Starting phenix.real_space_refine on Tue May 7 22:25:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xjm_38401/05_2024/8xjm_38401_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xjm_38401/05_2024/8xjm_38401.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xjm_38401/05_2024/8xjm_38401.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xjm_38401/05_2024/8xjm_38401.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xjm_38401/05_2024/8xjm_38401_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xjm_38401/05_2024/8xjm_38401_updated.pdb" } resolution = 2.85 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= -0.000 sd= 0.012 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 62 5.16 5 C 5627 2.51 5 N 1513 2.21 5 O 1647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 8849 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1821 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "E" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1771 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Chain: "R" Number of atoms: 2171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2171 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 5, 'TRANS': 281} Chain breaks: 1 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 2, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 60 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'7WT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.93, per 1000 atoms: 0.56 Number of scatterers: 8849 At special positions: 0 Unit cell: (108.07, 118.77, 110.21, 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 62 16.00 O 1647 8.00 N 1513 7.00 C 5627 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 186 " 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: 3.23 Conformation dependent library (CDL) restraints added in 1.7 seconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2128 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 13 sheets defined 35.9% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 118 through 129 Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 160 through 163 No H-bonds generated for 'chain 'A' and resid 160 through 163' Processing helix chain 'A' and resid 165 through 169 Processing helix chain 'A' and resid 184 through 202 removed outlier: 3.516A pdb=" N PHE A 197 " --> pdb=" O ILE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 244 Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'C' and resid 7 through 24 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'E' and resid 28 through 30 No H-bonds generated for 'chain 'E' and resid 28 through 30' Processing helix chain 'E' and resid 87 through 89 No H-bonds generated for 'chain 'E' and resid 87 through 89' Processing helix chain 'R' and resid 30 through 59 removed outlier: 3.542A pdb=" N GLN R 56 " --> pdb=" O MET R 52 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG R 57 " --> pdb=" O LYS R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 93 Processing helix chain 'R' and resid 98 through 101 No H-bonds generated for 'chain 'R' and resid 98 through 101' Processing helix chain 'R' and resid 106 through 138 Proline residue: R 122 - end of helix Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 149 through 167 Processing helix chain 'R' and resid 169 through 172 No H-bonds generated for 'chain 'R' and resid 169 through 172' Processing helix chain 'R' and resid 196 through 231 removed outlier: 3.972A pdb=" N LEU R 202 " --> pdb=" O ASP R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 244 through 278 removed outlier: 3.529A pdb=" N TRP R 262 " --> pdb=" O SER R 258 " (cutoff:3.500A) Proline residue: R 264 - end of helix removed outlier: 7.693A pdb=" N ASN R 277 " --> pdb=" O GLY R 273 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N HIS R 278 " --> pdb=" O ILE R 274 " (cutoff:3.500A) Processing helix chain 'R' and resid 283 through 304 removed outlier: 3.671A pdb=" N ASN R 296 " --> pdb=" O MET R 292 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN R 297 " --> pdb=" O ALA R 293 " (cutoff:3.500A) Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 309 through 320 Processing sheet with id= A, first strand: chain 'A' and resid 138 