Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 00:18:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id8_35359/04_2023/8id8_35359_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id8_35359/04_2023/8id8_35359.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id8_35359/04_2023/8id8_35359_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id8_35359/04_2023/8id8_35359_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id8_35359/04_2023/8id8_35359_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id8_35359/04_2023/8id8_35359.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id8_35359/04_2023/8id8_35359.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id8_35359/04_2023/8id8_35359_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id8_35359/04_2023/8id8_35359_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 60 5.16 5 C 5518 2.51 5 N 1468 2.21 5 O 1588 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 8635 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1752 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 Chain: "B" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2554 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "R" Number of atoms: 2170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2170 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 11, 'TRANS': 279} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 2, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 102 Chain: "S" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1715 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 217} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "Y" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 417 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'YN9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.99, per 1000 atoms: 0.58 Number of scatterers: 8635 At special positions: 0 Unit cell: (105.456, 125.736, 116.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 F 1 9.00 O 1588 8.00 N 1468 7.00 C 5518 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 111 " - pdb=" SG CYS R 194 " distance=2.03 Simple disulfide: pdb=" SG CYS S 160 " - pdb=" SG CYS S 230 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.33 Conformation dependent library (CDL) restraints added in 1.5 seconds 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2132 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 15 sheets defined 32.7% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 7 through 30 Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 277 removed outlier: 3.532A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 4.213A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.665A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.899A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 38 through 72 removed outlier: 4.584A pdb=" N ARG R 70 " --> pdb=" O ALA R 66 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ARG R 71 " --> pdb=" O ARG R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 100 removed outlier: 3.710A pdb=" N LEU R 86 " --> pdb=" O PHE R 82 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU R 87 " --> pdb=" O CYS R 83 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE R 88 " --> pdb=" O ALA R 84 " (cutoff:3.500A) Proline residue: R 93 - end of helix Processing helix chain 'R' and resid 108 through 141 removed outlier: 3.972A pdb=" N HIS R 112 " --> pdb=" O PRO R 108 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU R 113 " --> pdb=" O VAL R 109 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N PHE R 115 " --> pdb=" O CYS R 111 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N TYR R 116 " --> pdb=" O HIS R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 153 through 175 Proline residue: R 172 - end of helix removed outlier: 3.723A pdb=" N VAL R 175 " --> pdb=" O LEU R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 204 through 216 removed outlier: 3.820A pdb=" N SER R 210 " --> pdb=" O SER R 206 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 241 Processing helix chain 'R' and resid 252 through 276 removed outlier: 3.587A pdb=" N ARG R 261 " --> pdb=" O GLN R 257 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE R 263 " --> pdb=" O ASP R 259 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR R 265 " --> pdb=" O ARG R 261 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE R 273 " --> pdb=" O LEU R 269 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE R 274 " --> pdb=" O MET R 270 " (cutoff:3.500A) Processing helix chain 'R' and resid 278 through 293 removed outlier: 3.869A pdb=" N ASN R 291 " --> pdb=" O ILE R 287 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE R 292 " --> pdb=" O LEU R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 320 removed outlier: 3.502A pdb=" N ASN R 313 " --> pdb=" O PHE R 309 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER R 314 " --> pdb=" O THR R 310 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA R 315 " --> pdb=" O PHE R 311 " (cutoff:3.500A) Proline residue: R 318 - end of helix Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing helix chain 'Y' and resid 9 through 24 removed outlier: 3.790A pdb=" N ASN Y 24 " --> pdb=" O LYS Y 20 " (cutoff:3.500A) Processing helix chain 'Y' and resid 30 through 43 Processing helix chain 'Y' and resid 45 through 47 No H-bonds generated for 'chain 'Y' and resid 45 through 47' Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 7.331A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.613A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.940A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 178 through 180 removed outlier: 