Starting phenix.real_space_refine on Thu Feb 15 21:28:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td1_25820/02_2024/7td1_25820_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td1_25820/02_2024/7td1_25820.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td1_25820/02_2024/7td1_25820_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td1_25820/02_2024/7td1_25820_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td1_25820/02_2024/7td1_25820_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td1_25820/02_2024/7td1_25820.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td1_25820/02_2024/7td1_25820.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td1_25820/02_2024/7td1_25820_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td1_25820/02_2024/7td1_25820_trim_updated.pdb" } resolution = 3.08 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= 1.082 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: 6 Type Number sf(0) Gaussians P 1 5.49 5 S 59 5.16 5 C 4407 2.51 5 N 1164 2.21 5 O 1268 1.98 5 H 6593 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ASP 95": "OD1" <-> "OD2" Residue "R PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R GLU 145": "OE1" <-> "OE2" Residue "R ASP 191": "OD1" <-> "OD2" Residue "R TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ARG 233": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 238": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R GLU 301": "OE1" <-> "OE2" Residue "R PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ARG 314": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ASP 315": "OD1" <-> "OD2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 26": "OD1" <-> "OD2" Residue "A GLU 43": "OE1" <-> "OE2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "A TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 26": "OD1" <-> "OD2" Residue "G PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13492 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 4580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 4580 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 7, 'TRANS': 285} Chain breaks: 1 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 4849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 4849 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 68 Chain: "A" Number of atoms: 3355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3355 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "G" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 679 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "R" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'NKP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.12, per 1000 atoms: 0.45 Number of scatterers: 13492 At special positions: 0 Unit cell: (96.824, 96.824, 124.488, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 59 16.00 P 1 15.00 O 1268 8.00 N 1164 7.00 C 4407 6.00 H 6593 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 24 " - pdb=" SG CYS R 190 " distance=2.04 Simple disulfide: pdb=" SG CYS R 188 " - pdb=" SG CYS R 195 " distance=2.18 Simple disulfide: pdb=" SG CYS R 284 " - pdb=" SG CYS R 287 " 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: 10.22 Conformation dependent library (CDL) restraints added in 1.4 seconds 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1718 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 9 sheets defined 40.7% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'R' and resid 30 through 36 Processing helix chain 'R' and resid 47 through 76 Processing helix chain 'R' and resid 83 through 105 Processing helix chain 'R' and resid 110 through 115 Processing helix chain 'R' and resid 118 through 151 removed outlier: 3.706A pdb=" N ILE R 128 " --> pdb=" O ARG R 124 " (cutoff:3.500A) Processing helix chain 'R' and resid 163 through 181 Processing helix chain 'R' and resid 204 through 240 removed outlier: 4.726A pdb=" N ARG R 238 " --> pdb=" O GLN R 234 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N MET R 239 " --> pdb=" O ARG R 235 " (cutoff:3.500A) Processing helix chain 'R' and resid 252 through 283 removed outlier: 3.690A pdb=" N PHE R 267 " --> pdb=" O VAL R 263 " (cutoff:3.500A) Proline residue: R 273 - end of helix removed outlier: 3.668A pdb=" N LEU R 277 " --> pdb=" O PRO R 