Starting phenix.real_space_refine on Mon Mar 11 16:35:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh0_31982/03_2024/7vh0_31982_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh0_31982/03_2024/7vh0_31982.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh0_31982/03_2024/7vh0_31982_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh0_31982/03_2024/7vh0_31982_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh0_31982/03_2024/7vh0_31982_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh0_31982/03_2024/7vh0_31982.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh0_31982/03_2024/7vh0_31982.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh0_31982/03_2024/7vh0_31982_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh0_31982/03_2024/7vh0_31982_neut_updated.pdb" } resolution = 3.46 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= 0.030 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 58 5.16 5 C 5533 2.51 5 N 1463 2.21 5 O 1602 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 54": "OD1" <-> "OD2" Residue "A TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 20": "OD1" <-> "OD2" Residue "B GLU 186": "OE1" <-> "OE2" Residue "B ASP 229": "OD1" <-> "OD2" Residue "B TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 231": "OD1" <-> "OD2" Residue "B GLU 245": "OE1" <-> "OE2" Residue "B ASP 261": "OD1" <-> "OD2" Residue "B PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 275": "OE1" <-> "OE2" Residue "B PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 328": "OD1" <-> "OD2" Residue "C TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 153": "OD1" <-> "OD2" Residue "C GLU 260": "OE1" <-> "OE2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D GLU 47": "OE1" <-> "OE2" Residue "E PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 137": "OD1" <-> "OD2" Residue "E PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 220": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8656 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2122 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 11, 'TRANS': 261} Chain breaks: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 5, 'ASN:plan1': 1, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 44 Chain: "B" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1735 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 2, 'TRANS': 212} Chain breaks: 2 Chain: "C" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "D" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "E" Number of atoms: 1778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1778 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'JEV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.83, per 1000 atoms: 0.56 Number of scatterers: 8656 At special positions: 0 Unit cell: (90.95, 119.85, 128.35, 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 58 16.00 O 1602 8.00 N 1463 7.00 C 5533 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.13 Conformation dependent library (CDL) restraints added in 1.7 seconds 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2076 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 33 helices and 12 sheets defined 31.7% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 39 through 67 removed outlier: 3.562A pdb=" N VAL A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A 56 " --> pdb=" O ALA A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 72 No H-bonds generated for 'chain 'A' and resid 69 through 72' Processing helix chain 'A' and resid 76 through 91 removed outlier: 3.643A pdb=" N VAL A 80 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER A 81 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 85 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL A 88 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL A 89 " --> pdb=" O ASP A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 102 Processing helix chain 'A' and resid 110 through 116 Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.871A pdb=" N ILE A 125 " --> pdb=" O GLY A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 140 removed outlier: 4.146A pdb=" N TYR A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 