Starting phenix.real_space_refine on Fri Mar 15 16:10:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gn5_34155/03_2024/8gn5_34155.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gn5_34155/03_2024/8gn5_34155.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gn5_34155/03_2024/8gn5_34155.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gn5_34155/03_2024/8gn5_34155.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gn5_34155/03_2024/8gn5_34155.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gn5_34155/03_2024/8gn5_34155.pdb" } resolution = 4.02 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= 0.073 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 52 5.16 5 C 7588 2.51 5 N 2108 2.21 5 O 2348 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A GLU 125": "OE1" <-> "OE2" Residue "A GLU 152": "OE1" <-> "OE2" Residue "A GLU 307": "OE1" <-> "OE2" Residue "A TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 371": "OE1" <-> "OE2" Residue "A ARG 406": "NH1" <-> "NH2" Residue "A GLU 419": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 59": "OE1" <-> "OE2" Residue "B GLU 72": "OE1" <-> "OE2" Residue "B PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 152": "OE1" <-> "OE2" Residue "B GLU 307": "OE1" <-> "OE2" Residue "B GLU 371": "OE1" <-> "OE2" Residue "B GLU 419": "OE1" <-> "OE2" Residue "C GLU 52": "OE1" <-> "OE2" Residue "C GLU 72": "OE1" <-> "OE2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C GLU 125": "OE1" <-> "OE2" Residue "C GLU 159": "OE1" <-> "OE2" Residue "C GLU 371": "OE1" <-> "OE2" Residue "C PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 419": "OE1" <-> "OE2" Residue "D GLU 52": "OE1" <-> "OE2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D GLU 116": "OE1" <-> "OE2" Residue "D GLU 125": "OE1" <-> "OE2" Residue "D GLU 159": "OE1" <-> "OE2" Residue "D ASP 163": "OD1" <-> "OD2" Residue "D TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 371": "OE1" <-> "OE2" Residue "D GLU 419": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12096 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3024 Classifications: {'peptide': 396} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 376} Chain breaks: 1 Chain: "B" Number of atoms: 3024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3024 Classifications: {'peptide': 396} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 376} Chain breaks: 1 Chain: "C" Number of atoms: 3024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3024 Classifications: {'peptide': 396} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 376} Chain breaks: 1 Chain: "D" Number of atoms: 3024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3024 Classifications: {'peptide': 396} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 376} Chain breaks: 1 Time building chain proxies: 6.80, per 1000 atoms: 0.56 Number of scatterers: 12096 At special positions: 0 Unit cell: (137.747, 103.96, 166.336, 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 52 16.00 O 2348 8.00 N 2108 7.00 C 7588 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.19 Conformation dependent library (CDL) restraints added in 2.4 seconds 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2968 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 28 sheets defined 22.5% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 7 through 24 removed outlier: 4.066A pdb=" N LEU A 11 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP A 14 " --> pdb=" O THR A 10 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR A 24 " --> pdb=" O ILE A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 30 removed outlier: 3.522A pdb=" N ALA A 30 " --> pdb=" O ALA A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 95 removed outlier: 4.258A pdb=" N ARG A 95 " --> pdb=" O ASP A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 127 removed outlier: 4.797A pdb=" N ARG A 102 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ARG A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE A 104 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ASN A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 157 removed outlier: 4.152A pdb=" N ASP A 150 " --> pdb=" O ASN A 146 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N MET A 155 " --> pdb=" O ALA A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 removed outlier: 4.397A pdb=" N LYS A 176 " --> pdb=" O PRO A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 321 through 326 removed outlier: 3.511A pdb=" N ALA A 326 " --> pdb=" O PRO A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 419 No H-bonds generated for 'chain 'A' and resid 417 through 419' Processing helix chain 'B' and resid 8 through 22 removed outlier: 4.516A pdb=" N ASP B 14 " --> pdb=" O THR B 10 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU B 18 " --> pdb=" O ASP B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 91 through 95 removed outlier: 3.600A pdb=" N ARG B 95 " --> pdb=" O ASP B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 127 removed outlier: 4.278A pdb=" N ARG B 102 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ARG B 103 " --> pdb=" O ALA B 99 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE B 104 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS B 110 " --> pdb=" O SER B 106 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN B 114 " --> pdb=" O LYS B 110 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 159 removed outlier: 4.410A pdb=" N ASP B 150 " --> pdb=" O ASN B 146 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N MET B 155 " --> pdb=" O ALA B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.563A pdb=" N LYS B 176 " --> pdb=" O PRO B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'B' and resid 321 through 326 Processing helix chain 'B' and resid 417 through 419 No H-bonds generated for 'chain 'B' and resid 417 through 419' Processing helix chain 'C' and resid 7 through 23 removed outlier: 4.080A pdb=" N LEU C 11 " --> pdb=" O GLN C 7 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU C 18 " --> pdb=" O ASP C 14 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER C 21 " --> pdb=" O ILE C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 30 Processing helix chain 'C' and resid 91 through 95 removed outlier: 4.148A pdb=" N ARG C 95 " --> pdb=" O ASP C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 127 removed outlier: 4.676A pdb=" N ARG C 102 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG C 103 " --> pdb=" O ALA C 99 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE C 104 " --> pdb=" O TYR C 100 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ASN C 114 " --> pdb=" O LYS C 110 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 159 removed outlier: 3.805A pdb=" N ASP C 150 " --> pdb=" O ASN C 146 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N MET C 155 " --> pdb=" O ALA C 151 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG C 158 " --> pdb=" O ILE C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 178 removed outlier: 3.951A pdb=" N LYS C 176 " --> pdb=" O PRO C 172 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS C 177 " --> pdb=" O GLN C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 328 Processing helix chain 'C' and resid 417 through 419 No H-bonds generated for 'chain 'C' and resid 417 through 419' Processing helix chain 'D' and resid 7 through 24 removed outlier: 4.181A pdb=" N LEU D 11 " --> pdb=" O GLN D 7 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR D 24 " --> pdb=" O ILE D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 28 Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'D' and resid 96 through 127 removed outlier: 4.412A pdb=" N ARG D 102 " --> pdb=" O THR D 98 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG D 103 " --> pdb=" O ALA D 99 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE D 104 " --> pdb=" O TYR D 100 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASN D 114 " --> pdb=" O LYS D 110 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL D 115 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL D 119 " --> pdb=" O VAL D 115 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA D 124 " --> pdb=" O ALA D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 157 removed outlier: 4.041A pdb=" N ASP D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N MET D 155 " --> pdb=" O ALA D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 176 removed outlier: 3.786A pdb=" N LYS D 176 " --> pdb=" O PRO D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 326 removed outlier: 3.909A pdb=" N ALA D 326 " --> pdb=" O PRO D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 419 No H-bonds generated for 'chain 'D' and resid 417 through 419' Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 32 removed outlier: 6.827A pdb=" N LYS A 31 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ARG A 360 " --> pdb=" O ASN A 414 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN A 414 " --> pdb=" O ARG A 360 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 50 Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 59 removed outlier: 4.622A pdb=" N GLN A 58 " --> pdb=" O ASN B 84 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN B 84 " --> pdb=" O GLN A 58 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLY B 403 " --> pdb=" O LEU B 89 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 89 removed outlier: 4.125A pdb=" N GLY A 403 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ASN A 389 " --> pdb=" O TRP A 410 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 129 through 132 removed outlier: 6.352A pdb=" N LEU A 129 " --> pdb=" O VAL A 423 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N LEU A 425 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE A 131 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN A 351 " --> pdb=" O GLY A 424 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 242 through 243 Processing sheet with id=AA7, first strand: chain 'A' and resid 257 through 260 removed outlier: 3.706A pdb=" N ARG A 299 " --> pdb=" O GLU A 307 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N THR A 309 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N VAL A 297 " --> pdb=" O THR A 309 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 279 through 281 removed outlier: 5.382A pdb=" N PHE A 280 " --> pdb=" O LEU A 289 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 31 through 32 removed outlier: 3.600A pdb=" N ILE B 361 " --> pdb=" O LYS B 31 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 47 through 50 Processing sheet with id=AB2, first strand: chain 'B' and resid 129 through 132 removed outlier: 6.521A pdb=" N LEU B 129 " --> pdb=" O VAL B 423 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N LEU B 425 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE B 131 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASN B 351 " --> pdb=" O GLY B 424 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL B 352 " --> pdb=" O PHE B 169 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 241 through 243 Processing sheet with id=AB4, first strand: chain 'B' and resid 257 through 260 removed outlier: 3.795A pdb=" N ARG B 299 " --> pdb=" O GLU B 307 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N THR B 309 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N VAL B 297 " --> pdb=" O THR B 309 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 279 through 281 removed outlier: 5.520A pdb=" N PHE B 280 " --> pdb=" O LEU B 289 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 31 through 33 removed outlier: 6.784A pdb=" N LYS C 31 " --> pdb=" O ILE C 361 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 46 through 51 removed outlier: 4.200A pdb=" N LEU C 73 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 83 through 89 removed outlier: 3.601A pdb=" N GLY C 403 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASN C 389 " --> pdb=" O TRP C 410 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 129 through 132 removed outlier: 6.407A pdb=" N LEU C 129 " --> pdb=" O VAL C 423 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N LEU C 425 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE C 131 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N LEU C 212 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N TYR C 168 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 242 through 243 Processing sheet with id=AC2, first strand: chain 'C' and resid 257 through 260 removed outlier: 3.695A pdb=" N ARG C 299 " --> pdb=" O GLU C 307 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR C 309 " --> pdb=" O VAL C 297 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N VAL C 297 " --> pdb=" O THR C 309 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 279 through 281 removed outlier: 5.102A pdb=" N PHE C 280 " --> pdb=" O LEU C 289 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 31 through 33 Processing sheet with id=AC5, first strand: chain 'D' and resid 46 through 51 removed outlier: 4.180A pdb=" N LEU D 73 " --> pdb=" O VAL D 51 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 83 through 89 removed outlier: 3.589A pdb=" N GLY D 403 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER D 402 " --> pdb=" O ASP D 397 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASN D 389 " --> pdb=" O TRP D 410 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS D 377 " --> pdb=" O THR D 394 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 129 through 132 removed outlier: 6.401A pdb=" N LEU D 129 " --> pdb=" O VAL D 423 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N LEU D 425 " --> pdb=" O LEU D 129 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ILE D 131 " --> pdb=" O LEU D 425 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 242 through 243 Processing sheet with id=AC9, first strand: chain 'D' and resid 257 through 260 removed outlier: 3.704A pdb=" N ARG D 299 " --> pdb=" O GLU D 307 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR D 309 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N VAL D 297 " --> pdb=" O THR D 309 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 279 through 281 removed outlier: 5.613A pdb=" N PHE D 280 " --> pdb=" O LEU D 289 " (cutoff:3.500A) 385 hydrogen bonds defined for protein. 1011 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: 3.56 Time building geometry restraints manager: 4.