3.613A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.903A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.592A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.541A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.689A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 250 through 254 removed outlier: 3.625A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'R' and resid 177 through 181 Processing sheet with id= K, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= L, first strand: chain 'S' and resid 95 through 99 removed outlier: 6.023A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'S' and resid 92 through 94 Processing sheet with id= N, first strand: chain 'S' and resid 141 through 143 Processing sheet with id= O, first strand: chain 'S' and resid 230 through 232 removed outlier: 6.373A pdb=" N LEU S 179 " --> pdb=" O LEU S 188 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LEU S 188 " --> pdb=" O LEU S 179 " (cutoff:3.500A) 376 hydrogen bonds defined for protein. 1071 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: 2.46 Time building geometry restraints manager: 3.60 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: 2126 1.33 - 1.45: 1761 1.45 - 1.57: 4829 1.57 - 1.69: 4 1.69 - 1.82: 86 Bond restraints: 8806 Sorted by residual: bond pdb=" C1 YN9 R 401 " pdb=" C2 YN9 R 401 " ideal model delta sigma weight residual 1.386 1.486 -0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" C2 YN9 R 401 " pdb=" C4 YN9 R 401 " ideal model delta sigma weight residual 1.529 1.606 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" C11 YN9 R 401 " pdb=" C3 YN9 R 401 " ideal model delta sigma weight residual 1.385 1.457 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C10 YN9 R 401 " pdb=" C20 YN9 R 401 " ideal model delta sigma weight residual 1.386 1.458 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C18 YN9 R 401 " pdb=" C7 YN9 R 401 " ideal model delta sigma weight residual 1.386 1.455 -0.069 2.00e-02 2.50e+03 1.19e+01 ... (remaining 8801 not shown) Histogram of bond angle deviations from ideal: 99.37 - 106.30: 175 106.30 - 113.23: 4846 113.23 - 120.16: 3068 120.16 - 127.09: 3785 127.09 - 134.02: 84 Bond angle restraints: 11958 Sorted by residual: angle pdb=" C3 YN9 R 401 " pdb=" C1 YN9 R 401 " pdb=" C7 YN9 R 401 " ideal model delta sigma weight residual 103.24 118.53 -15.29 3.00e+00 1.11e-01 2.60e+01 angle pdb=" N TYR S 229 " pdb=" CA TYR S 229 " pdb=" C TYR S 229 " ideal model delta sigma weight residual 109.40 116.29 -6.89 1.63e+00 3.76e-01 1.79e+01 angle pdb=" C2 YN9 R 401 " pdb=" C1 YN9 R 401 " pdb=" C3 YN9 R 401 " ideal model delta sigma weight residual 136.76 125.37 11.39 3.00e+00 1.11e-01 1.44e+01 angle pdb=" N LEU R 173 " pdb=" CA LEU R 173 " pdb=" C LEU R 173 " ideal model delta sigma weight residual 111.82 116.17 -4.35 1.16e+00 7.43e-01 1.41e+01 angle pdb=" N ASP R 30 " pdb=" CA ASP R 30 " pdb=" C ASP R 30 " ideal model delta sigma weight residual 109.24 115.20 -5.96 1.67e+00 3.59e-01 1.27e+01 ... (remaining 11953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.75: 4599 14.75 - 29.49: 428 29.49 - 44.24: 127 44.24 - 58.99: 26 58.99 - 73.73: 7 Dihedral angle restraints: 5187 sinusoidal: 1895 harmonic: 3292 Sorted by residual: dihedral pdb=" CB CYS R 111 " pdb=" SG CYS R 111 " pdb=" SG CYS R 194 " pdb=" CB CYS R 194 " ideal model delta sinusoidal sigma weight residual 93.00 54.40 38.60 1 1.00e+01 1.00e-02 2.10e+01 dihedral pdb=" CA GLN S 143 " pdb=" C GLN S 143 " pdb=" N ALA S 144 " pdb=" CA ALA S 144 " ideal model delta harmonic sigma weight residual 180.00 -159.54 -20.46 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA ASP B 291 " pdb=" C ASP B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta harmonic sigma weight residual 180.00 161.25 18.75 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 5184 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 959 0.040 - 0.080: 323 0.080 - 0.119: 103 0.119 - 0.159: 17 0.159 - 0.199: 1 Chirality restraints: 1403 Sorted by residual: chirality pdb=" CA THR Y 52 " pdb=" N THR Y 52 " pdb=" C THR Y 52 " pdb=" CB THR Y 52 " both_signs ideal model delta sigma weight residual False 2.53 2.72 -0.20 2.00e-01 2.50e+01 9.89e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CA VAL S 37 " pdb=" N VAL S 37 " pdb=" C VAL S 37 " pdb=" CB VAL S 37 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.65e-01 ... (remaining 1400 not shown) Planarity restraints: 1500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 281 " 0.044 5.00e-02 4.00e+02 6.72e-02 7.22e+00 pdb=" N PRO A 282 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 282 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 282 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER S 106 " 0.034 5.00e-02 4.00e+02 5.21e-02 4.34e+00 pdb=" N PRO S 107 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO S 107 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO S 107 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL Y 54 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.32e+00 pdb=" C VAL Y 54 " -0.036 2.00e-02 2.50e+03 pdb=" O VAL Y 54 " 0.014 2.00e-02 2.50e+03 pdb=" N PRO Y 55 " 0.012 2.00e-02 2.50e+03 ... (remaining 1497 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.09: 3 2.09 - 2.80: 2119 2.80 - 3.50: 11329 3.50 - 4.20: 19759 4.20 - 4.90: 36053 Nonbonded interactions: 69263 Sorted by model distance: nonbonded pdb=" OH TYR A 230 " pdb=" CE1 PHE A 274 " model vdw 1.393 3.340 nonbonded pdb=" OD1 ASP A 341 " pdb=" NH1 ARG R 238 " model vdw 1.998 2.520 nonbonded pdb=" OH TYR A 230 " pdb=" CD1 PHE A 274 " model vdw 2.063 3.340 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.104 2.440 nonbonded pdb=" OH TYR R 165 " pdb=" OD1 ASN R 215 " model vdw 2.155 2.440 ... (remaining 69258 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: 0.430 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: 2.330 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 25.490 Find NCS groups from input model: 0.270 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:12.