Starting phenix.real_space_refine on Fri Jan 19 04:11:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tzf_26208/01_2024/7tzf_26208.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tzf_26208/01_2024/7tzf_26208.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tzf_26208/01_2024/7tzf_26208.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tzf_26208/01_2024/7tzf_26208.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tzf_26208/01_2024/7tzf_26208.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tzf_26208/01_2024/7tzf_26208.pdb" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 72 5.16 5 C 6640 2.51 5 N 1733 2.21 5 O 1896 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E GLU 74": "OE1" <-> "OE2" Residue "E GLU 117": "OE1" <-> "OE2" Residue "P ARG 11": "NH1" <-> "NH2" Residue "P TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 45": "NH1" <-> "NH2" Residue "R GLU 106": "OE1" <-> "OE2" Residue "R ARG 126": "NH1" <-> "NH2" Residue "R GLU 204": "OE1" <-> "OE2" Residue "R ARG 258": "NH1" <-> "NH2" Residue "R ARG 321": "NH1" <-> "NH2" Residue "R GLU 329": "OE1" <-> "OE2" Residue "R GLU 332": "OE1" <-> "OE2" Residue "R ARG 362": "NH1" <-> "NH2" Residue "R GLU 397": "OE1" <-> "OE2" Residue "R ARG 404": "NH1" <-> "NH2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A ARG 42": "NH1" <-> "NH2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 209": "OE1" <-> "OE2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A GLU 392": "OE1" <-> "OE2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "N GLU 6": "OE1" <-> "OE2" Residue "N ARG 98": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 10342 Number of models: 1 Model: "" Number of chains: 13 Chain: "E" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 755 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 7, 'TRANS': 106} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 90 Chain: "P" Number of atoms: 285 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 38, 274 Unusual residues: {'NH2': 1} Classifications: {'peptide': 37, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'PTRANS': 3, 'TRANS': 33} Conformer: "C" Number of residues, atoms: 38, 274 Unusual residues: {'NH2': 1} Classifications: {'peptide': 37, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'PTRANS': 3, 'TRANS': 33} bond proxies already assigned to first conformer: 266 Chain: "R" Number of atoms: 3006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 3006 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 16, 'TRANS': 350} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "A" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1898 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 2 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2600 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'P42': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 310 Unusual residues: {'NAG': 3, 'PLM': 11, 'Y01': 2} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "R" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG P 18 " occ=0.50 ... (20 atoms not shown) pdb=" NH2CARG P 18 " occ=0.62 Time building chain proxies: 6.46, per 1000 atoms: 0.62 Number of scatterers: 10342 At special positions: 0 Unit cell: (84.5, 99.45, 163.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 1 15.00 O 1896 8.00 N 1733 7.00 C 6640 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 72 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 104 " distance=2.03 Simple disulfide: pdb=" SG CYS P 2 " - pdb=" SG CYS P 7 " distance=2.03 Simple disulfide: pdb=" SG CYS R 55 " - pdb=" SG CYS R 81 " distance=2.03 Simple disulfide: pdb=" SG CYS R 72 " - pdb=" SG CYS R 112 " distance=2.03 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG E 201 " - " ASN E 71 " " NAG R 501 " - " ASN R 130 " " NAG R 502 " - " ASN R 73 " " NAG R 503 " - " ASN R 125 " Time building additional restraints: 4.61 Conformation dependent library (CDL) restraints added in 1.9 seconds 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2396 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 13 sheets defined 44.7% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'E' and resid 30 through 37 removed outlier: 4.046A pdb=" N LEU E 34 " --> pdb=" O GLU E 30 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU E 35 " --> pdb=" O THR E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 47 removed outlier: 3.803A pdb=" N LYS E 42 " --> pdb=" O PRO E 38 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA E 43 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA E 45 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET E 47 " --> pdb=" O ALA E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 81 removed outlier: 3.809A pdb=" N GLU E 67 " --> pdb=" O ILE E 63 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS E 72 " --> pdb=" O SER E 68 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA E 77 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL E 80 " --> pdb=" O GLU E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 101 removed outlier: 3.624A pdb=" N GLN E 99 " --> pdb=" O GLY E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 141 Proline residue: E 121 - end of helix Proline residue: E 126 - end of helix Processing helix chain 'P' and resid 4 through 6 No H-bonds generated for 'chain 'P' and resid 4 through 6' Processing helix chain 'P' and resid 7 through 20 Processing helix chain 'R' and resid 42 through 62 removed outlier: 4.041A pdb=" N GLN R 60 " --> pdb=" O TYR R 56 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN R 61 " --> pdb=" O ASP R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 136 removed outlier: 4.315A pdb=" N ASN R 135 " --> pdb=" O TYR R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 173 removed outlier: 3.771A pdb=" N VAL R 147 " --> pdb=" O LYS R 143 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 177 Processing helix chain 'R' and resid 178 through 205 Processing helix chain 'R' and resid 208 through 215 removed outlier: 3.530A pdb=" N VAL R 212 " --> pdb=" O ASN R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 249 removed outlier: 3.883A pdb=" N LYS R 220 " --> pdb=" O PRO R 216 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 267 Processing helix chain 'R' and resid 270 through 284 removed outlier: 3.529A pdb=" N THR R 274 " --> pdb=" O PRO R 270 " (cutoff:3.500A) Processing helix chain 'R' and resid 287 through 291 Processing helix chain 'R' and resid 295 through 297 No H-bonds generated for 'chain 'R' and resid 295 through 297' Processing helix chain 'R' and resid 298 through 330 Proline residue: R 304 - end of helix removed outlier: 3.619A pdb=" N THR R 330 " --> pdb=" O LYS R 326 " (cutoff:3.500A) Processing helix chain 'R' and resid 333 through 353 Proline residue: R 350 - end of helix Processing helix chain 'R' and resid 354 through 359 Processing helix chain 'R' and resid 365 through 382 Processing helix chain 'R' and resid 382 through 392 Processing helix chain 'R' and resid 395 through 407 Processing helix chain 'A' and resid 12 through 40 removed outlier: 4.078A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.814A pdb=" N MET A 60 " --> pdb=" O ILE A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.536A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.535A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.320A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.558A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 391 removed outlier: 4.404A pdb=" N ARG A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.559A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.505A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 71 through 72 Processing sheet with id=AA2, first strand: chain 'R' and resid 75 through 76 Processing sheet with id=AA3, first strand: chain 'R' and resid 90 through 94 removed outlier: 3.734A pdb=" N LYS R 110 " --> pdb=" O SER R 91 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.346A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.580A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.554A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.692A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.547A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.576A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.053A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.716A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.829A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 503 hydrogen bonds defined for protein. 1441 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: 3.13 Time building geometry restraints manager: 4.