Starting phenix.real_space_refine on Tue Nov 14 02:20:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2g_25612/11_2023/7t2g_25612_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2g_25612/11_2023/7t2g_25612.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2g_25612/11_2023/7t2g_25612.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2g_25612/11_2023/7t2g_25612.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2g_25612/11_2023/7t2g_25612_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2g_25612/11_2023/7t2g_25612_updated.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.028 sd= 0.242 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 59 5.16 5 C 4461 2.51 5 N 1154 2.21 5 O 1248 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 6922 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1690 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 2, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 59 Chain: "B" Number of atoms: 2481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2481 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 90 Chain: "C" Number of atoms: 348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 348 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "R" Number of atoms: 2403 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 299, 2364 Unusual residues: {'CLR': 2, 'EIG': 1} Classifications: {'peptide': 288, 'undetermined': 3, 'water': 8} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 277, None: 11} Not linked: pdbres="ILE R 352 " pdbres="EIG R 501 " Not linked: pdbres="EIG R 501 " pdbres="CLR R 502 " Not linked: pdbres="CLR R 502 " pdbres="CLR R 503 " Not linked: pdbres="CLR R 503 " pdbres="HOH R 601 " Not linked: pdbres="HOH R 601 " pdbres="HOH R 602 " ... (remaining 6 not shown) Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 25 Conformer: "B" Number of residues, atoms: 299, 2364 Unusual residues: {'CLR': 2, 'EIG': 1} Classifications: {'peptide': 288, 'undetermined': 3, 'water': 8} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 277, None: 11} Not linked: pdbres="ILE R 352 " pdbres="EIG R 501 " Not linked: pdbres="EIG R 501 " pdbres="CLR R 502 " Not linked: pdbres="CLR R 502 " pdbres="CLR R 503 " Not linked: pdbres="CLR R 503 " pdbres="HOH R 601 " Not linked: pdbres="HOH R 601 " pdbres="HOH R 602 " ... (remaining 6 not shown) Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 2379 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C01AEIG R 501 " occ=0.50 ... (58 atoms not shown) pdb=" O05BEIG R 501 " occ=0.50 Time building chain proxies: 5.69, per 1000 atoms: 0.82 Number of scatterers: 6922 At special positions: 0 Unit cell: (91.84, 98.4, 114.8, 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 59 16.00 O 1248 8.00 N 1154 7.00 C 4461 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 140 " - pdb=" SG CYS R 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.95 Conformation dependent library (CDL) restraints added in 1.7 seconds 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1706 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 9 sheets defined 43.4% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 208 through 215 removed outlier: 5.190A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N CYS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N PHE A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 231 removed outlier: 3.722A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 278 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 Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'B' and resid 6 through 25 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'C' and resid 10 through 23 Processing helix chain 'C' and resid 30 through 45 Processing helix chain 'R' and resid 66 through 95 Processing helix chain 'R' and resid 102 through 129 removed outlier: 3.630A pdb=" N THR R 120 " --> pdb=" O LEU R 116 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU R 121 " --> pdb=" O ALA R 117 " (cutoff:3.500A) Proline residue: R 122 - end of helix Processing helix chain 'R' and resid 136 through 170 Processing helix chain 'R' and resid 172 through 178 removed outlier: 4.142A pdb=" N ASP R 177 " --> pdb=" O VAL R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 205 removed outlier: 3.800A pdb=" N ALA R 197 " --> pdb=" O ILE R 193 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ILE R 198 " --> pdb=" O LEU R 194 " (cutoff:3.500A) Proline residue: R 201 - end of helix Processing helix chain 'R' and resid 225 through 240 Processing helix chain 'R' and resid 242 through 261 removed