Starting phenix.real_space_refine on Tue Feb 13 22:41:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h4i_34478/02_2024/8h4i_34478_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h4i_34478/02_2024/8h4i_34478.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h4i_34478/02_2024/8h4i_34478.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h4i_34478/02_2024/8h4i_34478.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h4i_34478/02_2024/8h4i_34478_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h4i_34478/02_2024/8h4i_34478_updated.pdb" } resolution = 3.06 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= 0.038 sd= 0.137 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 51 5.16 5 C 5087 2.51 5 N 1362 2.21 5 O 1465 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 49": "OD1" <-> "OD2" Residue "A ASP 240": "OD1" <-> "OD2" Residue "B ASP 38": "OD1" <-> "OD2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 312": "OD1" <-> "OD2" Residue "B ASP 323": "OD1" <-> "OD2" Residue "C TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 42": "OE1" <-> "OE2" Residue "D GLU 6": "OE1" <-> "OE2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R GLU 135": "OE1" <-> "OE2" Residue "R PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7965 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1874 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2547 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "C" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 409 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 957 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "R" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2178 Unusual residues: {'HXA': 1} Classifications: {'peptide': 283, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 13, 'TRANS': 269, None: 1} Not linked: pdbres="CYS R 326 " pdbres="HXA R 401 " Chain breaks: 2 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 10, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 65 Time building chain proxies: 4.64, per 1000 atoms: 0.58 Number of scatterers: 7965 At special positions: 0 Unit cell: (80.3, 102.3, 135.3, 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 51 16.00 O 1465 8.00 N 1362 7.00 C 5087 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS R 111 " - pdb=" SG CYS R 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.97 Conformation dependent library (CDL) restraints added in 1.5 seconds 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1952 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 11 sheets defined 36.9% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 14 through 39 removed outlier: 3.880A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 62 removed outlier: 4.182A pdb=" N ILE A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 238 Processing helix chain 'A' and resid 266 through 277 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 332 through 351 removed outlier: 3.905A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 391 removed outlier: 4.413A pdb=" N GLN A 390 " --> pdb=" O MET A 386 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.847A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) 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 9 through 22 Processing helix chain 'C' and resid 30 through 47 removed outlier: 3.631A pdb=" N HIS C 44 " --> pdb=" O TYR C 40 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA C 45 " --> pdb=" O CYS C 41 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LYS C 46 " --> pdb=" O GLU C 42 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLU C 47 " --> pdb=" O ALA C 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 31 No H-bonds generated for 'chain 'D' and resid 29 through 31' Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 88 through 90 No H-bonds generated for 'chain 'D' and resid 88 through 90' Processing helix chain 'R' and resid 34 through 66 removed outlier: 4.512A pdb=" N LEU R 37 " --> pdb=" O ASP R 34 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ALA R 40 " --> pdb=" O LEU R 37 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL R 65 " --> pdb=" O LEU R 62 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA R 66 " --> pdb=" O VAL R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 100 removed outlier: 3.567A pdb=" N VAL R 78 " --> pdb=" O ALA R 75 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU R 79 " --> pdb=" O CYS R 76 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE R 89 " --> pdb=" O LEU R 86 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER R 90 " --> pdb=" O LEU R 87 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ALA R 91 " --> pdb=" O PHE R 88 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE R 92 " --> pdb=" O ILE R 89 " (cutoff:3.500A) Proline residue: R 93 - end of helix Processing helix chain 'R' and resid 108 through 145 removed