Starting phenix.real_space_refine on Tue Jun 25 23:45:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tuz_26136/06_2024/7tuz_26136_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tuz_26136/06_2024/7tuz_26136.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tuz_26136/06_2024/7tuz_26136.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tuz_26136/06_2024/7tuz_26136.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tuz_26136/06_2024/7tuz_26136_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tuz_26136/06_2024/7tuz_26136_updated.pdb" } resolution = 3.12 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= 0.002 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 68 5.16 5 C 5681 2.51 5 N 1504 2.21 5 O 1657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ASP 22": "OD1" <-> "OD2" Residue "R ARG 31": "NH1" <-> "NH2" Residue "R TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 77": "OD1" <-> "OD2" Residue "R ARG 87": "NH1" <-> "NH2" Residue "R ARG 129": "NH1" <-> "NH2" Residue "R ARG 273": "NH1" <-> "NH2" Residue "R ARG 283": "NH1" <-> "NH2" Residue "A GLU 236": "OE1" <-> "OE2" Residue "A ASP 237": "OD1" <-> "OD2" Residue "A GLU 239": "OE1" <-> "OE2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B ASP 20": "OD1" <-> "OD2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 76": "OD1" <-> "OD2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "B PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 312": "OD1" <-> "OD2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "E PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 62": "OD1" <-> "OD2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E ASP 201": "OD1" <-> "OD2" Residue "E PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 220": "OE1" <-> "OE2" Residue "E GLU 222": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 8910 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2214 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 11, 'TRANS': 272} Chain breaks: 2 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "A" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1823 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 224} Chain breaks: 1 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "C" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 454 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 4, 'TRANS': 54} Chain: "E" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1782 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "R" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'KJX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.76, per 1000 atoms: 0.65 Number of scatterers: 8910 At special positions: 0 Unit cell: (104.125, 119.119, 110.789, 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 68 16.00 O 1657 8.00 N 1504 7.00 C 5681 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 104 " - pdb=" SG CYS R 181 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.04 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: 3.35 Conformation dependent library (CDL) restraints added in 1.5 seconds 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2142 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 13 sheets defined 34.6% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'R' and resid 25 through 58 removed outlier: 4.128A pdb=" N SER R 28 " --> pdb=" O ALA R 25 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA R 30 " --> pdb=" O HIS R 27 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG R 31 " --> pdb=" O SER R 28 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N MET R 34 " --> pdb=" O ARG R 31 " (cutoff:3.500A) Proline residue: R 35 - end of helix removed outlier: 3.531A pdb=" N ILE R 44 " --> pdb=" O VAL R 41 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY R 48 " --> pdb=" O GLY R 45 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU R 50 " --> pdb=" O VAL R 47 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU R 51 " --> pdb=" O GLY R 48 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLN R 58 " --> pdb=" O VAL R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 89 Proline residue: R 85 - end of helix removed outlier: 4.562A pdb=" N ALA R 89 " --> pdb=" O PRO R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 133 removed outlier: 4.066A pdb=" N PHE R 111 " --> pdb=" O ALA R 108 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE R 113 " --> pdb=" O VAL R 110 