through 144 removed outlier: 3.792A pdb=" N ALA A 105 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ASN A 80 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N LEU A 36 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N HIS A 82 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N LEU A 38 " --> pdb=" O HIS A 82 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N PHE A 84 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLY A 40 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N VAL A 86 " --> pdb=" O GLY A 40 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.688A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.855A 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: 6.945A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.070A 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: 6.713A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.675A 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: 6.837A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.297A 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: 6.499A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.899A 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: 6.479A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.218A 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: 3.525A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 2 through 6 Processing sheet with id= J, first strand: chain 'E' and resid 114 through 116 removed outlier: 5.950A pdb=" N ARG E 37 " --> pdb=" O TRP E 46 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N TRP E 46 " --> pdb=" O ARG E 37 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ALA E 39 " --> pdb=" O LEU E 44 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU E 44 " --> pdb=" O ALA E 39 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.585A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'E' and resid 155 through 160 Processing sheet with id= M, first strand: chain 'E' and resid 226 through 231 removed outlier: 6.112A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 424 hydrogen bonds defined for protein. 1221 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: 2.86 Time building geometry restraints manager: 3.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2873 1.34 - 1.46: 2157 1.46 - 1.58: 3901 1.58 - 1.69: 6 1.69 - 1.81: 90 Bond restraints: 9027 Sorted by residual: bond pdb=" C12 7WT R 601 " pdb=" C13 7WT R 601 " ideal model delta sigma weight residual 1.503 1.580 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" C10 7WT R 601 " pdb=" C11 7WT R 601 " ideal model delta sigma weight residual 1.524 1.585 -0.061 2.00e-02 2.50e+03 9.17e+00 bond pdb=" C04 7WT R 601 " pdb=" C08 7WT R 601 " ideal model delta sigma weight residual 1.524 1.582 -0.058 2.00e-02 2.50e+03 8.51e+00 bond pdb=" C09 7WT R 601 " pdb=" C10 7WT R 601 " ideal model delta sigma weight residual 1.528 1.584 -0.056 2.00e-02 2.50e+03 7.95e+00 bond pdb=" C02 7WT R 601 " pdb=" C03 7WT R 601 " ideal model delta sigma weight residual 1.527 1.578 -0.051 2.00e-02 2.50e+03 6.49e+00 ... (remaining 9022 not shown) Histogram of bond angle deviations from ideal: 100.17 - 106.93: 199 106.93 - 113.69: 5000 113.69 - 120.45: 3346 120.45 - 127.22: 3591 127.22 - 133.98: 92 Bond angle restraints: 12228 Sorted by residual: angle pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta sigma weight residual 121.54 126.17 -4.63 1.91e+00 2.74e-01 5.88e+00 angle pdb=" O TYR R 92 " pdb=" C TYR R 92 " pdb=" N ALA R 93 " ideal model delta sigma weight residual 122.12 124.45 -2.33 1.06e+00 8.90e-01 4.82e+00 angle pdb=" C06 7WT R 601 " pdb=" C05 7WT R 601 " pdb=" O07 7WT R 601 " ideal model delta sigma weight residual 113.84 107.65 6.19 3.00e+00 1.11e-01 4.25e+00 angle pdb=" CA TYR R 92 " pdb=" C TYR R 92 " pdb=" O TYR R 92 " ideal model delta sigma weight residual 120.55 118.50 2.05 1.06e+00 8.90e-01 3.73e+00 angle pdb=" C11 7WT R 601 " pdb=" C12 7WT R 601 " pdb=" C13 7WT R 601 " ideal model delta sigma weight residual 111.45 117.23 -5.78 3.00e+00 1.11e-01 3.71e+00 ... (remaining 12223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.63: 5281 27.63 - 55.25: 80 55.25 - 82.88: 6 82.88 - 110.50: 