150 Processing helix chain 'A' and resid 156 through 170 removed outlier: 3.553A pdb=" N ILE A 161 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N CYS A 162 " --> pdb=" O PRO A 158 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE A 164 " --> pdb=" O HIS A 160 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N TRP A 165 " --> pdb=" O ILE A 161 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR A 168 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 removed outlier: 3.898A pdb=" N VAL A 178 " --> pdb=" O ASN A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 199 through 208 removed outlier: 3.623A pdb=" N VAL A 204 " --> pdb=" O TYR A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 234 removed outlier: 4.360A pdb=" N VAL A 216 " --> pdb=" O PRO A 212 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR A 220 " --> pdb=" O VAL A 216 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TRP A 224 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LYS A 233 " --> pdb=" O GLN A 229 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 276 Proline residue: A 266 - end of helix Processing helix chain 'A' and resid 287 through 305 removed outlier: 3.840A pdb=" N SER A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N CYS A 302 " --> pdb=" O TYR A 298 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ALA A 305 " --> pdb=" O SER A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 322 removed outlier: 4.208A pdb=" N GLU A 318 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS A 320 " --> pdb=" O ARG A 316 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ARG A 321 " --> pdb=" O ARG A 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 28 removed outlier: 3.868A pdb=" N LEU B 23 " --> pdb=" O ILE B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 51 removed outlier: 3.541A pdb=" N THR B 48 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 210 No H-bonds generated for 'chain 'B' and resid 208 through 210' Processing helix chain 'B' and resid 212 through 215 Processing helix chain 'B' and resid 242 through 254 Processing helix chain 'B' and resid 271 through 277 Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 296 through 310 removed outlier: 3.852A pdb=" N LEU B 310 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 351 removed outlier: 3.708A pdb=" N VAL B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 25 removed outlier: 3.914A pdb=" N GLU C 10 " --> pdb=" O GLU C 6 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA C 11 " --> pdb=" O LEU C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 33 No H-bonds generated for 'chain 'C' and resid 30 through 33' Processing helix chain 'D' and resid 10 through 22 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 45 through 47 No H-bonds generated for 'chain 'D' 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 helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 221 through 223 No H-bonds generated for 'chain 'E' and resid 221 through 223' Processing sheet with id= A, first strand: chain 'B' and resid 320 through 323 removed outlier: 3.555A pdb=" N ALA B 220 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N CYS B 224 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP B 200 " --> pdb=" O VAL B 185 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 58 through 63 removed outlier: 7.095A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.856A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG C 137 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 178 through 180 Processing sheet with id= E, first strand: chain 'C' and resid 198 through 201 removed outlier: 6.054A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 262 through 265 removed outlier: 3.542A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER C 245 " --> pdb=" O THR C 249 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE C 241 " --> pdb=" O PHE C 253 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA C 231 " --> pdb=" O GLY C 244 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 294 through 298 Processing sheet with id= H, first strand: chain 'C' and resid 47 through 51 removed outlier: 7.212A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.550A pdb=" N MET E 83 " --> pdb=" O ARG E 18 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU E 20 " --> pdb=" O LEU E 81 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 93 through 99 removed outlier: 3.698A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 146 through 148 removed outlier: 7.049A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 155 through 160 319 hydrogen bonds defined for protein. 