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1664 1.32 - 1.44: 2889 1.44 - 1.57: 5888 1.57 - 1.69: 2 1.69 - 1.81: 102 Bond restraints: 10545 Sorted by residual: bond pdb=" C TYR P 37 " pdb=" N NH2 P 38 " ideal model delta sigma weight residual 2.329 1.324 1.005 1.40e-02 5.10e+03 5.15e+03 bond pdb=" N VAL P 32 " pdb=" CA VAL P 32 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.09e+01 bond pdb=" OBN P42 P 101 " pdb=" PBM P42 P 101 " ideal model delta sigma weight residual 1.657 1.605 0.052 2.00e-02 2.50e+03 6.69e+00 bond pdb=" N THR P 36 " pdb=" CA THR P 36 " ideal model delta sigma weight residual 1.453 1.486 -0.033 1.27e-02 6.20e+03 6.67e+00 bond pdb=" CA SER P 34 " pdb=" CB SER P 34 " ideal model delta sigma weight residual 1.528 1.493 0.036 1.56e-02 4.11e+03 5.21e+00 ... (remaining 10540 not shown) Histogram of bond angle deviations from ideal: 99.61 - 106.50: 279 106.50 - 113.38: 5633 113.38 - 120.27: 3966 120.27 - 127.16: 4247 127.16 - 134.05: 132 Bond angle restraints: 14257 Sorted by residual: angle pdb=" CA GLY P 33 " pdb=" C GLY P 33 " pdb=" O GLY P 33 " ideal model delta sigma weight residual 121.92 118.21 3.71 1.05e+00 9.07e-01 1.25e+01 angle pdb=" CA THR P 36 " pdb=" C THR P 36 " pdb=" O THR P 36 " ideal model delta sigma weight residual 121.88 118.40 3.48 1.13e+00 7.83e-01 9.50e+00 angle pdb=" CA SER P 34 " pdb=" C SER P 34 " pdb=" O SER P 34 " ideal model delta sigma weight residual 120.55 117.75 2.80 1.06e+00 8.90e-01 6.99e+00 angle pdb=" C LEU E 119 " pdb=" N ILE E 120 " pdb=" CA ILE E 120 " ideal model delta sigma weight residual 120.33 122.29 -1.96 8.00e-01 1.56e+00 6.02e+00 angle pdb=" CA VAL P 32 " pdb=" C VAL P 32 " pdb=" O VAL P 32 " ideal model delta sigma weight residual 120.78 118.05 2.73 1.25e+00 6.40e-01 4.78e+00 ... (remaining 14252 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.81: 6133 25.81 - 51.62: 272 51.62 - 77.42: 41 77.42 - 103.23: 9 103.23 - 129.04: 3 Dihedral angle restraints: 6458 sinusoidal: 2746 harmonic: 3712 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual 93.00 172.70 -79.70 1 1.00e+01 1.00e-02 7.88e+01 dihedral pdb=" CB CYS E 40 " pdb=" SG CYS E 40 " pdb=" SG CYS E 72 " pdb=" CB CYS E 72 " ideal model delta sinusoidal sigma weight residual 93.00 169.23 -76.23 1 1.00e+01 1.00e-02 7.32e+01 dihedral pdb=" CB CYS E 57 " pdb=" SG CYS E 57 " pdb=" SG CYS E 104 " pdb=" CB CYS E 104 " ideal model delta sinusoidal sigma weight residual -86.00 -32.98 -53.02 1 1.00e+01 1.00e-02 3.83e+01 ... (remaining 6455 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1276 0.050 - 0.100: 246 0.100 - 0.150: 54 0.150 - 0.199: 1 0.199 - 0.249: 1 Chirality restraints: 1578 Sorted by residual: chirality pdb=" CA TYR P 37 " pdb=" N TYR P 37 " pdb=" C TYR P 37 " pdb=" CB TYR P 37 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CBE P42 P 101 " pdb=" CAB P42 P 101 " pdb=" CBK P42 P 101 " pdb=" OBD P42 P 101 " both_signs ideal model delta sigma weight residual False -2.32 -2.52 0.19 2.00e-01 2.50e+01 9.45e-01 chirality pdb=" CBF Y01 R 507 " pdb=" CAS Y01 R 507 " pdb=" CBD Y01 R 507 " pdb=" CBH Y01 R 507 " both_signs ideal model delta sigma weight residual False -2.45 -2.59 0.14 2.00e-01 2.50e+01 4.96e-01 ... (remaining 1575 not shown) Planarity restraints: 1791 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN P 31 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.61e+00 pdb=" C ASN P 31 " -0.037 2.00e-02 2.50e+03 pdb=" O ASN P 31 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL P 32 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN P 35 " 0.006 2.00e-02 2.50e+03 1.32e-02 1.75e+00 pdb=" C ASN P 35 " -0.023 2.00e-02 2.50e+03 pdb=" O ASN P 35 " 0.008 2.00e-02 2.50e+03 pdb=" N THR P 36 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO B 236 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.018 5.00e-02 4.00e+02 ... (remaining 1788 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2322 2.78 - 3.31: 9517 3.31 - 3.84: 17592 3.84 - 4.37: 21836 4.37 - 4.90: 35982 Nonbonded interactions: 87249 Sorted by model distance: nonbonded pdb=" O LEU P 16 " pdb=" OG SER P 20 " model vdw 2.252 2.440 nonbonded pdb=" O TYR R 374 " pdb=" OG SER R 378 " model vdw 2.261 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.263 2.440 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.284 2.440 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.285 2.440 ... (remaining 87244 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=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: 6.690 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: 0.000 Extract box with map and model: 10.320 Check model and map are aligned: 0.160 Set scattering table: 0.080 Process input model: 31.800 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:10.