1 110.50 - 138.13: 1 Dihedral angle restraints: 5369 sinusoidal: 2074 harmonic: 3295 Sorted by residual: dihedral pdb=" C21 7WT R 601 " pdb=" C22 7WT R 601 " pdb=" C23 7WT R 601 " pdb=" C24 7WT R 601 " ideal model delta sinusoidal sigma weight residual 116.31 -105.56 -138.13 1 3.00e+01 1.11e-03 1.86e+01 dihedral pdb=" CA GLN B 75 " pdb=" C GLN B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta harmonic sigma weight residual 180.00 158.76 21.24 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA ARG E 191 " pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta harmonic sigma weight residual 180.00 161.33 18.67 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 5366 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1112 0.046 - 0.091: 220 0.091 - 0.137: 64 0.137 - 0.183: 0 0.183 - 0.228: 2 Chirality restraints: 1398 Sorted by residual: chirality pdb=" C03 7WT R 601 " pdb=" C02 7WT R 601 " pdb=" C04 7WT R 601 " pdb=" C20 7WT R 601 " both_signs ideal model delta sigma weight residual False -2.53 -2.75 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" C04 7WT R 601 " pdb=" C03 7WT R 601 " pdb=" C05 7WT R 601 " pdb=" C08 7WT R 601 " both_signs ideal model delta sigma weight residual False 2.63 2.81 -0.19 2.00e-01 2.50e+01 8.75e-01 chirality pdb=" C10 7WT R 601 " pdb=" C09 7WT R 601 " pdb=" C11 7WT R 601 " pdb=" O19 7WT R 601 " both_signs ideal model delta sigma weight residual False 2.40 2.53 -0.13 2.00e-01 2.50e+01 4.39e-01 ... (remaining 1395 not shown) Planarity restraints: 1548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO B 236 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER R 263 " -0.019 5.00e-02 4.00e+02 2.88e-02 1.32e+00 pdb=" N PRO R 264 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO R 264 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO R 264 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " 0.017 5.00e-02 4.00e+02 2.54e-02 1.03e+00 pdb=" N PRO B 194 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " 0.014 5.00e-02 4.00e+02 ... (remaining 1545 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 1946 2.78 - 3.31: 8361 3.31 - 3.84: 14843 3.84 - 4.37: 18554 4.37 - 4.90: 31718 Nonbonded interactions: 75422 Sorted by model distance: nonbonded pdb=" O VAL R 303 " pdb=" NH2 ARG R 308 " model vdw 2.256 2.520 nonbonded pdb=" O LYS C 20 " pdb=" ND2 ASN C 24 " model vdw 2.283 2.520 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.291 2.440 nonbonded pdb=" NE2 GLN A 52 " pdb=" O ALA A 218 " model vdw 2.294 2.520 nonbonded pdb=" O GLY R 40 " pdb=" ND2 ASN R 44 " model vdw 2.313 2.520 ... (remaining 75417 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 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: 1.910 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 26.520 Find NCS groups from input model: 0.240 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:13.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 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 : 0.003 0.077 9027 Z= 0.175 Angle : 0.416 6.186 12228 Z= 0.214 Chirality : 0.039 0.228 1398 Planarity : 0.003 0.038 1548 Dihedral : 10.253 138.130 3232 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.05 % Allowed : 3.16 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.55 (0.25), residues: 1122 helix: 1.91 (0.24), residues: 411 sheet: 0.80 (0.29), residues: 288 loop : 0.45 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 133 HIS 0.002 0.001 HIS B 91 PHE 0.009 0.001 PHE B 199 TYR 0.012 0.001 TYR E 190 ARG 0.002 0.000 ARG A 241 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 225 time to evaluate : 1.062 Fit side-chains REVERT: A 17 LYS cc_start: 0.8198 (mttt) cc_final: 0.7863 (mtmt) REVERT: A 83 MET cc_start: 0.8839 (ttp) cc_final: 0.8291 (ttp) REVERT: A 123 ASN cc_start: 0.8834 (m-40) cc_final: 0.8426 (m110) REVERT: A 136 THR cc_start: 0.8838 (p) cc_final: 0.8628 (m) REVERT: A 238 MET cc_start: 0.8575 (ttm) cc_final: 0.8321 (ttm) REVERT: A 242 GLU cc_start: 0.8819 (tt0) cc_final: 0.8563 (tt0) REVERT: B 59 TYR cc_start: 0.7829 (m-80) cc_final: 0.7327 (m-80) REVERT: B 101 MET cc_start: 0.9073 (mtp) cc_final: 0.8865 (mtp) REVERT: B 209 LYS cc_start: 0.8691 (mttm) cc_final: 