Starting phenix.real_space_refine on Tue Sep 24 18:25:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vy9_43650/09_2024/8vy9_43650.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vy9_43650/09_2024/8vy9_43650.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vy9_43650/09_2024/8vy9_43650.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vy9_43650/09_2024/8vy9_43650.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vy9_43650/09_2024/8vy9_43650.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vy9_43650/09_2024/8vy9_43650.cif" } resolution = 2.88 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= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 60 5.16 5 C 5574 2.51 5 N 1451 2.21 5 O 1580 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8668 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1722 Classifications: {'peptide': 224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 22} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 2458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2458 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 175 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 7, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 109 Chain: "C" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 328 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "D" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 2326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2326 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 286} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "R" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 51 Unusual residues: {'A1AEI': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.72, per 1000 atoms: 0.66 Number of scatterers: 8668 At special positions: 0 Unit cell: (87.6, 117.384, 134.904, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 F 3 9.00 O 1580 8.00 N 1451 7.00 C 5574 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.18 Conformation dependent library (CDL) restraints added in 1.1 seconds 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2120 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 13 sheets defined 39.1% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.687A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.576A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TRP A 211 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.570A pdb=" N ASN A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 4.544A pdb=" N THR A 279 " --> pdb=" O GLN A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.745A pdb=" N ILE A 285 " --> pdb=" O HIS A 282 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N CYS A 286 " --> pdb=" O LEU A 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 282 through 286' Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.601A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 13 through 24 removed outlier: 3.611A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.565A pdb=" N SER D 31 " --> pdb=" O ALA D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 212 removed outlier: 3.697A pdb=" N VAL D 212 " --> pdb=" O ALA D 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 37 Processing helix chain 'R' and resid 42 through 71 Processing helix chain 'R' and resid 74 through 77 Processing helix chain 'R' and resid 78 through 112 removed outlier: 4.146A pdb=" N THR R 86 " --> pdb=" O PHE R 82 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE R 95 " --> pdb=" O VAL R 91 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA R 100 " --> pdb=" O SER R 96 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 125 removed outlier: 3.790A pdb=" N ARG R 125 " --> pdb=" O TYR R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 137 Processing helix chain 'R' and resid 137 through 160 removed outlier: 3.573A pdb=" N LEU R 141 " --> pdb=" O THR R 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 213 removed outlier: 4.068A pdb=" N ILE R 179 " --> pdb=" O PHE R 175 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE R 189 " --> pdb=" O VAL R 185 " (cutoff:3.500A) Proline residue: R 190 - end of helix removed outlier: 3.760A pdb=" N LEU R 193 " --> pdb=" O ILE R 189 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 253 removed outlier: 3.932A pdb=" N SER R 232 " --> pdb=" O ARG R 228 