outlier: 5.137A pdb=" N PHE R 115 " --> pdb=" O CYS R 111 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TYR R 116 " --> pdb=" O HIS R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 169 Processing helix chain 'R' and resid 171 through 175 removed outlier: 3.759A pdb=" N VAL R 175 " --> pdb=" O PRO R 172 " (cutoff:3.500A) Processing helix chain 'R' and resid 201 through 215 Processing helix chain 'R' and resid 217 through 237 Processing helix chain 'R' and resid 260 through 268 removed outlier: 3.833A pdb=" N LEU R 268 " --> pdb=" O ARG R 264 " (cutoff:3.500A) Processing helix chain 'R' and resid 272 through 276 Processing helix chain 'R' and resid 278 through 290 Processing helix chain 'R' and resid 300 through 315 removed outlier: 3.809A pdb=" N ALA R 312 " --> pdb=" O ALA R 308 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASN R 313 " --> pdb=" O PHE R 309 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N SER R 314 " --> pdb=" O THR R 310 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ALA R 315 " --> pdb=" O PHE R 311 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 320 No H-bonds generated for 'chain 'R' and resid 317 through 320' Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.250A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.167A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.858A 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: 7.002A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.118A 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: 6.872A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.101A 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: 6.932A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.140A 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: 6.908A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.678A 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: 6.710A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.873A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.368A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'R' and resid 177 through 183 379 hydrogen bonds defined for protein. 969 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: 2.07 Time building geometry restraints manager: 3.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2113 1.33 - 1.45: 1557 1.45 - 1.57: 4388 1.57 - 1.69: 0 1.69 - 1.81: 71 Bond restraints: 8129 Sorted by residual: bond pdb=" C ASP B 66 " pdb=" N SER B 67 " ideal model delta sigma weight residual 1.332 1.289 0.044 1.40e-02 5.10e+03 9.72e+00 bond pdb=" C10 HXA R 401 " pdb=" C9 HXA R 401 " ideal model delta sigma weight residual 1.502 1.448 0.054 2.00e-02 2.50e+03 7.32e+00 bond pdb=" C18 HXA R 401 " pdb=" C19 HXA R 401 " ideal model delta sigma weight residual 1.503 1.450 0.053 2.00e-02 2.50e+03 7.14e+00 bond pdb=" C15 HXA R 401 " pdb=" C16 HXA R 401 " ideal model delta sigma weight residual 1.502 1.449 0.053 2.00e-02 2.50e+03 7.05e+00 bond pdb=" C11 HXA R 401 " pdb=" C12 HXA R 401 " ideal model delta sigma weight residual 1.502 1.452 0.050 2.00e-02 2.50e+03 6.16e+00 ... (remaining 8124 not shown) Histogram of bond angle deviations from ideal: 97.79 - 105.10: 126 105.10 - 112.41: 4140 112.41 - 119.72: 2825 119.72 - 127.04: 3855 127.04 - 134.35: 103 Bond angle restraints: 11049 Sorted by residual: angle pdb=" CA LEU D 79 " pdb=" CB LEU D 79 " pdb=" CG LEU D 79 " ideal model delta sigma weight residual 116.30 132.18 -15.88 3.50e+00 8.16e-02 2.06e+01 angle pdb=" N ASP B 205 " pdb=" CA ASP B 205 " pdb=" C ASP B 205 " ideal model delta sigma weight residual 110.80 101.25 9.55 2.13e+00 2.20e-01 2.01e+01 angle pdb=" C ASP B 66 " pdb=" N SER B 67 " pdb=" CA SER B 67 " ideal model delta sigma weight residual 121.54 114.34 7.20 1.91e+00 2.74e-01 1.42e+01 angle pdb=" CA TRP B 82 " pdb=" CB TRP B 82 " pdb=" CG TRP B 82 " ideal model delta sigma weight residual 113.60 120.26 -6.66 1.90e+00 2.77e-01 1.23e+01 angle pdb=" CA SER B 67 " pdb=" C SER B 67 " pdb=" N ARG B 68 " ideal model delta sigma weight residual 116.84 122.78 -5.94 1.71e+00 3.42e-01 1.21e+01 ... (remaining 11044 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 4401 17.69 - 35.38: 323 35.38 - 53.07: 59 53.07 - 70.76: 16 70.76 - 88.45: 7 Dihedral angle restraints: 4806 sinusoidal: 1798 harmonic: 3008 Sorted by residual: dihedral pdb=" CA THR B 65 " pdb=" C THR B 65 " pdb=" N ASP B 66 " pdb=" CA ASP B 66 " ideal model delta harmonic sigma weight residual 180.00 152.96 27.04 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 154.88 25.12 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA VAL D 64 " pdb=" C VAL D 64 " pdb=" N LYS D 65 " pdb=" CA LYS D 65 " ideal model delta harmonic sigma weight residual -180.00 -155.86 -24.14 0 5.00e+00 4.00e-02 2.33e+01 ... (remaining 4803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 679 0.041 - 0.082: 392 0.082 - 0.123: 164 0.123 - 0.164: 38 0.164 - 0.205: 11 Chirality restraints: 1284 Sorted by residual: chirality pdb=" CA TRP B 82 " pdb=" N TRP B 82 " pdb=" C TRP B 82 " pdb=" CB TRP B 82 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB VAL B 100 " pdb=" CA VAL B 100 " pdb=" CG1 VAL B 100 " pdb=" CG2 VAL B 100 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.73e-01 chirality pdb=" CB ILE R 92 " pdb=" CA ILE R 92 " pdb=" CG1 ILE R 92 " pdb=" CG2 ILE R 92 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.10e-01 ... (remaining 1281 not shown) Planarity restraints: 1407 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " -0.028 2.00e-02 2.50e+03 2.02e-02 8.13e+00 pdb=" CG TYR B 59 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 105 " -0.011 2.00e-02 2.50e+03 1.89e-02 7.11e+00 pdb=" CG TYR B 105 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR B 105 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR B 105 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR B 105 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 105 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR B 105 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 105 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 59 " -0.043 5.00e-02 4.00e+02 6.45e-02 6.65e+00 pdb=" N PRO C 60 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 60 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 60 " -0.036 5.00e-02 4.00e+02 ... (remaining 1404 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 206 2.70 - 3.25: 7255 3.25 - 3.80: 11379 3.80 - 4.35: 14421 4.35 - 4.90: 26103 Nonbonded interactions: 59364 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.147 2.440 nonbonded pdb=" OE2 GLU R 43 " pdb=" NH2 ARG R 99 " model vdw 2.159 2.520 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP C 48 " model vdw 2.190 2.440 nonbonded pdb=" OE2 GLU A 209 " pdb=" ND1 HIS A 220 " model vdw 2.203 2.520 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.260 2.440 ... (remaining 59359 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.890 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 24.510 Find NCS groups from input model: 0.210 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 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 0.082 8129 Z= 0.785 Angle : 1.045 15.878 11049 Z= 0.550 Chirality : 0.059 0.205 1284 Planarity : 0.006 0.064 1407 Dihedral : 13.700 88.446 2848 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.25), residues: 1019 helix: 1.17 (0.26), residues: 366 sheet: 0.40 (0.33), residues: 226 loop : -1.87 (0.26), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP A 234 HIS 0.015 0.004 HIS A 357 PHE 0.029 0.004 PHE D 108 TYR 0.045 0.004 TYR B 59 ARG 0.007 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.903 Fit side-chains REVERT: B 271 CYS cc_start: 0.7842 (m) cc_final: 0.7603 (m) REVERT: D 17 SER cc_start: 0.8714 (p) cc_final: 0.8441 (t) REVERT: R 197 ILE cc_start: 0.8872 (mt) cc_final: 0.8494 (tp) REVERT: R 267 PHE cc_start: 0.7472 (t80) cc_final: 0.7264 (t80) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.2915 time to fit residues: 34.2208 Evaluate side-chains 84 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 0.0470 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8129 Z= 0.177 Angle : 0.578 7.064 11049 Z= 0.314 Chirality : 0.043 0.163 1284 Planarity : 0.005 0.045 1407 Dihedral : 5.526 52.587 1124 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.24 % Allowed : 5.48 % Favored : 94.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.26), residues: 1019 helix: 1.47 (0.27), residues: 367 sheet: 0.56 (0.32), residues: 232 loop : -1.77 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.015 0.002 PHE A 212 TYR 0.034 0.001 TYR B 59 ARG 0.004 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 97 time to evaluate : 1.691 Fit side-chains REVERT: B 215 GLU cc_start: 0.7951 (pm20) cc_final: 0.7741 (pm20) REVERT: D 80 TYR cc_start: 0.8851 (m-80) cc_final: 0.8541 (m-80) REVERT: R 118 MET cc_start: 0.7286 (mtp) cc_final: 0.7025 (mtm) REVERT: R 197 ILE cc_start: 0.8800 (mt) cc_final: 0.8446 (tp) outliers start: 2 outliers final: 0 residues processed: 98 average time/residue: 0.2751 time to fit residues: 34.6080 Evaluate side-chains 85 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 62 optimal weight: 0.0010 chunk 25 optimal weight: 0.0030 chunk 91 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8129 Z= 0.180 Angle : 0.546 6.711 11049 Z= 0.292 Chirality : 0.042 0.153 1284 Planarity : 0.005 0.042 1407 Dihedral : 5.118 44.490 1124 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.24 % Allowed : 8.58 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.26), residues: 1019 helix: 1.58 (0.28), residues: 369 sheet: 0.63 (0.32), residues: 227 loop : -1.59 (0.27), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.016 0.002 PHE A 212 TYR 0.030 0.002 TYR B 59 ARG 0.005 