0.8466 (mmtp) REVERT: B 219 ARG cc_start: 0.7613 (mtp85) cc_final: 0.7259 (mtp85) REVERT: B 259 GLN cc_start: 0.7893 (pt0) cc_final: 0.7506 (pt0) REVERT: R 28 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7735 (pp) REVERT: R 57 ARG cc_start: 0.8165 (ttm170) cc_final: 0.7908 (ttp-110) outliers start: 10 outliers final: 3 residues processed: 231 average time/residue: 1.1766 time to fit residues: 289.9708 Evaluate side-chains 158 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 154 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain R residue 28 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 209 HIS ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN E 112 GLN E 171 ASN E 179 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9027 Z= 0.312 Angle : 0.543 6.848 12228 Z= 0.293 Chirality : 0.043 0.150 1398 Planarity : 0.004 0.042 1548 Dihedral : 6.718 134.929 1272 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 4.64 % Allowed : 10.13 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 2.04 (0.25), residues: 1122 helix: 2.64 (0.24), residues: 410 sheet: 0.83 (0.30), residues: 288 loop : 0.55 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 169 HIS 0.004 0.001 HIS B 91 PHE 0.013 0.002 PHE B 199 TYR 0.015 0.002 TYR E 190 ARG 0.005 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 144 time to evaluate : 1.022 Fit side-chains REVERT: A 17 LYS cc_start: 0.8086 (mttt) cc_final: 0.7825 (mtpt) REVERT: A 70 PHE cc_start: 0.7751 (t80) cc_final: 0.7410 (t80) REVERT: A 83 MET cc_start: 0.8939 (ttp) cc_final: 0.8377 (ttp) REVERT: A 222 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7721 (mm-30) REVERT: A 238 MET cc_start: 0.8640 (ttm) cc_final: 0.8414 (ttm) REVERT: B 197 ARG cc_start: 0.6831 (mmm160) cc_final: 0.6487 (mmm-85) REVERT: B 209 LYS cc_start: 0.8538 (mttm) cc_final: 0.8332 (mmtp) REVERT: B 219 ARG cc_start: 0.7706 (mtp85) cc_final: 0.7503 (mtt-85) REVERT: B 259 GLN cc_start: 0.8207 (pt0) cc_final: 0.7769 (pt0) REVERT: B 266 HIS cc_start: 0.7959 (t70) cc_final: 0.7723 (t70) REVERT: B 304 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7435 (ttm110) REVERT: B 314 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.7573 (ttt180) REVERT: C 21 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.8185 (tpp) REVERT: E 171 ASN cc_start: 0.9267 (m-40) cc_final: 0.8974 (m-40) REVERT: E 234 GLU cc_start: 0.8121 (pt0) cc_final: 0.7843 (pt0) REVERT: R 28 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7770 (pp) REVERT: R 246 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8011 (tp30) outliers start: 44 outliers final: 19 residues processed: 170 average time/residue: 1.3400 time to fit residues: 242.0968 Evaluate side-chains 161 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 136 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 246 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 81 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN B 266 HIS B 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9027 Z= 0.349 Angle : 0.548 8.181 12228 Z= 0.293 Chirality : 0.044 0.139 1398 Planarity : 0.004 0.047 1548 Dihedral : 6.646 126.951 1270 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 5.49 % Allowed : 11.60 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.87 (0.25), residues: 1122 helix: 2.55 (0.24), residues: 412 sheet: 0.76 (0.30), residues: 275 loop : 0.36 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 169 HIS 0.005 0.001 HIS B 91 PHE 0.012 0.002 PHE B 151 TYR 0.014 0.002 TYR E 190 ARG 0.005 0.000 ARG R 308 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 138 time to evaluate : 1.068 Fit side-chains REVERT: A 17 LYS cc_start: 0.8089 (mttt) cc_final: 0.7818 (mtpt) REVERT: A 25 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7595 (mt-10) REVERT: A 83 MET cc_start: 0.8973 (ttp) cc_final: 0.8518 (ttp) REVERT: A 222 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7632 (mm-30) REVERT: A 238 MET cc_start: 0.8672 (ttm) cc_final: 0.8464 (ttm) REVERT: B 59 TYR cc_start: 0.8308 (OUTLIER) cc_final: 0.7898 (m-80) REVERT: B 209 LYS cc_start: 0.8580 (mttm) cc_final: 0.8367 (mmtp) REVERT: B 234 PHE cc_start: 0.9404 (OUTLIER) cc_final: 0.8934 (m-80) REVERT: B 259 GLN cc_start: 0.8199 (pt0) cc_final: 0.7868 (pt0) REVERT: B 266 HIS cc_start: 0.8084 (t-90) cc_final: 0.7862 (t70) REVERT: B 304 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7363 (ttm110) REVERT: B 314 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.7636 (ttt180) REVERT: C 21 MET cc_start: 0.8388 (mmt) cc_final: 0.8170 (tpp) REVERT: C 46 LYS cc_start: 0.8447 (mmmt) cc_final: 0.8177 (mptp) REVERT: E 45 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7457 (tt0) REVERT: E 234 GLU cc_start: 0.8092 (pt0) cc_final: 0.7805 (pt0) REVERT: R 28 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7799 (pp) outliers start: 52 outliers final: 24 residues processed: 169 average time/residue: 1.3087 time to fit residues: 234.7927 Evaluate side-chains 165 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 133 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 52 MET Chi-restraints excluded: chain R residue 182 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 68 optimal weight: 0.0370 chunk 102 optimal weight: 4.9990 chunk 108 optimal weight: 20.0000 chunk 53 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN B 175 GLN B 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9027 Z= 0.332 Angle : 0.538 7.729 12228 Z= 0.287 Chirality : 0.043 0.139 1398 Planarity : 0.004 0.049 1548 Dihedral : 6.540 120.228 1270 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 5.38 % Allowed : 12.76 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.74 (0.25), residues: 1122 helix: 2.49 (0.24), residues: 412 sheet: 0.56 (0.30), residues: 280 loop : 0.35 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 169 HIS 0.004 0.001 HIS B 91 PHE 0.012 0.002 PHE B 151 TYR 0.015 0.002 TYR E 190 ARG 0.006 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 134 time to evaluate : 0.989 Fit side-chains REVERT: A 17 LYS cc_start: 0.8130 (mttt) cc_final: 0.7732 (mtmt) REVERT: A 25 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7689 (mt-10) REVERT: A 83 MET cc_start: 0.8966 (ttp) cc_final: 0.8457 (ttp) REVERT: A 166 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7487 (mm-30) REVERT: A 169 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7282 (mtm-85) REVERT: A 222 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7634 (mm-30) REVERT: B 59 TYR cc_start: 0.8336 (OUTLIER) cc_final: 0.7988 (m-80) REVERT: B 209 LYS cc_start: 0.8553 (mttm) cc_final: 0.8337 (mmtp) REVERT: B 234 PHE cc_start: 0.9412 (OUTLIER) cc_final: 0.8954 (m-80) REVERT: B 259 GLN cc_start: 0.8201 (pt0) cc_final: 0.7758 (pt0) REVERT: B 304 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7269 (ttm110) REVERT: B 314 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.7626 (ttt180) REVERT: C 21 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8152 (tpp) REVERT: E 234 GLU cc_start: 0.8086 (pt0) cc_final: 0.7814 (pt0) REVERT: R 28 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.7820 (pp) REVERT: R 246 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8061 (tp30) outliers start: 51 outliers final: 26 residues processed: 166 average time/residue: 1.3012 time to fit residues: 230.2322 Evaluate side-chains 168 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 132 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 52 MET Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 246 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 7.9990 chunk 1 optimal weight: 0.4980 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN B 88 ASN B 156 GLN B 293 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9027 Z= 0.194 Angle : 0.481 7.012 12228 Z= 0.257 Chirality : 0.041 0.177 1398 Planarity : 0.003 0.049 1548 Dihedral : 6.324 114.717 1270 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 4.54 % Allowed : 14.98 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.93 (0.25), residues: 1122 helix: 2.73 (0.24), residues: 412 sheet: 0.78 (0.30), residues: 270 loop : 0.28 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.004 0.001 HIS B 91 PHE 0.019 0.001 PHE R 90 TYR 0.014 0.001 TYR E 190 ARG 0.006 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 125 time to evaluate : 0.955 Fit side-chains REVERT: A 17 LYS