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N THR R 235 " --> pdb=" O LYS R 231 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR R 253 " --> pdb=" O ILE R 249 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 282 removed outlier: 3.577A pdb=" N ALA R 271 " --> pdb=" O VAL R 267 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N TYR R 272 " --> pdb=" O MET R 268 " (cutoff:3.500A) Proline residue: R 273 - end of helix removed outlier: 4.586A pdb=" N SER R 277 " --> pdb=" O PRO R 273 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N CYS R 278 " --> pdb=" O SER R 274 " (cutoff:3.500A) Processing helix chain 'R' and resid 284 through 302 removed outlier: 3.590A pdb=" N ARG R 299 " --> pdb=" O LEU R 295 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.833A pdb=" N CYS A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.574A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.741A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.835A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.599A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.862A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.655A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.563A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.793A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 12 removed outlier: 4.312A pdb=" N PHE D 110 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 135 through 136 removed outlier: 3.577A pdb=" N GLU D 234 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE D 177 " --> pdb=" O TRP D 164 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU D 166 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N LEU D 175 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 143 through 147 removed outlier: 3.635A pdb=" N ALA D 199 " --> pdb=" O SER D 196 " (cutoff:3.500A) 467 hydrogen bonds defined for protein. 1326 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: 2.46 Time building geometry restraints manager: 2.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2692 1.34 - 1.46: 1928 1.46 - 1.58: 4141 1.58 - 1.70: 2 1.70 - 1.82: 90 Bond restraints: 8853 Sorted by residual: bond pdb=" C10 A1AEI R 601 " pdb=" N11 A1AEI R 601 " ideal model delta sigma weight residual 1.364 1.457 -0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" C13 A1AEI R 601 " pdb=" C14 A1AEI R 601 " ideal model delta sigma weight residual 1.461 1.527 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" N16 A1AEI R 601 " pdb=" N17 A1AEI R 601 " ideal model delta sigma weight residual 1.275 1.335 -0.060 2.00e-02 2.50e+03 8.99e+00 bond pdb=" C16 CLR R 602 " pdb=" C17 CLR R 602 " ideal model delta sigma weight residual 1.554 1.606 -0.052 2.00e-02 2.50e+03 6.69e+00 bond pdb=" C23 CLR R 602 " pdb=" C24 CLR R 602 " ideal model delta sigma weight residual 1.525 1.571 -0.046 2.00e-02 2.50e+03 5.22e+00 ... (remaining 8848 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 11787 2.16 - 4.32: 187 4.32 - 6.49: 29 6.49 - 8.65: 9 8.65 - 10.81: 2 Bond angle restraints: 12014 Sorted by residual: angle pdb=" C ASP A 231 " pdb=" N MET A 232 " pdb=" CA MET A 232 " ideal model delta sigma weight residual 122.82 127.50 -4.68 1.42e+00 4.96e-01 1.09e+01 angle pdb=" CA TYR D 178 " pdb=" CB TYR D 178 " pdb=" CG TYR D 178 " ideal model delta sigma weight residual 113.90 119.71 -5.81 1.80e+00 3.09e-01 1.04e+01 angle pdb=" CA LEU R 261 " pdb=" CB LEU R 261 " pdb=" CG LEU R 261 " ideal model delta sigma weight residual 116.30 127.11 -10.81 3.50e+00 8.16e-02 9.54e+00 angle pdb=" N PHE R 247 " pdb=" CA PHE R 247 " pdb=" CB PHE R 247 " ideal model delta sigma weight residual 110.01 114.44 -4.43 1.45e+00 4.76e-01 9.34e+00 angle pdb=" C22 CLR R 602 " pdb=" C23 CLR R 602 " pdb=" C24 CLR R 602 " ideal model delta sigma weight residual 111.95 102.84 9.11 3.00e+00 1.11e-01 9.21e+00 ... (remaining 12009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.63: 4922 22.63 - 45.26: 268 45.26 - 67.89: 32 67.89 - 90.52: 6 90.52 - 113.15: 3 Dihedral angle restraints: 5231 sinusoidal: 1951 harmonic: 3280 Sorted by residual: dihedral pdb=" CB CYS D 147 " pdb=" SG CYS D 147 " pdb=" SG CYS D 217 " pdb=" CB CYS D 217 " ideal model delta sinusoidal sigma weight residual 93.00 167.08 -74.08 1 1.00e+01 1.00e-02 6.97e+01 dihedral pdb=" CA ASP A 231 " pdb=" C ASP A 231 " pdb=" N MET A 232 " pdb=" CA