273 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU R 278 " --> pdb=" O GLY R 274 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU R 279 " --> pdb=" O LEU R 275 " (cutoff:3.500A) Processing helix chain 'R' and resid 289 through 291 No H-bonds generated for 'chain 'R' and resid 289 through 291' Processing helix chain 'R' and resid 293 through 310 removed outlier: 3.852A pdb=" N SER R 304 " --> pdb=" O ALA R 300 " (cutoff:3.500A) Proline residue: R 308 - end of helix Processing helix chain 'R' and resid 316 through 321 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'A' and resid 9 through 30 Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 227 through 230 Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 277 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 309 removed outlier: 3.554A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.543A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 23 removed outlier: 3.635A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA G 23 " --> pdb=" O LEU G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing sheet with id= A, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.647A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.806A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 146 through 150 removed outlier: 6.967A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.172A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 229 through 234 removed outlier: 7.008A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 294 through 296 removed outlier: 3.996A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.765A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.802A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.675A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) 335 hydrogen bonds defined for protein. 966 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: 5.09 Time building geometry restraints manager: 10.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 6568 1.04 - 1.23: 143 1.23 - 1.43: 2856 1.43 - 1.63: 3974 1.63 - 1.82: 88 Bond restraints: 13629 Sorted by residual: bond pdb=" C ASN A 331 " pdb=" O ASN A 331 " ideal model delta sigma weight residual 1.236 1.156 0.080 1.26e-02 6.30e+03 4.07e+01 bond pdb=" N THR A 329 " pdb=" CA THR A 329 " ideal model delta sigma weight residual 1.462 1.505 -0.043 1.46e-02 4.69e+03 8.61e+00 bond pdb=" C THR A 329 " pdb=" O THR A 329 " ideal model delta sigma weight residual 1.233 1.269 -0.036 1.29e-02 6.01e+03 7.96e+00 bond pdb=" N LYS A 330 " pdb=" H LYS A 330 " ideal model delta sigma weight residual 0.860 0.911 -0.051 2.00e-02 2.50e+03 6.59e+00 bond pdb=" N THR A 329 " pdb=" H THR A 329 " ideal model delta sigma weight residual 0.860 0.911 -0.051 2.00e-02 2.50e+03 6.39e+00 ... (remaining 13624 not shown) Histogram of bond angle deviations from ideal: 100.40 - 107.12: 184 107.12 - 113.83: 15896 113.83 - 120.55: 4566 120.55 - 127.27: 3750 127.27 - 133.98: 69 Bond angle restraints: 24465 Sorted by residual: angle pdb=" CA ASP A 328 " pdb=" C ASP A 328 " pdb=" O ASP A 328 " ideal model delta sigma weight residual 119.97 115.18 4.79 1.15e+00 7.56e-01 1.73e+01 angle pdb=" CA ASN A 331 " pdb=" C ASN A 331 " pdb=" O ASN A 331 " ideal model delta sigma weight residual 119.97 115.47 4.50 1.15e+00 7.56e-01 1.53e+01 angle pdb=" C ASN A 331 " pdb=" N VAL A 332 " pdb=" CA VAL A 332 " ideal model delta sigma weight residual 120.55 126.50 -5.95 1.60e+00 3.91e-01 1.38e+01 angle pdb=" CA ASN A 331 " pdb=" CB ASN A 331 " pdb=" CG ASN A 331 " ideal model delta sigma weight residual 112.60 109.14 3.46 1.00e+00 1.00e+00 1.20e+01 angle pdb=" CA THR A 329 " pdb=" C THR A 329 " pdb=" O THR A 329 " ideal model delta sigma weight residual 121.28 117.59 3.69 1.19e+00 7.06e-01 9.63e+00 ... (remaining 24460 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 6076 17.88 - 35.77: 311 35.77 - 53.65: 73 53.65 - 71.53: 21 71.53 - 89.42: 4 Dihedral angle restraints: 6485 sinusoidal: 3335 harmonic: 3150 Sorted by residual: dihedral pdb=" CB CYS R 24 " pdb=" SG CYS R 24 " pdb=" SG CYS R 190 " pdb=" CB CYS R 190 " ideal model delta sinusoidal sigma weight residual 93.00 35.61 57.39 1 1.00e+01 1.00e-02 4.43e+01 dihedral pdb=" CB MET R 239 " pdb=" CG MET R 239 " pdb=" SD MET R 239 " pdb=" CE MET R 239 " ideal