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N THR R 115 " --> pdb=" O TYR R 112 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASN R 120 " --> pdb=" O ALA R 117 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LEU R 125 " --> pdb=" O MET R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 141 Processing helix chain 'R' and resid 145 through 167 Proline residue: R 165 - end of helix Processing helix chain 'R' and resid 184 through 187 No H-bonds generated for 'chain 'R' and resid 184 through 187' Processing helix chain 'R' and resid 193 through 229 removed outlier: 4.620A pdb=" N LEU R 198 " --> pdb=" O PRO R 194 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY R 199 " --> pdb=" O TRP R 195 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N LEU R 207 " --> pdb=" O ILE R 203 " (cutoff:3.500A) Proline residue: R 208 - end of helix Processing helix chain 'R' and resid 231 through 236 Processing helix chain 'R' and resid 238 through 273 removed outlier: 4.064A pdb=" N ALA R 242 " --> pdb=" O VAL R 238 " (cutoff:3.500A) Proline residue: R 259 - end of helix Processing helix chain 'R' and resid 282 through 311 removed outlier: 4.151A pdb=" N CYS R 295 " --> pdb=" O HIS R 291 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU R 296 " --> pdb=" O PHE R 292 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N CYS R 301 " --> pdb=" O MET R 297 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N CYS R 302 " --> pdb=" O ASN R 298 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET R 303 " --> pdb=" O PHE R 299 " (cutoff:3.500A) Proline residue: R 305 - end of helix Processing helix chain 'A' and resid 7 through 31 Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 228 through 231 Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 280 removed outlier: 3.890A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.787A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'B' and resid 3 through 23 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'C' and resid 8 through 23 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 45 through 47 No H-bonds generated for 'chain 'C' and resid 45 through 47' Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing sheet with id= A, first strand: chain 'A' and resid 263 through 269 removed outlier: 3.742A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.974A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.899A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.977A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.733A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.689A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.438A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 318 through 320 Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.714A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 140 through 142 Processing sheet with id= L, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.643A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'E' and resid 226 through 231 removed outlier: 5.981A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 405 hydrogen bonds defined for protein. 1032 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: 2.54 Time building geometry restraints manager: 3.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1448 1.27 - 1.41: 2296 1.41 - 1.54: 5205 1.54 - 1.68: 46 1.68 - 1.82: 100 Bond restraints: 9095 Sorted by residual: bond pdb=" C05 KJX R 401 " pdb=" C06 KJX R 401 " ideal model delta sigma weight residual 1.522 1.131 0.391 2.00e-02 2.50e+03 3.82e+02 bond pdb=" C04 KJX R 401 " pdb=" C09 KJX R 401 " ideal model delta sigma weight residual 1.528 1.193 0.335 2.00e-02 2.50e+03 2.80e+02 bond pdb=" C06 KJX R 401 " pdb=" C14 KJX R 401 " ideal model delta sigma weight residual 1.526 1.257 0.269 2.00e-02 2.50e+03 1.81e+02 bond pdb=" C10 KJX R 401 " pdb=" C17 KJX R 401 " ideal model delta sigma weight residual 1.519 1.251 0.268 2.00e-02 2.50e+03 1.80e+02 bond pdb=" C09 KJX R 401 " pdb=" C12 KJX R 401 " ideal model delta sigma weight residual 1.528 1.279 0.249 2.00e-02 2.50e+03 1.55e+02 ... (remaining 9090 not shown) Histogram of bond angle deviations from ideal: 98.55 - 105.65: 147 105.65 - 112.74: 4879 112.74 - 119.84: 2908 119.84 - 126.94: 4297 126.94 - 134.03: 99 Bond angle restraints: 12330 Sorted by residual: angle pdb=" C ALA R 102 " pdb=" N LEU R 103 " pdb=" CA LEU R 103 " ideal model delta sigma weight residual 120.38 125.62 -5.24 1.46e+00 4.69e-01 1.29e+01 