outlier: 3.747A pdb=" N SER R 261 " --> pdb=" O LEU R 257 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 305 Proline residue: R 295 - end of helix Processing helix chain 'R' and resid 314 through 336 removed outlier: 3.542A pdb=" N ASN R 328 " --> pdb=" O LEU R 324 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N SER R 329 " --> pdb=" O GLY R 325 " (cutoff:3.500A) Proline residue: R 333 - end of helix Processing helix chain 'R' and resid 341 through 349 removed outlier: 3.610A pdb=" N ARG R 345 " --> pdb=" O GLU R 341 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS R 346 " --> pdb=" O ASN R 342 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU R 349 " --> pdb=" O ARG R 345 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.524A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.773A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.008A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.524A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.696A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.560A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.339A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.524A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'R' and resid 208 through 211 365 hydrogen bonds defined for protein. 1065 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: 2.18 Time building geometry restraints manager: 3.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1094 1.30 - 1.43: 1855 1.43 - 1.56: 4029 1.56 - 1.69: 6 1.69 - 1.82: 83 Bond restraints: 7067 Sorted by residual: bond pdb=" C08BEIG R 501 " pdb=" N01BEIG R 501 " ideal model delta sigma weight residual 1.448 1.271 0.177 2.00e-02 2.50e+03 7.83e+01 bond pdb=" C17BEIG R 501 " pdb=" C19BEIG R 501 " ideal model delta sigma weight residual 1.470 1.611 -0.141 2.00e-02 2.50e+03 4.98e+01 bond pdb=" C08BEIG R 501 " pdb=" C09BEIG R 501 " ideal model delta sigma weight residual 1.529 1.404 0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" C LEU B 252 " pdb=" O LEU B 252 " ideal model delta sigma weight residual 1.235 1.169 0.066 1.22e-02 6.72e+03 2.97e+01 bond pdb=" C17AEIG R 501 " pdb=" C20AEIG R 501 " ideal model delta sigma weight residual 1.348 1.445 -0.097 2.00e-02 2.50e+03 2.35e+01 ... (remaining 7062 not shown) Histogram of bond angle deviations from ideal: 94.75 - 103.13: 54 103.13 - 111.51: 3257 111.51 - 119.88: 3032 119.88 - 128.26: 3220 128.26 - 136.63: 69 Bond angle restraints: 9632 Sorted by residual: angle pdb=" C09BEIG R 501 " pdb=" C08BEIG R 501 " pdb=" C12BEIG R 501 " ideal model delta sigma weight residual 114.95 94.75 20.20 3.00e+00 1.11e-01 4.53e+01 angle pdb=" N GLY B 64 " pdb=" CA GLY B 64 " pdb=" C GLY B 64 " ideal model delta sigma weight residual 112.82 105.38 7.44 1.38e+00 5.25e-01 2.90e+01 angle pdb=" N ASN R 328 " pdb=" CA ASN R 328 " pdb=" C ASN R 328 " ideal model delta sigma weight residual 112.54 106.25 6.29 1.22e+00 6.72e-01 2.66e+01 angle pdb=" N SER R 329 " pdb=" CA SER R 329 " pdb=" C SER R 329 " ideal model delta sigma weight residual 112.23 105.84 6.39 1.26e+00 6.30e-01 2.57e+01 angle pdb=" N LYS C 32 " pdb=" CA LYS C 32 " pdb=" C LYS C 32 " ideal model delta sigma weight residual 112.90 106.27 6.63 1.31e+00 5.83e-01 2.56e+01 ... (remaining 9627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.02: 3869 17.02 - 34.03: 225 34.03 - 51.05: 35 51.05 - 68.07: 18 68.07 - 85.09: 4 Dihedral angle restraints: 4151 sinusoidal: 1522 harmonic: 2629 Sorted by residual: dihedral pdb=" CA PHE B 151 " pdb=" C PHE B 151 " pdb=" N LEU B 152 " pdb=" CA LEU B 152 " ideal model delta harmonic sigma weight residual 180.00 161.17 18.83 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 161.18 18.82 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA ASN B 293 " pdb=" C ASN B 293 " pdb=" N CYS B 294 " pdb=" CA CYS B 294 " ideal model delta harmonic sigma weight residual 180.00 163.67 16.33 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 4148 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1069 0.096 - 0.192: 68 0.192 - 0.288: 1 0.288 - 0.383: 1 0.383 - 0.479: 1 Chirality restraints: 1140 Sorted by residual: chirality pdb=" C08BEIG R 501 " pdb=" C09BEIG R 501 " pdb=" C10BEIG R 501 " pdb=" C12BEIG R 501 " both_signs ideal model delta sigma weight residual False -2.77 -2.29 -0.48 2.00e-01 2.50e+01 5.74e+00 chirality pdb=" C14BEIG R 501 " pdb=" C13BEIG R 501 " pdb=" C15BEIG R 501 " pdb=" C17BEIG R 501 " both_signs ideal model delta sigma weight residual False -2.26 -2.58 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" C10AEIG R 501 " pdb=" C08AEIG R 501 " pdb=" C13AEIG R 501 " pdb=" N02AEIG R 501 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 1137 not shown) Planarity restraints: 1190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C14BEIG R 501 " -0.022 2.00e-02 2.50e+03 4.86e-02 2.95e+01 pdb=" C17BEIG R 501 " 0.016 2.00e-02 2.50e+03 pdb=" C19BEIG R 501 " 0.029 2.00e-02 2.50e+03 pdb=" C20BEIG R 501 " -0.082 2.00e-02 2.50e+03 pdb=" O03BEIG R 501 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 251 " 0.413 9.50e-02 1.11e+02 1.85e-01 2.10e+01 pdb=" NE ARG B 251 " -0.026 2.00e-02 2.50e+03 pdb=" CZ ARG B 251 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG B 251 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 251 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 252 " -0.020 2.00e-02 2.50e+03 4.11e-02 1.69e+01 pdb=" C LEU B 252 " 0.071 2.00e-02 2.50e+03 pdb=" O LEU B 252 " -0.027 2.00e-02 2.50e+03 pdb=" N PHE B 253 " -0.024 2.00e-02 2.50e+03 ... (remaining 1187 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1012 2.75 - 3.29: 7313 3.29 - 3.83: 12874 3.83 - 4.36: 16084 4.36 - 4.90: 25918 Nonbonded interactions: 63201 Sorted by model distance: nonbonded pdb=" O ASP B 195 " pdb=" OG1 THR B 196 " model vdw 2.214 2.440 nonbonded pdb=" OD1 ASN B 110 " pdb=" NZ LYS B 127 " model vdw 2.284 2.520 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.300 2.440 nonbonded pdb=" O MET B 325 " pdb=" ND2 ASN B 340 " model vdw 2.308 2.520 nonbonded pdb=" OD2 ASP R 147 " pdb=" OH TYR R 326 " model vdw 2.314 2.440 ... (remaining 63196 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=0.43 max=1.00 mean=0.99 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: 0.410 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: 1.950 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 25.560 Find NCS groups from input model: 0.210 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: 0.010 Load rotamer database and sin/cos tables:12.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 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 : 0.007 0.177 7067 Z= 0.476 Angle : 0.880 20.195 9632 Z= 0.534 Chirality : 0.049 0.479 1140 Planarity : 0.008 0.185 1190 Dihedral : 12.300 85.085 2442 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.00 % Allowed : 7.30 % Favored : 91.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.61 (0.28), residues: 890 helix: 1.29 (0.27), residues: 376 sheet: 0.19 (0.37), residues: 175 loop : -0.38 (0.35), residues: 339 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 165 time to evaluate : 0.833 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 168 average time/residue: 1.1580 time to fit residues: 205.2051 Evaluate side-chains 154 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 152 time to evaluate : 0.719 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.9688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 26 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 HIS B 17 GLN B 75 GLN B 259 GLN B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 109 ASN ** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 7067 Z= 0.352 Angle : 0.643 6.172 9632 Z= 0.343 Chirality : 0.045 0.172 1140 Planarity : 0.005 0.035 1190 Dihedral : 6.666 65.385 1017 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.15 % Allowed : 12.02 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.61 (0.27), residues: 890 helix: 1.59 (0.25), residues: 390 sheet: -0.00 (0.37), residues: 173 loop : -0.75 (0.34), residues: 327 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 159 time to evaluate : 0.799 Fit side-chains outliers start: 22 outliers final: 7 residues processed: 166 average time/residue: 1.1872 time to fit residues: 207.9548 Evaluate side-chains 158 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 151 time to evaluate : 0.793 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 3 average time/residue: 0.4310 time to fit residues: 2.5120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 195 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 ASN R 109 ASN R 150 ASN ** R 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7067 Z= 0.275 Angle : 0.578 5.598 9632 Z= 0.307 Chirality : 0.043 0.175 1140 Planarity : 0.004 0.036 1190 Dihedral : 6.055 56.902 1017 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.58 % Allowed : 13.59 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.66 (0.28), residues: 890 helix: 1.71 (0.25), residues: 397 sheet: -0.10 (0.37), residues: 173 loop : -0.84 (0.34), residues: 320 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 