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3853 1.34 - 1.46: 1717 1.46 - 1.58: 6653 1.58 - 1.71: 1 1.71 - 1.83: 100 Bond restraints: 12324 Sorted by residual: bond pdb=" CA ARG B 109 " pdb=" C ARG B 109 " ideal model delta sigma weight residual 1.524 1.585 -0.061 1.27e-02 6.20e+03 2.32e+01 bond pdb=" CA ARG A 406 " pdb=" C ARG A 406 " ideal model delta sigma weight residual 1.522 1.567 -0.045 1.14e-02 7.69e+03 1.59e+01 bond pdb=" CA ARG A 162 " pdb=" C ARG A 162 " ideal model delta sigma weight residual 1.531 1.580 -0.049 1.39e-02 5.18e+03 1.25e+01 bond pdb=" CA ARG B 162 " pdb=" C ARG B 162 " ideal model delta sigma weight residual 1.521 1.564 -0.043 1.23e-02 6.61e+03 1.24e+01 bond pdb=" CA ARG A 417 " pdb=" C ARG A 417 " ideal model delta sigma weight residual 1.524 1.566 -0.042 1.26e-02 6.30e+03 1.12e+01 ... (remaining 12319 not shown) Histogram of bond angle deviations from ideal: 97.05 - 104.73: 266 104.73 - 112.40: 5444 112.40 - 120.08: 5726 120.08 - 127.75: 5242 127.75 - 135.43: 90 Bond angle restraints: 16768 Sorted by residual: angle pdb=" N ARG B 90 " pdb=" CA ARG B 90 " pdb=" C ARG B 90 " ideal model delta sigma weight residual 110.33 101.78 8.55 1.29e+00 6.01e-01 4.39e+01 angle pdb=" CA ASP A 253 " pdb=" CB ASP A 253 " pdb=" CG ASP A 253 " ideal model delta sigma weight residual 112.60 118.99 -6.39 1.00e+00 1.00e+00 4.08e+01 angle pdb=" CA PHE C 256 " pdb=" CB PHE C 256 " pdb=" CG PHE C 256 " ideal model delta sigma weight residual 113.80 119.79 -5.99 1.00e+00 1.00e+00 3.58e+01 angle pdb=" N ARG A 90 " pdb=" CA ARG A 90 " pdb=" C ARG A 90 " ideal model delta sigma weight residual 110.41 103.08 7.33 1.23e+00 6.61e-01 3.55e+01 angle pdb=" CA ASP B 347 " pdb=" CB ASP B 347 " pdb=" CG ASP B 347 " ideal model delta sigma weight residual 112.60 118.23 -5.63 1.00e+00 1.00e+00 3.17e+01 ... (remaining 16763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 6854 17.87 - 35.75: 487 35.75 - 53.62: 65 53.62 - 71.49: 23 71.49 - 89.36: 11 Dihedral angle restraints: 7440 sinusoidal: 2868 harmonic: 4572 Sorted by residual: dihedral pdb=" CA ASN C 84 " pdb=" C ASN C 84 " pdb=" N ASP C 85 " pdb=" CA ASP C 85 " ideal model delta harmonic sigma weight residual 180.00 150.65 29.35 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA ASN B 84 " pdb=" C ASN B 84 " pdb=" N ASP B 85 " pdb=" CA ASP B 85 " ideal model delta harmonic sigma weight residual 180.00 151.01 28.99 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA ALA C 151 " pdb=" C ALA C 151 " pdb=" N GLU C 152 " pdb=" CA GLU C 152 " ideal model delta harmonic sigma weight residual 180.00 151.33 28.67 0 5.00e+00 4.00e-02 3.29e+01 ... (remaining 7437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1029 0.069 - 0.138: 636 0.138 - 0.208: 203 0.208 - 0.277: 53 0.277 - 0.346: 19 Chirality restraints: 1940 Sorted by residual: chirality pdb=" CA THR C 221 " pdb=" N THR C 221 " pdb=" C THR C 221 " pdb=" CB THR C 221 " both_signs ideal model delta sigma weight residual False 2.53 2.18 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CA THR A 260 " pdb=" N THR A 260 " pdb=" C THR A 260 " pdb=" CB THR A 260 " both_signs ideal model delta sigma weight residual False 2.53 2.19 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CA THR A 221 " pdb=" N THR A 221 " pdb=" C THR A 221 " pdb=" CB THR A 221 " both_signs ideal model delta sigma weight residual False 2.53 2.21 0.32 2.00e-01 2.50e+01 2.52e+00 ... (remaining 1937 not shown) Planarity restraints: 2200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 410 " 0.132 2.00e-02 2.50e+03 6.92e-02 1.20e+02 pdb=" CG TRP B 410 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP B 410 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP B 410 " -0.046 2.00e-02 2.50e+03 pdb=" NE1 TRP B 410 " -0.055 2.00e-02 2.50e+03 pdb=" CE2 TRP B 410 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP B 410 " -0.107 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 410 " 0.075 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 410 " -0.028 2.00e-02 2.50e+03 pdb=" CH2 TRP B 410 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 410 " 0.126 2.00e-02 2.50e+03 6.00e-02 9.01e+01 pdb=" CG TRP A 410 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP A 410 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP A 410 " -0.058 2.00e-02 2.50e+03 pdb=" NE1 TRP A 410 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 TRP A 410 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 410 " -0.073 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 410 " 0.066 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 410 " -0.020 2.00e-02 2.50e+03 pdb=" CH2 TRP A 410 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 410 " 0.114 2.00e-02 2.50e+03 5.66e-02 8.00e+01 pdb=" CG TRP C 410 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP C 410 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP C 410 " -0.041 2.00e-02 2.50e+03 pdb=" NE1 TRP C 410 " -0.038 2.00e-02 2.50e+03 pdb=" CE2 TRP C 410 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP C 410 " -0.063 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 410 " 0.076 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 410 " -0.035 2.00e-02 2.50e+03 pdb=" CH2 TRP C 410 " 0.050 2.00e-02 2.50e+03 ... (remaining 2197 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 523 2.75 - 3.29: 12244 3.29 - 3.83: 15994 3.83 - 4.36: 19935 4.36 - 4.90: 33011 Nonbonded interactions: 81707 Sorted by model distance: nonbonded pdb=" OE2 GLU B 52 " pdb=" NH1 ARG B 417 " model vdw 2.215 2.520 nonbonded pdb=" N ARG B 90 " pdb=" O ARG B 90 " model vdw 2.446 2.496 nonbonded pdb=" N ARG C 90 " pdb=" O ARG C 90 " model vdw 2.497 2.496 nonbonded pdb=" OE2 GLU B 15 " pdb=" NH1 ARG B 101 " model vdw 2.504 2.520 nonbonded pdb=" NH2 ARG A 162 " pdb=" O ASP A 356 " model vdw 2.507 2.520 ... (remaining 81702 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.110 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: 1.530 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 34.250 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.070 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 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 : 0.012 0.061 12324 Z= 0.754 Angle : 1.811 9.043 16768 Z= 1.214 Chirality : 0.097 0.346 1940 Planarity : 0.012 0.097 2200 Dihedral : 13.402 89.362 4472 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 1.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.19), residues: 1568 helix: -1.84 (0.27), residues: 250 sheet: -0.04 (0.26), residues: 344 loop : -0.87 (0.18), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.132 0.022 TRP B 410 HIS 0.009 0.002 HIS B 287 PHE 0.101 0.014 PHE D 280 TYR 0.103 0.022 TYR A 175 ARG 0.007 0.001 ARG C 158 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 680 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 THR cc_start: 0.9395 (p) cc_final: 0.9092 (t) REVERT: A 66 LYS cc_start: 0.8323 (mtpp) cc_final: 0.7827 (mtmm) REVERT: A 93 ASP cc_start: 0.8780 (m-30) cc_final: 0.8415 (m-30) REVERT: A 121 ASN cc_start: 0.9135 (t0) cc_final: 0.8730 (t0) REVERT: A 169 PHE cc_start: 0.9110 (m-80) cc_final: 0.8835 (m-10) REVERT: A 216 LYS cc_start: 0.9274 (mmtt) cc_final: 0.8946 (mmtt) REVERT: A 284 MET cc_start: 0.8832 (mmt) cc_final: 0.8409 (mmt) REVERT: A 291 GLN cc_start: 0.8961 (pm20) cc_final: 0.8633 (pm20) REVERT: A 311 LYS cc_start: 0.9423 (tttt) cc_final: 0.8892 (tttp) REVERT: A 317 ASP cc_start: 0.8293 (t0) cc_final: 0.7451 (t0) REVERT: A 319 SER cc_start: 0.8898 (m) cc_final: 0.8556 (p) REVERT: A 321 SER cc_start: 0.8526 (t) cc_final: 0.8080 (t) REVERT: A 331 ASN cc_start: 0.8957 (t0) cc_final: 0.8599 (t0) REVERT: A 336 ASP cc_start: 0.9144 (t0) cc_final: 0.8944 (t70) REVERT: A 349 ARG cc_start: 0.8271 (ttm-80) cc_final: 0.8068 (tpt-90) REVERT: A 356 ASP cc_start: 0.8799 (t0) cc_final: 0.8530 (t0) REVERT: A 357 ASP cc_start: 0.8637 (m-30) cc_final: 0.8187 (m-30) REVERT: A 359 ILE cc_start: 0.9279 (mt) cc_final: 0.8969 (mm) REVERT: B 45 ASN cc_start: 0.8674 (t0) cc_final: 0.8275 (t0) REVERT: B 48 TRP cc_start: 0.9173 (m100) cc_final: 0.8693 (m100) REVERT: B 135 ASP cc_start: 