Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 19:32:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rmi_24572/04_2023/7rmi_24572_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rmi_24572/04_2023/7rmi_24572.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rmi_24572/04_2023/7rmi_24572.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rmi_24572/04_2023/7rmi_24572.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rmi_24572/04_2023/7rmi_24572_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rmi_24572/04_2023/7rmi_24572_updated.pdb" } resolution = 3.2 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= -0.006 sd= 0.375 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1045 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 4667 2.51 5 N 1220 2.21 5 O 1266 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None 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: 7205 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1517 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 4, 'TRANS': 189} Chain breaks: 3 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 5, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 73 Chain: "R" Number of atoms: 2221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2221 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 13, 'TRANS': 271} Chain breaks: 1 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "S" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'NH2': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 5} Chain: "B" Number of atoms: 2319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2319 Classifications: {'peptide': 322} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 5, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 7, 'ASN:plan1': 5, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 113 Chain: "G" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 245 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 1, 'TRANS': 36} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 45 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: "N" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 851 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 4.40, per 1000 atoms: 0.61 Number of scatterers: 7205 At special positions: 0 Unit cell: (67.635, 98.53, 128.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1266 8.00 N 1220 7.00 C 4667 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 180 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " 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: 3.04 Conformation dependent library (CDL) restraints added in 1.1 seconds 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1822 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 11 sheets defined 35.9% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 26 through 38 removed outlier: 3.773A pdb=" N GLN A 31 " --> pdb=" O GLU A 27 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP A 33 " --> pdb=" O GLN A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 253 through 277 removed outlier: 3.632A pdb=" N LEU A 266 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLN A 267 " --> pdb=" O ASN A 264 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU A 268 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 332 through 349 removed outlier: 3.741A pdb=" N ARG A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'R' and resid 29 through 59 Processing helix chain 'R' and resid 66 through 93 removed outlier: 4.660A pdb=" N PHE R 70 " --> pdb=" O THR R 67 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER R 80 " --> pdb=" O ALA R 77 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA R 83 " --> pdb=" O SER R 80 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE R 84 " --> pdb=" O MET R 81 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASN R 85 " --> pdb=" O ALA R 82 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR R 86 " --> pdb=" O ALA R 83 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL R 87 " --> pdb=" O PHE R 84 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL R 88 " --> pdb=" O ASN R 85 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN R 89 " --> pdb=" O THR R 86 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR R 91 " --> pdb=" O VAL R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 134 Proline residue: R 112 - end of helix Processing helix chain 'R' and resid 144 through 167 Proline residue: R 164 - end of helix Processing helix chain 'R' and resid 191 through 204 Processing helix chain 'R' and resid 206 through 223 Processing helix chain 'R' and resid 240 through 272 Proline residue: R 263 - end of helix Proline residue: R 271 - end of helix Processing helix chain 'R' and resid 275 through 277 No H-bonds generated for 'chain 'R' and resid 275 through 277' Processing helix chain 'R' and resid 282 through 298 removed outlier: 4.324A pdb=" N SER R 297 " --> pdb=" O LEU R 293 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N THR R 298 " --> pdb=" O ALA R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 300 through 308 Processing helix chain 'R' and resid 310 through 319 Processing helix chain 'B' and resid 15 through 24 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 