Starting phenix.real_space_refine on Fri Dec 8 08:37:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kh5_37237/12_2023/8kh5_37237_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kh5_37237/12_2023/8kh5_37237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kh5_37237/12_2023/8kh5_37237.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kh5_37237/12_2023/8kh5_37237.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kh5_37237/12_2023/8kh5_37237_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kh5_37237/12_2023/8kh5_37237_updated.pdb" } resolution = 2.83 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= 0.003 sd= 0.143 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 57 5.16 5 C 5034 2.51 5 N 1339 2.21 5 O 1407 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: 7838 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2214 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 12, 'TRANS': 268} Chain breaks: 1 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 64 Chain: "B" Number of atoms: 1778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1778 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 96 Chain: "C" Number of atoms: 2467 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 338, 2460 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 175 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 7, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 116 Conformer: "B" Number of residues, atoms: 338, 2460 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 175 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 7, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 116 bond proxies already assigned to first conformer: 2496 Chain: "E" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 946 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 345 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 88 Unusual residues: {'CLR': 2, 'LPS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.12, per 1000 atoms: 0.78 Number of scatterers: 7838 At special positions: 0 Unit cell: (74.52, 97.2, 130.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 57 16.00 P 1 15.00 O 1407 8.00 N 1339 7.00 C 5034 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 91 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 99 " - pdb=" SG CYS E 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.04 Conformation dependent library (CDL) restraints added in 2.2 seconds 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 10 sheets defined 39.0% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 16 through 50 removed outlier: 4.321A pdb=" N VAL A 31 " --> pdb=" O THR A 27 " (cutoff:3.500A) Proline residue: A 32 - end of helix Processing helix chain 'A' and resid 56 through 81 Proline residue: A 73 - end of helix Processing helix chain 'A' and resid 88 through 121 removed outlier: 3.630A pdb=" N LYS A 98 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TYR A 99 " --> pdb=" O PHE A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 126 No H-bonds generated for 'chain 'A' and resid 123 through 126' Processing helix chain 'A' and resid 134 through 155 removed outlier: 3.526A pdb=" N CYS A 146 " --> pdb=" O TRP A 142 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N PHE A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) Proline residue: A 153 - end of helix Processing helix chain 'A' and resid 179 through 212 Proline residue: A 197 - end of helix Processing helix chain 'A' and resid 224 through 257 removed outlier: 3.623A pdb=" N LEU A 229 " --> pdb=" O LYS A 225 " (cutoff:3.500A) Proline residue: A 245 - end of helix Proline residue: A 251 - end of helix Processing helix chain 'A' and resid 264 through 293 Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'B' and resid 13 through 38 removed outlier: 3.595A pdb=" N ALA B 18 " --> pdb=" O ASN B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 59 Processing helix chain 'B' and resid 232 through 235 No H-bonds generated for 'chain 'B' and resid 232 through 235' Processing helix chain 'B' and resid 266 through 278 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 308 through 311 No H-bonds generated for 'chain 'B' and resid 308 through 311' Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 332 through 351 removed outlier: 3.651A pdb=" N ILE B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 392 removed outlier: 3.787A pdb=" N GLU B 392 " --> pdb=" O LEU B 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 25 Processing helix chain 'C' and resid 30 through 35 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'D' and resid 9 through 23 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 56 through 58 No H-bonds generated for 'chain 'D' and resid 56 through 58' Processing sheet with id= A, first strand: chain 'B' and resid 359 through 363 removed outlier: 7.189A pdb=" N VAL B 287 " --> pdb=" O TYR B 360 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N HIS B 362 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU B 289 " --> pdb=" O HIS B 362 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA B 243 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ASN B 218 " --> pdb=" O HIS B 41 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N LEU B 43 " --> pdb=" O ASN B 218 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N HIS B 220 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N LEU B 45 " --> pdb=" O HIS B 220 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N PHE B 222 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.788A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.983A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.785A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.824A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.590A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.422A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 47 through 52 removed outlier: 6.652A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.046A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) 393 hydrogen bonds defined for protein. 1137 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: 2.36 Time building geometry restraints manager: 3.26 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: 1234 1.30 - 1.43: 2168 1.43 - 1.55: 4530 1.55 - 1.68: 4 1.68 - 1.81: 78 Bond restraints: 8014 Sorted by residual: bond pdb=" C PRO A 123 " pdb=" O PRO A 123 " ideal model delta sigma weight residual 1.237 1.410 -0.173 1.26e-02 6.30e+03 1.88e+02 bond pdb=" C31 LPS A 402 " pdb=" O32 LPS A 402 " ideal model delta sigma weight residual 1.398 1.180 0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" CA ALA A 140 " pdb=" C ALA A 140 " ideal model delta sigma weight residual 1.524 1.412 0.112 1.29e-02 6.01e+03 7.53e+01 bond pdb=" C ASP A 16 " pdb=" O ASP A 16 " ideal model delta sigma weight residual 1.235 1.314 -0.079 1.26e-02 6.30e+03 3.94e+01 bond pdb=" C PHE A 126 " pdb=" O PHE A 126 " ideal model delta sigma weight residual 1.236 1.169 0.067 1.15e-02 7.56e+03 3.44e+01 ... (remaining 8009 not shown) Histogram of bond angle deviations from ideal: 99.54 - 106.44: 205 106.44 - 113.34: 4419 113.34 - 120.23: 2786 120.23 - 127.13: 3433 127.13 - 134.03: 84 Bond angle restraints: 10927 Sorted by residual: angle pdb=" N PHE A 126 " pdb=" CA PHE A 126 " pdb=" C PHE A 126 " ideal model delta sigma weight residual 111.07 123.34 -12.27 1.07e+00 8.73e-01 1.32e+02 angle pdb=" N CYS A 129 " pdb=" CA CYS A 129 " pdb=" C CYS A 129 " ideal model delta sigma weight residual 112.92 100.41 12.51 1.23e+00 6.61e-01 1.03e+02 angle pdb=" N LYS A 130 " pdb=" CA LYS A 130 " pdb=" C LYS A 130 " ideal model delta sigma weight residual 112.57 102.29 10.28 1.13e+00 7.83e-01 8.28e+01 angle pdb=" CA PHE A 126 " pdb=" C PHE A 126 " pdb=" N HIS A 127 " ideal model delta sigma weight residual 117.07 126.17 -9.10 1.14e+00 7.69e-01 6.37e+01 angle pdb=" O PHE A 126 " pdb=" C PHE A 126 " pdb=" N HIS A 127 " ideal model delta sigma weight residual 122.07 114.52 7.55 1.03e+00 9.43e-01 5.37e+01 ... (remaining 10922 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.07: 4301 15.07 - 30.14: 382 30.14 - 45.21: 103 45.21 - 60.29: 19 60.29 - 75.36: 8 Dihedral angle restraints: 4813 sinusoidal: 1799 harmonic: 3014 Sorted by residual: dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual 93.00 147.71 -54.71 1 1.00e+01 1.00e-02 4.05e+01 dihedral pdb=" N PHE A 124 " pdb=" C PHE A 124 " pdb=" CA PHE A 124 " pdb=" CB PHE A 124 " ideal model delta harmonic sigma weight residual 122.80 110.88 11.92 0 2.50e+00 1.60e-01 2.27e+01 dihedral pdb=" CB CYS A 91 " pdb=" SG CYS A 91 " pdb=" SG CYS A 168 " pdb=" CB CYS A 168 " ideal model delta sinusoidal sigma weight residual 93.00 131.85 -38.85 1 1.00e+01 1.00e-02 2.12e+01 ... (remaining 4810 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.443: 1274 0.443 - 0.886: 1 0.886 - 1.329: 0 1.329 - 1.772: 0 1.772 - 2.214: 1 Chirality restraints: 1276 Sorted by residual: chirality pdb=" C31 LPS A 402 " pdb=" C32 LPS A 402 " pdb=" O31 LPS A 402 " pdb=" O32 LPS A 402 " both_signs ideal model delta sigma weight residual False -2.18 0.04 -2.21 2.00e-01 2.50e+01 1.23e+02 chirality pdb=" CA PHE A 126 " pdb=" N PHE A 126 " pdb=" C PHE A 126 " pdb=" CB PHE A 126 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.49e+00 chirality pdb=" C13 CLR A 401 " pdb=" C12 CLR A 401 " pdb=" C14 CLR A 401 " pdb=" C17 CLR A 401 " both_signs ideal model delta sigma weight residual False -2.93 -2.52 -0.41 2.00e-01 2.50e+01 4.14e+00 ... (remaining 1273 not shown) Planarity restraints: 1371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 124 " 0.025 2.00e-02 2.50e+03 4.90e-02 2.40e+01 pdb=" C PHE A 124 " -0.085 2.00e-02 2.50e+03 pdb=" O PHE A 124 " 0.031 2.00e-02 2.50e+03 pdb=" N ARG A 125 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 126 " -0.025 2.00e-02 2.50e+03 4.67e-02 2.18e+01 pdb=" C PHE A 126 " 0.081 2.00e-02 2.50e+03 pdb=" O PHE A 126 " -0.028 2.00e-02 2.50e+03 pdb=" N HIS A 127 