angle pdb=" C14 KJX R 401 " pdb=" C19 KJX R 401 " pdb=" C17 KJX R 401 " ideal model delta sigma weight residual 125.07 114.43 10.64 3.00e+00 1.11e-01 1.26e+01 angle pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta sigma weight residual 122.08 126.65 -4.57 1.47e+00 4.63e-01 9.65e+00 angle pdb=" C ASN A 269 " pdb=" N LYS A 270 " pdb=" CA LYS A 270 " ideal model delta sigma weight residual 122.46 126.77 -4.31 1.41e+00 5.03e-01 9.36e+00 angle pdb=" N LEU R 84 " pdb=" CA LEU R 84 " pdb=" C LEU R 84 " ideal model delta sigma weight residual 109.81 116.39 -6.58 2.21e+00 2.05e-01 8.87e+00 ... (remaining 12325 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 4969 17.31 - 34.61: 416 34.61 - 51.92: 62 51.92 - 69.22: 7 69.22 - 86.53: 4 Dihedral angle restraints: 5458 sinusoidal: 2141 harmonic: 3317 Sorted by residual: dihedral pdb=" CA GLN B 75 " pdb=" C GLN B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta harmonic sigma weight residual 180.00 150.50 29.50 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA PHE R 111 " pdb=" C PHE R 111 " pdb=" N TYR R 112 " pdb=" CA TYR R 112 " ideal model delta harmonic sigma weight residual -180.00 -158.55 -21.45 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA ILE R 113 " pdb=" C ILE R 113 " pdb=" N ASN R 114 " pdb=" CA ASN R 114 " ideal model delta harmonic sigma weight residual 180.00 -159.92 -20.08 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 5455 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.280: 1410 0.280 - 0.559: 2 0.559 - 0.839: 1 0.839 - 1.119: 0 1.119 - 1.398: 1 Chirality restraints: 1414 Sorted by residual: chirality pdb=" C06 KJX R 401 " pdb=" C05 KJX R 401 " pdb=" C07 KJX R 401 " pdb=" C14 KJX R 401 " both_signs ideal model delta sigma weight residual False -2.58 -1.19 -1.40 2.00e-01 2.50e+01 4.89e+01 chirality pdb=" C04 KJX R 401 " pdb=" C05 KJX R 401 " pdb=" C08 KJX R 401 " pdb=" C09 KJX R 401 " both_signs ideal model delta sigma weight residual False -2.94 -2.15 -0.80 2.00e-01 2.50e+01 1.59e+01 chirality pdb=" C08 KJX R 401 " pdb=" C04 KJX R 401 " pdb=" C13 KJX R 401 " pdb=" C15 KJX R 401 " both_signs ideal model delta sigma weight residual False 2.55 2.98 -0.43 2.00e-01 2.50e+01 4.61e+00 ... (remaining 1411 not shown) Planarity restraints: 1554 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 KJX R 401 " 0.091 2.00e-02 2.50e+03 1.23e-01 1.90e+02 pdb=" C14 KJX R 401 " -0.119 2.00e-02 2.50e+03 pdb=" C17 KJX R 401 " -0.107 2.00e-02 2.50e+03 pdb=" C19 KJX R 401 " 0.196 2.00e-02 2.50e+03 pdb=" C21 KJX R 401 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.030 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PRO B 236 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR R 184 " 0.031 5.00e-02 4.00e+02 4.57e-02 3.35e+00 pdb=" N PRO R 185 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO R 185 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO R 185 " 0.026 5.00e-02 4.00e+02 ... (remaining 1551 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 337 2.71 - 3.26: 8792 3.26 - 3.80: 14216 3.80 - 4.35: 18010 4.35 - 4.90: 30689 Nonbonded interactions: 72044 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.161 2.440 nonbonded pdb=" O THR R 123 " pdb=" OG SER R 126 " model vdw 2.214 2.440 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 175 " model vdw 2.214 2.440 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.216 2.440 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP C 48 " model vdw 2.255 2.440 ... (remaining 72039 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 5.170 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 27.090 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 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 : 0.011 0.391 9095 Z= 0.738 Angle : 0.733 10.643 12330 Z= 0.403 Chirality : 0.066 1.398 1414 Planarity : 0.005 0.123 1554 Dihedral : 12.680 86.527 3307 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.10 % Allowed : 3.74 % Favored : 96.