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 89 time to evaluate : 0.867 Fit side-chains REVERT: C 38 MET cc_start: 0.7378 (mtm) cc_final: 0.7090 (mmm) REVERT: D 80 TYR cc_start: 0.8846 (m-80) cc_final: 0.8588 (m-80) REVERT: R 118 MET cc_start: 0.7262 (mtp) cc_final: 0.7035 (mtm) outliers start: 2 outliers final: 0 residues processed: 90 average time/residue: 0.2848 time to fit residues: 32.6958 Evaluate side-chains 87 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 43 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 81 optimal weight: 0.0040 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8129 Z= 0.161 Angle : 0.513 7.879 11049 Z= 0.274 Chirality : 0.041 0.146 1284 Planarity : 0.004 0.042 1407 Dihedral : 4.871 37.609 1124 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.72 % Allowed : 9.42 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.26), residues: 1019 helix: 1.68 (0.29), residues: 369 sheet: 0.67 (0.32), residues: 229 loop : -1.56 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.015 0.001 PHE A 212 TYR 0.023 0.001 TYR B 59 ARG 0.005 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 0.914 Fit side-chains REVERT: C 38 MET cc_start: 0.7363 (mtm) cc_final: 0.7064 (mmm) REVERT: D 80 TYR cc_start: 0.8814 (m-80) cc_final: 0.8529 (m-80) outliers start: 6 outliers final: 4 residues processed: 89 average time/residue: 0.2803 time to fit residues: 32.0618 Evaluate side-chains 87 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 83 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 213 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 67 optimal weight: 0.0170 chunk 0 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 75 GLN D 77 ASN R 182 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8129 Z= 0.232 Angle : 0.569 7.001 11049 Z= 0.301 Chirality : 0.043 0.146 1284 Planarity : 0.005 0.043 1407 Dihedral : 4.944 34.479 1124 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.83 % Allowed : 9.89 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.26), residues: 1019 helix: 1.57 (0.29), residues: 371 sheet: 0.64 (0.33), residues: 229 loop : -1.50 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.017 0.002 PHE A 212 TYR 0.029 0.002 TYR B 59 ARG 0.006 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 86 time to evaluate : 0.984 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 90 average time/residue: 0.3346 time to fit residues: 39.0859 Evaluate side-chains 89 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 84 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain R residue 67 ARG Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 213 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 57 optimal weight: 0.0670 chunk 24 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 81 optimal weight: 0.0030 chunk 45 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 overall best weight: 0.4728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 75 GLN D 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8129 Z= 0.137 Angle : 0.487 6.484 11049 Z= 0.261 Chirality : 0.041 0.137 1284 Planarity : 0.004 0.041 1407 Dihedral : 4.659 38.090 1124 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.60 % Allowed : 10.61 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.27), residues: 1019 helix: 1.75 (0.29), residues: 369 sheet: 0.69 (0.33), residues: 231 loop : -1.46 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.013 0.001 PHE A 212 TYR 0.026 0.001 TYR B 59 ARG 0.005 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 91 time to evaluate : 0.950 Fit side-chains REVERT: A 272 ASP cc_start: 0.7621 (m-30) cc_final: 0.7326 (m-30) REVERT: C 38 MET cc_start: 0.7331 (mtm) cc_final: 0.7046 (mmm) REVERT: R 67 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.8044 (ttp80) outliers start: 5 outliers final: 3 residues processed: 94 average time/residue: 0.2683 time to fit residues: 32.4626 Evaluate side-chains 95 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 91 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain R residue 67 ARG Chi-restraints excluded: chain R residue 194 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8129 Z= 0.347 Angle : 0.646 7.690 11049 Z= 0.339 Chirality : 0.045 0.136 1284 Planarity : 0.005 0.056 1407 Dihedral : 5.112 35.038 1124 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.07 % Allowed : 11.32 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.26), residues: 1019 helix: 1.47 (0.29), residues: 368 sheet: 0.56 (0.33), residues: 229 loop : -1.45 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 82 HIS 0.007 0.002 HIS A 357 PHE 0.018 0.002 PHE A 212 TYR 0.038 0.002 TYR B 59 ARG 0.006 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 91 time to evaluate : 0.976 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 96 average time/residue: 0.2876 time to fit residues: 35.0188 Evaluate side-chains 91 