879 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: 2.32 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1405 1.31 - 1.43: 2463 1.43 - 1.56: 4893 1.56 - 1.69: 1 1.69 - 1.81: 82 Bond restraints: 8844 Sorted by residual: bond pdb=" C12 JEV A 401 " pdb=" O1 JEV A 401 " ideal model delta sigma weight residual 1.488 1.321 0.167 2.00e-02 2.50e+03 6.98e+01 bond pdb=" CA ILE A 142 " pdb=" C ILE A 142 " ideal model delta sigma weight residual 1.523 1.454 0.069 1.27e-02 6.20e+03 2.99e+01 bond pdb=" CA THR A 252 " pdb=" C THR A 252 " ideal model delta sigma weight residual 1.521 1.460 0.061 1.14e-02 7.69e+03 2.85e+01 bond pdb=" C15 JEV A 401 " pdb=" O1 JEV A 401 " ideal model delta sigma weight residual 1.434 1.351 0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" CA TYR A 200 " pdb=" C TYR A 200 " ideal model delta sigma weight residual 1.522 1.466 0.057 1.37e-02 5.33e+03 1.72e+01 ... (remaining 8839 not shown) Histogram of bond angle deviations from ideal: 99.28 - 106.23: 191 106.23 - 113.19: 4742 113.19 - 120.14: 3110 120.14 - 127.09: 3852 127.09 - 134.05: 104 Bond angle restraints: 11999 Sorted by residual: angle pdb=" N THR A 198 " pdb=" CA THR A 198 " pdb=" C THR A 198 " ideal model delta sigma weight residual 112.90 101.76 11.14 1.31e+00 5.83e-01 7.23e+01 angle pdb=" N THR A 201 " pdb=" CA THR A 201 " pdb=" C THR A 201 " ideal model delta sigma weight residual 111.36 102.13 9.23 1.09e+00 8.42e-01 7.17e+01 angle pdb=" N VAL B 50 " pdb=" CA VAL B 50 " pdb=" C VAL B 50 " ideal model delta sigma weight residual 113.43 104.43 9.00 1.09e+00 8.42e-01 6.82e+01 angle pdb=" N THR E 144 " pdb=" CA THR E 144 " pdb=" C THR E 144 " ideal model delta sigma weight residual 112.93 104.71 8.22 1.12e+00 7.97e-01 5.39e+01 angle pdb=" N LEU B 227 " pdb=" CA LEU B 227 " pdb=" C LEU B 227 " ideal model delta sigma weight residual 113.50 105.48 8.02 1.23e+00 6.61e-01 4.25e+01 ... (remaining 11994 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.97: 4566 16.97 - 33.93: 498 33.93 - 50.90: 118 50.90 - 67.87: 26 67.87 - 84.84: 8 Dihedral angle restraints: 5216 sinusoidal: 1996 harmonic: 3220 Sorted by residual: dihedral pdb=" C TYR A 200 " pdb=" N TYR A 200 " pdb=" CA TYR A 200 " pdb=" CB TYR A 200 " ideal model delta harmonic sigma weight residual -122.60 -133.36 10.76 0 2.50e+00 1.60e-01 1.85e+01 dihedral pdb=" CA LEU E 117 " pdb=" C LEU E 117 " pdb=" N THR E 118 " pdb=" CA THR E 118 " ideal model delta harmonic sigma weight residual -180.00 -158.96 -21.04 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" N TYR A 200 " pdb=" C TYR A 200 " pdb=" CA TYR A 200 " pdb=" CB TYR A 200 " ideal model delta harmonic sigma weight residual 122.80 132.98 -10.18 0 2.50e+00 1.60e-01 1.66e+01 ... (remaining 5213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 1305 0.111 - 0.222: 51 0.222 - 0.333: 7 0.333 - 0.444: 2 0.444 - 0.555: 1 Chirality restraints: 1366 Sorted by residual: chirality pdb=" CA TYR A 200 " pdb=" N TYR A 200 " pdb=" C TYR A 200 " pdb=" CB TYR A 200 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.56 2.00e-01 2.50e+01 7.70e+00 chirality pdb=" CA SER A 145 " pdb=" N SER A 145 " pdb=" C SER A 145 " pdb=" CB SER A 145 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" CA GLU B 186 " pdb=" N GLU B 186 " pdb=" C GLU B 186 " pdb=" CB GLU B 186 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.27e+00 ... (remaining 1363 not shown) Planarity restraints: 1512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 139 " 0.019 2.00e-02 2.50e+03 3.91e-02 1.53e+01 pdb=" C TYR A 139 " -0.068 2.00e-02 2.50e+03 pdb=" O TYR A 139 " 0.025 2.00e-02 2.50e+03 pdb=" N LEU A 140 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 285 " -0.050 5.00e-02 4.00e+02 7.65e-02 