cc_start: 0.8081 (mttt) cc_final: 0.7802 (mtpt) REVERT: A 25 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7681 (mt-10) REVERT: A 83 MET cc_start: 0.8869 (ttp) cc_final: 0.8324 (ttp) REVERT: A 166 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7497 (mm-30) REVERT: A 222 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7657 (mm-30) REVERT: A 225 ARG cc_start: 0.8239 (ttm-80) cc_final: 0.7936 (tpp-160) REVERT: B 59 TYR cc_start: 0.8200 (OUTLIER) cc_final: 0.7901 (m-80) REVERT: B 197 ARG cc_start: 0.7233 (mmm160) cc_final: 0.6996 (mmm160) REVERT: B 234 PHE cc_start: 0.9407 (OUTLIER) cc_final: 0.8908 (m-80) REVERT: B 270 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8272 (pp) REVERT: B 304 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7148 (ttm110) REVERT: B 314 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.7581 (ttt180) REVERT: E 45 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7424 (tt0) REVERT: E 234 GLU cc_start: 0.8101 (pt0) cc_final: 0.7815 (pt0) REVERT: R 28 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7979 (pp) REVERT: R 246 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7855 (tt0) outliers start: 43 outliers final: 13 residues processed: 150 average time/residue: 1.2997 time to fit residues: 207.1847 Evaluate side-chains 147 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 124 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 246 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 108 optimal weight: 20.0000 chunk 89 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.0170 chunk 35 optimal weight: 7.9990 chunk 56 optimal weight: 8.9990 chunk 104 optimal weight: 4.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN B 293 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9027 Z= 0.155 Angle : 0.461 6.571 12228 Z= 0.245 Chirality : 0.040 0.180 1398 Planarity : 0.003 0.047 1548 Dihedral : 6.016 103.611 1270 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.06 % Allowed : 16.46 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 2.02 (0.25), residues: 1122 helix: 2.85 (0.24), residues: 417 sheet: 0.83 (0.30), residues: 269 loop : 0.23 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS B 91 PHE 0.013 0.001 PHE R 90 TYR 0.013 0.001 TYR E 190 ARG 0.005 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 129 time to evaluate : 0.943 Fit side-chains REVERT: A 17 LYS cc_start: 0.8038 (mttt) cc_final: 0.7735 (mtpt) REVERT: A 83 MET cc_start: 0.8847 (ttp) cc_final: 0.8327 (ttp) REVERT: A 225 ARG cc_start: 0.8234 (ttm-80) cc_final: 0.7960 (tpp-160) REVERT: B 59 TYR cc_start: 0.8194 (OUTLIER) cc_final: 0.7936 (m-80) REVERT: B 234 PHE cc_start: 0.9403 (OUTLIER) cc_final: 0.8913 (m-80) REVERT: B 270 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8264 (pp) REVERT: B 304 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.7115 (ttm110) REVERT: B 314 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7574 (ttt180) REVERT: E 45 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7398 (tt0) REVERT: E 202 ARG cc_start: 0.7538 (ptp90) cc_final: 0.7055 (ptp90) REVERT: E 234 GLU cc_start: 0.8139 (pt0) cc_final: 0.7888 (pt0) REVERT: R 28 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8012 (pp) REVERT: R 246 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7861 (tt0) outliers start: 29 outliers final: 14 residues processed: 150 average time/residue: 1.3414 time to fit residues: 213.9068 Evaluate side-chains 144 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 122 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 246 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN B 175 GLN B 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9027 Z= 0.294 Angle : 0.526 7.411 12228 Z= 0.277 Chirality : 0.043 0.238 1398 Planarity : 0.004 0.046 1548 Dihedral : 6.212 110.810 1270 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.11 % Allowed : 15.72 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.83 (0.25), residues: 1122 helix: 2.71 (0.24), residues: 411 sheet: 0.69 (0.30), residues: 270 loop : 0.18 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.004 0.001 HIS B 91 PHE 0.012 0.001 PHE B 151 TYR 0.016 0.001 TYR C 40 ARG 0.007 