157 time to evaluate : 0.836 Fit side-chains outliers start: 18 outliers final: 7 residues processed: 166 average time/residue: 1.1251 time to fit residues: 196.9360 Evaluate side-chains 153 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 146 time to evaluate : 0.810 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 1 average time/residue: 1.0528 time to fit residues: 2.1832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 86 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 ASN B 32 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 7067 Z= 0.295 Angle : 0.593 5.731 9632 Z= 0.314 Chirality : 0.043 0.158 1140 Planarity : 0.004 0.037 1190 Dihedral : 6.107 57.993 1017 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.58 % Allowed : 15.45 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.27), residues: 890 helix: 1.68 (0.25), residues: 396 sheet: -0.21 (0.36), residues: 174 loop : -0.89 (0.33), residues: 320 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 152 time to evaluate : 0.718 Fit side-chains outliers start: 18 outliers final: 9 residues processed: 161 average time/residue: 1.1799 time to fit residues: 200.2110 Evaluate side-chains 158 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 149 time to evaluate : 0.780 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 3 average time/residue: 0.4637 time to fit residues: 2.5793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 59 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 77 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 17 optimal weight: 0.0980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 195 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7067 Z= 0.196 Angle : 0.520 5.494 9632 Z= 0.278 Chirality : 0.041 0.153 1140 Planarity : 0.004 0.039 1190 Dihedral : 5.529 56.113 1017 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.86 % Allowed : 17.17 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.76 (0.28), residues: 890 helix: 1.86 (0.25), residues: 397 sheet: -0.22 (0.36), residues: 179 loop : -0.77 (0.35), residues: 314 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 156 time to evaluate : 0.769 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 164 average time/residue: 1.1926 time to fit residues: 206.0587 Evaluate side-chains 152 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 145 time to evaluate : 0.796 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.1468 time to fit residues: 1.4925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 86 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 45 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 195 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 259 GLN B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 ASN ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7067 Z= 0.221 Angle : 0.544 6.311 9632 Z= 0.288 Chirality : 0.041 0.150 1140 Planarity : 0.004 0.036 1190 Dihedral : 5.512 56.868 1017 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.43 % Allowed : 17.88 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.73 (0.27), residues: 890 helix: 1.83 (0.25), residues: 397 sheet: -0.23 (0.36), residues: 179 loop : -0.78 (0.34), residues: 314 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 149 time to evaluate : 0.781 Fit side-chains outliers start: 17 outliers final: 5 residues processed: 159 average time/residue: 1.1891 time to fit residues: 199.0893 Evaluate side-chains 148 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 143 time to evaluate : 0.806 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.2093 time to fit residues: 1.3603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 ASN ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 7067 Z= 0.324 Angle : 0.626 6.420 9632 Z= 0.330 Chirality : 0.044 0.160 1140 Planarity : 0.004 0.032 1190 Dihedral : 5.898 58.903 1017 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.00 % Allowed : 19.17 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.50 (0.27), residues: 890 helix: 1.60 (0.25), residues: 397 sheet: -0.32 (0.36), residues: 180 loop : -0.86 (0.34), residues: 313 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 147 time to evaluate : 0.711 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 156 average time/residue: 1.1796 time to fit residues: 193.8893 Evaluate side-chains 154 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 144 time to evaluate : 0.753 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 3 average time/residue: 0.4961 time to fit residues: 