MET A 232 " ideal model delta harmonic sigma weight residual 180.00 157.15 22.85 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA TYR D 178 " pdb=" C TYR D 178 " pdb=" N ARG D 179 " pdb=" CA ARG D 179 " ideal model delta harmonic sigma weight residual 180.00 157.16 22.84 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 5228 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1113 0.056 - 0.112: 233 0.112 - 0.168: 45 0.168 - 0.224: 6 0.224 - 0.280: 1 Chirality restraints: 1398 Sorted by residual: chirality pdb=" C17 CLR R 602 " pdb=" C13 CLR R 602 " pdb=" C16 CLR R 602 " pdb=" C20 CLR R 602 " both_signs ideal model delta sigma weight residual False 2.55 2.83 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" C13 CLR R 602 " pdb=" C12 CLR R 602 " pdb=" C14 CLR R 602 " pdb=" C17 CLR R 602 " both_signs ideal model delta sigma weight residual False -2.93 -3.13 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CB VAL R 251 " pdb=" CA VAL R 251 " pdb=" CG1 VAL R 251 " pdb=" CG2 VAL R 251 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.95e-01 ... (remaining 1395 not shown) Planarity restraints: 1490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE R 247 " 0.028 2.00e-02 2.50e+03 2.77e-02 1.34e+01 pdb=" CG PHE R 247 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 PHE R 247 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE R 247 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE R 247 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE R 247 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE R 247 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 240 " -0.021 2.00e-02 2.50e+03 1.31e-02 3.42e+00 pdb=" CG TYR R 240 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR R 240 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR R 240 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR R 240 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR R 240 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR R 240 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR R 240 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO B 236 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.025 5.00e-02 4.00e+02 ... (remaining 1487 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1779 2.78 - 3.31: 7571 3.31 - 3.84: 14554 3.84 - 4.37: 16340 4.37 - 4.90: 29477 Nonbonded interactions: 69721 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.245 3.040 nonbonded pdb=" OD1 ASP R 221 " pdb=" OG1 THR R 224 " model vdw 2.269 3.040 nonbonded pdb=" O LEU R 133 " pdb=" OG1 THR R 137 " model vdw 2.287 3.040 nonbonded pdb=" O ILE D 126 " pdb=" OG1 THR D 226 " model vdw 2.299 3.040 nonbonded pdb=" OG SER R 254 " pdb=" OE1 GLU R 255 " model vdw 2.303 3.040 ... (remaining 69716 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 2.110 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 22.780 Find NCS groups from input model: 0.100 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:10.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 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 : 0.005 0.093 8853 Z= 0.319 Angle : 0.702 10.811 12014 Z= 0.358 Chirality : 0.049 0.280 1398 Planarity : 0.005 0.045 1490 Dihedral : 14.270 113.148 3108 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.69 (0.24), residues: 1118 helix: 0.23 (0.23), residues: 410 sheet: 0.30 (0.31), residues: 282 loop : -1.63 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 169 HIS 0.008 0.001 HIS D 220 PHE 0.065 0.002 PHE R 247 TYR 0.030 0.002 TYR D 178 ARG 0.002 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 0.906 Fit side-chains REVERT: A 186 GLU cc_start: 0.7520 (tt0) cc_final: 0.7300 (tt0) REVERT: B 70 LEU cc_start: 0.8316 (tt) cc_final: 0.8103 (tt) REVERT: B 189 SER cc_start: 0.8649 (p) cc_final: 0.8423 (t) REVERT: B 263 THR cc_start: 0.8624 (t) cc_final: 0.8280 (m) REVERT: D 21 SER cc_start: 0.8211 (m) cc_final: 0.7701 (p) REVERT: D 23 SER cc_start: 0.8253 (m) cc_final: 0.8043 (t) REVERT: D 192 SER cc_start: 0.8536 (m) cc_final: 0.8253 (t) REVERT: D 218 MET cc_start: 0.8168 (ttp) cc_final: 0.7956 (ttm) REVERT: R 152 ILE cc_start: 0.8314 (mm) cc_final: 0.7806 (tt) REVERT: R 280 LEU cc_start: 0.8725 (mt) cc_final: 0.8458 (mt) outliers start: 0 outliers final: 1 residues processed: 242 average time/residue: 0.8877 time to fit residues: 