model delta sinusoidal sigma weight residual 180.00 121.69 58.31 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CA ASP A 272 " pdb=" CB ASP A 272 " pdb=" CG ASP A 272 " pdb=" OD1 ASP A 272 " ideal model delta sinusoidal sigma weight residual -30.00 -82.18 52.18 1 2.00e+01 2.50e-03 9.28e+00 ... (remaining 6482 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 802 0.031 - 0.062: 204 0.062 - 0.094: 75 0.094 - 0.125: 36 0.125 - 0.156: 5 Chirality restraints: 1122 Sorted by residual: chirality pdb=" CA LYS A 330 " pdb=" N LYS A 330 " pdb=" C LYS A 330 " pdb=" CB LYS A 330 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.10e-01 chirality pdb=" CA ILE B 123 " pdb=" N ILE B 123 " pdb=" C ILE B 123 " pdb=" CB ILE B 123 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CA ASP A 328 " pdb=" N ASP A 328 " pdb=" C ASP A 328 " pdb=" CB ASP A 328 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.24e-01 ... (remaining 1119 not shown) Planarity restraints: 2085 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.151 2.00e-02 2.50e+03 1.64e-01 4.05e+02 pdb=" CG ASN A 331 " -0.003 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " 0.144 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.024 2.00e-02 2.50e+03 pdb="HD21 ASN A 331 " -0.250 2.00e-02 2.50e+03 pdb="HD22 ASN A 331 " 0.236 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 331 " -0.016 2.00e-02 2.50e+03 3.37e-02 1.14e+01 pdb=" C ASN A 331 " 0.058 2.00e-02 2.50e+03 pdb=" O ASN A 331 " -0.022 2.00e-02 2.50e+03 pdb=" N VAL A 332 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 331 " -0.017 2.00e-02 2.50e+03 3.17e-02 1.01e+01 pdb=" N VAL A 332 " 0.055 2.00e-02 2.50e+03 pdb=" CA VAL A 332 " -0.015 2.00e-02 2.50e+03 pdb=" H VAL A 332 " -0.023 2.00e-02 2.50e+03 ... (remaining 2082 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 709 2.21 - 2.81: 27781 2.81 - 3.40: 35521 3.40 - 4.00: 47147 4.00 - 4.60: 73844 Nonbonded interactions: 185002 Sorted by model distance: nonbonded pdb=" O ASN B 340 " pdb="HD22 ASN G 59 " model vdw 1.612 1.850 nonbonded pdb=" O ILE B 58 " pdb=" HG SER B 316 " model vdw 1.653 1.850 nonbonded pdb=" O LYS B 57 " pdb=" HG SER B 74 " model vdw 1.668 1.850 nonbonded pdb=" O ASP B 333 " pdb=" HG SER B 334 " model vdw 1.678 1.850 nonbonded pdb=" O ASP B 170 " pdb=" H GLY B 174 " model vdw 1.708 1.850 ... (remaining 184997 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=0.00 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: 0.080 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: 0.210 Extract box with map and model: 1.420 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 45.440 Find NCS groups from input model: 0.250 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: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 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 0.080 7036 Z= 0.171 Angle : 0.430 5.952 9562 Z= 0.268 Chirality : 0.037 0.156 1122 Planarity : 0.002 0.034 1204 Dihedral : 11.994 89.418 2416 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.28 % Allowed : 4.81 % Favored : 94.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.27), residues: 892 helix: 1.18 (0.26), residues: 383 sheet: -1.55 (0.34), residues: 190 loop : -1.46 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 121 HIS 0.002 0.000 HIS R 227 PHE 0.007 0.001 PHE A 189 TYR 0.009 0.001 TYR R 231 ARG 0.001 0.000 ARG R 152 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 159 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Evaluate side-chains 185 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 183 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 152 ARG cc_start: 0.7191 (ptp90) cc_final: 0.6877 (ptt180) REVERT: R 209 PHE cc_start: 0.7263 (t80) cc_final: 0.7041 (t80) REVERT: B 259 GLN cc_start: 0.7803 (pt0) cc_final: 0.7275 (pt0) REVERT: B 268 ASN cc_start: 0.7425 (t0) cc_final: 0.7134 (t0) REVERT: B 269 ILE cc_start: 0.8480 (mt) cc_final: 0.8243 (mt) REVERT: B 340 ASN cc_start: 0.6060 (t0) cc_final: 0.5846 (t0) REVERT: A 310 LEU cc_start: 0.8419 (mt) cc_final: 0.8175 (mt) REVERT: A 349 LYS cc_start: 0.8380 (ttmt) cc_final: 0.7999 (mttt) outliers start: 2 outliers final: 2 residues processed: 185 average time/residue: 0.5015 time to fit residues: 117.5256 Evaluate side-chains 154 