14 through 23 Processing helix chain 'G' and resid 30 through 44 removed outlier: 3.774A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.622A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 247 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'R' and resid 169 through 174 Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.055A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.936A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.972A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.944A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 7.011A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.557A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.690A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.602A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'N' and resid 122 through 124 removed outlier: 5.932A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 336 hydrogen bonds defined for protein. 891 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: 2.04 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2260 1.35 - 1.46: 1946 1.46 - 1.58: 3096 1.58 - 1.70: 0 1.70 - 1.82: 75 Bond restraints: 7377 Sorted by residual: bond pdb=" CB ASN B 155 " pdb=" CG ASN B 155 " ideal model delta sigma weight residual 1.516 1.569 -0.053 2.50e-02 1.60e+03 4.47e+00 bond pdb=" CG1 ILE R 290 " pdb=" CD1 ILE R 290 " ideal model delta sigma weight residual 1.513 1.449 0.064 3.90e-02 6.57e+02 2.73e+00 bond pdb=" C LEU R 262 " pdb=" N PRO R 263 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.25e-02 6.40e+03 2.29e+00 bond pdb=" CB GLN N 39 " pdb=" CG GLN N 39 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.22e+00 bond pdb=" C PHE R 163 " pdb=" N PRO R 164 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.28e-02 6.10e+03 1.97e+00 ... (remaining 7372 not shown) Histogram of bond angle deviations from ideal: 97.22 - 104.59: 96 104.59 - 111.96: 3489 111.96 - 119.33: 2518 119.33 - 126.70: 3840 126.70 - 134.07: 126 Bond angle restraints: 10069 Sorted by residual: angle pdb=" CB MET G 21 " pdb=" CG MET G 21 " pdb=" SD MET G 21 " ideal model delta sigma weight residual 112.70 124.23 -11.53 3.00e+00 1.11e-01 1.48e+01 angle pdb=" C ASN A 292 " pdb=" N LYS A 293 " pdb=" CA LYS A 293 " ideal model delta sigma weight residual 122.82 128.27 -5.45 1.42e+00 4.96e-01 1.47e+01 angle pdb=" CA LEU B 308 " pdb=" CB LEU B 308 " pdb=" CG LEU B 308 " ideal model delta sigma weight residual 116.30 128.82 -12.52 3.50e+00 8.16e-02 1.28e+01 angle pdb=" CA ASN B 155 " pdb=" CB ASN B 155 " pdb=" CG ASN B 155 " ideal model delta sigma weight residual 112.60 116.09 -3.49 1.00e+00 1.00e+00 1.21e+01 angle pdb=" CB GLN N 39 " pdb=" CG GLN N 39 " pdb=" CD GLN N 39 " ideal model delta sigma weight residual 112.60 118.41 -5.81 1.70e+00 3.46e-01 1.17e+01 ... (remaining 10064 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.03: 3906 17.03 - 34.06: 293 34.06 - 51.10: 49 51.10 - 68.13: 4 68.13 - 85.16: 5 Dihedral angle restraints: 4257 sinusoidal: 1445 harmonic: 2812 Sorted by residual: dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual 180.00 -152.34 -27.66 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -153.61 -26.39 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA MET R 299 " pdb=" C MET R 299 " pdb=" N TYR R 300 " pdb=" CA TYR R 300 " ideal model delta harmonic sigma weight residual -180.00 -158.03 -21.97 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 4254 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 814 0.048 - 0.095: 268 0.095 - 0.143: 74 0.143 - 0.191: 19 0.191 - 0.239: 2 Chirality restraints: 1177 Sorted by residual: chirality pdb=" CB VAL A 241 " pdb=" CA VAL A 241 " pdb=" CG1 VAL A 241 " pdb=" CG2 VAL A 241 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CG LEU B 255 " pdb=" CB LEU B 255 " pdb=" CD1 LEU B 255 " pdb=" CD2 LEU B 255 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.19e-01 chirality pdb=" CB ILE N 70 " pdb=" CA ILE N 70 " pdb=" CG1 ILE N 70 " pdb=" CG2 ILE N 70 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.96e-01 ... (remaining 1174 not shown) Planarity restraints: 1256 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 332 " -0.043 2.00e-02 2.50e+03 3.80e-02 3.60e+01 pdb=" CG TRP B 332 " 0.102 2.00e-02 2.50e+03 pdb=" CD1 TRP B 332 " -0.045 2.00e-02 2.50e+03 pdb=" CD2 TRP B 332 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 332 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 332 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 332 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 332 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 332 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP B 332 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.050 5.00e-02 4.00e+02 7.50e-02 8.99e+00 pdb=" N PRO B 236 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 82 " 0.013 2.00e-02 2.50e+03 2.55e-02 6.51e+00 pdb=" C ALA R 82 " -0.044 2.00e-02 2.50e+03 pdb=" O ALA R 82 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA R 83 " 0.015 2.00e-02 2.50e+03 ... (remaining 1253 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2080 2.82 - 3.34: 6168 3.34 - 3.86: 11920 3.86 - 4.38: 12987 4.38 - 4.90: 23831 Nonbonded interactions: 56986 Sorted by