0.7792 (m-30) cc_final: 0.7560 (m-30) REVERT: B 180 TYR cc_start: 0.7959 (m-80) cc_final: 0.6696 (m-80) REVERT: B 213 ARG cc_start: 0.8022 (mtt-85) cc_final: 0.7644 (mtm-85) REVERT: B 230 VAL cc_start: 0.9173 (t) cc_final: 0.8887 (p) REVERT: B 249 LYS cc_start: 0.8410 (mtmt) cc_final: 0.8099 (mtpp) REVERT: B 284 MET cc_start: 0.8858 (mmm) cc_final: 0.8406 (mmt) REVERT: C 63 LEU cc_start: 0.7966 (mt) cc_final: 0.7729 (mp) REVERT: C 126 MET cc_start: 0.8437 (ttm) cc_final: 0.8090 (ttm) REVERT: C 143 ASP cc_start: 0.8340 (t70) cc_final: 0.8048 (t0) REVERT: C 145 TRP cc_start: 0.9426 (t60) cc_final: 0.9041 (t60) REVERT: C 279 LYS cc_start: 0.7771 (mttp) cc_final: 0.7156 (mmmt) REVERT: C 346 LYS cc_start: 0.8580 (tttt) cc_final: 0.8293 (ttmm) REVERT: C 359 ILE cc_start: 0.9236 (mt) cc_final: 0.8910 (mm) REVERT: C 389 ASN cc_start: 0.9165 (m-40) cc_final: 0.8481 (m110) REVERT: D 18 GLU cc_start: 0.8118 (tt0) cc_final: 0.7590 (mm-30) REVERT: D 42 ARG cc_start: 0.7543 (mmt180) cc_final: 0.7187 (mmt180) REVERT: D 96 ASP cc_start: 0.8308 (t0) cc_final: 0.7903 (t0) REVERT: D 116 GLU cc_start: 0.8181 (tt0) cc_final: 0.7980 (tt0) REVERT: D 126 MET cc_start: 0.8074 (ttm) cc_final: 0.7691 (ttp) REVERT: D 173 GLN cc_start: 0.7473 (tt0) cc_final: 0.7049 (tm-30) REVERT: D 216 LYS cc_start: 0.9275 (mmtt) cc_final: 0.8624 (mmmt) REVERT: D 243 LEU cc_start: 0.8338 (mt) cc_final: 0.8073 (mt) REVERT: D 253 ASP cc_start: 0.7502 (t0) cc_final: 0.7103 (t0) REVERT: D 279 LYS cc_start: 0.8322 (mttt) cc_final: 0.7809 (mmtt) REVERT: D 292 ASP cc_start: 0.9191 (p0) cc_final: 0.8529 (p0) REVERT: D 349 ARG cc_start: 0.8869 (ttm-80) cc_final: 0.8509 (mtp-110) REVERT: D 362 VAL cc_start: 0.9547 (t) cc_final: 0.9152 (m) REVERT: D 377 LYS cc_start: 0.8951 (tppt) cc_final: 0.8691 (tptt) outliers start: 0 outliers final: 0 residues processed: 680 average time/residue: 0.2401 time to fit residues: 226.9644 Evaluate side-chains 515 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 515 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 122 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 91 optimal weight: 30.0000 chunk 141 optimal weight: 9.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 HIS A 370 HIS A 389 ASN A 428 GLN B 74 ASN B 84 ASN B 369 ASN ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 ASN ** C 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 344 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12324 Z= 0.191 Angle : 0.622 6.801 16768 Z= 0.343 Chirality : 0.044 0.201 1940 Planarity : 0.004 0.040 2200 Dihedral : 6.575 50.713 1680 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 (0.20), residues: 1568 helix: -0.82 (0.30), residues: 256 sheet: 0.24 (0.25), residues: 430 loop : -0.82 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 241 HIS 0.005 0.001 HIS D 287 PHE 0.016 0.002 PHE B 147 TYR 0.012 0.001 TYR B 175 ARG 0.005 0.001 ARG A 101 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 570 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.8702 (tttm) cc_final: 0.8130 (tttm) REVERT: A 90 ARG cc_start: 0.7669 (mmm-85) cc_final: 0.7361 (mmm-85) REVERT: A 121 ASN cc_start: 0.8877 (t0) cc_final: 0.8169 (t0) REVERT: A 125 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7426 (mt-10) REVERT: A 213 ARG cc_start: 0.8002 (ptt180) cc_final: 0.7487 (ptt180) REVERT: A 284 MET cc_start: 0.8797 (mmt) cc_final: 0.8463 (mmt) REVERT: A 311 LYS cc_start: 0.9392 (tttt) cc_final: 0.8859 (tttm) REVERT: A 317 ASP cc_start: 0.8371 (t0) cc_final: 0.7924 (t0) REVERT: A 331 ASN cc_start: 0.8811 (t0) cc_final: 0.8425 (t0) REVERT: A 356 ASP cc_start: 0.8807 (t0) cc_final: 0.7674 (t0) REVERT: A 359 ILE cc_start: 0.9256 (mt) cc_final: 0.9019 (mm) REVERT: A 362 VAL cc_start: 0.9275 (t) cc_final: 0.9015 (m) REVERT: B 15 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8166 (mm-30) REVERT: B 48 TRP cc_start: 0.9123 (m100) cc_final: 0.8781 (m100) REVERT: B 249 LYS cc_start: 0.8503 (mtmt) cc_final: 0.8301 (mtpt) REVERT: B 268 LYS cc_start: 0.9023 (mtpt) cc_final: 0.8645 (mtpt) REVERT: B 284 MET cc_start: 0.8734 (mmm) cc_final: 0.8338 (mmt) REVERT: B 338 MET cc_start: 0.8616 (mmm) cc_final: 0.8204 (mmm) REVERT: C 48 TRP cc_start: 0.9143 (m100) cc_final: 0.8675 (m100) REVERT: C 71 LEU cc_start: 0.8407 (tp) cc_final: 0.8172 (tp) REVERT: C 75 VAL cc_start: 0.8887 (t) cc_final: 0.8593 (t) REVERT: C 81 GLU cc_start: 0.7904 (mp0) cc_final: 0.7627 (mp0) REVERT: C 97 GLU cc_start: 0.8227 (tt0) cc_final: 0.7944 (tt0) REVERT: C 131 ILE cc_start: 0.9311 (mm) cc_final: 0.8994 (mm) REVERT: C 143 ASP cc_start: 0.8095 (t70) cc_final: 0.7551 (t0) REVERT: C 145 TRP cc_start: 0.9349 (t60) cc_final: 0.9078 (t60) REVERT: C 234 GLN cc_start: 0.8567 (mt0) cc_final: 0.7834 (mp-120) REVERT: C 241 TRP cc_start: 0.8286 (m100) cc_final: 0.8017 (m100) REVERT: C 279 LYS cc_start: 0.7874 (mttp) cc_final: 0.7335 (mmmt) REVERT: C 327 TYR cc_start: 0.8504 (m-80) cc_final: 0.8232 (m-80) REVERT: C 344 ASN cc_start: 0.8088 (t0) cc_final: 0.7880 (t0) REVERT: C 359 ILE cc_start: 0.9239 (mt) cc_final: 0.8898 (mm) REVERT: C 389 ASN cc_start: 0.9034 (m-40) cc_final: 0.8074 (m110) REVERT: D 42 ARG cc_start: 0.7445 (mmt180) cc_final: 0.7110 (mmt180) REVERT: D 44 SER cc_start: 0.8679 (t) cc_final: 0.8408 (p) REVERT: D 85 ASP cc_start: 0.8881 (t0) cc_final: 0.8427 (t0) REVERT: D 118 LYS cc_start: 0.8860 (tppt) cc_final: 0.8403 (ttmm) REVERT: D 163 ASP cc_start: 0.8337 (t0) cc_final: 0.7986 (t0) REVERT: D 173 GLN cc_start: 0.7930 (tt0) cc_final: 0.7385 (tm-30) REVERT: D 216 LYS cc_start: 0.9288 (mmtt) cc_final: 0.8781 (mmmt) REVERT: D 241 TRP cc_start: 0.7384 (m100) cc_final: 0.6967 (m100) REVERT: D 292 ASP cc_start: 0.9250 (p0) cc_final: 0.8686 (p0) REVERT: D 338 MET cc_start: 0.7059 (mmt) cc_final: 0.6684 (mmm) REVERT: D 357 ASP cc_start: 0.8630 (t70) cc_final: 0.8104 (t70) REVERT: D 371 GLU cc_start: 0.8821 (pp20) cc_final: 0.8206 (pp20) REVERT: D 407 ILE cc_start: 0.7915 (pt) cc_final: 0.7542 (mt) outliers start: 0 outliers final: 0 residues processed: 570 average time/residue: 0.2266 time to fit residues: 187.8656 Evaluate side-chains 467 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 467 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 117 optimal weight: 10.0000 chunk 96 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 141 optimal weight: 7.9990 chunk 153 optimal weight: 8.9990 chunk 126 optimal weight: 4.9990 chunk 140 optimal weight: 20.0000 chunk 48 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 HIS A 74 ASN A 113 ASN ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN B 54 HIS B 370 HIS B 389 ASN C 88 GLN C 161 ASN ** C 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 389 ASN C 414 ASN D 74 ASN D 305 HIS D 364 GLN ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12324 Z= 0.293 Angle : 0.629 7.518 16768 Z= 0.342 Chirality : 0.045 0.183 1940 Planarity : 0.004 0.054 2200 Dihedral : 6.012 46.478 1680 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.08 % Allowed : 3.69 % Favored : 96.