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 122 " -0.040 5.00e-02 4.00e+02 5.99e-02 5.74e+00 pdb=" N PRO A 123 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 123 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 123 " -0.032 5.00e-02 4.00e+02 ... (remaining 1368 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 137 2.66 - 3.22: 7483 3.22 - 3.78: 12704 3.78 - 4.34: 17671 4.34 - 4.90: 29189 Nonbonded interactions: 67184 Sorted by model distance: nonbonded pdb=" OD1 ASP E 50 " pdb=" OG SER E 59 " model vdw 2.103 2.440 nonbonded pdb=" O ILE C 58 " pdb=" OG SER C 316 " model vdw 2.189 2.440 nonbonded pdb=" OH TYR A 78 " pdb=" OD2 ASP A 171 " model vdw 2.197 2.440 nonbonded pdb=" NH1 ARG B 228 " pdb=" OD1 ASP C 186 " model vdw 2.249 2.520 nonbonded pdb=" O CYS C 149 " pdb=" NH1 ARG C 150 " model vdw 2.254 2.520 ... (remaining 67179 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 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: 1.740 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 27.460 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 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 : 0.008 0.218 8014 Z= 0.535 Angle : 0.852 17.124 10927 Z= 0.505 Chirality : 0.084 2.214 1276 Planarity : 0.005 0.060 1371 Dihedral : 12.854 75.356 2856 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.26 % Allowed : 0.77 % Favored : 98.97 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.27), residues: 1018 helix: 1.86 (0.27), residues: 402 sheet: 0.40 (0.34), residues: 218 loop : -0.56 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 142 HIS 0.011 0.002 HIS C 142 PHE 0.028 0.002 PHE A 239 TYR 0.031 0.002 TYR C 59 ARG 0.004 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 204 time to evaluate : 0.905 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 206 average time/residue: 1.0699 time to fit residues: 234.8558 Evaluate side-chains 133 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 131 time to evaluate : 0.851 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.2127 time to fit residues: 1.7165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS A 131 GLN B 23 ASN B 213 GLN ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 ASN C 119 ASN C 175 GLN C 176 GLN C 220 GLN C 259 GLN E 31 ASN D 44 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8014 Z= 0.284 Angle : 0.603 7.521 10927 Z= 0.317 Chirality : 0.045 0.148 1276 Planarity : 0.005 0.059 1371 Dihedral : 6.243 54.188 1272 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.22 % Allowed : 12.23 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.27), residues: 1018 helix: 1.95 (0.26), residues: 410 sheet: 0.39 (0.32), residues: 221 loop : -0.40 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 339 HIS 0.010 0.002 HIS B 220 PHE 0.027 0.002 PHE A 119 TYR 0.025 0.002 TYR C 59 ARG 0.009 0.001 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 147 time to evaluate : 0.872 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 10 residues processed: 161 average time/residue: 1.2396 time to fit residues: 211.0996 Evaluate side-chains 132 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 122 time to evaluate : 0.847 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.0707 time to fit residues: 1.4136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 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 284 ASN B 213 GLN B 227 GLN ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 ASN C 156 GLN C 175 GLN C 220 GLN E 31 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8014 Z= 0.245 Angle : 0.543 5.118 10927 Z= 0.288 Chirality : 0.043 0.149 1276 Planarity : 0.004 0.057 1371 Dihedral : 5.868 54.115 1272 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.47 % Allowed : 15.19 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.26), residues: 1018 helix: 2.13 (0.26), residues: 409 sheet: 0.30 (0.32), residues: 221 loop : -0.42 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 82 HIS 0.009 0.001 HIS B 357 PHE 0.027 0.002 PHE A 119 TYR 0.029 0.002 TYR C 59 ARG 0.006 0.001 ARG B 280 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 127 time to evaluate : 0.903 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 12 residues processed: 145 average time/residue: 1.2807 time to fit residues: 196.0178 Evaluate side-chains 126 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 114 time to evaluate : 0.884 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 0.0695 time to fit residues: 1.2562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 chunk 86 optimal weight: 0.8980 chunk 26 optimal weight: 0.0470 chunk 80 optimal weight: 8.9990 chunk 54 optimal weight: 0.0970 overall best weight: 0.5676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 GLN B 213 GLN ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN C 175 GLN C 220 GLN E 31 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8014 Z= 0.166 Angle : 0.506 8.013 10927 Z= 0.265 Chirality : 0.041 0.133 1276 Planarity : 0.004 0.057 