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 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 : 0.010 1.005 10545 Z= 0.737 Angle : 0.529 7.284 14257 Z= 0.296 Chirality : 0.041 0.249 1578 Planarity : 0.003 0.032 1787 Dihedral : 14.486 129.040 4035 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.43 % Allowed : 11.76 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.21), residues: 1257 helix: -2.10 (0.18), residues: 493 sheet: -0.34 (0.32), residues: 237 loop : -1.42 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.004 0.001 HIS R 302 PHE 0.011 0.001 PHE B 151 TYR 0.010 0.001 TYR R 391 ARG 0.004 0.000 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 177 time to evaluate : 1.225 Fit side-chains revert: symmetry clash REVERT: P 11 ARG cc_start: 0.8475 (mtm-85) cc_final: 0.8186 (mtm-85) REVERT: P 15 PHE cc_start: 0.8283 (t80) cc_final: 0.8066 (t80) REVERT: R 99 PHE cc_start: 0.5097 (m-80) cc_final: 0.4885 (m-10) REVERT: R 141 LYS cc_start: 0.6809 (tttt) cc_final: 0.6605 (mtmt) REVERT: R 338 TYR cc_start: 0.5831 (m-80) cc_final: 0.5349 (m-10) REVERT: A 209 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.6677 (mp0) REVERT: A 296 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7280 (mp) REVERT: B 46 ARG cc_start: 0.6580 (mtp85) cc_final: 0.6202 (mmm-85) REVERT: B 96 ARG cc_start: 0.7217 (mtp-110) cc_final: 0.6985 (ttp-170) REVERT: B 134 ARG cc_start: 0.6994 (ptt90) cc_final: 0.6791 (ptt90) REVERT: B 197 ARG cc_start: 0.7020 (mmm-85) cc_final: 0.6788 (mmt90) REVERT: B 268 ASN cc_start: 0.7287 (p0) cc_final: 0.7058 (p0) REVERT: G 16 VAL cc_start: 0.7614 (t) cc_final: 0.7342 (m) REVERT: N 1 GLN cc_start: 0.7578 (tp-100) cc_final: 0.7363 (tp40) REVERT: N 33 LYS cc_start: 0.8575 (ttmt) cc_final: 0.8371 (ttpt) outliers start: 15 outliers final: 5 residues processed: 189 average time/residue: 1.4792 time to fit residues: 296.5913 Evaluate side-chains 151 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 144 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 4.9990 chunk 93 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 0.0020 chunk 62 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 111 optimal weight: 20.0000 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 97 HIS ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 14 ASN P 31 ASN P 35 ASN R 52 GLN R 93 GLN R 184 HIS ** R 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 288 ASN R 336 HIS R 399 GLN A 35 GLN A 59 GLN A 254 ASN A 357 HIS B 6 GLN B 35 ASN B 75 GLN B 340 ASN N 82 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10545 Z= 0.149 Angle : 0.510 8.074 14257 Z= 0.272 Chirality : 0.041 0.136 1578 Planarity : 0.004 0.036 1787 Dihedral : 8.682 124.257 1825 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.72 % Allowed : 15.58 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.22), residues: 1257 helix: 0.26 (0.22), residues: 500 sheet: 0.08 (0.33), residues: 222 loop : -1.05 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.003 0.001 HIS A 357 PHE 0.014 0.001 PHE E 69 TYR 0.010 0.001 TYR R 131 ARG 0.006 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 154 time to evaluate : 1.237 Fit side-chains revert: symmetry clash REVERT: R 158 LEU cc_start: 0.7181 (OUTLIER) cc_final: 0.6924 (tp) REVERT: R 339 LEU cc_start: 0.7194 (tm) cc_final: 0.6846 (tp) REVERT: A 21 GLU cc_start: 0.5897 (OUTLIER) cc_final: 0.5558 (tm-30) REVERT: A 50 GLU cc_start: 0.4701 (mm-30) cc_final: 0.3972 (mm-30) REVERT: A 209 GLU cc_start: 0.6766 (mt-10) cc_final: 0.6502 (mp0) REVERT: B 46 ARG cc_start: 0.6493 (mtp85) cc_final: 0.6087 (mmm-85) REVERT: B 137 ARG cc_start: 0.7603 (tpp-160) cc_final: 0.7396 (tpt170) REVERT: G 20 LYS cc_start: 0.7194 (mttm) cc_final: 0.6936 (mttm) REVERT: N 39 GLN cc_start: 0.8687 (tt0) cc_final: 0.8448 (tt0) outliers start: 18 outliers final: 7 residues processed: 164 average time/residue: 1.4016 time to fit residues: 245.2957 Evaluate side-chains 156 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 147 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 43 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 110 optimal weight: 0.6980 chunk 38 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 223 HIS R 233 ASN R 318 ASN R 399 GLN A 35 GLN A 59 GLN B 35 ASN N 84 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10545 Z= 0.292 Angle : 0.646 7.413 14257 Z= 0.340 Chirality : 0.046 0.212 1578 Planarity : 0.005 0.045 1787 Dihedral : 10.706 140.739 1818 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.35 % Allowed : 15.49 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.23), residues: 1257 helix: 0.82 (0.22), residues: 494 sheet: 0.14 (0.32), residues: 229 loop : -0.79 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 234 HIS 0.011 0.001 HIS A 41 PHE 0.016 0.002 PHE B 151 TYR 0.017 0.002 TYR E 66 ARG 0.007 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 157 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: R 158 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7325 (tt) REVERT: R 332 GLU cc_start: 0.5797 (mm-30) cc_final: 0.5453 (mt-10) REVERT: R 338 TYR cc_start: 0.5629 (m-10) cc_final: 0.5092 (m-10) REVERT: R 396 ASN cc_start: 0.6908 (OUTLIER) cc_final: 0.6618 (t0) REVERT: A 21 GLU cc_start: 0.5936 (OUTLIER) cc_final: 0.5555 (tm-30) REVERT: A 209 GLU cc_start: 0.7012 (mt-10) cc_final: 0.6633 (mp0) REVERT: B 46 ARG cc_start: 0.6623 (mtp85) cc_final: 0.6139 (mmm-85) REVERT: G 20 LYS cc_start: 0.7140 (mttm) cc_final: 0.6861 (mttm) REVERT: G 21 MET cc_start: 0.6553 (mmm) cc_final: 0.6290 (tpp) REVERT: N 39 GLN cc_start: 0.8675 (tt0) cc_final: 0.8410 (tt0) outliers start: 35 outliers final: 12 residues processed: 178 average time/residue: 1.4205 time to fit residues: 269.0579 Evaluate side-chains 166 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 151 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 396 ASN Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 78 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 7.9990 chunk 84 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 118 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 99 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 GLN A 59 GLN B 35 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 10545 Z= 0.321 Angle : 0.667 7.103 14257 Z= 0.349 Chirality : 0.047 0.161 1578 Planarity : 0.005 0.047 1787 Dihedral : 11.703 128.095 1815 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.25 % Allowed : 16.54 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.23), residues: 1257 helix: 0.90 (0.23), residues: 492 sheet: 0.11 (0.33), residues: 234 loop : -0.80 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 234 HIS 0.010 0.002 HIS A 41 PHE 0.019 0.002 PHE B 151 TYR 0.016 0.002 TYR R 131 ARG 0.010 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 149 time to evaluate : 1.216 Fit side-chains revert: symmetry clash REVERT: R 49 MET cc_start: 0.2616 (mmp) cc_final: 0.2359 (mmt) REVERT: R 338 TYR cc_start: 0.5641 (m-10) cc_final: 0.5266 (m-10) REVERT: R 396 ASN cc_start: 0.6785 (OUTLIER) cc_final: 0.6464 (t0) REVERT: A 21 GLU cc_start: 0.6028 (OUTLIER) cc_final: 0.5596 (tm-30) REVERT: A 58 LYS cc_start: 0.5958 (OUTLIER) cc_final: 0.5574 (ttpt) REVERT: A 209 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6608 (mp0) REVERT: B 44 GLN cc_start: 0.5390 (mm-40) cc_final: 0.5110 (mm-40) REVERT: B 46 ARG cc_start: 0.6629 (mtp85) cc_final: 0.6147 (mmm-85) REVERT: B 195 ASP cc_start: 0.7427 (p0) cc_final: 0.7081 (p0) REVERT: G 20 LYS cc_start: 0.7171 (mttm) cc_final: 0.6928 (mttm) REVERT: G 21 MET cc_start: 0.6562 (mmm) cc_final: 0.6282 (tpp) REVERT: N 39 GLN cc_start: 0.8670 (tt0) cc_final: 0.8396 (tt0) outliers start: 34 outliers final: 18 residues processed: 169 average time/residue: 1.4631 time to fit residues: 263.2316 Evaluate side-chains 164 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 142 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain R residue 165 ILE Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain R residue 396 ASN Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 