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.22), residues: 1123 helix: -0.54 (0.24), residues: 406 sheet: -1.68 (0.26), residues: 309 loop : -2.09 (0.26), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 211 HIS 0.012 0.001 HIS R 37 PHE 0.017 0.002 PHE B 199 TYR 0.016 0.002 TYR R 90 ARG 0.003 0.000 ARG E 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 181 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 34 MET cc_start: 0.7449 (mmm) cc_final: 0.6953 (mmm) REVERT: R 87 ARG cc_start: 0.6850 (tpp80) cc_final: 0.6489 (tpt-90) REVERT: R 149 LYS cc_start: 0.7782 (tppt) cc_final: 0.7109 (tptt) REVERT: R 160 PHE cc_start: 0.7758 (m-10) cc_final: 0.7489 (m-80) REVERT: R 225 ARG cc_start: 0.8117 (ttm110) cc_final: 0.7593 (ttm110) REVERT: B 3 GLU cc_start: 0.9081 (tp30) cc_final: 0.8768 (tp30) REVERT: B 10 GLU cc_start: 0.9182 (tp30) cc_final: 0.8546 (tp30) REVERT: B 23 LYS cc_start: 0.8924 (ttpp) cc_final: 0.8717 (tmmt) REVERT: B 217 MET cc_start: 0.8398 (ptm) cc_final: 0.8080 (ptm) REVERT: C 17 GLU cc_start: 0.8985 (tp30) cc_final: 0.8553 (tp30) REVERT: E 153 GLU cc_start: 0.8340 (pt0) cc_final: 0.7822 (pt0) REVERT: E 220 GLU cc_start: 0.8172 (mp0) cc_final: 0.7771 (mp0) REVERT: E 223 ASP cc_start: 0.8220 (m-30) cc_final: 0.7757 (m-30) outliers start: 1 outliers final: 0 residues processed: 182 average time/residue: 0.3089 time to fit residues: 70.3309 Evaluate side-chains 131 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 33 optimal weight: 0.0870 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 0.1980 chunk 100 optimal weight: 4.9990 overall best weight: 0.8562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 244 ASN R 282 GLN R 298 ASN A 52 GLN A 213 HIS A 331 ASN B 88 ASN B 91 HIS B 119 ASN B 259 GLN B 293 ASN C 44 HIS ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 232 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9095 Z= 0.175 Angle : 0.515 9.255 12330 Z= 0.270 Chirality : 0.041 0.142 1414 Planarity : 0.004 0.042 1554 Dihedral : 4.969 62.719 1299 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.35 % Allowed : 9.66 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.22 (0.24), residues: 1123 helix: 0.41 (0.26), residues: 413 sheet: -1.27 (0.26), residues: 301 loop : -1.56 (0.28), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 211 HIS 0.005 0.001 HIS E 35 PHE 0.010 0.001 PHE R 111 TYR 0.011 0.001 TYR E 190 ARG 0.005 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 149 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 34 MET cc_start: 0.7364 (mmm) cc_final: 0.6919 (mmm) REVERT: R 128 ASP cc_start: 0.7995 (t70) cc_final: 0.7703 (t0) REVERT: R 149 LYS cc_start: 0.7776 (tppt) cc_final: 0.7121 (tptt) REVERT: R 225 ARG cc_start: 0.7917 (ttm110) cc_final: 0.7691 (ttm110) REVERT: B 3 GLU cc_start: 0.9116 (tp30) cc_final: 0.8794 (tp30) REVERT: B 10 GLU cc_start: 0.9180 (tp30) cc_final: 0.8521 (tp30) REVERT: B 23 LYS cc_start: 0.8908 (ttpp) cc_final: 0.8681 (tmmt) REVERT: B 59 TYR cc_start: 0.8951 (m-80) cc_final: 0.8611 (m-80) REVERT: C 17 GLU cc_start: 0.8956 (tp30) cc_final: 0.8710 (tp30) REVERT: C 20 LYS cc_start: 0.8855 (mtmt) cc_final: 0.8416 (mttp) REVERT: E 220 GLU cc_start: 0.8074 (mp0) cc_final: 0.7769 (mp0) REVERT: E 223 ASP cc_start: 0.8148 (m-30) cc_final: 0.7905 (m-30) outliers start: 13 outliers final: 8 residues processed: 156 average time/residue: 0.2679 time to fit residues: 54.5487 Evaluate side-chains 144 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 136 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 HIS Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain A residue 3 CYS Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 70 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 89 optimal weight: 0.0870 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 overall best weight: 2.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 220 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9095 Z= 0.340 Angle : 0.555 6.602 12330 Z= 0.295 Chirality : 0.043 0.145 1414 Planarity : 0.004 0.043 1554 Dihedral : 5.032 62.700 1299 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.39 % Allowed : 11.32 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.24), residues: 1123 helix: 0.72 (0.27), residues: 410 sheet: -1.13 (0.27), residues: 299 loop : -1.35 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS R 261 PHE 0.011 0.001 PHE B 253 TYR 0.015 0.002 TYR R 260 ARG 0.004 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 135 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 34 MET cc_start: 0.7338 (mmm) cc_final: 0.6785 (mmm) REVERT: R 128 ASP cc_start: 0.8036 (t70) cc_final: 0.7712 (t0) REVERT: R 147 HIS cc_start: 0.7262 (m-70) cc_final: 0.6527 (t-170) REVERT: R 149 LYS cc_start: 0.7899 (tppt) cc_final: 0.7252 (tptt) REVERT: A 296 TYR cc_start: 0.8870 (t80) cc_final: 0.8606 (t80) REVERT: B 3 GLU cc_start: 0.9120 (tp30) cc_final: 0.8820 (tp30) REVERT: B 10 GLU cc_start: 0.9191 (tp30) cc_final: 0.8678 (tp30) REVERT: B 23 LYS cc_start: 0.8938 (ttpp) cc_final: 0.8702 (tmmt) REVERT: B 262 MET cc_start: 0.8334 (mmm) cc_final: 0.8098 (tpp) REVERT: C 17 GLU cc_start: 0.8984 (tp30) cc_final: 0.8643 (tp30) REVERT: E 220 GLU cc_start: 0.8014 (mp0) cc_final: 0.7389 (mp0) REVERT: E 223 ASP cc_start: 0.8131 (m-30) cc_final: 0.6799 (m-30) outliers start: 23 outliers final: 16 residues processed: 151 average time/residue: 0.2692 time to fit residues: 53.0928 Evaluate side-chains 147 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 131 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 37 HIS Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain R residue 229 GLN Chi-restraints excluded: chain A residue 3 CYS Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.9980 chunk 52 optimal weight: 0.0980 chunk 11 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 101 optimal weight: 0.0050 chunk 107 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 49 ASN ** R 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 298 ASN B 36 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9095 Z= 0.141 Angle : 0.473 5.806 12330 Z= 0.252 Chirality : 0.040 0.139 1414 Planarity : 0.003 0.041 1554 Dihedral : 4.726 62.038 1299 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.49 % Allowed : 13.40 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.43 (0.25), residues: 1123 helix: 1.05 (0.27), residues: 409 sheet: -0.83 (0.27), residues: 311 loop : -1.10 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS E 35 PHE 0.010 0.001 PHE B 199 TYR 0.010 0.001 TYR E 190 ARG 0.005 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 152 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 128 ASP cc_start: 0.7991 (t70) cc_final: 0.7690 (t0) REVERT: R 147 HIS cc_start: 0.7259 (m-70) cc_final: 0.6505 (t-170) REVERT: R 149 LYS cc_start: 0.7885 (tppt) cc_final: 0.7294 (tptt) REVERT: R 315 TYR cc_start: 0.6664 (m-80) cc_final: 0.6343 (m-10) REVERT: A 20 ASP cc_start: 0.8488 (m-30) cc_final: 0.8278 (m-30) REVERT: B 3 GLU cc_start: 0.9117 (tp30) cc_final: 0.8787 (tp30) REVERT: B 10 GLU cc_start: 0.9172 (tp30) cc_final: 0.8628 (tp30) REVERT: B 23 LYS cc_start: 0.8907 (ttpp) cc_final: 0.8675 (tmmt) REVERT: C 15 LEU cc_start: 0.9155 (tp) cc_final: 0.8828 (tt) REVERT: C 17 GLU cc_start: 0.8971 (tp30) cc_final: 0.8726 (tp30) REVERT: C 20 LYS cc_start: 0.8894 (mtmt) cc_final: 0.8468 (mttp) REVERT: E 220 GLU cc_start: 0.7960 (mp0) cc_final: 0.7637 (mp0) REVERT: E 223 ASP cc_start: 0.8209 (m-30) cc_final: 0.7148 (m-30) outliers start: 24 outliers final: 14 residues processed: 166 average time/residue: 0.2483 time to fit residues: 54.3223 Evaluate side-chains 150 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 136 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 HIS Chi-restraints excluded: chain R residue 229 GLN Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 192 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN E 171 ASN E 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9095 Z= 0.334 Angle : 0.561 7.789 12330 Z= 0.296 Chirality : 0.042 0.142 1414 Planarity : 0.004 0.041 1554 Dihedral : 4.895 60.914 1299 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.91 % Allowed : 14.54 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.42 (0.25), residues: 1123 helix: 1.03 (0.27), residues: 408 sheet: -0.79 (0.28), residues: 297 loop : -1.09 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS R 261 PHE 0.012 0.001 PHE B 253 TYR 0.017 0.001 TYR R 260 ARG 0.005 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 134 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 34 MET cc_start: 0.6756 (mmp) cc_final: 0.6487 (mmp) REVERT: R 128 ASP cc_start: 0.8007 (t70) cc_final: 0.7691 (t0) REVERT: R 147 HIS cc_start: 0.7291 (m-70) cc_final: 0.6539 (t-170) REVERT: R 149 LYS cc_start: 0.7897 (tppt) cc_final: 0.7307 (tptt) REVERT: R 315 TYR cc_start: 0.6674 (m-80) cc_final: 0.6352 (m-10) REVERT: B 3 GLU cc_start: 0.9134 (tp30) cc_final: 0.8831 (tp30) REVERT: B 10 GLU cc_start: 0.9189 (tp30) cc_final: 0.8677 (tp30) REVERT: B 23 LYS cc_start: 0.8946 (ttpp) cc_final: 0.8703 (tmmt) REVERT: C 15 LEU cc_start: 0.9125 (tp) cc_final: 0.8735 (tt) REVERT: C 17 GLU cc_start: 0.8990 (tp30) cc_final: 0.8688 (tp30) REVERT: E 51 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.7886 (tp) REVERT: E 220 GLU cc_start: 0.7977 (mp0) cc_final: 0.7615 (mp0) REVERT: E 223 ASP cc_start: 0.8124 (m-30) cc_final: 0.7306 (m-30) outliers start: 28 outliers final: 20 residues processed: 152 average time/residue: 0.2464 time to fit residues: 49.8874 Evaluate side-chains 151 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 130 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 HIS Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain R residue 187 PHE Chi-restraints excluded: chain R residue 229 GLN Chi-restraints excluded: chain A residue 3 CYS Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 233 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.9980 chunk 26 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 89 optimal weight: 0.0870 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 56 optimal weight: 0.4980 chunk 103 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 298 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN E 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9095 Z= 0.162 Angle : 0.489 6.549 12330 Z= 0.259 Chirality : 0.040 0.141 1414 Planarity : 0.003 0.039 1554 Dihedral : 4.667 59.585 1299 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.28 % Allowed : 16.41 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.16 (0.25), residues: 1123 helix: 1.23 (0.27), residues: 409 sheet: -0.66 (0.27), residues: 309 loop : -0.92 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS E 35 PHE 0.017 0.001 PHE R 299 TYR 0.010 0.001 TYR E 190 ARG 0.007 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 147 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 128 ASP cc_start: 0.7949 (t70) cc_final: 0.7666 (t0) REVERT: R 147 HIS cc_start: 0.7244 (m-70) cc_final: 0.6501 (t-170) REVERT: R 149 LYS cc_start: 0.7915 (tppt) cc_final: 0.7357 (tptt) REVERT: R 315 TYR cc_start: 0.6704 (m-80) cc_final: 0.6431 (m-10) REVERT: A 20 ASP cc_start: 0.8476 (m-30) cc_final: 0.8259 (m-30) REVERT: B 3 GLU cc_start: 0.9115 (tp30) cc_final: 0.8805 (tp30) REVERT: B 10 GLU cc_start: 0.9175 (tp30) cc_final: 0.8523 (tp30) REVERT: B 23 LYS cc_start: 0.8907 (ttpp) cc_final: 0.8678 (tmmt) REVERT: C 15 LEU cc_start: 0.9124 (tp) cc_final: 0.8777 (tt) REVERT: C 17 GLU cc_start: 0.8973 (tp30) cc_final: 0.8750 (tp30) REVERT: C 20 LYS cc_start: 0.8886 (mtmt) cc_final: 0.8471 (mttp) REVERT: E 220 GLU cc_start: 0.7873 (mp0) cc_final: 0.7583 (mp0) REVERT: E 223 ASP cc_start: 0.8231 (m-30) cc_final: 0.7312 (m-30) outliers start: 22 outliers final: 18 residues processed: 162 average time/residue: 0.2517 time to fit residues: 53.7434 Evaluate side-chains 158 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 140 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 HIS Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain R residue 229 GLN Chi-restraints excluded: chain R residue 298 ASN Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 192 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS B 268 ASN E 171 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9095 Z= 0.251 Angle : 0.523 7.329 12330 Z= 0.276 Chirality : 0.041 0.141 1414 Planarity : 0.004 0.044 1554 Dihedral : 4.705 59.393 1299 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.80 % Allowed : 16.51 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.12 (0.25), residues: 1123 helix: 1.30 (0.27), residues: 407 sheet: -0.61 (0.28), residues: 298 loop : -0.96 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS E 35 PHE 0.015 0.001 PHE R 299 TYR 0.013 0.001 TYR R 260 ARG 0.007 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 136 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 128 ASP cc_start: 0.7962 (t70) cc_final: 0.7670 (t0) REVERT: R 147 HIS cc_start: 0.7257 (m-70) cc_final: 0.6546 (t-170) REVERT: R 149 LYS cc_start: 0.7924 (tppt) cc_final: 0.7323 (tptt) REVERT: R 315 TYR cc_start: 0.6729 (m-80) cc_final: 0.6453 (m-10) REVERT: A 20 ASP cc_start: 0.8479 (m-30) cc_final: 0.8270 (m-30) REVERT: B 3 GLU cc_start: 0.9129 (tp30) cc_final: 0.8824 (tp30) REVERT: B 10 GLU cc_start: 0.9184 (tp30) cc_final: 0.8535 (tp30) REVERT: B 23 LYS cc_start: 0.8934 (ttpp) cc_final: 0.8693 (tmmt) REVERT: C 15 LEU cc_start: 0.9125 (tp) cc_final: 0.8752 (tt) REVERT: C 17 GLU cc_start: 0.8984 (tp30) cc_final: 0.8747 (tp30) REVERT: C 20 LYS cc_start: 0.8917 (mtmt) cc_final: 0.8532 (mttp) REVERT: E 51 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7766 (tp) REVERT: E 220 GLU cc_start: 0.7890 (mp0) cc_final: 0.7586 (mp0) REVERT: E 223 ASP cc_start: 0.8219 (m-30) cc_final: 0.7366 (m-30) REVERT: E 233 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8725 (tt) outliers start: 27 outliers final: 22 residues processed: 157 average time/residue: 0.2353 time to fit residues: 48.9622 Evaluate side-chains 158 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 134 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 HIS Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain R residue 187 PHE Chi-restraints excluded: chain R residue 195 TRP Chi-restraints excluded: chain R residue 229 GLN Chi-restraints excluded: chain A residue 3 CYS Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 233 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 10.0000 chunk 68 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9095 Z= 0.268 Angle : 0.529 6.977 12330 Z= 0.280 Chirality : 0.042 0.141 1414 Planarity : 0.004 0.040 1554 Dihedral : 4.720 59.908 1299 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.12 % Allowed : 16.30 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.11 (0.25), residues: 1123 helix: 1.31 (0.27), residues: 408 sheet: -0.62 (0.28), residues: 297 loop : -0.95 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS E 35 PHE 0.016 0.001 PHE R 299 TYR 0.013 0.001 TYR R 260 ARG 0.007 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 135 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 128 ASP cc_start: 0.8038 (t70) cc_final: 0.7712 (t70) REVERT: R 147 HIS cc_start: 0.7255 (m-70) cc_final: 0.6520 (t-170) REVERT: R 149 LYS cc_start: 0.7933 (tppt) cc_final: 0.7375 (tptt) REVERT: R 275 SER cc_start: 0.5465 (m) cc_final: 0.5241 (t) REVERT: R 315 TYR cc_start: 0.6749 (m-80) cc_final: 0.6493 (m-10) REVERT: B 3 GLU cc_start: 0.9145 (tp30) cc_final: 0.8843 (tp30) REVERT: B 10 GLU cc_start: 0.9188 (tp30) cc_final: 0.8545 (tp30) REVERT: B 23 LYS cc_start: 0.8938 (ttpp) cc_final: 0.8699 (tmmt) REVERT: B 215 GLU cc_start: 0.8279 (mp0) cc_final: 0.7996 (mp0) REVERT: C 8 SER cc_start: 0.8001 (OUTLIER) cc_final: 0.7787 (t) REVERT: C 15 LEU cc_start: 0.9103 (tp) cc_final: 0.8724 (tt) REVERT: C 17 GLU cc_start: 0.8985 (tp30) cc_final: 0.8691 (tp30) REVERT: E 51 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7809 (tp) REVERT: E 118 THR cc_start: 0.8898 (OUTLIER) cc_final: 0.8671 (p) REVERT: E 220 GLU cc_start: 0.7901 (mp0) cc_final: 0.7629 (mp0) REVERT: E 223 ASP cc_start: 0.8218 (m-30) cc_final: 0.7458 (m-30) REVERT: E 233 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8749 (tt) outliers start: 30 outliers final: 24 residues processed: 158 average time/residue: 0.2361 time to fit residues: 49.4332 Evaluate side-chains 161 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 133 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 HIS Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain R residue 131 ILE Chi-restraints excluded: chain R residue 187 PHE Chi-restraints excluded: chain R residue 195 TRP Chi-restraints excluded: chain R residue 229 GLN Chi-restraints excluded: chain A residue 3 CYS Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 233 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 105 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 298 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9095 Z= 0.162 Angle : 0.500 7.259 12330 Z= 0.263 Chirality : 0.041 0.141 1414 Planarity : 0.003 0.048 1554 Dihedral : 4.535 59.818 1299 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.70 % Allowed : 17.55 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.09 (0.26), residues: 1123 helix: 1.31 (0.27), residues: 417 sheet: -0.42 (0.29), residues: 286 loop : -0.77 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS E 35 PHE 0.016 0.001 PHE R 42 TYR 0.009 0.001 TYR E 190 ARG 0.014 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 144 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 128 ASP cc_start: 0.8000 (t70) cc_final: 0.7681 (t0) REVERT: R 147 HIS cc_start: 0.7214 (m-70) cc_final: 0.6494 (t-170) REVERT: R 149 LYS cc_start: 0.7913 (tppt) cc_final: 0.7354 (tptt) REVERT: R 160 PHE cc_start: 0.7563 (m-10) cc_final: 0.7258 (m-80) REVERT: R 315 TYR cc_start: 0.6790 (m-80) cc_final: 0.6558 (m-10) REVERT: A 20 ASP cc_start: 0.8488 (m-30) cc_final: 0.8267 (m-30) REVERT: B 3 GLU cc_start: 0.9133 (tp30) cc_final: 0.8829 (tp30) REVERT: B 10 GLU cc_start: 0.9174 (tp30) cc_final: 0.8523 (tp30) REVERT: B 23 LYS cc_start: 0.8916 (ttpp) cc_final: 0.8682 (tmmt) REVERT: B 215 GLU cc_start: 