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 126 time to evaluate : 0.890 Fit side-chains REVERT: A 17 LYS cc_start: 0.8063 (mttt) cc_final: 0.7691 (mtmt) REVERT: A 25 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7699 (mt-10) REVERT: A 83 MET cc_start: 0.8881 (ttp) cc_final: 0.8349 (ttp) REVERT: A 222 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7609 (mm-30) REVERT: B 59 TYR cc_start: 0.8254 (OUTLIER) cc_final: 0.7973 (m-80) REVERT: B 234 PHE cc_start: 0.9403 (OUTLIER) cc_final: 0.8946 (m-80) REVERT: B 304 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.7163 (ttm110) REVERT: B 314 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.7621 (ttt180) REVERT: E 45 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7454 (tt0) REVERT: E 234 GLU cc_start: 0.8138 (pt0) cc_final: 0.7900 (pt0) REVERT: R 28 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8019 (pp) REVERT: R 246 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7943 (tp30) outliers start: 39 outliers final: 19 residues processed: 151 average time/residue: 1.3083 time to fit residues: 210.2030 Evaluate side-chains 149 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 121 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 52 MET Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 246 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 73 optimal weight: 0.0980 chunk 53 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9027 Z= 0.166 Angle : 0.470 7.973 12228 Z= 0.249 Chirality : 0.041 0.198 1398 Planarity : 0.003 0.048 1548 Dihedral : 5.842 95.396 1270 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.06 % Allowed : 16.67 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 2.00 (0.25), residues: 1122 helix: 2.88 (0.24), residues: 411 sheet: 0.80 (0.30), residues: 266 loop : 0.23 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS B 91 PHE 0.011 0.001 PHE B 199 TYR 0.013 0.001 TYR E 190 ARG 0.008 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 125 time to evaluate : 0.923 Fit side-chains REVERT: A 17 LYS cc_start: 0.8038 (mttt) cc_final: 0.7751 (mtpt) REVERT: A 25 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7687 (mt-10) REVERT: A 83 MET cc_start: 0.8855 (ttp) cc_final: 0.8276 (ttp) REVERT: A 208 ARG cc_start: 0.7323 (mtp180) cc_final: 0.6511 (mmp-170) REVERT: A 222 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7634 (mm-30) REVERT: A 225 ARG cc_start: 0.8200 (ttm-80) cc_final: 0.7935 (tpp-160) REVERT: B 59 TYR cc_start: 0.8234 (OUTLIER) cc_final: 0.7979 (m-80) REVERT: B 234 PHE cc_start: 0.9391 (OUTLIER) cc_final: 0.8897 (m-80) REVERT: B 304 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7111 (ttm110) REVERT: B 314 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7588 (ttt180) REVERT: E 45 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7457 (tt0) REVERT: E 234 GLU cc_start: 0.8131 (pt0) cc_final: 0.7886 (pt0) REVERT: R 28 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7910 (pp) REVERT: R 246 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7859 (tt0) outliers start: 29 outliers final: 15 residues processed: 145 average time/residue: 1.3092 time to fit residues: 201.7652 Evaluate side-chains 152 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 128 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 246 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9027 Z= 0.185 Angle : 0.475 8.105 12228 Z= 0.252 Chirality : 0.041 0.188 1398 Planarity : 0.003 0.047 1548 Dihedral : 5.544 75.662 1270 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.06 % Allowed : 17.09 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 2.04 (0.25), residues: 1122 helix: 2.94 (0.24), residues: 410 sheet: 0.82 (0.30), residues: 266 loop : 0.22 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS B 91 PHE 0.010 0.001 PHE B 199 TYR 0.013 0.001 TYR E 190 ARG 0.007 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 130 time to evaluate : 0.982 Fit side-chains REVERT: A 17 LYS cc_start: 0.8017 (mttt) cc_final: 0.7733 (mtpt) REVERT: A 25 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7696 (mt-10) REVERT: A 83 MET cc_start: 0.8889 (ttp) cc_final: 0.8362 (ttp) REVERT: A 208 