9.37e+00 pdb=" N PRO A 286 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 286 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 286 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 152 " 0.014 2.00e-02 2.50e+03 2.75e-02 7.54e+00 pdb=" C TYR A 152 " -0.047 2.00e-02 2.50e+03 pdb=" O TYR A 152 " 0.018 2.00e-02 2.50e+03 pdb=" N ARG A 153 " 0.016 2.00e-02 2.50e+03 ... (remaining 1509 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2178 2.79 - 3.32: 7812 3.32 - 3.85: 13675 3.85 - 4.37: 15696 4.37 - 4.90: 27484 Nonbonded interactions: 66845 Sorted by model distance: nonbonded pdb=" OG SER C 147 " pdb=" O MET C 188 " model vdw 2.266 2.440 nonbonded pdb=" O ARG C 22 " pdb=" NE2 GLN C 259 " model vdw 2.279 2.520 nonbonded pdb=" NH2 ARG E 67 " pdb=" OD1 ASP E 90 " model vdw 2.281 2.520 nonbonded pdb=" OG1 THR C 321 " pdb=" OD1 ASP C 323 " model vdw 2.299 2.440 nonbonded pdb=" OG SER C 281 " pdb=" OD2 ASP D 48 " model vdw 2.300 2.440 ... (remaining 66840 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: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.930 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 26.400 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 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 : 0.005 0.167 8844 Z= 0.341 Angle : 0.810 11.135 11999 Z= 0.508 Chirality : 0.055 0.555 1366 Planarity : 0.005 0.077 1512 Dihedral : 15.442 84.837 3137 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.23 % Favored : 93.49 % Rotamer: Outliers : 3.66 % Allowed : 2.26 % Favored : 94.08 % Cbeta Deviations : 0.10 % 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: -1.57 (0.25), residues: 1091 helix: -0.47 (0.30), residues: 339 sheet: -0.48 (0.31), residues: 288 loop : -1.77 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 211 HIS 0.005 0.001 HIS A 156 PHE 0.021 0.001 PHE A 91 TYR 0.026 0.001 TYR A 200 ARG 0.008 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 208 time to evaluate : 0.931 Fit side-chains REVERT: A 64 SER cc_start: 0.6767 (m) cc_final: 0.6271 (p) REVERT: A 259 ILE cc_start: 0.8667 (tp) cc_final: 0.8438 (tp) REVERT: B 53 MET cc_start: 0.6220 (OUTLIER) cc_final: 0.5978 (mmp) REVERT: B 296 TYR cc_start: 0.7513 (t80) cc_final: 0.7278 (t80) REVERT: C 308 LEU cc_start: 0.8487 (mp) cc_final: 0.8250 (mp) REVERT: E 160 ARG cc_start: 0.7553 (ttm110) cc_final: 0.7040 (ttm-80) outliers start: 34 outliers final: 11 residues processed: 227 average time/residue: 0.2184 time to fit residues: 66.3715 Evaluate side-chains 181 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 169 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 140 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.0770 chunk 82 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 overall best weight: 1.3344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 ASN A 156 HIS A 300 ASN B 52 GLN B 269 ASN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN C 176 GLN ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8844 Z= 0.214 Angle : 0.569 7.788 11999 Z= 0.295 Chirality : 0.042 0.210 1366 Planarity : 0.004 0.061 1512 Dihedral : 7.011 78.063 1231 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.15 % Allowed : 11.19 % Favored : 86.65 % 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: -1.32 (0.25), residues: 1091 helix: -0.21 (0.29), residues: 353 sheet: -0.37 (0.31), residues: 282 loop : -1.66 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 211 HIS 0.003 0.001 HIS C 91 PHE 0.015 0.002 PHE C 151 TYR 0.018 0.001 TYR A 200 ARG 0.004 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 189 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 PHE cc_start: 0.8267 (t80) cc_final: 0.7894 (t80) REVERT: A 259 ILE cc_start: 0.8689 (tp) cc_final: 0.8470 (tp) REVERT: A 300 ASN cc_start: 0.8033 (t0) cc_final: 0.7812 (t0) REVERT: B 53 MET cc_start: 0.6284 (OUTLIER) cc_final: 0.6068 (mmm) REVERT: B 229 ASP cc_start: 0.8136 (m-30) cc_final: 0.7392 (m-30) REVERT: C 308 LEU cc_start: 0.8600 (mp) cc_final: 0.8345 (mp) outliers start: 20 outliers final: 16 residues processed: 200 average time/residue: 0.2195 time to fit residues: 58.6932 Evaluate side-chains 188 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 