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.87 (0.20), residues: 1568 helix: -0.69 (0.30), residues: 266 sheet: 0.25 (0.25), residues: 430 loop : -0.94 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 410 HIS 0.004 0.001 HIS D 305 PHE 0.018 0.002 PHE B 170 TYR 0.015 0.002 TYR D 100 ARG 0.008 0.001 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 527 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8295 (mtm) cc_final: 0.8074 (mtm) REVERT: A 49 MET cc_start: 0.8768 (ttp) cc_final: 0.8519 (mtp) REVERT: A 116 GLU cc_start: 0.8663 (tp30) cc_final: 0.8461 (tp30) REVERT: A 121 ASN cc_start: 0.8922 (t0) cc_final: 0.8492 (t0) REVERT: A 284 MET cc_start: 0.8481 (mmt) cc_final: 0.8266 (mmt) REVERT: A 291 GLN cc_start: 0.8892 (pm20) cc_final: 0.8690 (pm20) REVERT: A 311 LYS cc_start: 0.9448 (tttt) cc_final: 0.8965 (tttm) REVERT: A 317 ASP cc_start: 0.8493 (t0) cc_final: 0.8163 (t0) REVERT: A 359 ILE cc_start: 0.9320 (mt) cc_final: 0.9108 (mm) REVERT: B 15 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8231 (mm-30) REVERT: B 110 LYS cc_start: 0.8805 (tmmt) cc_final: 0.8488 (tmmt) REVERT: B 135 ASP cc_start: 0.8192 (m-30) cc_final: 0.7947 (m-30) REVERT: B 249 LYS cc_start: 0.8493 (mtmt) cc_final: 0.8282 (mtpp) REVERT: B 268 LYS cc_start: 0.8984 (mtpt) cc_final: 0.8646 (mtpt) REVERT: B 338 MET cc_start: 0.8756 (mmm) cc_final: 0.8078 (tpp) REVERT: C 71 LEU cc_start: 0.8507 (tp) cc_final: 0.7944 (tt) REVERT: C 81 GLU cc_start: 0.7926 (mp0) cc_final: 0.7706 (mp0) REVERT: C 97 GLU cc_start: 0.8153 (tt0) cc_final: 0.7846 (tt0) REVERT: C 145 TRP cc_start: 0.9330 (t60) cc_final: 0.9078 (t60) REVERT: C 241 TRP cc_start: 0.8433 (m100) cc_final: 0.8206 (m100) REVERT: C 279 LYS cc_start: 0.7979 (mttp) cc_final: 0.7717 (mmmt) REVERT: C 344 ASN cc_start: 0.8078 (t0) cc_final: 0.7712 (t0) REVERT: C 357 ASP cc_start: 0.8610 (t0) cc_final: 0.8383 (t0) REVERT: C 359 ILE cc_start: 0.9215 (mt) cc_final: 0.8902 (mm) REVERT: C 361 ILE cc_start: 0.9471 (mt) cc_final: 0.9233 (mm) REVERT: C 363 SER cc_start: 0.8461 (t) cc_final: 0.8114 (t) REVERT: C 389 ASN cc_start: 0.8900 (m110) cc_final: 0.7812 (m110) REVERT: C 395 GLN cc_start: 0.9380 (tp40) cc_final: 0.9108 (tp40) REVERT: C 397 ASP cc_start: 0.8039 (t70) cc_final: 0.7733 (t70) REVERT: C 401 LEU cc_start: 0.7816 (mp) cc_final: 0.7526 (mp) REVERT: D 42 ARG cc_start: 0.7405 (mmt180) cc_final: 0.7043 (mmt180) REVERT: D 44 SER cc_start: 0.8637 (t) cc_final: 0.8251 (p) REVERT: D 66 LYS cc_start: 0.7176 (mmtm) cc_final: 0.6593 (tppt) REVERT: D 71 LEU cc_start: 0.7340 (tp) cc_final: 0.7056 (tp) REVERT: D 74 ASN cc_start: 0.9074 (m-40) cc_final: 0.8850 (m110) REVERT: D 110 LYS cc_start: 0.8553 (tttt) cc_final: 0.8343 (ttpt) REVERT: D 118 LYS cc_start: 0.8901 (tppt) cc_final: 0.8296 (ttmm) REVERT: D 163 ASP cc_start: 0.8421 (t0) cc_final: 0.8190 (t0) REVERT: D 216 LYS cc_start: 0.9117 (mmtt) cc_final: 0.8283 (mmmt) REVERT: D 234 GLN cc_start: 0.7831 (mp10) cc_final: 0.7549 (mp10) REVERT: D 241 TRP cc_start: 0.7865 (m100) cc_final: 0.7606 (m100) REVERT: D 279 LYS cc_start: 0.8211 (mmtp) cc_final: 0.7014 (mmtp) REVERT: D 281 LEU cc_start: 0.8346 (mp) cc_final: 0.8057 (mp) REVERT: D 292 ASP cc_start: 0.9260 (p0) cc_final: 0.8617 (p0) REVERT: D 320 LEU cc_start: 0.7754 (mp) cc_final: 0.7441 (mp) REVERT: D 338 MET cc_start: 0.7207 (mmt) cc_final: 0.6875 (mmm) REVERT: D 349 ARG cc_start: 0.8692 (ttm-80) cc_final: 0.8124 (ttm110) REVERT: D 357 ASP cc_start: 0.8650 (t70) cc_final: 0.8083 (t70) REVERT: D 371 GLU cc_start: 0.8918 (pp20) cc_final: 0.8541 (pp20) REVERT: D 407 ILE cc_start: 0.8094 (pt) cc_final: 0.7643 (mt) outliers start: 1 outliers final: 0 residues processed: 528 average time/residue: 0.2156 time to fit residues: 165.0154 Evaluate side-chains 473 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 473 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 67 optimal weight: 8.9990 chunk 95 optimal weight: 6.9990 chunk 142 optimal weight: 6.9990 chunk 150 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 134 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN A 329 ASN ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 ASN C 88 GLN ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 ASN C 414 ASN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 364 GLN ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12324 Z= 0.274 Angle : 0.604 8.656 16768 Z= 0.326 Chirality : 0.044 0.154 1940 Planarity : 0.004 0.044 2200 Dihedral : 5.687 45.807 1680 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.08 % Allowed : 2.62 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.86 (0.20), residues: 1568 helix: -0.51 (0.31), residues: 262 sheet: 0.13 (0.25), residues: 430 loop : -0.92 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP C 410 HIS 0.003 0.001 HIS B 370 PHE 0.013 0.002 PHE B 170 TYR 0.018 0.002 TYR C 100 ARG 0.005 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 532 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.8773 (ttp) cc_final: 0.8520 (mtp) REVERT: A 53 GLN cc_start: 0.8589 (pm20) cc_final: 0.7944 (pm20) REVERT: A 121 ASN cc_start: 0.8862 (t0) cc_final: 0.8463 (t0) REVERT: A 284 MET cc_start: 0.8482 (mmt) cc_final: 0.8266 (mmt) REVERT: A 311 LYS cc_start: 0.9507 (tttt) cc_final: 0.8993 (tttm) REVERT: A 317 ASP cc_start: 0.8419 (t0) cc_final: 0.8200 (t0) REVERT: A 385 ASP cc_start: 0.9319 (p0) cc_final: 0.8957 (p0) REVERT: B 15 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8256 (mm-30) REVERT: B 110 LYS cc_start: 0.8900 (tmmt) cc_final: 0.8660 (tmmt) REVERT: B 162 ARG cc_start: 0.9003 (tpp80) cc_final: 0.8720 (mmt90) REVERT: B 249 LYS cc_start: 0.8441 (mtmt) cc_final: 0.8188 (mtpp) REVERT: B 268 LYS cc_start: 0.8973 (mtpt) cc_final: 0.8635 (mtpt) REVERT: B 410 TRP cc_start: 0.9337 (t60) cc_final: 0.9072 (t60) REVERT: C 81 GLU cc_start: 0.7903 (mp0) cc_final: 0.7693 (mp0) REVERT: C 145 TRP cc_start: 0.9211 (t60) cc_final: 0.8765 (t60) REVERT: C 155 MET cc_start: 0.9005 (ttp) cc_final: 0.8649 (ttp) REVERT: C 279 LYS cc_start: 0.7993 (mttp) cc_final: 0.7768 (mmmt) REVERT: C 327 TYR cc_start: 0.8579 (m-80) cc_final: 0.8231 (m-10) REVERT: C 338 MET cc_start: 0.7562 (mmt) cc_final: 0.7102 (mmt) REVERT: C 344 ASN cc_start: 0.7942 (t0) cc_final: 0.7427 (t0) REVERT: C 359 ILE cc_start: 0.9237 (mt) cc_final: 0.8900 (mm) REVERT: C 425 LEU cc_start: 0.8944 (mt) cc_final: 0.8734 (mt) REVERT: D 42 ARG cc_start: 0.7434 (mmt180) cc_final: 0.7037 (mmt180) REVERT: D 44 SER cc_start: 0.8582 (t) cc_final: 0.8241 (p) REVERT: D 66 LYS cc_start: 0.7342 (mmtm) cc_final: 0.6777 (tppt) REVERT: D 116 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8218 (tm-30) REVERT: D 118 LYS cc_start: 0.8896 (tppt) cc_final: 0.8356 (ttmm) REVERT: D 163 ASP cc_start: 0.8347 (t0) cc_final: 0.8111 (t0) REVERT: D 164 MET cc_start: 0.4227 (ttp) cc_final: 0.3998 (ttp) REVERT: D 241 TRP cc_start: 0.7908 (m100) cc_final: 0.7617 (m100) REVERT: D 253 ASP cc_start: 0.7882 (t0) cc_final: 0.7579 (t0) REVERT: D 279 LYS cc_start: 0.8024 (mmtp) cc_final: 0.6846 (mmtp) REVERT: D 292 ASP cc_start: 0.9354 (p0) cc_final: 0.8459 (p0) REVERT: D 320 LEU cc_start: 0.7918 (mp) cc_final: 0.7605 (mp) REVERT: D 338 MET cc_start: 0.7352 (mmt) cc_final: 0.7005 (mmm) REVERT: D 370 HIS cc_start: 0.8927 (m-70) cc_final: 0.8481 (m90) REVERT: D 371 GLU cc_start: 0.8977 (pp20) cc_final: 0.8492 (pp20) REVERT: D 407 ILE cc_start: 0.8025 (pt) cc_final: 0.7622 (mt) outliers start: 1 outliers final: 0 residues processed: 533 average time/residue: 0.2069 time to fit residues: 160.7028 Evaluate side-chains 469 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 469 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 2 optimal weight: 0.0170 chunk 112 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 chunk 128 optimal weight: 6.9990 chunk 104 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 135 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 overall best weight: 5.