Starting phenix.real_space_refine on Fri Dec 8 04:12:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2g_25612/12_2023/7t2g_25612_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2g_25612/12_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_25612/12_2023/7t2g_25612.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2g_25612/12_2023/7t2g_25612.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2g_25612/12_2023/7t2g_25612_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2g_25612/12_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-1.21rc1-5172/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: 5.37, per 1000 atoms: 0.78 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: 2.64 Conformation dependent library (CDL) restraints added in 1.5 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: 1.43 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: 2.22 Time building geometry restraints manager: 2.84 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: 4044 17.02 - 34.03: 238 34.03 - 51.05: 35 51.05 - 68.07: 18 68.07 - 85.09: 4 Dihedral angle restraints: 4339 sinusoidal: 1710 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 4336 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: 0.380 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: 1.940 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 23.820 Find NCS groups from input model: 0.200 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:11.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.000 ------------------------------------------------------------------------------- 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 : 12.032 85.085 2630 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 192 HIS 0.010 0.001 HIS B 225 PHE 0.015 0.002 PHE B 151 TYR 0.019 0.002 TYR R 326 ARG 0.005 0.001 ARG B 251 *********************** 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 : 0.831 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 168 average time/residue: 1.1536 time to fit residues: 204.2698 Evaluate side-chains 154 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 152 time to evaluate : 0.815 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 1.1007 ------------------------------------------------------------------------------- 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: 0.7944 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 7067 Z= 0.351 Angle : 0.641 6.267 9632 Z= 0.343 Chirality : 0.045 0.171 1140 Planarity : 0.005 0.036 1190 Dihedral : 6.826 63.696 1205 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.43 % Allowed : 11.59 % Favored : 84.98 % 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: 1.58 (0.25), residues: 390 sheet: 0.00 (0.37), residues: 173 loop : -0.75 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP B 82 HIS 0.010 0.002 HIS B 54 PHE 0.019 0.002 PHE B 151 TYR 0.015 0.002 TYR R 326 ARG 0.003 0.001 ARG C 27 *********************** 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 182 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 158 time to evaluate : 0.766 Fit side-chains outliers start: 24 outliers final: 8 residues processed: 165 average time/residue: 1.1094 time to fit residues: 193.3459 Evaluate side-chains 157 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 149 time to evaluate : 0.759 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 4 average time/residue: 0.5569 time to fit residues: 3.4743 ------------------------------------------------------------------------------- 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: 0.7980 chunk 25 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 195 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 ASN B 259 GLN B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 ASN R 109 ASN R 150 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7067 Z= 0.241 Angle : 0.553 5.512 9632 Z= 0.295 Chirality : 0.042 0.172 1140 Planarity : 0.004 0.037 1190 Dihedral : 6.049 55.959 1205 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.86 % Allowed : 14.59 % Favored : 83.55 % 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: 0.74 (0.28), residues: 890 helix: 1.78 (0.25), residues: 397 sheet: -0.05 (0.36), residues: 174 loop : -0.81 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.005 0.001 HIS B 54 PHE 0.014 0.002 PHE B 151 TYR 0.009 0.001 TYR R 326 ARG 0.006 0.001 ARG R 280 *********************** 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 172 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 159 time to evaluate : 0.769 Fit side-chains outliers start: 13 outliers final: 5 residues processed: 165 average time/residue: 1.1882 time to fit residues: 206.5114 Evaluate side-chains 152 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 147 time to evaluate : 0.768 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 1 average time/residue: 1.0817 time to fit residues: 2.1673 ------------------------------------------------------------------------------- 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: 6.9990 chunk 42 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 chunk 86 optimal weight: 0.1980 chunk 77 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2034 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= 0.191 Angle : 0.508 5.469 9632 Z= 0.271 Chirality : 0.041 0.151 1140 Planarity : 0.003 0.039 1190 Dihedral : 5.641 55.822 1205 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.58 % Allowed : 15.88 % Favored : 81.55 % 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: 