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 152 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 272 THR Chi-restraints excluded: chain B residue 70 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN G 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7036 Z= 0.344 Angle : 0.560 5.032 9562 Z= 0.305 Chirality : 0.042 0.143 1122 Planarity : 0.004 0.055 1204 Dihedral : 6.152 54.896 990 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.98 % Allowed : 9.76 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.28), residues: 892 helix: 1.70 (0.26), residues: 387 sheet: -1.09 (0.36), residues: 182 loop : -1.28 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP R 121 HIS 0.007 0.001 HIS A 322 PHE 0.022 0.002 PHE A 196 TYR 0.015 0.002 TYR B 145 ARG 0.007 0.001 ARG R 115 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 159 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Evaluate side-chains 200 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 186 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 97 PHE cc_start: 0.8308 (t80) cc_final: 0.8001 (t80) REVERT: R 152 ARG cc_start: 0.7441 (ptp90) cc_final: 0.6846 (ptt180) REVERT: R 209 PHE cc_start: 0.8043 (t80) cc_final: 0.7796 (t80) REVERT: B 83 ASP cc_start: 0.8191 (t0) cc_final: 0.7759 (t70) REVERT: B 201 SER cc_start: 0.9082 (m) cc_final: 0.8833 (p) REVERT: B 259 GLN cc_start: 0.7984 (pt0) cc_final: 0.7290 (pt0) REVERT: A 310 LEU cc_start: 0.8480 (mt) cc_final: 0.8258 (mt) REVERT: A 349 LYS cc_start: 0.8347 (ttmt) cc_final: 0.8025 (mttt) REVERT: A 354 PHE cc_start: 0.7902 (t80) cc_final: 0.7614 (t80) outliers start: 14 outliers final: 11 residues processed: 191 average time/residue: 0.4497 time to fit residues: 110.6781 Evaluate side-chains 186 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 175 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 304 SER Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 293 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 40 HIS A 255 ASN A 306 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7036 Z= 0.273 Angle : 0.468 4.672 9562 Z= 0.256 Chirality : 0.039 0.138 1122 Planarity : 0.004 0.045 1204 Dihedral : 6.032 55.998 989 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.40 % Allowed : 12.73 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.28), residues: 892 helix: 2.11 (0.26), residues: 382 sheet: -1.01 (0.37), residues: 189 loop : -1.05 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 82 HIS 0.009 0.001 HIS R 40 PHE 0.010 0.001 PHE R 209 TYR 0.011 0.001 TYR R 231 ARG 0.005 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 159 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Evaluate side-chains 200 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 183 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 ARG cc_start: 0.8224 (tpp80) cc_final: 0.8004 (ttm-80) REVERT: R 97 PHE cc_start: 0.8363 (t80) cc_final: 0.8117 (t80) REVERT: R 123 LEU cc_start: 0.8760 (tt) cc_final: 0.8508 (tt) REVERT: R 209 PHE cc_start: 0.8122 (t80) cc_final: 0.7848 (t80) REVERT: B 52 ARG cc_start: 0.7871 (mtt90) cc_final: 0.7657 (mtt90) REVERT: B 201 SER cc_start: 0.9017 (m) cc_final: 0.8784 (p) REVERT: B 259 GLN cc_start: 0.8076 (pt0) cc_final: 0.7411 (pt0) REVERT: A 310 LEU cc_start: 0.8454 (mt) cc_final: 0.8235 (mt) REVERT: A 349 LYS cc_start: 0.8272 (ttmt) cc_final: 0.7936 (mttt) outliers start: 17 outliers final: 16 residues processed: 190 average time/residue: 0.4619 time to fit residues: 112.6629 Evaluate side-chains 195 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 179 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 272 THR Chi-restraints excluded: chain R residue 304 SER Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 344 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 40 HIS B 259 GLN ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 7036 Z= 0.361 Angle : 0.512 4.814 9562 Z= 0.283 Chirality : 0.040 0.138 1122 Planarity : 0.004 0.039 1204 Dihedral : 6.357 59.847 989 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.83 % Allowed : 14.57 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.28), residues: 892 helix: 2.02 (0.26), residues: 383 sheet: -0.93 (0.38), residues: 184 loop : -1.12 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 121 HIS 0.010 