171 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 139 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 82 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 HIS A 175 ASN B 269 ASN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8844 Z= 0.180 Angle : 0.537 6.380 11999 Z= 0.276 Chirality : 0.041 0.168 1366 Planarity : 0.003 0.055 1512 Dihedral : 6.189 76.418 1222 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.48 % Allowed : 14.21 % Favored : 83.32 % 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: -1.17 (0.25), residues: 1091 helix: -0.08 (0.29), residues: 364 sheet: -0.37 (0.30), residues: 285 loop : -1.54 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 211 HIS 0.003 0.001 HIS C 91 PHE 0.014 0.001 PHE C 151 TYR 0.015 0.001 TYR A 200 ARG 0.004 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 173 time to evaluate : 1.076 Fit side-chains revert: symmetry clash REVERT: A 183 TYR cc_start: 0.7412 (t80) cc_final: 0.7070 (t80) REVERT: B 53 MET cc_start: 0.6845 (tpt) cc_final: 0.6138 (mmm) REVERT: C 172 GLU cc_start: 0.7979 (tp30) cc_final: 0.7755 (tp30) REVERT: E 76 LYS cc_start: 0.8677 (mmtm) cc_final: 0.8058 (tptm) outliers start: 23 outliers final: 19 residues processed: 187 average time/residue: 0.2294 time to fit residues: 57.7590 Evaluate side-chains 181 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 162 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 210 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.9990 chunk 74 optimal weight: 0.2980 chunk 51 optimal weight: 8.9990 chunk 10 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS A 304 ASN B 269 ASN ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN ** D 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 17 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8844 Z= 0.245 Angle : 0.553 10.778 11999 Z= 0.287 Chirality : 0.042 0.258 1366 Planarity : 0.003 0.049 1512 Dihedral : 5.887 76.004 1218 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.91 % Allowed : 16.68 % Favored : 80.41 % 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: -1.10 (0.25), residues: 1091 helix: 0.00 (0.29), residues: 363 sheet: -0.40 (0.30), residues: 285 loop : -1.49 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 165 HIS 0.003 0.001 HIS C 91 PHE 0.016 0.002 PHE C 151 TYR 0.015 0.001 TYR E 102 ARG 0.004 0.000 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 166 time to evaluate : 1.085 Fit side-chains revert: symmetry clash REVERT: A 183 TYR cc_start: 0.7323 (t80) cc_final: 0.6945 (t80) REVERT: B 53 MET cc_start: 0.6824 (tpt) cc_final: 0.6145 (mmm) REVERT: D 17 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8126 (tm-30) REVERT: D 51 LEU cc_start: 0.8850 (tp) cc_final: 0.8608 (mt) outliers start: 27 outliers final: 22 residues processed: 182 average time/residue: 0.2353 time to fit residues: 57.4382 Evaluate side-chains 188 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 165 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 210 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 HIS ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN ** D 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 8844 Z= 0.426 Angle : 0.640 9.272 11999 Z= 0.335 Chirality : 0.045 0.237 1366 Planarity : 0.004 0.048 1512 Dihedral : 6.098 73.864 1215 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 3.12 % Allowed : 18.73 % Favored : 78.15 % 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: -1.37 (0.25), residues: 1091 helix: -0.12 (0.28), residues: 364 sheet: -0.71 (0.30), residues: 286 loop : -1.60 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 165 HIS 0.006 0.001 HIS C 91 PHE 0.022 0.002 PHE E 68 TYR 0.020 0.002 TYR E 102 ARG 0.004 0.000 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 161 time to evaluate : 0.846 Fit side-chains REVERT: A 183 TYR cc_start: 0.7371 (t80) cc_final: 0.6976 (t80) REVERT: E 220 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8481 (mm-30) outliers start: 29 outliers final: 24 residues processed: 180 average time/residue: 0.2267 time to fit residues: 54.4275 Evaluate side-chains 180 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 156 