2.7677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 67 optimal weight: 0.1980 chunk 78 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 48 optimal weight: 0.0870 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 195 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7067 Z= 0.203 Angle : 0.546 6.375 9632 Z= 0.287 Chirality : 0.041 0.153 1140 Planarity : 0.003 0.036 1190 Dihedral : 5.483 56.620 1017 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.86 % Allowed : 19.89 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.66 (0.27), residues: 890 helix: 1.75 (0.25), residues: 397 sheet: -0.23 (0.36), residues: 179 loop : -0.79 (0.34), residues: 314 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 148 time to evaluate : 0.729 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 157 average time/residue: 1.2057 time to fit residues: 199.0486 Evaluate side-chains 151 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 144 time to evaluate : 0.791 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.2029 time to fit residues: 1.2819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 72 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 84 optimal weight: 0.0980 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 ASN ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7067 Z= 0.283 Angle : 0.609 6.978 9632 Z= 0.319 Chirality : 0.044 0.154 1140 Planarity : 0.004 0.032 1190 Dihedral : 5.770 58.464 1017 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.57 % Allowed : 20.74 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 (0.27), residues: 890 helix: 1.62 (0.25), residues: 397 sheet: -0.26 (0.36), residues: 180 loop : -0.85 (0.34), residues: 313 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 145 time to evaluate : 0.702 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 153 average time/residue: 1.2082 time to fit residues: 194.3886 Evaluate side-chains 151 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 143 time to evaluate : 0.770 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 0.2091 time to fit residues: 1.3635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 7 optimal weight: 0.0170 chunk 54 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 21 optimal weight: 0.2980 chunk 65 optimal weight: 0.0470 chunk 10 optimal weight: 0.0670 overall best weight: 0.2854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 195 HIS A 269 ASN B 32 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 293 ASN B 340 ASN ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7067 Z= 0.158 Angle : 0.517 7.199 9632 Z= 0.272 Chirality : 0.041 0.155 1140 Planarity : 0.003 0.037 1190 Dihedral : 5.157 55.562 1017 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.86 % Allowed : 21.03 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.83 (0.28), residues: 890 helix: 1.87 (0.25), residues: 397 sheet: -0.07 (0.36), residues: 179 loop : -0.75 (0.34), residues: 314 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 163 time to evaluate : 0.792 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 174 average time/residue: 1.1459 time to fit residues: 210.4706 Evaluate side-chains 161 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 154 time to evaluate : 0.755 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.2157 time to fit residues: 1.2957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 0.0370 chunk 70 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 72 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 51 optimal weight: 0.0870 chunk 80 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 195 HIS A 213 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 ASN ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.129150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.113696 restraints weight = 24464.509| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.01 r_work: 0.3292 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3287 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3287 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7067 Z= 0.172 Angle : 0.531 7.411 9632 Z= 0.278 Chirality : 0.041 0.154 1140 Planarity : 0.003 0.036 1190 Dihedral : 5.183 55.643 1017 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.43 % Allowed : 21.75 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.28), residues: 890 helix: 1.89 (0.25), residues: 392 sheet: 0.01 (0.37), residues: 181 loop : -0.70 (0.34), residues: 317 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3452.77 seconds wall clock time: 61 minutes 56.41 seconds (3716.41 seconds total)