0.8302 (mp0) cc_final: 0.8022 (mp0) REVERT: C 8 SER cc_start: 0.7930 (OUTLIER) cc_final: 0.7713 (t) REVERT: C 15 LEU cc_start: 0.9116 (tp) cc_final: 0.8797 (tt) REVERT: C 17 GLU cc_start: 0.8955 (tp30) cc_final: 0.8751 (tp30) REVERT: C 20 LYS cc_start: 0.8905 (mtmt) cc_final: 0.8487 (mttp) REVERT: E 222 GLU cc_start: 0.8439 (pm20) cc_final: 0.8239 (pm20) REVERT: E 223 ASP cc_start: 0.8269 (m-30) cc_final: 0.7413 (m-30) REVERT: E 233 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8657 (tt) outliers start: 26 outliers final: 19 residues processed: 164 average time/residue: 0.2415 time to fit residues: 52.7862 Evaluate side-chains 157 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 136 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 HIS Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain R residue 131 ILE Chi-restraints excluded: chain R residue 229 GLN Chi-restraints excluded: chain R residue 298 ASN Chi-restraints excluded: chain A residue 3 CYS Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 233 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 93 optimal weight: 0.1980 chunk 26 optimal weight: 30.0000 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.120 9095 Z= 0.277 Angle : 0.869 59.189 12330 Z= 0.508 Chirality : 0.045 0.552 1414 Planarity : 0.004 0.045 1554 Dihedral : 4.611 59.853 1299 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.28 % Allowed : 17.55 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.10 (0.26), residues: 1123 helix: 1.32 (0.27), residues: 417 sheet: -0.40 (0.29), residues: 286 loop : -0.77 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.014 0.001 HIS R 291 PHE 0.021 0.001 PHE R 299 TYR 0.009 0.001 TYR E 190 ARG 0.013 0.000 ARG A 32 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 136 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 128 ASP cc_start: 0.8003 (t70) cc_final: 0.7683 (t0) REVERT: R 147 HIS cc_start: 0.7215 (m-70) cc_final: 0.6495 (t-170) REVERT: R 149 LYS cc_start: 0.7914 (tppt) cc_final: 0.7355 (tptt) REVERT: R 160 PHE cc_start: 0.7565 (m-10) cc_final: 0.7260 (m-80) REVERT: R 315 TYR cc_start: 0.6789 (m-80) cc_final: 0.6561 (m-10) REVERT: A 20 ASP cc_start: 0.8490 (m-30) cc_final: 0.8270 (m-30) REVERT: B 3 GLU cc_start: 0.9133 (tp30) cc_final: 0.8828 (tp30) REVERT: B 10 GLU cc_start: 0.9175 (tp30) cc_final: 0.8525 (tp30) REVERT: B 23 LYS cc_start: 0.8917 (ttpp) cc_final: 0.8683 (tmmt) REVERT: B 215 GLU cc_start: 0.8305 (mp0) cc_final: 0.8023 (mp0) REVERT: C 8 SER cc_start: 0.7933 (OUTLIER) cc_final: 0.7714 (t) REVERT: C 15 LEU cc_start: 0.9116 (tp) cc_final: 0.8798 (tt) REVERT: C 17 GLU cc_start: 0.8956 (tp30) cc_final: 0.8754 (tp30) REVERT: C 20 LYS cc_start: 0.8903 (mtmt) cc_final: 0.8478 (mttp) REVERT: E 233 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8661 (tt) outliers start: 22 outliers final: 18 residues processed: 150 average time/residue: 0.2450 time to fit residues: 48.4922 Evaluate side-chains 155 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 135 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 HIS Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain R residue 131 ILE Chi-restraints excluded: chain R residue 229 GLN Chi-restraints excluded: chain R residue 273 ARG Chi-restraints excluded: chain A residue 3 CYS Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 233 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 11 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 5 optimal weight: 0.0770 chunk 63 optimal weight: 3.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.101415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.069659 restraints weight = 17252.900| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.90 r_work: 0.2862 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.120 9095 Z= 0.277 Angle : 0.869 59.189 12330 Z= 0.508 Chirality : 0.045 0.552 1414 Planarity : 0.004 0.045 1554 Dihedral : 4.611 59.853 1299 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.08 % Allowed : 17.76 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.10 (0.26), residues: 1123 helix: 1.32 (0.27), residues: 417 sheet: -0.40 (0.29), residues: 286 loop : -0.77 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.014 0.001 HIS R 291 PHE 0.021 0.001 PHE R 299 TYR 0.009 0.001 TYR E 190 ARG 0.013 0.000 ARG A 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2218.77 seconds wall clock time: 40 minutes 11.13 seconds (2411.13 seconds total)