78 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 233 ASN R 286 ASN R 318 ASN A 35 GLN A 59 GLN B 35 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 84 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10545 Z= 0.253 Angle : 0.597 6.713 14257 Z= 0.313 Chirality : 0.044 0.138 1578 Planarity : 0.004 0.042 1787 Dihedral : 11.258 130.524 1815 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.96 % Allowed : 17.30 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.23), residues: 1257 helix: 1.16 (0.23), residues: 500 sheet: 0.14 (0.33), residues: 234 loop : -0.71 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 234 HIS 0.008 0.001 HIS A 41 PHE 0.016 0.002 PHE B 151 TYR 0.013 0.002 TYR R 131 ARG 0.009 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 153 time to evaluate : 1.196 Fit side-chains REVERT: R 49 MET cc_start: 0.2824 (mmp) cc_final: 0.2576 (mmt) REVERT: R 332 GLU cc_start: 0.5815 (OUTLIER) cc_final: 0.5429 (mt-10) REVERT: R 338 TYR cc_start: 0.5551 (m-10) cc_final: 0.5215 (m-10) REVERT: R 396 ASN cc_start: 0.6811 (OUTLIER) cc_final: 0.6467 (t0) REVERT: A 21 GLU cc_start: 0.6020 (OUTLIER) cc_final: 0.5590 (tm-30) REVERT: A 209 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6618 (mp0) REVERT: B 44 GLN cc_start: 0.5342 (mm-40) cc_final: 0.5078 (mm-40) REVERT: B 46 ARG cc_start: 0.6584 (mtp85) cc_final: 0.6121 (mmm-85) REVERT: G 21 MET cc_start: 0.6526 (mmm) cc_final: 0.6274 (tpp) REVERT: N 39 GLN cc_start: 0.8675 (tt0) cc_final: 0.8419 (tt0) outliers start: 31 outliers final: 17 residues processed: 171 average time/residue: 1.4872 time to fit residues: 271.1527 Evaluate side-chains 165 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 144 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 218 SER Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain R residue 332 GLU Chi-restraints excluded: chain R residue 396 ASN Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 30 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 0.6980 chunk 23 optimal weight: 0.1980 chunk 69 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 399 GLN A 35 GLN A 59 GLN B 35 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10545 Z= 0.154 Angle : 0.505 6.399 14257 Z= 0.267 Chirality : 0.041 0.139 1578 Planarity : 0.003 0.042 1787 Dihedral : 10.125 123.428 1815 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.01 % Allowed : 17.97 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.23), residues: 1257 helix: 1.55 (0.23), residues: 504 sheet: 0.28 (0.33), residues: 221 loop : -0.66 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 234 HIS 0.003 0.001 HIS R 302 PHE 0.015 0.001 PHE B 199 TYR 0.010 0.001 TYR R 149 ARG 0.009 0.001 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 153 time to evaluate : 1.159 Fit side-chains revert: symmetry clash REVERT: R 49 MET cc_start: 0.2789 (mmp) cc_final: 0.2542 (mmt) REVERT: R 158 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7171 (tp) REVERT: R 229 MET cc_start: 0.8043 (tpp) cc_final: 0.7826 (tpp) REVERT: R 396 ASN cc_start: 0.6803 (OUTLIER) cc_final: 0.6437 (t0) REVERT: A 21 GLU cc_start: 0.6004 (OUTLIER) cc_final: 0.5606 (tm-30) REVERT: A 209 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6597 (mp0) REVERT: A 314 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6528 (pt0) REVERT: B 44 GLN cc_start: 0.5218 (mm-40) cc_final: 0.4974 (mm-40) REVERT: B 46 ARG cc_start: 0.6515 (mtp85) cc_final: 0.6072 (mmm-85) REVERT: G 21 MET cc_start: 0.6525 (mmm) cc_final: 0.6303 (tpp) REVERT: N 39 GLN cc_start: 0.8664 (tt0) cc_final: 0.8416 (tt0) outliers start: 21 outliers final: 10 residues processed: 166 average time/residue: 1.3605 time to fit residues: 241.3320 Evaluate side-chains 158 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 143 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain R residue 396 ASN Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain N residue 105 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 86 optimal weight: 0.2980 chunk 100 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 121 HIS ** R 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 399 GLN A 59 GLN B 35 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10545 Z= 0.136 Angle : 0.476 5.829 14257 Z= 0.252 Chirality : 