1371 Dihedral : 5.500 49.482 1272 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.60 % Allowed : 15.57 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.26), residues: 1018 helix: 2.31 (0.26), residues: 410 sheet: 0.27 (0.32), residues: 226 loop : -0.32 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 82 HIS 0.005 0.001 HIS B 357 PHE 0.026 0.001 PHE A 119 TYR 0.018 0.001 TYR B 391 ARG 0.010 0.001 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 142 time to evaluate : 0.805 Fit side-chains outliers start: 28 outliers final: 12 residues processed: 162 average time/residue: 1.1975 time to fit residues: 205.6439 Evaluate side-chains 141 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 129 time to evaluate : 0.891 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 0 time to fit residues: 1.2172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.0670 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 82 optimal weight: 0.0030 chunk 66 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 86 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 87 optimal weight: 0.4980 overall best weight: 0.4128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 ASN B 29 GLN B 213 GLN B 292 ASN ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN C 119 ASN C 156 GLN C 175 GLN C 220 GLN C 259 GLN E 31 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8014 Z= 0.163 Angle : 0.498 6.398 10927 Z= 0.261 Chirality : 0.040 0.136 1276 Planarity : 0.004 0.055 1371 Dihedral : 5.321 46.822 1272 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.35 % Allowed : 16.99 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.27), residues: 1018 helix: 2.39 (0.26), residues: 410 sheet: 0.27 (0.31), residues: 231 loop : -0.33 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 82 HIS 0.004 0.001 HIS B 220 PHE 0.025 0.001 PHE A 119 TYR 0.014 0.001 TYR E 80 ARG 0.007 0.001 ARG B 317 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 141 time to evaluate : 0.965 Fit side-chains outliers start: 26 outliers final: 12 residues processed: 160 average time/residue: 1.1502 time to fit residues: 195.5685 Evaluate side-chains 144 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 132 time to evaluate : 0.869 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 0.0735 time to fit residues: 1.3328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 chunk 44 optimal weight: 0.0770 chunk 8 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 93 optimal weight: 0.0170 chunk 10 optimal weight: 0.8980 overall best weight: 0.5576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 ASN B 29 GLN B 292 ASN ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN C 175 GLN C 220 GLN E 31 ASN E 82 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8014 Z= 0.177 Angle : 0.518 8.250 10927 Z= 0.264 Chirality : 0.041 0.229 1276 Planarity : 0.004 0.055 1371 Dihedral : 5.252 44.730 1272 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.70 % Allowed : 19.31 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.26), residues: 1018 helix: 2.45 (0.26), residues: 407 sheet: 0.37 (0.32), residues: 225 loop : -0.34 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 82 HIS 0.005 0.001 HIS B 357 PHE 0.026 0.001 PHE A 119 TYR 0.011 0.001 TYR B 391 ARG 0.012 0.001 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 135 time to evaluate : 1.047 Fit side-chains outliers start: 21 outliers final: 13 residues processed: 151 average time/residue: 1.1455 time to fit residues: 184.0642 Evaluate side-chains 139 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 126 time to evaluate : 0.883 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 11 residues processed: 2 average time/residue: 0.0770 time to fit residues: 1.5764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 81 optimal weight: 0.0670 chunk 96 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 44 optimal weight: 10.0000 chunk 59 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 ASN B 29 GLN B 292 ASN ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 GLN C 220 GLN E 31 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8014 Z= 0.185 Angle : 0.502 8.101 10927 Z= 0.261 Chirality : 0.041 0.189 1276 Planarity : 0.004 0.055 1371 Dihedral : 5.242 46.227 1272 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.83 % Allowed : 19.05 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.26), residues: 1018 helix: 2.45 (0.26), residues: 406 sheet: 0.38 (0.31), residues: 230 loop : -0.35 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.005 0.001 HIS B 357 PHE 0.026 0.001 PHE A 119 TYR 0.019 0.001 TYR A 78 ARG 0.009 0.001 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 132 time to evaluate : 0.808 Fit side-chains outliers start: 22 outliers final: 13 residues processed: 149 average time/residue: 1.0379 time to fit residues: 165.0439 Evaluate side-chains 137 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 124 time to evaluate : 0.877 