233.7217 Evaluate side-chains 207 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 206 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 19 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 57 optimal weight: 0.2980 chunk 45 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.7741 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8853 Z= 0.222 Angle : 0.544 6.405 12014 Z= 0.285 Chirality : 0.041 0.147 1398 Planarity : 0.004 0.036 1490 Dihedral : 5.390 48.616 1280 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.09 % Allowed : 12.47 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.34 (0.25), residues: 1118 helix: 1.61 (0.25), residues: 407 sheet: 0.66 (0.30), residues: 281 loop : -1.47 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS D 220 PHE 0.033 0.002 PHE R 247 TYR 0.024 0.001 TYR D 178 ARG 0.005 0.000 ARG R 55 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 213 time to evaluate : 0.947 Fit side-chains REVERT: A 186 GLU cc_start: 0.7574 (tt0) cc_final: 0.7341 (tt0) REVERT: A 313 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7665 (tttm) REVERT: D 23 SER cc_start: 0.8355 (m) cc_final: 0.8110 (p) REVERT: D 192 SER cc_start: 0.8527 (m) cc_final: 0.8246 (t) REVERT: R 13 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8216 (tt) REVERT: R 101 THR cc_start: 0.8937 (OUTLIER) cc_final: 0.8692 (t) REVERT: R 152 ILE cc_start: 0.8276 (mm) cc_final: 0.7781 (tt) REVERT: R 267 VAL cc_start: 0.7915 (t) cc_final: 0.7683 (p) REVERT: R 280 LEU cc_start: 0.8731 (mt) cc_final: 0.8481 (mt) REVERT: R 286 LYS cc_start: 0.8026 (ttmm) cc_final: 0.7719 (ttpt) outliers start: 28 outliers final: 11 residues processed: 222 average time/residue: 0.9257 time to fit residues: 222.2829 Evaluate side-chains 210 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 196 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 145 ILE Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 292 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 84 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 101 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 90 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7753 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8853 Z= 0.241 Angle : 0.538 9.727 12014 Z= 0.279 Chirality : 0.041 0.156 1398 Planarity : 0.003 0.034 1490 Dihedral : 5.167 50.085 1278 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.54 % Allowed : 16.89 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.58 (0.26), residues: 1118 helix: 1.94 (0.25), residues: 410 sheet: 0.62 (0.32), residues: 273 loop : -1.34 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS D 35 PHE 0.027 0.002 PHE R 247 TYR 0.027 0.001 TYR D 178 ARG 0.005 0.000 ARG R 55 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 206 time to evaluate : 0.905 Fit side-chains REVERT: A 186 GLU cc_start: 0.7545 (tt0) cc_final: 0.7301 (tt0) REVERT: A 313 LYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7683 (tttm) REVERT: A 341 ASP cc_start: 0.8212 (t70) cc_final: 0.7915 (t70) REVERT: A 345 LYS cc_start: 0.8222 (mtmt) cc_final: 0.8005 (mtmm) REVERT: B 49 ARG cc_start: 0.8419 (mmt-90) cc_final: 0.8045 (mpt180) REVERT: B 155 ASN cc_start: 0.8427 (t0) cc_final: 0.8139 (t0) REVERT: B 160 SER cc_start: 0.8317 (OUTLIER) cc_final: 0.8114 (p) REVERT: B 237 ASN cc_start: 0.7955 (t0) cc_final: 0.7726 (t0) REVERT: D 21 SER cc_start: 0.8327 (m) cc_final: 0.7927 (p) REVERT: D 23 SER cc_start: 0.8361 (m) cc_final: 0.8160 (p) REVERT: D 192 SER cc_start: 0.8550 (m) cc_final: 0.8256 (t) REVERT: D 218 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7978 (ttp) REVERT: R 13 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8238 (tt) REVERT: R 152 ILE cc_start: 0.8254 (mm) cc_final: 0.7779 (tt) REVERT: R 211 LYS cc_start: 0.7220 (OUTLIER) cc_final: 0.6953 (ttpp) REVERT: R 280 LEU cc_start: 0.8745 (mt) cc_final: 0.8436 (mt) REVERT: R 286 LYS cc_start: 0.7947 (ttmm) cc_final: 0.7680 (ttmt) outliers start: 23 outliers final: 11 residues processed: 213 average time/residue: 0.9103 time to fit residues: 209.7512 Evaluate side-chains 216 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 200 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 211 LYS Chi-restraints excluded: chain R residue 292 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 48 optimal weight: 0.0870 