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 210 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 105 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 GLN B 269 ASN ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8844 Z= 0.278 Angle : 0.563 7.706 11999 Z= 0.292 Chirality : 0.042 0.198 1366 Planarity : 0.003 0.046 1512 Dihedral : 5.808 75.911 1214 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.44 % Allowed : 20.24 % Favored : 76.32 % 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: -1.29 (0.25), residues: 1091 helix: 0.01 (0.28), residues: 364 sheet: -0.74 (0.30), residues: 286 loop : -1.57 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 165 HIS 0.004 0.001 HIS C 91 PHE 0.019 0.002 PHE E 68 TYR 0.016 0.001 TYR E 190 ARG 0.003 0.000 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 166 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: A 183 TYR cc_start: 0.7311 (t80) cc_final: 0.6858 (t80) REVERT: B 229 ASP cc_start: 0.7746 (m-30) cc_final: 0.7001 (t70) REVERT: C 172 GLU cc_start: 0.8093 (tp30) cc_final: 0.7877 (tp30) REVERT: C 292 PHE cc_start: 0.8383 (m-80) cc_final: 0.8165 (m-80) outliers start: 32 outliers final: 20 residues processed: 189 average time/residue: 0.2400 time to fit residues: 60.5823 Evaluate side-chains 180 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 160 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 210 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 59 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 chunk 105 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 GLN ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8844 Z= 0.181 Angle : 0.537 9.459 11999 Z= 0.277 Chirality : 0.041 0.186 1366 Planarity : 0.003 0.044 1512 Dihedral : 5.583 75.861 1214 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.80 % Allowed : 20.88 % Favored : 76.32 % 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: -1.15 (0.25), residues: 1091 helix: 0.19 (0.29), residues: 356 sheet: -0.68 (0.30), residues: 284 loop : -1.52 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 165 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.001 PHE E 68 TYR 0.015 0.001 TYR E 190 ARG 0.003 0.000 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 172 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 165 TRP cc_start: 0.6247 (t-100) cc_final: 0.5623 (t-100) REVERT: A 183 TYR cc_start: 0.7258 (t80) cc_final: 0.6861 (t80) REVERT: B 229 ASP cc_start: 0.7697 (m-30) cc_final: 0.7006 (t70) REVERT: C 292 PHE cc_start: 0.8349 (m-80) cc_final: 0.8107 (m-80) outliers start: 26 outliers final: 22 residues processed: 191 average time/residue: 0.2191 time to fit residues: 56.4370 Evaluate side-chains 187 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 165 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 233 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.2980 chunk 31 optimal weight: 8.9990 chunk 20 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 GLN ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 8844 Z= 0.372 Angle : 0.625 13.138 11999 Z= 0.324 Chirality : 0.044 0.288 1366 Planarity : 0.004 0.044 1512 Dihedral : 5.842 75.179 1214 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 4.41 % Allowed : 20.67 % Favored : 74.92 % 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: -1.39 (0.25), residues: 1091 helix: -0.04 (0.28), residues: 363 sheet: -0.86 (0.30), residues: 286 loop : -1.60 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 165 HIS 0.005 0.001 HIS C 91 PHE 0.023 0.002 PHE E 68 TYR 0.018 0.002 TYR E 102 ARG 0.002 0.000 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 163 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: A 165 TRP cc_start: 0.6325 (t-100) cc_final: 0.5667 (t-100) REVERT: A 183 TYR cc_start: 0.7233 (t80) cc_final: 0.6817 (t80) REVERT: B 229 ASP cc_start: 0.7722 (m-30) cc_final: 0.7015 (t0) REVERT: C 292 PHE cc_start: 0.8497 (m-80) cc_final: 0.8203 (m-80) outliers start: 41 outliers final: 31 residues processed: 188 average time/residue: 0.2195 time to fit residues: 56.2537 Evaluate side-chains 188 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 157 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 