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN A 113 ASN ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN C 88 GLN ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 ASN D 74 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12324 Z= 0.283 Angle : 0.599 6.378 16768 Z= 0.324 Chirality : 0.044 0.177 1940 Planarity : 0.004 0.050 2200 Dihedral : 5.625 42.821 1680 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.89 (0.20), residues: 1568 helix: -0.48 (0.31), residues: 260 sheet: 0.09 (0.25), residues: 430 loop : -0.95 (0.20), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 410 HIS 0.003 0.001 HIS B 370 PHE 0.013 0.002 PHE C 170 TYR 0.022 0.002 TYR D 100 ARG 0.005 0.000 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 528 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.8790 (ttp) cc_final: 0.8521 (mtp) REVERT: A 53 GLN cc_start: 0.8651 (pm20) cc_final: 0.8014 (pm20) REVERT: A 121 ASN cc_start: 0.8867 (t0) cc_final: 0.8483 (t0) REVERT: A 164 MET cc_start: 0.6629 (mpp) cc_final: 0.5547 (mpp) REVERT: A 284 MET cc_start: 0.8460 (mmt) cc_final: 0.8239 (mmt) REVERT: A 311 LYS cc_start: 0.9448 (tttt) cc_final: 0.8956 (tttm) REVERT: A 385 ASP cc_start: 0.9300 (p0) cc_final: 0.8989 (p0) REVERT: B 162 ARG cc_start: 0.9044 (tpp80) cc_final: 0.8744 (mmt90) REVERT: B 249 LYS cc_start: 0.8467 (mtmt) cc_final: 0.8153 (mtpp) REVERT: B 268 LYS cc_start: 0.8974 (mtpt) cc_final: 0.8635 (mtpt) REVERT: B 320 LEU cc_start: 0.9353 (mp) cc_final: 0.9148 (mp) REVERT: B 410 TRP cc_start: 0.9329 (t60) cc_final: 0.9109 (t60) REVERT: B 425 LEU cc_start: 0.9150 (mp) cc_final: 0.8902 (mp) REVERT: C 81 GLU cc_start: 0.7923 (mp0) cc_final: 0.7713 (mp0) REVERT: C 145 TRP cc_start: 0.9172 (t60) cc_final: 0.8733 (t60) REVERT: C 159 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7847 (mt-10) REVERT: C 327 TYR cc_start: 0.8606 (m-80) cc_final: 0.8237 (m-10) REVERT: C 333 SER cc_start: 0.9165 (p) cc_final: 0.8937 (p) REVERT: C 344 ASN cc_start: 0.8154 (t0) cc_final: 0.7634 (t0) REVERT: C 359 ILE cc_start: 0.9306 (mt) cc_final: 0.9004 (mm) REVERT: D 42 ARG cc_start: 0.7433 (mmt180) cc_final: 0.7052 (mmt180) REVERT: D 44 SER cc_start: 0.8590 (t) cc_final: 0.8239 (p) REVERT: D 66 LYS cc_start: 0.7381 (mmtm) cc_final: 0.6842 (tppt) REVERT: D 84 ASN cc_start: 0.7983 (p0) cc_final: 0.7616 (p0) REVERT: D 116 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8239 (tm-30) REVERT: D 118 LYS cc_start: 0.8859 (tppt) cc_final: 0.8319 (ttmm) REVERT: D 163 ASP cc_start: 0.8288 (t0) cc_final: 0.8028 (t0) REVERT: D 241 TRP cc_start: 0.7875 (m100) cc_final: 0.7548 (m100) REVERT: D 253 ASP cc_start: 0.8098 (t0) cc_final: 0.7669 (t0) REVERT: D 279 LYS cc_start: 0.8030 (mmtp) cc_final: 0.7219 (mmtm) REVERT: D 292 ASP cc_start: 0.9287 (p0) cc_final: 0.8556 (p0) REVERT: D 320 LEU cc_start: 0.7827 (mp) cc_final: 0.7610 (mp) REVERT: D 349 ARG cc_start: 0.8573 (ttm-80) cc_final: 0.8112 (ttm110) REVERT: D 370 HIS cc_start: 0.8861 (m-70) cc_final: 0.8476 (m90) REVERT: D 371 GLU cc_start: 0.8966 (pp20) cc_final: 0.8419 (pp20) outliers start: 0 outliers final: 0 residues processed: 528 average time/residue: 0.2070 time to fit residues: 160.1191 Evaluate side-chains 468 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 468 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 6.9990 chunk 135 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 150 optimal weight: 20.0000 chunk 125 optimal weight: 4.9990 chunk 69 optimal weight: 20.0000 chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 GLN ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 ASN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 428 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12324 Z= 0.273 Angle : 0.608 10.002 16768 Z= 0.324 Chirality : 0.043 0.148 1940 Planarity : 0.004 0.049 2200 Dihedral : 5.565 42.951 1680 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.91 (0.20), residues: 1568 helix: -0.34 (0.31), residues: 260 sheet: 0.08 (0.25), residues: 428 loop : -1.02 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 354 HIS 0.003 0.001 HIS B 370 PHE 0.027 0.002 PHE B 156 TYR 0.014 0.002 TYR C 100 ARG 0.006 0.000 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 522 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.8821 (ttp) cc_final: 0.8527 (mtp) REVERT: A 121 ASN cc_start: 0.8879 (t0) cc_final: 0.8503 (t0) REVERT: A 284 MET cc_start: 0.8415 (mmt) cc_final: 0.8050 (mmt) REVERT: A 291 GLN cc_start: 0.8937 (pm20) cc_final: 0.8715 (pm20) REVERT: A 311 LYS cc_start: 0.9463 (tttt) cc_final: 0.8971 (tttm) REVERT: B 162 ARG cc_start: 0.9084 (tpp80) cc_final: 0.8809 (mmt90) REVERT: B 249 LYS cc_start: 0.8424 (mtmt) cc_final: 0.8108 (mtpp) REVERT: B 268 LYS cc_start: 0.8918 (mtpt) cc_final: 0.8601 (mtpt) REVERT: B 336 ASP cc_start: 0.8369 (t70) cc_final: 0.8158 (t0) REVERT: B 376 MET cc_start: 0.7584 (ttm) cc_final: 0.7380 (ttm) REVERT: B 425 LEU cc_start: 0.9169 (mp) cc_final: 0.8925 (mp) REVERT: C 145 TRP cc_start: 0.9151 (t60) cc_final: 0.8738 (t60) REVERT: C 327 TYR cc_start: 0.8636 (m-80) cc_final: 0.8267 (m-10) REVERT: C 333 SER cc_start: 0.9182 (p) cc_final: 0.8962 (p) REVERT: C 344 ASN cc_start: 0.8135 (t0) cc_final: 0.7567 (t0) REVERT: C 359 ILE cc_start: 0.9307 (mt) cc_final: 0.9035 (mm) REVERT: C 395 GLN cc_start: 0.9354 (tp-100) cc_final: 0.8872 (tp-100) REVERT: D 44 SER cc_start: 0.8524 (t) cc_final: 0.8186 (p) REVERT: D 66 LYS cc_start: 0.7411 (mmtm) cc_final: 0.6861 (tppt) REVERT: D 84 ASN cc_start: 0.8221 (p0) cc_final: 0.7919 (p0) REVERT: D 116 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8251 (tm-30) REVERT: D 118 LYS cc_start: 0.8844 (tppt) cc_final: 0.8297 (ttmm) REVERT: D 163 ASP cc_start: 0.8518 (t0) cc_final: 0.8201 (t0) REVERT: D 177 LYS cc_start: 0.9161 (mmmm) cc_final: 0.8909 (mttp) REVERT: D 216 LYS cc_start: 0.9139 (mmmt) cc_final: 0.8813 (mmtt) REVERT: D 241 TRP cc_start: 0.7838 (m100) cc_final: 0.7411 (m100) REVERT: D 279 LYS cc_start: 0.7990 (mmtp) cc_final: 0.7186 (mmtm) REVERT: D 292 ASP cc_start: 0.9261 (p0) cc_final: 0.8485 (p0) REVERT: D 321 SER cc_start: 0.8736 (t) cc_final: 0.8144 (t) REVERT: D 324 GLN cc_start: 0.8758 (mt0) cc_final: 0.7980 (mp10) REVERT: D 349 ARG cc_start: 0.8564 (ttm-80) cc_final: 0.8037 (ttm110) REVERT: D 370 HIS cc_start: 0.8892 (m-70) cc_final: 0.8467 (m90) REVERT: D 371 GLU cc_start: 0.8967 (pp20) cc_final: 0.8406 (pp20) REVERT: D 407 ILE cc_start: 0.8034 (pt) cc_final: 0.7663 (mt) outliers start: 0 outliers final: 0 residues processed: 522 average time/residue: 0.2133 time to fit residues: 161.8442 Evaluate side-chains 476 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 476 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 0.0670 chunk 17 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 110 optimal weight: 0.9990 chunk 127 optimal weight: 6.9990 chunk 84 optimal weight: 0.2980 chunk 150 optimal weight: 0.7980 chunk 94 optimal weight: 6.9990 chunk 91 optimal weight: 20.0000 chunk 69 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 overall best weight: 1.4322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN A 113 ASN ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 GLN ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 ASN D 74 ASN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12324 Z= 0.143 Angle : 0.540 10.821 16768 Z= 0.287 Chirality : 0.042 0.152 1940 Planarity : 0.004 0.050 2200 Dihedral : 4.976 48.039 1680 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.64 (0.21), residues: 1568 helix: 0.13 (0.31), residues: 266 sheet: 0.31 (0.26), residues: 418 loop : -0.96 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 410 HIS 0.004 0.000 HIS D 287 PHE 0.018 0.001 PHE C 169 TYR 