chunk 68 optimal weight: 0.1980 chunk 102 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 53 optimal weight: 0.3980 chunk 96 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 90 optimal weight: 0.0980 overall best weight: 0.2958 ------------------------------------------------------------------------------- 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: 0.7719 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8853 Z= 0.152 Angle : 0.495 7.067 12014 Z= 0.258 Chirality : 0.040 0.138 1398 Planarity : 0.003 0.031 1490 Dihedral : 4.890 48.280 1278 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.87 % Allowed : 18.54 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.26), residues: 1118 helix: 2.31 (0.25), residues: 410 sheet: 0.74 (0.31), residues: 280 loop : -1.26 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS R 94 PHE 0.030 0.001 PHE R 17 TYR 0.018 0.001 TYR D 178 ARG 0.004 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 203 time to evaluate : 0.975 Fit side-chains REVERT: A 52 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7883 (mt0) REVERT: A 186 GLU cc_start: 0.7490 (tt0) cc_final: 0.7264 (tt0) REVERT: A 323 MET cc_start: 0.8304 (mtt) cc_final: 0.7968 (mtt) REVERT: A 345 LYS cc_start: 0.8187 (mtmt) cc_final: 0.7947 (mtmm) REVERT: B 14 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8230 (mm) REVERT: B 49 ARG cc_start: 0.8380 (mmt-90) cc_final: 0.8032 (mpt180) REVERT: B 50 THR cc_start: 0.8449 (t) cc_final: 0.8222 (m) REVERT: B 155 ASN cc_start: 0.8444 (t0) cc_final: 0.8165 (t0) REVERT: D 192 SER cc_start: 0.8546 (m) cc_final: 0.8218 (t) REVERT: R 13 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8219 (tt) REVERT: R 152 ILE cc_start: 0.8249 (mm) cc_final: 0.7771 (tt) REVERT: R 195 LEU cc_start: 0.7775 (tp) cc_final: 0.6982 (tt) REVERT: R 280 LEU cc_start: 0.8721 (mt) cc_final: 0.8408 (mt) REVERT: R 286 LYS cc_start: 0.7926 (ttmm) cc_final: 0.7693 (ttmt) outliers start: 26 outliers final: 9 residues processed: 213 average time/residue: 0.8912 time to fit residues: 205.8994 Evaluate side-chains 211 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 199 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain R residue 13 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 0.1980 chunk 92 optimal weight: 0.2980 chunk 74 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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: 0.7795 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 8853 Z= 0.405 Angle : 0.594 7.916 12014 Z= 0.310 Chirality : 0.045 0.190 1398 Planarity : 0.004 0.040 1490 Dihedral : 5.354 54.199 1278 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.09 % Allowed : 20.64 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.75 (0.26), residues: 1118 helix: 2.12 (0.25), residues: 411 sheet: 0.70 (0.32), residues: 275 loop : -1.30 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.005 0.001 HIS D 35 PHE 0.034 0.002 PHE R 63 TYR 0.032 0.002 TYR D 178 ARG 0.008 0.000 ARG R 55 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 205 time to evaluate : 1.202 Fit side-chains REVERT: A 186 GLU cc_start: 0.7558 (tt0) cc_final: 0.7340 (tt0) REVERT: A 345 LYS cc_start: 0.8316 (mtmt) cc_final: 0.8057 (mtmm) REVERT: B 14 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8280 (mm) REVERT: B 49 ARG cc_start: 0.8485 (mmt-90) cc_final: 0.8154 (mpt180) REVERT: B 65 THR cc_start: 0.8173 (m) cc_final: 0.7923 (p) REVERT: B 155 ASN cc_start: 0.8455 (t0) cc_final: 0.8182 (t0) REVERT: B 188 MET cc_start: 0.8438 (mmm) cc_final: 0.8168 (mmm) REVERT: B 256 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7440 (mtt180) REVERT: B 333 ASP cc_start: 0.8006 (p0) cc_final: 0.7702 (p0) REVERT: D 21 SER cc_start: 0.8393 (m) cc_final: 0.7985 (p) REVERT: D 128 MET cc_start: 0.8817 (mmm) cc_final: 0.7790 (mmm) REVERT: D 192 SER cc_start: 0.8560 (m) cc_final: 0.8296 (t) REVERT: D 218 MET cc_start: 0.8205 (ttp) cc_final: 0.7938 (ttp) REVERT: R 13 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8364 (tt) REVERT: R 152 ILE cc_start: 0.8243 (mm) cc_final: 0.7804 (tt) REVERT: R 286 LYS cc_start: 0.7964 (ttmm) cc_final: 0.7704 (ttpt) outliers start: 28 outliers final: 10 residues processed: 216 average time/residue: 0.9650 time to fit residues: 225.9762 Evaluate side-chains 209 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 196 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain R residue 13 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 0.0050 chunk 104 optimal weight: 0.