model distance: nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.296 2.440 nonbonded pdb=" O ASP N 90 " pdb=" OH TYR N 94 " model vdw 2.296 2.440 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.301 2.440 nonbonded pdb=" O VAL R 116 " pdb=" OG SER R 119 " model vdw 2.324 2.440 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.328 2.440 ... (remaining 56981 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 7.720 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 23.100 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 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 0.068 7377 Z= 0.277 Angle : 0.843 12.516 10069 Z= 0.456 Chirality : 0.053 0.239 1177 Planarity : 0.007 0.075 1256 Dihedral : 12.681 85.159 2426 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.26), residues: 934 helix: -0.65 (0.24), residues: 338 sheet: 0.24 (0.36), residues: 201 loop : -1.09 (0.30), residues: 395 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 0.814 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.1814 time to fit residues: 38.4240 Evaluate side-chains 113 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.814 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.8980 chunk 70 optimal weight: 9.9990 chunk 39 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 267 GLN B 220 GLN B 230 ASN B 295 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 7377 Z= 0.179 Angle : 0.518 5.108 10069 Z= 0.279 Chirality : 0.042 0.136 1177 Planarity : 0.004 0.053 1256 Dihedral : 4.257 23.471 1029 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.27), residues: 934 helix: 0.67 (0.27), residues: 344 sheet: 0.39 (0.36), residues: 206 loop : -0.81 (0.31), residues: 384 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 122 time to evaluate : 0.816 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 123 average time/residue: 0.1834 time to fit residues: 30.9860 Evaluate side-chains 114 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 109 time to evaluate : 0.849 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0668 time to fit residues: 1.7282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 chunk 84 optimal weight: 5.9990 chunk 91 optimal weight: 0.0170 chunk 75 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 67 optimal weight: 7.9990 overall best weight: 1.6422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN R 136 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 7377 Z= 0.273 Angle : 0.563 6.511 10069 Z= 0.299 Chirality : 0.043 0.168 1177 Planarity : 0.004 0.049 1256 Dihedral : 4.245 22.569 1029 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.27), residues: 934 helix: 0.64 (0.27), residues: 357 sheet: 0.40 (0.35), residues: 200 loop : -0.87 (0.31), residues: 377 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 123 time to evaluate : 0.896 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 127 average time/residue: 0.1907 time to fit residues: 32.9874 Evaluate side-chains 120 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 111 time to evaluate : 0.861 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0664 time to fit residues: 2.2534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 0.9990 chunk 63 optimal weight: 0.0370 chunk 43 optimal weight: 0.0570 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 80 optimal weight: 20.0000 chunk 24 optimal weight: 0.7980 overall best weight: 0.5776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 267 GLN A 271 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 7377 Z= 0.152 Angle : 0.497 6.138 10069 Z= 0.262 Chirality : 0.041 0.133 1177 Planarity : 0.003 0.045 1256 Dihedral : 4.023 21.796 1029 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.27), residues: 934 helix: 0.96 (0.27), residues: 355 sheet: 0.59 (0.36), residues: 195 loop : -0.79 (0.31), residues: 384 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 120 time to evaluate : 0.893 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 125 average time/residue: 0.1831 time to fit residues: 31.5843 Evaluate side-chains 120 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 114 time to evaluate : 0.923 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0812 time to fit residues: 2.0339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 37 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 0 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 80 optimal weight: 0.0370 chunk 22 optimal weight: 0.6980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 7377 Z= 0.158 Angle : 0.488 6.556 10069 Z= 0.257 Chirality : 0.041 0.134 1177 Planarity : 0.003 0.043 1256 Dihedral : 3.910 20.563 1029 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.27), residues: 934 helix: 1.11 (0.28), residues: 356 sheet: 0.51 (0.35), residues: 208 loop : -0.69 (0.32), residues: 370 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 117 time to evaluate : 0.885 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 119 average time/residue: 0.1883 time to fit residues: 30.9077 Evaluate side-chains 115 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 111 time to evaluate : 0.865 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0766 time to fit residues: 