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 88 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain R residue 213 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 66 optimal weight: 0.0870 chunk 48 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 75 GLN D 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8129 Z= 0.170 Angle : 0.531 8.205 11049 Z= 0.283 Chirality : 0.042 0.147 1284 Planarity : 0.004 0.049 1407 Dihedral : 4.804 35.019 1124 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.72 % Allowed : 11.80 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.27), residues: 1019 helix: 1.61 (0.29), residues: 370 sheet: 0.62 (0.33), residues: 235 loop : -1.42 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.025 0.001 TYR B 59 ARG 0.005 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 87 time to evaluate : 0.910 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 89 average time/residue: 0.2639 time to fit residues: 30.7479 Evaluate side-chains 89 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 85 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain R residue 270 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 71 optimal weight: 0.0070 chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 0.1980 chunk 85 optimal weight: 0.7980 chunk 59 optimal weight: 0.2980 chunk 95 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8129 Z= 0.139 Angle : 0.495 8.048 11049 Z= 0.262 Chirality : 0.041 0.145 1284 Planarity : 0.004 0.043 1407 Dihedral : 4.549 38.372 1124 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.72 % Allowed : 11.80 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.27), residues: 1019 helix: 1.81 (0.29), residues: 368 sheet: 0.68 (0.32), residues: 234 loop : -1.34 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.013 0.001 PHE A 212 TYR 0.017 0.001 TYR B 59 ARG 0.005 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 87 time to evaluate : 0.893 Fit side-chains REVERT: C 38 MET cc_start: 0.7319 (mtm) cc_final: 0.7041 (mmm) REVERT: R 67 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.8035 (ttp80) outliers start: 6 outliers final: 4 residues processed: 89 average time/residue: 0.2587 time to fit residues: 30.1397 Evaluate side-chains 91 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 86 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain R residue 67 ARG Chi-restraints excluded: chain R residue 194 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 100 optimal weight: 0.3980 chunk 92 optimal weight: 1.9990 chunk 80 optimal weight: 0.0270 chunk 8 optimal weight: 0.8980 chunk 61 optimal weight: 0.0010 chunk 49 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 85 optimal weight: 0.3980 chunk 24 optimal weight: 0.8980 overall best weight: 0.3444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8129 Z= 0.128 Angle : 0.494 9.446 11049 Z= 0.257 Chirality : 0.040 0.144 1284 Planarity : 0.004 0.041 1407 Dihedral : 4.354 41.015 1124 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.72 % Allowed : 12.51 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.27), residues: 1019 helix: 1.87 (0.29), residues: 369 sheet: 0.90 (0.32), residues: 230 loop : -1.30 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.013 0.001 PHE A 212 TYR 0.012 0.001 TYR B 59 ARG 0.006 0.000 ARG B 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 0.948 Fit side-chains REVERT: A 272 ASP cc_start: 0.7642 (m-30) cc_final: 0.7324 (m-30) REVERT: B 214 ARG cc_start: 0.6970 (mtm110) cc_final: 0.6735 (mtp-110) REVERT: C 38 MET cc_start: 0.7313 (mtm) cc_final: 0.7048 (mmm) REVERT: R 100 TRP cc_start: 0.8358 (m100) cc_final: 0.7927 (m100) outliers start: 6 outliers final: 3 residues processed: 94 average time/residue: 0.2616 time to fit residues: 31.8965 Evaluate side-chains 91 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 88 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain R residue 92 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.1980 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.117593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.092362 restraints weight = 12266.168| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.26 r_work: 0.3082 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8129 Z= 0.187 Angle : 0.541 9.514 11049 Z= 0.282 Chirality : 0.042 0.149 1284 Planarity : 0.004 0.043 1407 Dihedral : 4.517 40.829 1124 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.48 % Allowed : 12.75 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.27), residues: 1019 helix: 1.85 (0.29), residues: 369 sheet: 0.73 (0.32), residues: 241 loop : -1.26 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.015 0.001 PHE A 212 TYR 0.023 0.001 TYR B 59 ARG 0.006 0.000 ARG B 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1940.20 seconds wall clock time: 35 minutes 49.35 seconds (2149.35 seconds total)