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 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 : 0.004 0.100 8806 Z= 0.284 Angle : 0.665 15.292 11958 Z= 0.363 Chirality : 0.044 0.199 1403 Planarity : 0.004 0.067 1500 Dihedral : 13.179 73.733 3049 Min Nonbonded Distance : 1.393 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.25), residues: 1115 helix: 1.13 (0.29), residues: 353 sheet: -0.82 (0.29), residues: 284 loop : -0.94 (0.26), residues: 478 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 152 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 154 average time/residue: 1.1766 time to fit residues: 193.5793 Evaluate side-chains 119 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 118 time to evaluate : 0.984 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.1202 time to fit residues: 1.5667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 64 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS A 204 GLN B 32 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 8806 Z= 0.176 Angle : 0.519 8.117 11958 Z= 0.271 Chirality : 0.041 0.152 1403 Planarity : 0.004 0.056 1500 Dihedral : 4.894 66.532 1220 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer Outliers : 2.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.25), residues: 1115 helix: 1.49 (0.29), residues: 355 sheet: -0.72 (0.30), residues: 277 loop : -0.91 (0.26), residues: 483 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 123 time to evaluate : 0.913 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 7 residues processed: 132 average time/residue: 1.2135 time to fit residues: 170.8110 Evaluate side-chains 121 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 1.045 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 3 average time/residue: 0.4754 time to fit residues: 3.0679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 8806 Z= 0.306 Angle : 0.585 9.117 11958 Z= 0.307 Chirality : 0.043 0.146 1403 Planarity : 0.004 0.063 1500 Dihedral : 5.106 71.611 1220 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer Outliers : 2.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.25), residues: 1115 helix: 1.38 (0.29), residues: 356 sheet: -0.57 (0.29), residues: 293 loop : -0.97 (0.27), residues: 466 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 128 time to evaluate : 1.030 Fit side-chains outliers start: 24 outliers final: 9 residues processed: 138 average time/residue: 1.1996 time to fit residues: 176.9468 Evaluate side-chains 129 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 120 time to evaluate : 0.956 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 6 residues processed: 3 average time/residue: 0.4836 time to fit residues: 3.1256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 101 optimal weight: 0.2980 chunk 107 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 28 optimal weight: 0.1980 chunk 89 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN R 317 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 8806 Z= 0.234 Angle : 0.537 8.358 11958 Z= 0.282 Chirality : 0.042 0.177 1403 Planarity : 0.004 0.062 1500 Dihedral : 5.031 76.117 1220 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer Outliers : 2.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.25), residues: 1115 helix: 1.57 (0.29), residues: 350 sheet: -0.55 (0.29), residues: 285 loop : -0.81 (0.27), residues: 480 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 125 time to evaluate : 1.046 Fit side-chains outliers start: 25 outliers final: 11 residues processed: 139 average time/residue: 1.1295 time to fit residues: 168.3144 Evaluate side-chains 131 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 120 time to evaluate : 0.974 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 3 average time/residue: 0.9365 time to fit residues: 4.3919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 21 optimal weight: 0.2980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN R 317 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 8806 Z= 0.172 Angle : 0.490 6.971 11958 Z= 0.260 Chirality : 0.041 0.179 1403 Planarity : 0.004 0.056 1500 Dihedral : 4.876 81.542 1220 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer Outliers : 2.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.25), residues: 1115 helix: 1.66 (0.29), residues: 356 sheet: -0.40 (0.30), residues: 287 loop : -0.86 (0.26), residues: 472 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 129 time to evaluate : 0.999 Fit side-chains outliers start: 24 outliers final: 11 residues processed: 140 average time/residue: 1.1099 time to fit residues: 166.7422 Evaluate side-chains 134 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 123 time to evaluate : 0.924 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 7 residues processed: 4 average time/residue: 0.3837 time to fit residues: 3.1259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 56 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 12 optimal weight: 0.0770 chunk 61 optimal weight: 1.9990 overall best weight: 1.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 32 GLN S 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 8806 Z= 0.215 Angle : 0.540 12.267 11958 Z= 0.280 Chirality : 0.042 0.185 1403 Planarity : 0.004 0.057 1500 Dihedral : 5.009 87.629 1220 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer Outliers : 3.