1.6780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 7377 Z= 0.171 Angle : 0.503 6.712 10069 Z= 0.264 Chirality : 0.041 0.135 1177 Planarity : 0.003 0.042 1256 Dihedral : 3.889 19.908 1029 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.28), residues: 934 helix: 1.17 (0.28), residues: 357 sheet: 0.66 (0.35), residues: 204 loop : -0.75 (0.32), residues: 373 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 118 time to evaluate : 0.813 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 122 average time/residue: 0.1632 time to fit residues: 28.2545 Evaluate side-chains 119 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 113 time to evaluate : 0.808 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0730 time to fit residues: 1.8654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 75 optimal weight: 0.0980 chunk 89 optimal weight: 0.9980 chunk 56 optimal weight: 0.0980 chunk 54 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 7377 Z= 0.156 Angle : 0.495 6.545 10069 Z= 0.259 Chirality : 0.041 0.132 1177 Planarity : 0.003 0.042 1256 Dihedral : 3.836 18.992 1029 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.28), residues: 934 helix: 1.27 (0.28), residues: 357 sheet: 0.74 (0.35), residues: 204 loop : -0.69 (0.32), residues: 373 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 119 time to evaluate : 0.892 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 122 average time/residue: 0.1726 time to fit residues: 29.8761 Evaluate side-chains 122 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 116 time to evaluate : 0.943 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0723 time to fit residues: 1.9894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 70 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 7377 Z= 0.258 Angle : 0.560 7.869 10069 Z= 0.294 Chirality : 0.043 0.139 1177 Planarity : 0.003 0.041 1256 Dihedral : 4.053 21.188 1029 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.28), residues: 934 helix: 1.12 (0.28), residues: 353 sheet: 0.72 (0.36), residues: 196 loop : -0.72 (0.32), residues: 385 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 118 time to evaluate : 0.818 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 121 average time/residue: 0.1788 time to fit residues: 30.4899 Evaluate side-chains 118 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 116 time to evaluate : 0.861 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0715 time to fit residues: 1.4825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 88 optimal weight: 0.0870 overall best weight: 0.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN ** R 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 7377 Z= 0.191 Angle : 0.533 7.095 10069 Z= 0.278 Chirality : 0.042 0.133 1177 Planarity : 0.003 0.041 1256 Dihedral : 3.991 20.485 1029 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.28), residues: 934 helix: 1.22 (0.28), residues: 354 sheet: 0.79 (0.36), residues: 196 loop : -0.69 (0.32), residues: 384 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 122 time to evaluate : 0.917 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 125 average time/residue: 0.1750 time to fit residues: 30.6872 Evaluate side-chains 124 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 120 time to evaluate : 0.913 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0726 time to fit residues: 1.7525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 61 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN R 108 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 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 : 0.003 0.033 7377 Z= 0.179 Angle : 0.542 7.634 10069 Z= 0.281 Chirality : 0.041 0.140 1177 Planarity : 0.003 0.041 1256 Dihedral : 3.950 19.861 1029 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.28), residues: 934 helix: 1.24 (0.28), residues: 354 sheet: 0.81 (0.36), residues: 197 loop : -0.68 (0.32), residues: 383 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.734 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1786 time to fit residues: 30.2800 Evaluate side-chains 121 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.886 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 0.5980 chunk 68 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 30 optimal weight: 0.0050 chunk 75 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 overall best weight: 1.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN ** R 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.133478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.115145 restraints weight = 15433.477| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 3.24 r_work: 0.3539 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 7377 Z= 0.211 Angle : 0.555 7.002 10069 Z= 0.288 Chirality : 0.042 0.157 1177 Planarity : 0.003 0.041 1256 Dihedral : 3.978 19.987 1029 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.28), residues: 934 helix: 1.24 (0.28), residues: 354 sheet: 0.79 (0.36), residues: 197 loop : -0.68 (0.32), residues: 383 =============================================================================== Job complete usr+sys time: 1749.54 seconds wall clock time: 32 minutes 14.84 seconds (1934.84 seconds total)