0.017 0.001 TYR D 100 ARG 0.005 0.000 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 569 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLN cc_start: 0.8640 (pm20) cc_final: 0.8343 (pm20) REVERT: A 249 LYS cc_start: 0.7837 (mtpp) cc_final: 0.7500 (mtpt) REVERT: A 268 LYS cc_start: 0.8658 (mtmm) cc_final: 0.8375 (ptpp) REVERT: A 284 MET cc_start: 0.8374 (mmt) cc_final: 0.7955 (mmt) REVERT: A 311 LYS cc_start: 0.9514 (tttt) cc_final: 0.9153 (tttm) REVERT: A 317 ASP cc_start: 0.8473 (t0) cc_final: 0.8262 (t0) REVERT: A 331 ASN cc_start: 0.9004 (t0) cc_final: 0.8700 (t0) REVERT: B 83 ASP cc_start: 0.8952 (t0) cc_final: 0.8663 (t0) REVERT: B 118 LYS cc_start: 0.9168 (tppp) cc_final: 0.8847 (ttpt) REVERT: B 164 MET cc_start: 0.7965 (mmm) cc_final: 0.7277 (tpp) REVERT: B 228 ILE cc_start: 0.9370 (mm) cc_final: 0.9156 (mm) REVERT: B 268 LYS cc_start: 0.8927 (mtpt) cc_final: 0.8593 (mtpt) REVERT: B 376 MET cc_start: 0.7648 (ttm) cc_final: 0.7393 (ttm) REVERT: C 71 LEU cc_start: 0.8494 (tp) cc_final: 0.8052 (tt) REVERT: C 81 GLU cc_start: 0.7954 (mp0) cc_final: 0.7722 (mp0) REVERT: C 145 TRP cc_start: 0.9135 (t60) cc_final: 0.8805 (t60) REVERT: C 159 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7641 (mt-10) REVERT: C 327 TYR cc_start: 0.8592 (m-80) cc_final: 0.8098 (m-10) REVERT: C 333 SER cc_start: 0.9142 (p) cc_final: 0.8904 (p) REVERT: C 344 ASN cc_start: 0.7981 (t0) cc_final: 0.7548 (t0) REVERT: C 359 ILE cc_start: 0.9199 (mt) cc_final: 0.8907 (mm) REVERT: D 42 ARG cc_start: 0.7361 (mmt180) cc_final: 0.7032 (mmt180) REVERT: D 66 LYS cc_start: 0.7428 (mmtm) cc_final: 0.6892 (tppt) REVERT: D 84 ASN cc_start: 0.8276 (p0) cc_final: 0.7932 (p0) REVERT: D 116 GLU cc_start: 0.8438 (tm-30) cc_final: 0.8147 (tm-30) REVERT: D 118 LYS cc_start: 0.8849 (tppt) cc_final: 0.8292 (ttmt) REVERT: D 163 ASP cc_start: 0.8395 (t0) cc_final: 0.8078 (t0) REVERT: D 177 LYS cc_start: 0.9144 (mmmm) cc_final: 0.8941 (mttp) REVERT: D 241 TRP cc_start: 0.7734 (m100) cc_final: 0.7424 (m100) REVERT: D 292 ASP cc_start: 0.9248 (p0) cc_final: 0.8533 (p0) REVERT: D 320 LEU cc_start: 0.7825 (mp) cc_final: 0.7625 (mp) REVERT: D 349 ARG cc_start: 0.8423 (ttm-80) cc_final: 0.8176 (ttm110) REVERT: D 370 HIS cc_start: 0.8868 (m-70) cc_final: 0.8348 (m90) REVERT: D 371 GLU cc_start: 0.8965 (pp20) cc_final: 0.8380 (pp20) REVERT: D 407 ILE cc_start: 0.7895 (pt) cc_final: 0.7627 (mt) REVERT: D 417 ARG cc_start: 0.9238 (ttp-170) cc_final: 0.8953 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 569 average time/residue: 0.2077 time to fit residues: 172.4646 Evaluate side-chains 488 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 488 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 45 optimal weight: 0.0470 chunk 29 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 chunk 118 optimal weight: 9.9990 chunk 136 optimal weight: 30.0000 chunk 144 optimal weight: 10.0000 overall best weight: 2.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 74 ASN ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 ASN A 234 GLN ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 ASN D 283 GLN D 329 ASN ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12324 Z= 0.189 Angle : 0.553 7.005 16768 Z= 0.294 Chirality : 0.042 0.195 1940 Planarity : 0.004 0.050 2200 Dihedral : 4.979 46.806 1680 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.63 (0.21), residues: 1568 helix: 0.23 (0.31), residues: 264 sheet: 0.27 (0.26), residues: 420 loop : -0.96 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 410 HIS 0.004 0.001 HIS D 287 PHE 0.014 0.001 PHE D 169 TYR 0.018 0.001 TYR B 175 ARG 0.004 0.000 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 554 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 THR cc_start: 0.9360 (p) cc_final: 0.9099 (t) REVERT: A 53 GLN cc_start: 0.8657 (pm20) cc_final: 0.8340 (pm20) REVERT: A 241 TRP cc_start: 0.7847 (p-90) cc_final: 0.7565 (p-90) REVERT: A 249 LYS cc_start: 0.7998 (mtpp) cc_final: 0.7668 (mtpt) REVERT: A 268 LYS cc_start: 0.8716 (mtmm) cc_final: 0.8497 (ptpp) REVERT: A 311 LYS cc_start: 0.9462 (tttt) cc_final: 0.8974 (tttm) REVERT: B 15 GLU cc_start: 0.7696 (mm-30) cc_final: 0.6958 (mm-30) REVERT: B 83 ASP cc_start: 0.8972 (t0) cc_final: 0.8715 (t0) REVERT: B 118 LYS cc_start: 0.9168 (tppp) cc_final: 0.8862 (ttpt) REVERT: B 164 MET cc_start: 0.7956 (mmm) cc_final: 0.7252 (tpp) REVERT: B 268 LYS cc_start: 0.8934 (mtpt) cc_final: 0.8622 (mtpt) REVERT: B 376 MET cc_start: 0.7157 (ttm) cc_final: 0.6875 (ttm) REVERT: B 417 ARG cc_start: 0.9409 (mtm-85) cc_final: 0.9120 (mtm110) REVERT: B 425 LEU cc_start: 0.9093 (mp) cc_final: 0.8859 (mp) REVERT: C 40 MET cc_start: 0.7957 (ttm) cc_final: 0.7733 (ttm) REVERT: C 71 LEU cc_start: 0.8509 (tp) cc_final: 0.8063 (tt) REVERT: C 81 GLU cc_start: 0.8150 (mp0) cc_final: 0.7929 (mp0) REVERT: C 159 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7668 (mt-10) REVERT: C 327 TYR cc_start: 0.8643 (m-80) cc_final: 0.8159 (m-10) REVERT: C 333 SER cc_start: 0.9145 (p) cc_final: 0.8934 (p) REVERT: C 344 ASN cc_start: 0.7978 (t0) cc_final: 0.7582 (t0) REVERT: C 359 ILE cc_start: 0.9299 (mt) cc_final: 0.8998 (mm) REVERT: C 395 GLN cc_start: 0.9277 (tp40) cc_final: 0.8849 (tp-100) REVERT: D 42 ARG cc_start: 0.7436 (mmt180) cc_final: 0.7090 (mmt180) REVERT: D 66 LYS cc_start: 0.7453 (mmtm) cc_final: 0.6910 (tppt) REVERT: D 84 ASN cc_start: 0.8319 (p0) cc_final: 0.7970 (p0) REVERT: D 116 GLU cc_start: 0.8436 (tm-30) cc_final: 0.8134 (tm-30) REVERT: D 118 LYS cc_start: 0.8813 (tppt) cc_final: 0.8187 (ttpt) REVERT: D 163 ASP cc_start: 0.8449 (t0) cc_final: 0.8140 (t0) REVERT: D 177 LYS cc_start: 0.9175 (mmmm) cc_final: 0.8964 (mttp) REVERT: D 216 LYS cc_start: 0.8792 (mmmt) cc_final: 0.8536 (mmtt) REVERT: D 292 ASP cc_start: 0.9245 (p0) cc_final: 0.8564 (p0) REVERT: D 320 LEU cc_start: 0.7907 (mp) cc_final: 0.7696 (mp) REVERT: D 349 ARG cc_start: 0.8432 (ttm-80) cc_final: 0.7877 (ttm110) REVERT: D 370 HIS cc_start: 0.8846 (m-70) cc_final: 0.8305 (m90) REVERT: D 371 GLU cc_start: 0.8988 (pp20) cc_final: 0.8369 (pp20) REVERT: D 407 ILE cc_start: 0.7950 (pt) cc_final: 0.7640 (mt) REVERT: D 417 ARG cc_start: 0.9255 (ttp-170) cc_final: 0.8941 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 554 average time/residue: 0.2009 time to fit residues: 163.5142 Evaluate side-chains 487 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 487 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 144 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 chunk 61 optimal weight: 9.9990 chunk 110 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 74 ASN A 234 GLN B 74 ASN ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 ASN D 7 GLN D 251 ASN D 283 GLN D 329 ASN D 395 GLN ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12324 Z= 0.219 Angle : 0.586 10.342 16768 Z= 0.305 Chirality : 0.043 0.194 1940 Planarity : 0.004 0.051 2200 Dihedral : 5.081 46.449 1680 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.08 % Allowed : 0.62 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.67 (0.21), residues: 1568 helix: 0.16 (0.32), residues: 254 sheet: 0.31 (0.26), residues: 418 loop : -0.99 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 410 HIS 0.004 0.001 HIS D 287 PHE 0.014 0.001 PHE C 86 TYR 0.028 0.001 TYR D 100 ARG 0.004 0.000 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 545 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLN cc_start: 0.8636 (pm20) cc_final: 0.7920 (pm20) REVERT: A 268 LYS cc_start: 0.8724 (mtmm) cc_final: 0.8443 (ptpp) REVERT: A 311 LYS cc_start: 0.9456 (tttt) cc_final: 0.8977 (tttm) REVERT: A 317 ASP cc_start: 0.8512 (t0) cc_final: 0.8277 (t0) REVERT: A 331 ASN cc_start: 0.8979 (t0) cc_final: 0.8651 (t0) REVERT: B 15 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7334 (mm-30) REVERT: B 83 ASP cc_start: 0.9010 (t0) cc_final: 0.8735 (t0) REVERT: B 164 MET cc_start: 0.8039 (mmm) cc_final: 0.7356 (tpp) REVERT: B 268 LYS cc_start: 0.8874 (mtpt) cc_final: 0.8567 (mtpt) REVERT: B 376 MET cc_start: 0.6826 (ttm) cc_final: 0.6535 (ttm) REVERT: B 425 LEU cc_start: 0.9170 (mp) cc_final: 0.8917 (mp) REVERT: C 40 MET cc_start: 0.7821 (ttm) cc_final: 0.7618 (ttm) REVERT: C 71 LEU cc_start: 0.8486 (tp) cc_final: 0.8180 (tt) REVERT: C 81 GLU cc_start: 0.8113 (mp0) cc_final: 0.7904 (mp0) REVERT: C 145 TRP cc_start: 0.9289 (t60) cc_final: 0.8827 (t60) REVERT: C 159 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7743 (mt-10) REVERT: C 333 SER cc_start: 0.9158 (p) cc_final: 0.8945 (p) REVERT: C 344 ASN cc_start: 0.8212 (t0) cc_final: 0.7670 (t0) REVERT: C 359 ILE cc_start: 0.9306 (mt) cc_final: 0.9002 (mm) REVERT: C 395 GLN cc_start: 0.9272 (tp40) cc_final: 0.8841 (tp-100) REVERT: D 42 ARG cc_start: 0.7456 (mmt180) cc_final: 0.7135 (mmt180) REVERT: D 66 LYS cc_start: 0.7487 (mmtm) cc_final: 0.6925 (tppt) REVERT: D 84 ASN cc_start: 0.8366 (p0) cc_final: 0.7976 (p0) REVERT: D 116 GLU cc_start: 0.8363 (tm-30) cc_final: 0.8097 (tm-30) REVERT: D 118 LYS cc_start: 0.8824 (tppt) cc_final: 0.8201 (ttpt) REVERT: D 163 ASP cc_start: 0.8468 (t0) cc_final: 0.8158 (t0) REVERT: D 174 ASP cc_start: 0.8583 (m-30) cc_final: 0.8381 (m-30) REVERT: D 216 LYS cc_start: 0.8822 (mmmt) cc_final: 0.8600 (mmtt) REVERT: D 279 LYS cc_start: 0.8024 (mmtp) cc_final: 0.7202 (mmtm) REVERT: D 292 ASP cc_start: 0.9254 (p0) cc_final: 0.8501 (p0) REVERT: D 320 LEU cc_start: 0.8013 (mp) cc_final: 0.7711 (mp) REVERT: D 321 SER cc_start: 0.8621 (t) cc_final: 0.8125 (t) REVERT: D 324 GLN cc_start: 0.8723 (mt0) cc_final: 0.8044 (mp10) REVERT: D 349 ARG cc_start: 0.8539 (ttm-80) cc_final: 0.8258 (ttm110) REVERT: D 370 HIS cc_start: 0.8904 (m-70) cc_final: 0.8411 (m90) REVERT: D 371 GLU cc_start: 0.8964 (pp20) cc_final: 0.8368 (pp20) REVERT: D 407 ILE cc_start: 0.7931 (pt) cc_final: 0.7581 (mt) REVERT: D 417 ARG cc_start: 0.9262 (ttp-170) cc_final: 0.8929 (mtm-85) outliers start: 1 outliers final: 0 residues processed: 545 average time/residue: 0.2087 time to fit residues: 167.4831 Evaluate side-chains 486 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 486 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 155 optimal weight: 0.5980 chunk 143 optimal weight: 10.0000 chunk 123 optimal weight: 20.0000 chunk 12 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 74 ASN B 74 ASN ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 ASN D 74 ASN D 251 ASN D 395 GLN ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.4935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12324 Z= 0.138 Angle : 0.557 12.470 16768 Z= 0.287 Chirality : 0.042 0.198 1940 Planarity : 0.004 0.051 2200 Dihedral : 4.699 50.809 1680 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.08 % Allowed : 0.38 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 (0.21), residues: 1568 helix: 0.26 (0.31), residues: 276 sheet: 0.59 (0.26), residues: 400 loop : -1.01 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 410 HIS 0.005 0.001 HIS D 287 PHE 0.016 0.001 PHE D 169 TYR 0.027 0.001 TYR D 100 ARG 0.004 0.000 ARG C 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 538 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 THR cc_start: 0.9338 (p) cc_final: 0.9084 (t) REVERT: A 53 GLN cc_start: 0.8505 (pm20) cc_final: 0.8244 (pm20) REVERT: A 155 MET cc_start: 0.8641 (ttp) cc_final: 0.8361 (ttp) REVERT: A 249 LYS cc_start: 0.8162 (mtpp) cc_final: 0.7594 (mtpt) REVERT: A 311 LYS cc_start: 0.9503 (tttt) cc_final: 0.9050 (tttm) REVERT: B 5 GLU cc_start: 0.8561 (tt0) cc_final: 0.8018 (tm-30) REVERT: B 7 GLN cc_start: 0.8185 (pt0) cc_final: 0.7944 (pp30) REVERT: B 15 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7529 (mm-30) REVERT: B 28 GLN cc_start: 0.9323 (mm-40) cc_final: 0.9061 (mm-40) REVERT: B 83 ASP cc_start: 0.8869 (t0) cc_final: 0.8636 (t0) REVERT: B 164 MET cc_start: 0.7875 (mmm) cc_final: 0.7253 (tpp) REVERT: B 268 LYS cc_start: 0.8900 (mtpt) cc_final: 0.8594 (mtpt) REVERT: B 376 MET cc_start: 0.6911 (ttm) cc_final: 0.6589 (ttm) REVERT: C 71 LEU cc_start: 0.8422 (tp) cc_final: 0.8138 (tt) REVERT: C 81 GLU cc_start: 0.8058 (mp0) cc_final: 0.7849 (mp0) REVERT: C 145 TRP cc_start: 0.9180 (t60) cc_final: 0.8004 (t60) REVERT: C 159 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7570 (mt-10) REVERT: C 344 ASN cc_start: 0.8048 (t0) cc_final: 0.7530 (t0) REVERT: C 359 ILE cc_start: 0.9281 (mt) cc_final: 0.9004 (mm) REVERT: D 24 THR cc_start: 0.8879 (p) cc_final: 0.8618 (p) REVERT: D 42 ARG cc_start: 0.7384 (mmt180) cc_final: 0.7105 (mmt180) REVERT: D 66 LYS cc_start: 0.7380 (mmtm) cc_final: 0.6789 (tppt) REVERT: D 84 ASN cc_start: 0.8189 (p0) cc_final: 0.7797 (p0) REVERT: D 116 GLU cc_start: 0.8324 (tm-30) cc_final: 0.8014 (tm-30) REVERT: D 118 LYS cc_start: 0.8793 (tppt) cc_final: 0.8130 (ttpt) REVERT: D 163 ASP cc_start: 0.8471 (t0) cc_final: 0.8168 (t0) REVERT: D 173 GLN cc_start: 0.8833 (tm-30) cc_final: 0.8393 (tm-30) REVERT: D 174 ASP cc_start: 0.8362 (m-30) cc_final: 0.8054 (m-30) REVERT: D 177 LYS cc_start: 0.9100 (mttt) cc_final: 0.8879 (mttp) REVERT: D 216 LYS cc_start: 0.8828 (mmmt) cc_final: 0.8554 (mmtt) REVERT: D 242 GLN cc_start: 0.7750 (tm-30) cc_final: 0.7503 (tm-30) REVERT: D 292 ASP cc_start: 0.9257 (p0) cc_final: 0.8557 (p0) REVERT: D 370 HIS cc_start: 0.8895 (m-70) cc_final: 0.8441 (m90) REVERT: D 371 GLU cc_start: 0.8958 (pp20) cc_final: 0.8404 (pp20) REVERT: D 407 ILE cc_start: 0.7854 (pt) cc_final: 0.7579 (mt) outliers start: 1 outliers final: 0 residues processed: 538 average time/residue: 0.2030 time to fit residues: 161.7474 Evaluate side-chains 498 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 498 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 114 optimal weight: 0.1980 chunk 18 optimal weight: 0.7980 chunk 34 optimal weight: 8.9990 chunk 123 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 15 optimal weight: 20.0000 chunk 22 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 GLN ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 ASN C 395 GLN D 251 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.127596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.107779 restraints weight = 18438.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.111521 restraints weight = 9399.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.114029 restraints weight = 5796.497| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.4975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12324 Z= 0.164 Angle : 0.559 12.158 16768 Z= 0.288 Chirality : 0.042 0.207 1940 Planarity : 0.004 0.054 2200 Dihedral : 4.694 49.560 1680 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.08 % Allowed : 0.23 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.52 (0.21), residues: 1568 helix: 0.31 (0.31), residues: 276 sheet: 0.60 (0.26), residues: 412 loop : -1.04 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 410 HIS 0.004 0.001 HIS D 287 PHE 0.016 0.001 PHE C 86 TYR 0.025 0.002 TYR B 100 ARG 0.006 0.000 ARG C 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3251.50 seconds wall clock time: 58 minutes 45.36 seconds (3525.36 seconds total)