ARG cc_start: 0.7370 (mtp180) cc_final: 0.6546 (mmp-170) REVERT: A 222 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7617 (mm-30) REVERT: A 225 ARG cc_start: 0.8125 (ttm-80) cc_final: 0.7898 (tpp-160) REVERT: B 59 TYR cc_start: 0.8262 (OUTLIER) cc_final: 0.7993 (m-80) REVERT: B 234 PHE cc_start: 0.9393 (OUTLIER) cc_final: 0.8901 (m-80) REVERT: B 259 GLN cc_start: 0.8210 (pt0) cc_final: 0.7924 (pt0) REVERT: B 304 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7088 (ttm110) REVERT: B 314 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.7586 (ttt180) REVERT: E 45 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7475 (tt0) REVERT: E 234 GLU cc_start: 0.8132 (pt0) cc_final: 0.7916 (pt0) REVERT: R 28 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7878 (pp) REVERT: R 246 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7931 (tt0) outliers start: 29 outliers final: 15 residues processed: 150 average time/residue: 1.3883 time to fit residues: 221.0238 Evaluate side-chains 154 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 130 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 246 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 111 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 9 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9027 Z= 0.160 Angle : 0.471 8.812 12228 Z= 0.248 Chirality : 0.041 0.203 1398 Planarity : 0.003 0.047 1548 Dihedral : 5.396 76.574 1270 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.64 % Allowed : 17.83 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 2.08 (0.25), residues: 1122 helix: 2.95 (0.24), residues: 415 sheet: 0.81 (0.29), residues: 269 loop : 0.26 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS B 91 PHE 0.010 0.001 PHE B 199 TYR 0.012 0.001 TYR E 190 ARG 0.010 0.000 ARG B 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 134 time to evaluate : 1.089 Fit side-chains REVERT: A 17 LYS cc_start: 0.8009 (mttt) cc_final: 0.7721 (mtpt) REVERT: A 25 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7694 (mt-10) REVERT: A 83 MET cc_start: 0.8862 (ttp) cc_final: 0.8265 (ttp) REVERT: A 208 ARG cc_start: 0.7355 (mtp180) cc_final: 0.6529 (mmp-170) REVERT: B 59 TYR cc_start: 0.8250 (OUTLIER) cc_final: 0.7996 (m-80) REVERT: B 197 ARG cc_start: 0.7126 (mmm160) cc_final: 0.6838 (mmm160) REVERT: B 234 PHE cc_start: 0.9393 (OUTLIER) cc_final: 0.8904 (m-80) REVERT: B 259 GLN cc_start: 0.8200 (pt0) cc_final: 0.7847 (pt0) REVERT: B 314 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.7584 (ttt180) REVERT: C 46 LYS cc_start: 0.8779 (pptt) cc_final: 0.8344 (mmmt) REVERT: E 45 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7443 (tt0) REVERT: E 234 GLU cc_start: 0.8124 (pt0) cc_final: 0.7911 (pt0) REVERT: R 28 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7935 (pp) REVERT: R 246 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7929 (tt0) outliers start: 25 outliers final: 13 residues processed: 152 average time/residue: 1.3501 time to fit residues: 217.7788 Evaluate side-chains 151 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 131 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 246 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 91 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN B 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.153666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.121051 restraints weight = 10207.209| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.77 r_work: 0.3037 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9027 Z= 0.223 Angle : 0.503 8.592 12228 Z= 0.265 Chirality : 0.042 0.235 1398 Planarity : 0.004 0.046 1548 Dihedral : 5.447 75.057 1269 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.43 % Allowed : 18.14 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 2.00 (0.25), residues: 1122 helix: 2.89 (0.24), residues: 410 sheet: 0.82 (0.29), residues: 266 loop : 0.21 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.003 0.001 HIS E 34 PHE 0.017 0.001 PHE E 67 TYR 0.012 0.001 TYR E 190 ARG 0.009 0.000 ARG B 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4019.95 seconds wall clock time: 72 minutes 37.60 seconds (4357.60 seconds total)