0.001 HIS R 40 PHE 0.012 0.001 PHE A 196 TYR 0.012 0.001 TYR R 231 ARG 0.006 0.001 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 159 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Evaluate side-chains 198 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 178 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 201 SER cc_start: 0.9035 (m) cc_final: 0.8831 (p) REVERT: B 259 GLN cc_start: 0.8108 (pt0) cc_final: 0.7501 (pt0) REVERT: A 349 LYS cc_start: 0.8316 (ttmt) cc_final: 0.7960 (mttt) outliers start: 20 outliers final: 19 residues processed: 188 average time/residue: 0.4643 time to fit residues: 113.3833 Evaluate side-chains 194 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 175 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 SER Chi-restraints excluded: chain R residue 40 HIS Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 188 CYS Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 272 THR Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 304 SER Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 344 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 72 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7036 Z= 0.231 Angle : 0.469 6.240 9562 Z= 0.259 Chirality : 0.038 0.138 1122 Planarity : 0.004 0.045 1204 Dihedral : 6.245 56.968 989 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.11 % Allowed : 14.71 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.29), residues: 892 helix: 2.23 (0.26), residues: 384 sheet: -0.85 (0.38), residues: 184 loop : -1.04 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 82 HIS 0.024 0.002 HIS R 40 PHE 0.009 0.001 PHE A 196 TYR 0.016 0.001 TYR A 302 ARG 0.007 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 159 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Evaluate side-chains 197 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 175 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 53 MET cc_start: 0.7638 (tpp) cc_final: 0.7105 (tpp) REVERT: B 83 ASP cc_start: 0.8176 (t0) cc_final: 0.7552 (t0) REVERT: B 259 GLN cc_start: 0.8073 (pt0) cc_final: 0.7428 (pt0) REVERT: A 349 LYS cc_start: 0.8283 (ttmt) cc_final: 0.7948 (mttt) outliers start: 22 outliers final: 19 residues processed: 186 average time/residue: 0.4658 time to fit residues: 111.5561 Evaluate side-chains 196 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 177 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 SER Chi-restraints excluded: chain R residue 113 THR Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 188 CYS Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 272 THR Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 304 SER Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 344 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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: 0.7510 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 7036 Z= 0.297 Angle : 0.487 5.084 9562 Z= 0.266 Chirality : 0.039 0.139 1122 Planarity : 0.004 0.058 1204 Dihedral : 6.480 56.074 989 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.69 % Allowed : 15.70 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.28), residues: 892 helix: 2.25 (0.26), residues: 388 sheet: -0.87 (0.38), residues: 184 loop : -1.06 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 121 HIS 0.004 0.001 HIS A 322 PHE 0.011 0.001 PHE A 196 TYR 0.023 0.001 TYR A 302 ARG 0.009 0.001 ARG R 115 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 159 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Evaluate side-chains 195 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 176 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 53 MET cc_start: 0.7680 (tpp) cc_final: 0.7202 (tpp) REVERT: R 239 MET cc_start: 0.8657 (mmp) cc_final: 0.8396 (mmp) REVERT: B 83 ASP cc_start: 0.8202 (t0) cc_final: 0.7590 (t0) REVERT: B 259 GLN cc_start: 0.8017 (pt0) cc_final: 0.7400 (pt0) REVERT: A 349 LYS cc_start: 0.8300 (ttmt) cc_final: 0.7953 (mttt) outliers start: 19 outliers final: 18 residues processed: 185 average time/residue: 0.4577 time to fit residues: 109.1669 Evaluate side-chains 190 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 172 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 SER Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 188 