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 1 average time/residue: 0.0722 time to fit residues: 1.3180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 chunk 87 optimal weight: 0.5980 chunk 92 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 GLN B 213 GLN ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 GLN C 220 GLN E 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8014 Z= 0.197 Angle : 0.521 8.447 10927 Z= 0.267 Chirality : 0.041 0.172 1276 Planarity : 0.004 0.054 1371 Dihedral : 5.263 47.828 1272 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.06 % Allowed : 20.46 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.26), residues: 1018 helix: 2.48 (0.26), residues: 405 sheet: 0.41 (0.31), residues: 230 loop : -0.39 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.006 0.001 HIS B 220 PHE 0.028 0.002 PHE A 77 TYR 0.014 0.001 TYR A 78 ARG 0.008 0.000 ARG B 317 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 130 time to evaluate : 0.884 Fit side-chains outliers start: 16 outliers final: 12 residues processed: 142 average time/residue: 1.0571 time to fit residues: 160.4821 Evaluate side-chains 137 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 125 time to evaluate : 0.857 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 0.0754 time to fit residues: 1.3562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 84 optimal weight: 0.4980 chunk 89 optimal weight: 1.9990 chunk 58 optimal weight: 0.3980 chunk 94 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 ASN B 29 GLN B 292 ASN ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 GLN C 220 GLN E 31 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8014 Z= 0.218 Angle : 0.526 7.051 10927 Z= 0.272 Chirality : 0.042 0.185 1276 Planarity : 0.004 0.054 1371 Dihedral : 5.420 48.636 1272 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.80 % Allowed : 21.49 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.26), residues: 1018 helix: 2.48 (0.26), residues: 405 sheet: 0.34 (0.31), residues: 232 loop : -0.41 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.006 0.001 HIS B 357 PHE 0.027 0.002 PHE A 119 TYR 0.016 0.001 TYR E 80 ARG 0.009 0.000 ARG B 317 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 129 time to evaluate : 0.901 Fit side-chains outliers start: 14 outliers final: 14 residues processed: 142 average time/residue: 1.1269 time to fit residues: 170.8128 Evaluate side-chains 135 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 121 time to evaluate : 0.910 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 13 residues processed: 1 average time/residue: 1.6137 time to fit residues: 2.8303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 48 optimal weight: 0.2980 chunk 63 optimal weight: 0.0370 chunk 84 optimal weight: 0.5980 chunk 24 optimal weight: 10.0000 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 GLN ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN E 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8014 Z= 0.176 Angle : 0.508 8.477 10927 Z= 0.260 Chirality : 0.041 0.143 1276 Planarity : 0.004 0.054 1371 Dihedral : 5.191 50.878 1272 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.93 % Allowed : 22.01 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.26), residues: 1018 helix: 2.44 (0.26), residues: 407 sheet: 0.40 (0.31), residues: 230 loop : -0.40 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.005 0.001 HIS B 357 PHE 0.035 0.001 PHE A 77 TYR 0.015 0.001 TYR A 78 ARG 0.009 0.000 ARG B 317 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 130 time to evaluate : 0.981 Fit side-chains outliers start: 15 outliers final: 12 residues processed: 142 average time/residue: 1.2265 time to fit residues: 185.0942 Evaluate side-chains 135 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 123 time to evaluate : 0.802 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 0.0715 time to fit residues: 1.3620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 ASN B 29 GLN B 292 ASN ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 GLN C 220 GLN E 31 ASN E 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.155659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.118939 restraints weight = 17118.503| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.91 r_work: 0.3282 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8014 Z= 0.200 Angle : 0.517 7.290 10927 Z= 0.267 Chirality : 0.042 0.172 1276 Planarity : 0.004 0.054 1371 Dihedral : 5.262 49.340 1272 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.93 % Allowed : 22.14 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.26), residues: 1018 helix: 2.42 (0.26), residues: 407 sheet: 0.41 (0.31), residues: 230 loop : -0.41 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.006 0.001 HIS B 357 PHE 0.027 0.001 PHE A 119 TYR 0.016 0.001 TYR E 80 ARG 0.009 0.000 ARG B 317 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3496.57 seconds wall clock time: 62 minutes 49.61 seconds (3769.61 seconds total)