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- 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: 0.7762 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8853 Z= 0.226 Angle : 0.537 9.796 12014 Z= 0.277 Chirality : 0.042 0.184 1398 Planarity : 0.003 0.036 1490 Dihedral : 5.113 51.296 1278 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.65 % Allowed : 21.30 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.94 (0.26), residues: 1118 helix: 2.37 (0.25), residues: 411 sheet: 0.79 (0.32), residues: 273 loop : -1.27 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS D 35 PHE 0.031 0.002 PHE R 63 TYR 0.024 0.001 TYR D 178 ARG 0.007 0.000 ARG R 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 209 time to evaluate : 1.103 Fit side-chains REVERT: A 186 GLU cc_start: 0.7526 (tt0) cc_final: 0.7315 (tt0) REVERT: B 14 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8272 (mm) REVERT: B 49 ARG cc_start: 0.8416 (mmt-90) cc_final: 0.7948 (mpt180) REVERT: B 65 THR cc_start: 0.8153 (m) cc_final: 0.7901 (p) REVERT: B 155 ASN cc_start: 0.8451 (t0) cc_final: 0.8166 (t0) REVERT: B 333 ASP cc_start: 0.8027 (p0) cc_final: 0.7720 (p0) REVERT: D 21 SER cc_start: 0.8352 (m) cc_final: 0.7947 (p) REVERT: D 34 MET cc_start: 0.8751 (mmp) cc_final: 0.8493 (mmm) REVERT: D 128 MET cc_start: 0.8815 (mmm) cc_final: 0.7747 (mmm) REVERT: D 192 SER cc_start: 0.8553 (m) cc_final: 0.8254 (t) REVERT: D 218 MET cc_start: 0.8193 (ttp) cc_final: 0.7917 (ttp) REVERT: R 13 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8343 (tt) REVERT: R 152 ILE cc_start: 0.8245 (mm) cc_final: 0.7831 (tt) REVERT: R 195 LEU cc_start: 0.7819 (tp) cc_final: 0.7001 (tt) REVERT: R 261 LEU cc_start: 0.8507 (tt) cc_final: 0.8297 (tp) REVERT: R 286 LYS cc_start: 0.7951 (ttmm) cc_final: 0.7700 (ttpt) REVERT: R 301 MET cc_start: 0.6235 (tpt) cc_final: 0.5887 (tpt) outliers start: 24 outliers final: 11 residues processed: 216 average time/residue: 0.9057 time to fit residues: 211.9186 Evaluate side-chains 208 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 195 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain R residue 13 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 107 optimal weight: 0.0970 chunk 67 optimal weight: 0.0040 chunk 65 optimal weight: 0.5980 chunk 49 optimal weight: 0.1980 chunk 66 optimal weight: 0.0770 chunk 43 optimal weight: 2.9990 overall best weight: 0.1948 ------------------------------------------------------------------------------- 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: 0.7714 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8853 Z= 0.139 Angle : 0.507 9.627 12014 Z= 0.261 Chirality : 0.040 0.164 1398 Planarity : 0.003 0.032 1490 Dihedral : 4.857 47.916 1278 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.10 % Allowed : 23.18 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.21 (0.26), residues: 1118 helix: 2.57 (0.25), residues: 412 sheet: 1.11 (0.32), residues: 265 loop : -1.19 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS R 94 PHE 0.034 0.001 PHE R 63 TYR 0.015 0.001 TYR D 178 ARG 0.007 0.000 ARG R 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 201 time to evaluate : 0.945 Fit side-chains REVERT: A 186 GLU cc_start: 0.7501 (tt0) cc_final: 0.7288 (tt0) REVERT: A 277 LYS cc_start: 0.8461 (ttpp) cc_final: 0.8236 (ttmt) REVERT: A 323 MET cc_start: 0.8256 (mtt) cc_final: 0.7932 (mtt) REVERT: B 14 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8186 (mm) REVERT: B 49 ARG cc_start: 0.8397 (mmt-90) cc_final: 0.8024 (mpt180) REVERT: B 65 THR cc_start: 0.8087 (m) cc_final: 0.7823 (p) REVERT: B 155 ASN cc_start: 0.8473 (t0) cc_final: 0.8226 (t0) REVERT: B 188 MET cc_start: 0.8351 (mmm) cc_final: 0.8024 (mmm) REVERT: B 333 ASP cc_start: 0.7989 (p0) cc_final: 0.7680 (p0) REVERT: D 128 MET cc_start: 0.8743 (mmm) cc_final: 0.7615 (mmm) REVERT: D 183 LEU cc_start: 0.8692 (mt) cc_final: 0.8468 (mm) REVERT: D 192 SER cc_start: 0.8535 (m) cc_final: 0.8204 (t) REVERT: D 201 THR cc_start: 0.8271 (m) cc_final: 0.8001 (p) REVERT: R 152 ILE cc_start: 0.8237 (mm) cc_final: 0.7784 (tt) REVERT: R 195 LEU cc_start: 0.7738 (tp) cc_final: 0.6914 (tt) REVERT: R 261 LEU cc_start: 0.8480 (tt) cc_final: 0.8272 (tp) REVERT: R 280 LEU cc_start: 0.8773 (mt) cc_final: 0.8414 (mt) REVERT: R 286 LYS cc_start: 0.7937 (ttmm) cc_final: 0.7715 (ttpt) REVERT: R 301 MET cc_start: 0.6174 (tpt) cc_final: 0.5848 (tpt) outliers start: 19 outliers final: 10 residues processed: 209 average time/residue: 0.8885 time to fit residues: 201.3900 Evaluate side-chains 204 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 193 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain R residue 179 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 73 optimal weight: 0.4980 chunk 53 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.7756 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8853 Z= 0.234 Angle : 0.538 9.320 12014 Z= 0.278 Chirality : 0.042 0.180 1398 Planarity : 0.003 0.047 1490 Dihedral : 5.001 51.720 1278 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.32 % Allowed : 23.84 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.26), residues: 1118 helix: 2.51 (0.25), residues: 412 sheet: 0.86 (0.31), residues: 281 loop : -1.18 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS D 35 PHE 0.036 0.002 PHE R 63 TYR 0.024 0.001 TYR D 178 ARG 0.014 0.000 ARG R 55 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 196 time to evaluate : 0.884 Fit side-chains REVERT: A 186 GLU cc_start: 0.7533 (tt0) cc_final: 0.7313 (tt0) REVERT: A 277 LYS cc_start: 0.8475 (ttpp) cc_final: 0.8229 (ttmt) REVERT: B 14 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8251 (mm) REVERT: B 49 ARG cc_start: 0.8405 (mmt-90) cc_final: 0.8077 (mpt180) REVERT: B 65 THR cc_start: 0.8143 (m) cc_final: 0.7870 (p) REVERT: B 155 ASN cc_start: 0.8480 (t0) cc_final: 0.8191 (t0) REVERT: B 188 MET cc_start: 0.8378 (mmm) cc_final: 0.8075 (mmm) REVERT: B 333 ASP cc_start: 0.7973 (p0) cc_final: 0.7655 (p0) REVERT: D 21 SER cc_start: 0.8348 (m) cc_final: 0.7949 (p) REVERT: D 34 MET cc_start: 0.8708 (mmp) cc_final: 0.8433 (mmm) REVERT: D 128 MET cc_start: 0.8735 (mmm) cc_final: 0.7615 (mmm) REVERT: D 183 LEU cc_start: 0.8731 (mt) cc_final: 0.8509 (mm) REVERT: D 192 SER cc_start: 0.8570 (m) cc_final: 0.8269 (t) REVERT: D 201 THR cc_start: 0.8329 (m) cc_final: 0.8044 (p) REVERT: D 226 THR cc_start: 0.8972 (OUTLIER) cc_final: 0.8724 (p) REVERT: R 13 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8327 (tt) REVERT: R 152 ILE cc_start: 0.8250 (mm) cc_final: 0.7833 (tt) REVERT: R 195 LEU cc_start: 0.7816 (tp) cc_final: 0.7011 (tt) REVERT: R 261 LEU cc_start: 0.8496 (tt) cc_final: 0.8288 (tp) REVERT: R 286 LYS cc_start: 0.7923 (ttmm) cc_final: 0.7687 (ttpt) REVERT: R 301 MET cc_start: 0.6224 (tpt) cc_final: 0.5900 (tpt) outliers start: 21 outliers final: 11 residues processed: 205 average time/residue: 0.9419 time to fit residues: 208.6859 Evaluate side-chains 211 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 197 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 270 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.0170 chunk 100 optimal weight: 0.0670 chunk 103 optimal weight: 0.0050 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 overall best weight: 0.2770 ------------------------------------------------------------------------------- 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: 0.7719 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8853 Z= 0.151 Angle : 0.522 9.187 12014 Z= 0.267 Chirality : 0.041 0.174 1398 Planarity : 0.003 0.040 1490 Dihedral : 4.853 49.690 1278 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.99 % Allowed : 24.17 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.22 (0.26), residues: 1118 helix: 2.61 (0.25), residues: 412 sheet: 1.07 (0.32), residues: 264 loop : -1.19 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS R 208 PHE 0.040 0.001 PHE R 63 TYR 0.017 0.001 TYR D 178 ARG 0.011 0.000 ARG R 55 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 200 time to evaluate : 0.894 Fit side-chains REVERT: A 18 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7849 (mtm) REVERT: A 186 GLU cc_start: 0.7503 (tt0) cc_final: 0.7286 (tt0) REVERT: A 323 MET cc_start: 0.8266 (mtt) cc_final: 0.7925 (mtt) REVERT: B 14 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8184 (mm) REVERT: B 49 ARG cc_start: 0.8376 (mmt-90) cc_final: 0.8007 (mpt180) REVERT: B 65 THR cc_start: 0.8090 (m) cc_final: 0.7828 (p) REVERT: B 155 ASN cc_start: 0.8461 (t0) cc_final: 0.8200 (t0) REVERT: B 188 MET cc_start: 0.8350 (mmm) cc_final: 0.8023 (mmm) REVERT: B 192 LEU cc_start: 0.8369 (mp) cc_final: 0.8135 (mp) REVERT: B 333 ASP cc_start: 0.7954 (p0) cc_final: 0.7642 (p0) REVERT: D 183 LEU cc_start: 0.8706 (mt) cc_final: 0.8486 (mm) REVERT: D 192 SER cc_start: 0.8548 (m) cc_final: 0.8221 (t) REVERT: D 201 THR cc_start: 0.8275 (m) cc_final: 0.7996 (p) REVERT: D 226 THR cc_start: 0.8953 (OUTLIER) cc_final: 0.8723 (p) REVERT: R 152 ILE cc_start: 0.8246 (mm) cc_final: 0.7832 (tt) REVERT: R 280 LEU cc_start: 0.8791 (mt) cc_final: 0.8454 (mt) REVERT: R 286 LYS cc_start: 0.7916 (ttmm) cc_final: 0.7689 (ttpt) REVERT: R 301 MET cc_start: 0.6215 (tpt) cc_final: 0.5877 (tpt) outliers start: 18 outliers final: 11 residues processed: 205 average time/residue: 0.9011 time to fit residues: 200.0731 Evaluate side-chains 210 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 196 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 179 ILE 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: 0.9990 chunk 73 optimal weight: 0.0000 chunk 111 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 94 optimal weight: 0.4980 overall best weight: 0.5986 ------------------------------------------------------------------------------- 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: 0.7744 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8853 Z= 0.221 Angle : 0.548 10.269 12014 Z= 0.279 Chirality : 0.042 0.200 1398 Planarity : 0.003 0.041 1490 Dihedral : 4.951 51.903 1278 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.99 % Allowed : 23.95 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.17 (0.26), residues: 1118 helix: 2.55 (0.25), residues: 412 sheet: 0.96 (0.32), residues: 270 loop : -1.18 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS D 35 PHE 0.032 0.002 PHE R 63 TYR 0.023 0.001 TYR D 178 ARG 0.013 0.000 ARG R 55 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 198 time to evaluate : 0.956 Fit side-chains REVERT: A 18 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7843 (mtm) REVERT: A 186 GLU cc_start: 0.7528 (tt0) cc_final: 0.7320 (tt0) REVERT: B 14 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8238 (mm) REVERT: B 49 ARG cc_start: 0.8408 (mmt-90) cc_final: 0.8084 (mpt180) REVERT: B 65 THR cc_start: 0.8132 (m) cc_final: 0.7861 (p) REVERT: B 155 ASN cc_start: 0.8447 (t0) cc_final: 0.8197 (t0) REVERT: B 188 MET cc_start: 0.8374 (mmm) cc_final: 0.8055 (mmm) REVERT: B 333 ASP cc_start: 0.7953 (p0) cc_final: 0.7632 (p0) REVERT: D 21 SER cc_start: 0.8340 (m) cc_final: 0.7930 (p) REVERT: D 183 LEU cc_start: 0.8726 (mt) cc_final: 0.8507 (mm) REVERT: D 192 SER cc_start: 0.8580 (m) cc_final: 0.8262 (t) REVERT: D 201 THR cc_start: 0.8309 (m) cc_final: 0.8024 (p) REVERT: D 226 THR cc_start: 0.8974 (OUTLIER) cc_final: 0.8726 (p) REVERT: R 13 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8344 (tt) REVERT: R 152 ILE cc_start: 0.8246 (mm) cc_final: 0.7838 (tt) REVERT: R 286 LYS cc_start: 0.7929 (ttmm) cc_final: 0.7701 (ttpt) REVERT: R 301 MET cc_start: 0.6224 (tpt) cc_final: 0.5872 (tpt) outliers start: 18 outliers final: 11 residues processed: 205 average time/residue: 0.9243 time to fit residues: 205.3408 Evaluate side-chains 210 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 195 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 179 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.133552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.115431 restraints weight = 12121.263| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.01 r_work: 0.3408 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8853 Z= 0.285 Angle : 0.576 9.905 12014 Z= 0.295 Chirality : 0.043 0.203 1398 Planarity : 0.003 0.042 1490 Dihedral : 5.138 53.490 1278 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.21 % Allowed : 23.84 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.04 (0.26), residues: 1118 helix: 2.37 (0.25), residues: 414 sheet: 0.93 (0.32), residues: 262 loop : -1.16 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS D 35 PHE 0.024 0.002 PHE R 63 TYR 0.026 0.001 TYR D 178 ARG 0.014 0.001 ARG R 55 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 3887.50 seconds wall clock time: 68 minutes 20.31 seconds (4100.31 seconds total)