CYS Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 272 THR Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 304 SER Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 344 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 84 optimal weight: 20.0000 chunk 53 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 39 optimal weight: 0.0870 chunk 52 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 overall best weight: 2.1964 ------------------------------------------------------------------------------- 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: 0.7491 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7036 Z= 0.214 Angle : 0.455 4.885 9562 Z= 0.247 Chirality : 0.038 0.138 1122 Planarity : 0.004 0.054 1204 Dihedral : 6.463 57.749 989 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.97 % Allowed : 15.56 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.29), residues: 892 helix: 2.47 (0.26), residues: 389 sheet: -0.81 (0.38), residues: 184 loop : -0.97 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 121 HIS 0.003 0.001 HIS B 142 PHE 0.008 0.001 PHE A 196 TYR 0.020 0.001 TYR A 302 ARG 0.010 0.001 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 159 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 173 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 53 MET cc_start: 0.7651 (tpp) cc_final: 0.7189 (tpp) REVERT: B 83 ASP cc_start: 0.8110 (t0) cc_final: 0.7508 (t0) REVERT: B 259 GLN cc_start: 0.8083 (pt0) cc_final: 0.7526 (pt0) REVERT: A 349 LYS cc_start: 0.8269 (ttmt) cc_final: 0.7921 (mttt) outliers start: 21 outliers final: 20 residues processed: 185 average time/residue: 0.4505 time to fit residues: 107.6091 Evaluate side-chains 193 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 173 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 29 SER Chi-restraints excluded: chain R residue 113 THR Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 188 CYS Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 272 THR Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 304 SER Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 344 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 77 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 7036 Z= 0.363 Angle : 0.520 4.695 9562 Z= 0.287 Chirality : 0.040 0.141 1122 Planarity : 0.004 0.056 1204 Dihedral : 6.534 57.080 989 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.25 % Allowed : 14.71 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.28), residues: 892 helix: 2.16 (0.26), residues: 389 sheet: -0.91 (0.38), residues: 186 loop : -1.17 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 121 HIS 0.004 0.001 HIS A 322 PHE 0.012 0.001 PHE A 196 TYR 0.022 0.002 TYR A 302 ARG 0.010 0.001 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 159 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Evaluate side-chains 199 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 176 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 53 MET cc_start: 0.7764 (tpp) cc_final: 0.7291 (tpp) REVERT: B 259 GLN cc_start: 0.7958 (pt0) cc_final: 0.7383 (pt0) REVERT: A 349 LYS cc_start: 0.8333 (ttmt) cc_final: 0.7984 (mttt) outliers start: 23 outliers final: 21 residues processed: 187 average time/residue: 0.4605 time to fit residues: 112.1043 Evaluate side-chains 194 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 173 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 29 SER Chi-restraints excluded: chain R residue 37 SER Chi-restraints excluded: chain R residue 113 THR Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 188 CYS Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 272 THR Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 304 SER Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 344 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 62 optimal weight: 0.2980 chunk 24 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 83 optimal weight: 20.0000 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7036 Z= 0.141 Angle : 0.443 5.254 9562 Z= 0.237 Chirality : 0.038 0.136 1122 Planarity : 0.004 0.052 1204 Dihedral : 6.121 56.560 989 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.55 % Allowed : 16.27 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.29), residues: 892 helix: 2.68 (0.26), residues: 388 sheet: -0.86 (0.37), residues: 191 loop : -0.88 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 99 HIS 0.002 0.000 HIS B 142 PHE 0.008 0.001 PHE A 354 TYR 0.020 0.001 TYR A 302 ARG 0.008 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 159 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Evaluate side-chains 190 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 172 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 53 MET cc_start: 0.7653 (tpp) cc_final: 0.7208 (tpp) REVERT: B 259 GLN cc_start: 0.8107 (pt0) cc_final: 0.7539 (pt0) REVERT: A 242 ARG cc_start: 0.8269 (mtp85) cc_final: 0.7986 (mtp-110) REVERT: A 349 LYS cc_start: 0.8234 (ttmt) cc_final: 0.7895 (mttt) outliers start: 18 outliers final: 15 residues processed: 181 average time/residue: 0.4656 time to fit residues: 108.1336 Evaluate side-chains 183 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 168 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 29 SER Chi-restraints excluded: chain R residue 37 SER Chi-restraints excluded: chain R residue 113 THR Chi-restraints excluded: chain R residue 188 CYS Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 304 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 344 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 8.9990 chunk 39 optimal weight: 0.5980 chunk 58 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 42 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7036 Z= 0.207 Angle : 0.456 5.409 9562 Z= 0.246 Chirality : 0.038 0.153 1122 Planarity : 0.004 0.047 1204 Dihedral : 6.028 56.723 989 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.98 % Allowed : 16.97 % Favored : 81.05 % 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: 1.05 (0.29), residues: 892 helix: 2.66 (0.26), residues: 389 sheet: -0.74 (0.38), residues: 184 loop : -0.91 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 121 HIS 0.003 0.001 HIS B 142 PHE 0.008 0.001 PHE A 196 TYR 0.022 0.001 TYR A 302 ARG 0.008 0.001 ARG A 32 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 159 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue MET 174 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Evaluate side-chains 187 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 173 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 53 MET cc_start: 0.7693 (tpp) cc_final: 0.7244 (tpp) REVERT: R 275 LEU cc_start: 0.8158 (tp) cc_final: 0.7591 (tp) REVERT: B 259 GLN cc_start: 0.8069 (pt0) cc_final: 0.7504 (pt0) REVERT: B 262 MET cc_start: 0.7172 (tpp) cc_final: 0.6967 (tpp) REVERT: A 242 ARG cc_start: 0.8283 (mtp85) cc_final: 0.8004 (mtp-110) REVERT: A 349 LYS cc_start: 0.8271 (ttmt) cc_final: 0.7924 (mttt) outliers start: 14 outliers final: 14 residues processed: 182 average time/residue: 0.4653 time to fit residues: 109.3016 Evaluate side-chains 185 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 171 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 29 SER Chi-restraints excluded: chain R residue 37 SER Chi-restraints excluded: chain R residue 113 THR Chi-restraints excluded: chain R residue 188 CYS Chi-restraints excluded: chain R residue 272 THR Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 304 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 344 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 29 optimal weight: 50.0000 chunk 71 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.147427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.115490 restraints weight = 24430.307| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.50 r_work: 0.3145 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 7036 Z= 0.328 Angle : 0.501 5.276 9562 Z= 0.275 Chirality : 0.040 0.139 1122 Planarity : 0.004 0.044 1204 Dihedral : 6.268 57.586 989 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.26 % Allowed : 16.55 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.29), residues: 892 helix: 2.41 (0.26), residues: 390 sheet: -0.77 (0.38), residues: 184 loop : -1.05 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 121 HIS 0.004 0.001 HIS A 322 PHE 0.011 0.001 PHE A 196 TYR 0.021 0.002 TYR A 302 ARG 0.008 0.001 ARG A 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3931.50 seconds wall clock time: 70 minutes 14.98 seconds (4214.98 seconds total)