1.91 (0.25), residues: 397 sheet: -0.11 (0.36), residues: 174 loop : -0.78 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS B 54 PHE 0.013 0.001 PHE B 199 TYR 0.013 0.001 TYR R 149 ARG 0.007 0.000 ARG R 280 *********************** 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 173 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 155 time to evaluate : 0.690 Fit side-chains outliers start: 18 outliers final: 6 residues processed: 164 average time/residue: 1.1566 time to fit residues: 199.7329 Evaluate side-chains 154 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 148 time to evaluate : 0.689 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 3 average time/residue: 0.4462 time to fit residues: 2.4366 ------------------------------------------------------------------------------- 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: 0.5980 chunk 35 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 59 optimal weight: 0.0870 chunk 0 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2008 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= 0.219 Angle : 0.532 5.478 9632 Z= 0.284 Chirality : 0.041 0.146 1140 Planarity : 0.004 0.036 1190 Dihedral : 5.613 56.188 1205 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.29 % Allowed : 16.88 % Favored : 80.83 % 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: 0.78 (0.27), residues: 890 helix: 1.87 (0.25), residues: 397 sheet: -0.15 (0.36), residues: 174 loop : -0.79 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.005 0.001 HIS B 54 PHE 0.012 0.002 PHE B 151 TYR 0.010 0.001 TYR R 326 ARG 0.003 0.000 ARG A 208 *********************** 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: 16 poor density : 153 time to evaluate : 0.828 Fit side-chains outliers start: 16 outliers final: 6 residues processed: 161 average time/residue: 1.1747 time to fit residues: 199.3724 Evaluate side-chains 155 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 149 time to evaluate : 0.811 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 0.1540 time to fit residues: 1.4435 ------------------------------------------------------------------------------- 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: 3.9990 chunk 21 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 7 optimal weight: 0.0570 chunk 28 optimal weight: 0.4980 chunk 45 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 ** 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7067 Z= 0.171 Angle : 0.501 5.426 9632 Z= 0.268 Chirality : 0.040 0.148 1140 Planarity : 0.003 0.037 1190 Dihedral : 5.385 57.633 1205 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % 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: 0.85 (0.27), residues: 890 helix: 1.94 (0.25), residues: 397 sheet: -0.08 (0.36), residues: 176 loop : -0.78 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.003 0.001 HIS B 54 PHE 0.012 0.001 PHE B 199 TYR 0.015 0.001 TYR R 149 ARG 0.002 0.000 ARG A 208 *********************** 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 174 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 157 time to evaluate : 0.834 Fit side-chains outliers start: 17 outliers final: 5 residues processed: 165 average time/residue: 1.1429 time to fit residues: 199.1385 Evaluate side-chains 153 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 148 time to evaluate : 0.783 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.1459 time to fit residues: 1.4692 ------------------------------------------------------------------------------- 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: 3.9990 chunk 72 optimal weight: 0.1980 chunk 85 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 293 ASN 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7067 Z= 0.277 Angle : 0.585 6.639 9632 Z= 0.309 Chirality : 0.043 0.167 1140 Planarity : 0.004 0.034 1190 Dihedral : 5.743 57.591 1205 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.15 % Allowed : 19.46 % Favored : 78.40 % 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: 0.68 (0.27), residues: 890 helix: 1.74 (0.25), residues: 397 sheet: -0.19 (0.36), residues: 179 loop : -0.78 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.006 0.001 HIS B 54 PHE 0.015 0.002 PHE A 189 TYR 0.011 0.002 TYR R 326 ARG 0.003 0.000 ARG A 208 *********************** 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 165 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 150 time to evaluate : 0.702 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 157 average time/residue: 1.1741 time to fit residues: 194.2571 Evaluate side-chains 154 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 148 time to evaluate : 0.782 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 0.6355 time to fit residues: 2.4316 ------------------------------------------------------------------------------- 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: 1.9990 chunk 54 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 67 optimal weight: 0.3980 chunk 78 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 74 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 293 ASN R 109 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2183 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= 0.199 Angle : 0.535 6.318 9632 Z= 0.284 Chirality : 0.041 0.154 1140 Planarity : 0.003 0.037 1190 Dihedral : 5.453 56.235 1205 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.72 % Allowed : 19.89 % Favored : 78.40 % 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: 0.77 (0.27), residues: 890 helix: 1.78 (0.25), residues: 397 sheet: 0.01 (0.37), residues: 175 loop : -0.79 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.003 0.001 HIS B 54 PHE 0.012 0.001 PHE B 199 TYR 0.012 0.001 TYR B 59 ARG 0.003 0.000 ARG A 208 *********************** 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 164 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 152 time to evaluate : 0.790 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 162 average time/residue: 1.2055 time to fit residues: 205.5689 Evaluate side-chains 154 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 148 time to evaluate : 0.781 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 1.0563 ------------------------------------------------------------------------------- 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: 0.9980 chunk 62 optimal weight: 4.9990 chunk 24 optimal weight: 0.4980 chunk 72 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 84 optimal weight: 0.0670 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 0.0370 chunk 58 optimal weight: 0.6980 overall best weight: 0.4396 ------------------------------------------------------------------------------- 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 75 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 293 ASN R 104 ASN R 109 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7067 Z= 0.164 Angle : 0.501 6.530 9632 Z= 0.266 Chirality : 0.040 0.154 1140 Planarity : 0.003 0.039 1190 Dihedral : 5.241 56.091 1205 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.72 % Allowed : 20.46 % Favored : 77.83 % 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: 0.86 (0.28), residues: 890 helix: 1.88 (0.25), residues: 398 sheet: -0.03 (0.36), residues: 178 loop : -0.72 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.003 0.001 HIS B 54 PHE 0.012 0.001 PHE B 199 TYR 0.014 0.001 TYR R 149 ARG 0.003 0.000 ARG A 208 *********************** 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 170 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 158 time to evaluate : 0.797 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 165 average time/residue: 1.2080 time to fit residues: 210.2949 Evaluate side-chains 159 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 151 time to evaluate : 0.774 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 0.1362 time to fit residues: 1.4845 ------------------------------------------------------------------------------- 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: 4.9990 chunk 81 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 7 optimal weight: 0.2980 chunk 54 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 chunk 21 optimal weight: 0.0670 chunk 65 optimal weight: 0.0030 chunk 10 optimal weight: 0.4980 overall best weight: 0.3528 ------------------------------------------------------------------------------- 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 304 GLN B 32 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 293 ASN R 109 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7067 Z= 0.156 Angle : 0.499 6.867 9632 Z= 0.265 Chirality : 0.040 0.155 1140 Planarity : 0.003 0.038 1190 Dihedral : 5.129 56.142 1205 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % 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: 0.95 (0.28), residues: 890 helix: 1.91 (0.25), residues: 397 sheet: 0.21 (0.37), residues: 171 loop : -0.73 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.002 0.001 HIS B 54 PHE 0.012 0.001 PHE B 199 TYR 0.010 0.001 TYR R 128 ARG 0.004 0.000 ARG A 21 ********************** 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 163 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 153 time to evaluate : 0.684 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 161 average time/residue: 1.1512 time to fit residues: 195.3182 Evaluate side-chains 156 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 151 time to evaluate : 0.764 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 1.0353 ------------------------------------------------------------------------------- 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: 0.9990 chunk 70 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 51 optimal weight: 0.0670 chunk 80 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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** A 304 GLN 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 Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.129342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.113107 restraints weight = 25650.659| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.14 r_work: 0.3302 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 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 = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3299 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7067 Z= 0.177 Angle : 0.519 6.838 9632 Z= 0.275 Chirality : 0.041 0.152 1140 Planarity : 0.003 0.037 1190 Dihedral : 5.257 56.234 1205 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.72 % Allowed : 21.46 % 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: 0.88 (0.28), residues: 890 helix: 1.87 (0.25), residues: 397 sheet: 0.09 (0.37), residues: 178 loop : -0.76 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS B 54 PHE 0.013 0.001 PHE B 199 TYR 0.017 0.001 TYR R 149 ARG 0.007 0.000 ARG R 280 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3473.72 seconds wall clock time: 62 minutes 19.53 seconds (3739.53 seconds total)