0.040 0.140 1578 Planarity : 0.004 0.047 1787 Dihedral : 9.345 115.395 1815 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.82 % Allowed : 18.74 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.24), residues: 1257 helix: 1.83 (0.23), residues: 505 sheet: 0.29 (0.33), residues: 211 loop : -0.60 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 234 HIS 0.004 0.001 HIS B 266 PHE 0.015 0.001 PHE B 199 TYR 0.010 0.001 TYR R 149 ARG 0.011 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 149 time to evaluate : 1.211 Fit side-chains REVERT: R 49 MET cc_start: 0.2790 (mmp) cc_final: 0.2573 (mmt) REVERT: R 338 TYR cc_start: 0.5577 (m-10) cc_final: 0.5331 (m-10) REVERT: A 21 GLU cc_start: 0.5937 (OUTLIER) cc_final: 0.5513 (tm-30) REVERT: A 209 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.6542 (mp0) REVERT: A 314 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6521 (pt0) REVERT: B 44 GLN cc_start: 0.5206 (mm-40) cc_final: 0.4962 (mm-40) REVERT: B 46 ARG cc_start: 0.6487 (mtp85) cc_final: 0.6049 (mmm-85) REVERT: G 21 MET cc_start: 0.6533 (mmm) cc_final: 0.6323 (tpp) REVERT: N 39 GLN cc_start: 0.8648 (tt0) cc_final: 0.8397 (tt0) outliers start: 19 outliers final: 10 residues processed: 160 average time/residue: 1.4449 time to fit residues: 247.1381 Evaluate side-chains 157 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 144 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 99 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 107 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 399 GLN A 35 GLN A 59 GLN A 390 GLN B 35 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10545 Z= 0.275 Angle : 0.604 6.406 14257 Z= 0.318 Chirality : 0.044 0.156 1578 Planarity : 0.004 0.040 1787 Dihedral : 10.667 124.565 1815 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.10 % Allowed : 18.16 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.23), residues: 1257 helix: 1.43 (0.23), residues: 504 sheet: 0.28 (0.33), residues: 226 loop : -0.69 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 234 HIS 0.008 0.001 HIS A 41 PHE 0.015 0.002 PHE B 151 TYR 0.012 0.002 TYR R 391 ARG 0.009 0.001 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 145 time to evaluate : 1.251 Fit side-chains revert: symmetry clash REVERT: R 49 MET cc_start: 0.2929 (mmp) cc_final: 0.2655 (mmt) REVERT: R 104 PRO cc_start: 0.5852 (Cg_exo) cc_final: 0.5536 (Cg_endo) REVERT: R 158 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7234 (tp) REVERT: R 338 TYR cc_start: 0.5575 (m-10) cc_final: 0.5373 (m-10) REVERT: A 209 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6636 (mp0) REVERT: A 311 TYR cc_start: 0.7443 (OUTLIER) cc_final: 0.6806 (m-10) REVERT: B 44 GLN cc_start: 0.5390 (mm-40) cc_final: 0.5106 (mm-40) REVERT: B 46 ARG cc_start: 0.6574 (mtp85) cc_final: 0.6111 (mmm-85) REVERT: G 21 MET cc_start: 0.6550 (mmm) cc_final: 0.6250 (tpp) REVERT: N 39 GLN cc_start: 0.8670 (tt0) cc_final: 0.8405 (tt0) outliers start: 22 outliers final: 14 residues processed: 158 average time/residue: 1.4467 time to fit residues: 243.9695 Evaluate side-chains 159 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 142 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 105 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 9.9990 chunk 110 optimal weight: 0.6980 chunk 113 optimal weight: 4.9990 chunk 66 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 399 GLN A 35 GLN A 59 GLN B 35 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10545 Z= 0.196 Angle : 0.543 6.174 14257 Z= 0.286 Chirality : 0.042 0.138 1578 Planarity : 0.004 0.042 1787 Dihedral : 10.324 122.612 1815 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.49 % Allowed : 17.59 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.23), residues: 1257 helix: 1.52 (0.23), residues: 506 sheet: 0.34 (0.33), residues: 224 loop : -0.68 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 234 HIS 0.006 0.001 HIS A 41 PHE 0.017 0.002 PHE B 199 TYR 0.011 0.001 TYR A 339 ARG 0.009 0.001 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 143 time to evaluate : 1.109 Fit side-chains revert: symmetry clash REVERT: R 49 MET cc_start: 0.2903 (mmp) cc_final: 0.2629 (mmt) REVERT: R 104 PRO cc_start: 0.5845 (Cg_exo) cc_final: 0.5544 (Cg_endo) REVERT: R 158 