233 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.4980 chunk 100 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 chunk 76 optimal weight: 0.0980 chunk 30 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 92 optimal weight: 0.3980 chunk 64 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 GLN ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8844 Z= 0.164 Angle : 0.582 14.556 11999 Z= 0.289 Chirality : 0.042 0.271 1366 Planarity : 0.003 0.042 1512 Dihedral : 5.578 76.540 1214 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.26 % Allowed : 22.82 % Favored : 74.92 % 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: -1.17 (0.25), residues: 1091 helix: 0.33 (0.30), residues: 349 sheet: -0.71 (0.30), residues: 283 loop : -1.63 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 165 HIS 0.003 0.001 HIS E 35 PHE 0.020 0.001 PHE E 68 TYR 0.016 0.001 TYR E 190 ARG 0.005 0.000 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 170 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: A 183 TYR cc_start: 0.7201 (t80) cc_final: 0.6835 (t80) REVERT: B 53 MET cc_start: 0.6772 (tpt) cc_final: 0.6289 (mmp) REVERT: B 229 ASP cc_start: 0.7706 (m-30) cc_final: 0.7091 (t0) REVERT: C 292 PHE cc_start: 0.8407 (m-80) cc_final: 0.8093 (m-80) REVERT: D 21 MET cc_start: 0.7956 (mmp) cc_final: 0.7550 (mmm) outliers start: 21 outliers final: 19 residues processed: 186 average time/residue: 0.2101 time to fit residues: 53.1180 Evaluate side-chains 184 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 165 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 233 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 1.9990 chunk 71 optimal weight: 0.2980 chunk 108 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8844 Z= 0.308 Angle : 0.618 12.363 11999 Z= 0.313 Chirality : 0.044 0.280 1366 Planarity : 0.004 0.042 1512 Dihedral : 5.632 74.953 1213 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 2.80 % Allowed : 22.93 % Favored : 74.27 % 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: -1.28 (0.25), residues: 1091 helix: 0.26 (0.29), residues: 353 sheet: -0.85 (0.30), residues: 286 loop : -1.66 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 165 HIS 0.004 0.001 HIS C 91 PHE 0.020 0.002 PHE E 68 TYR 0.017 0.002 TYR B 230 ARG 0.003 0.000 ARG E 160 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 161 time to evaluate : 0.947 Fit side-chains revert: symmetry clash REVERT: A 165 TRP cc_start: 0.6173 (t-100) cc_final: 0.5070 (t-100) REVERT: A 183 TYR cc_start: 0.7225 (t80) cc_final: 0.6792 (t80) REVERT: B 53 MET cc_start: 0.6806 (tpt) cc_final: 0.6340 (mmp) REVERT: B 229 ASP cc_start: 0.7731 (m-30) cc_final: 0.7107 (t0) REVERT: C 292 PHE cc_start: 0.8435 (m-80) cc_final: 0.8103 (m-80) REVERT: E 76 LYS cc_start: 0.8510 (mmtm) cc_final: 0.7924 (tptm) outliers start: 26 outliers final: 23 residues processed: 181 average time/residue: 0.2211 time to fit residues: 53.8200 Evaluate side-chains 183 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 160 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 233 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 10 optimal weight: 0.4980 chunk 15 optimal weight: 9.9990 chunk 76 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.162644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.107589 restraints weight = 11330.245| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 3.21 r_work: 0.3111 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8844 Z= 0.175 Angle : 0.571 11.316 11999 Z= 0.286 Chirality : 0.042 0.271 1366 Planarity : 0.003 0.041 1512 Dihedral : 5.495 75.681 1213 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.48 % Allowed : 23.36 % Favored : 74.17 % 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: -1.14 (0.25), residues: 1091 helix: 0.45 (0.30), residues: 351 sheet: -0.71 (0.30), residues: 283 loop : -1.69 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 165 HIS 0.003 0.001 HIS E 35 PHE 0.015 0.001 PHE E 68 TYR 0.016 0.001 TYR E 190 ARG 0.003 0.000 ARG E 160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2373.02 seconds wall clock time: 43 minutes 27.99 seconds (2607.99 seconds total)