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.25), residues: 1115 helix: 1.68 (0.28), residues: 357 sheet: -0.43 (0.30), residues: 291 loop : -0.79 (0.27), residues: 467 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 128 time to evaluate : 0.998 Fit side-chains outliers start: 28 outliers final: 15 residues processed: 145 average time/residue: 1.1406 time to fit residues: 177.1547 Evaluate side-chains 137 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 122 time to evaluate : 0.921 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 9 residues processed: 6 average time/residue: 0.4601 time to fit residues: 4.5116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 49 optimal weight: 0.3980 chunk 42 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 8806 Z= 0.161 Angle : 0.501 10.796 11958 Z= 0.263 Chirality : 0.041 0.194 1403 Planarity : 0.004 0.052 1500 Dihedral : 4.778 83.343 1220 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 3.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.25), residues: 1115 helix: 1.69 (0.28), residues: 362 sheet: -0.32 (0.30), residues: 283 loop : -0.71 (0.27), residues: 470 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 124 time to evaluate : 1.077 Fit side-chains outliers start: 29 outliers final: 17 residues processed: 144 average time/residue: 1.1351 time to fit residues: 175.3398 Evaluate side-chains 140 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 0.992 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 14 residues processed: 3 average time/residue: 1.1076 time to fit residues: 4.9285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.3980 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 97 optimal weight: 0.0970 chunk 102 optimal weight: 3.9990 chunk 93 optimal weight: 0.1980 chunk 99 optimal weight: 3.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS B 32 GLN B 340 ASN S 184 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 8806 Z= 0.133 Angle : 0.487 10.179 11958 Z= 0.253 Chirality : 0.041 0.194 1403 Planarity : 0.003 0.046 1500 Dihedral : 4.295 68.210 1220 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer Outliers : 2.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.25), residues: 1115 helix: 1.82 (0.28), residues: 363 sheet: -0.14 (0.30), residues: 282 loop : -0.63 (0.27), residues: 470 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 131 time to evaluate : 0.960 Fit side-chains outliers start: 21 outliers final: 13 residues processed: 147 average time/residue: 1.2287 time to fit residues: 192.9946 Evaluate side-chains 130 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 117 time to evaluate : 1.009 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 0 time to fit residues: 1.3900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 90 optimal weight: 0.0060 chunk 94 optimal weight: 0.4980 chunk 99 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 8806 Z= 0.152 Angle : 0.527 10.565 11958 Z= 0.272 Chirality : 0.041 0.204 1403 Planarity : 0.004 0.047 1500 Dihedral : 4.207 59.149 1220 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer Outliers : 2.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.25), residues: 1115 helix: 1.87 (0.28), residues: 362 sheet: -0.07 (0.31), residues: 282 loop : -0.52 (0.28), residues: 471 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 125 time to evaluate : 1.027 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 16 residues processed: 140 average time/residue: 1.2150 time to fit residues: 181.7675 Evaluate side-chains 138 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 122 time to evaluate : 0.902 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 3 average time/residue: 0.4318 time to fit residues: 2.7823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 101 optimal weight: 0.0980 chunk 88 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 69 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 8806 Z= 0.160 Angle : 0.531 9.464 11958 Z= 0.275 Chirality : 0.042 0.203 1403 Planarity : 0.004 0.047 1500 Dihedral : 4.085 50.727 1220 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer Outliers : 2.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.25), residues: 1115 helix: 2.00 (0.28), residues: 359 sheet: -0.05 (0.31), residues: 282 loop : -0.56 (0.28), residues: 474 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 123 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 17 residues processed: 142 average time/residue: 1.2235 time to fit residues: 185.5170 Evaluate side-chains 137 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 120 time to evaluate : 1.026 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 17 residues processed: 1 average time/residue: 0.1318 time to fit residues: 1.6603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.0770 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 63 optimal weight: 6.9990 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.178564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.141203 restraints weight = 9039.256| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.14 r_work: 0.3326 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 8806 Z= 0.210 Angle : 0.564 9.249 11958 Z= 0.293 Chirality : 0.043 0.212 1403 Planarity : 0.004 0.052 1500 Dihedral : 4.243 50.015 1220 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 2.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.25), residues: 1115 helix: 1.87 (0.28), residues: 362 sheet: -0.17 (0.30), residues: 285 loop : -0.55 (0.28), residues: 468 =============================================================================== Job complete usr+sys time: 3474.58 seconds wall clock time: 62 minutes 26.95 seconds (3746.95 seconds total)