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7176 (tp) REVERT: R 332 GLU cc_start: 0.5937 (OUTLIER) cc_final: 0.5488 (mt-10) REVERT: R 396 ASN cc_start: 0.6782 (OUTLIER) cc_final: 0.6420 (t0) REVERT: A 21 GLU cc_start: 0.5996 (OUTLIER) cc_final: 0.5582 (tm-30) REVERT: A 209 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.6621 (mp0) REVERT: A 314 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6644 (pt0) REVERT: B 44 GLN cc_start: 0.5387 (mm-40) cc_final: 0.5096 (mm-40) REVERT: B 46 ARG cc_start: 0.6559 (mtp85) cc_final: 0.6106 (mmm-85) REVERT: N 39 GLN cc_start: 0.8649 (tt0) cc_final: 0.8394 (tt0) outliers start: 26 outliers final: 16 residues processed: 161 average time/residue: 1.4508 time to fit residues: 248.4117 Evaluate side-chains 163 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 141 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain R residue 332 GLU Chi-restraints excluded: chain R residue 396 ASN Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 105 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 122 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 399 GLN A 35 GLN A 59 GLN B 35 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10545 Z= 0.165 Angle : 0.514 5.865 14257 Z= 0.270 Chirality : 0.041 0.140 1578 Planarity : 0.004 0.041 1787 Dihedral : 9.857 117.394 1815 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.29 % Allowed : 17.97 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.23), residues: 1257 helix: 1.68 (0.23), residues: 506 sheet: 0.35 (0.33), residues: 221 loop : -0.62 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 234 HIS 0.004 0.001 HIS A 41 PHE 0.016 0.001 PHE B 199 TYR 0.011 0.001 TYR R 338 ARG 0.010 0.000 ARG B 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 144 time to evaluate : 1.230 Fit side-chains revert: symmetry clash REVERT: R 49 MET cc_start: 0.2845 (mmp) cc_final: 0.2618 (mmt) REVERT: R 104 PRO cc_start: 0.5824 (Cg_exo) cc_final: 0.5547 (Cg_endo) REVERT: R 332 GLU cc_start: 0.5929 (OUTLIER) cc_final: 0.5564 (mt-10) REVERT: R 396 ASN cc_start: 0.6803 (OUTLIER) cc_final: 0.6428 (t0) REVERT: A 21 GLU cc_start: 0.5974 (OUTLIER) cc_final: 0.5550 (tm-30) REVERT: A 209 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6628 (mp0) REVERT: A 314 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6613 (pt0) REVERT: B 44 GLN cc_start: 0.5318 (mm-40) cc_final: 0.5038 (mm-40) REVERT: B 46 ARG cc_start: 0.6525 (mtp85) cc_final: 0.6077 (mmm-85) REVERT: G 21 MET cc_start: 0.6558 (mmm) cc_final: 0.6299 (tpp) REVERT: N 39 GLN cc_start: 0.8638 (tt0) cc_final: 0.8391 (tt0) outliers start: 24 outliers final: 15 residues processed: 160 average time/residue: 1.4764 time to fit residues: 252.3018 Evaluate side-chains 163 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 143 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain R residue 332 GLU Chi-restraints excluded: chain R residue 396 ASN Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 105 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 40 optimal weight: 10.0000 chunk 100 optimal weight: 0.2980 chunk 12 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 399 GLN A 35 GLN A 59 GLN A 390 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN N 84 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.179466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.143731 restraints weight = 26635.603| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 4.57 r_work: 0.3090 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3079 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3079 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10545 Z= 0.138 Angle : 0.483 5.418 14257 Z= 0.253 Chirality : 0.040 0.140 1578 Planarity : 0.003 0.040 1787 Dihedral : 9.223 107.853 1815 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.63 % Allowed : 18.93 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.23), residues: 1257 helix: 1.83 (0.23), residues: 509 sheet: 0.37 (0.33), residues: 211 loop : -0.63 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 234 HIS 0.003 0.001 HIS R 302 PHE 0.015 0.001 PHE B 199 TYR 0.013 0.001 TYR R 338 ARG 0.010 0.000 ARG B 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4952.77 seconds wall clock time: 88 minutes 41.34 seconds (5321.34 seconds total)