Starting phenix.real_space_refine on Wed Mar 12 07:42:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wjx_37591/03_2025/8wjx_37591.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wjx_37591/03_2025/8wjx_37591.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wjx_37591/03_2025/8wjx_37591.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wjx_37591/03_2025/8wjx_37591.map" model { file = "/net/cci-nas-00/data/ceres_data/8wjx_37591/03_2025/8wjx_37591.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wjx_37591/03_2025/8wjx_37591.cif" } resolution = 3.2 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= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 50 5.16 5 C 4866 2.51 5 N 1293 2.21 5 O 1324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7535 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1793 Classifications: {'peptide': 239} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 6, 'TRANS': 232} Chain breaks: 1 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 13, 'ARG:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 118 Chain: "B" Number of atoms: 2284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2284 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 5, 'TRANS': 323} Unresolved non-hydrogen bonds: 240 Unresolved non-hydrogen angles: 300 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 6, 'ASN:plan1': 8, 'ASP:plan': 17, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 177 Chain: "G" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 250 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 38} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "N" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 888 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 120} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 42 Chain: "R" Number of atoms: 2265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2265 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 10, 'TRANS': 286} Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 1, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 88 Chain: "R" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'ADP': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.38, per 1000 atoms: 0.71 Number of scatterers: 7535 At special positions: 0 Unit cell: (82, 96, 128, 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 50 16.00 P 2 15.00 O 1324 8.00 N 1293 7.00 C 4866 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 42 " - pdb=" SG CYS R 296 " distance=2.03 Simple disulfide: pdb=" SG CYS R 124 " - pdb=" SG CYS R 202 " 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: 1.88 Conformation dependent library (CDL) restraints added in 1.1 seconds 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1938 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 12 sheets defined 40.7% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 Processing helix chain 'A' and resid 52 through 62 removed outlier: 3.594A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 236 removed outlier: 4.580A pdb=" N TRP A 234 " --> pdb=" O GLU A 230 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A 235 " --> pdb=" O ARG A 231 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLN A 236 " --> pdb=" O ARG A 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 230 through 236' Processing helix chain 'A' and resid 237 through 239 No H-bonds generated for 'chain 'A' and resid 237 through 239' Processing helix chain 'A' and resid 255 through 269 Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 297 through 302 removed outlier: 3.972A pdb=" N TYR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 306 Processing helix chain 'A' and resid 321 through 341 removed outlier: 3.636A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 381 Processing helix chain 'B' and resid 13 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 20 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 47 through 52 Processing helix chain 'R' and resid 52 through 79 removed outlier: 3.903A pdb=" N LEU R 67 " --> pdb=" O ILE R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 113 removed outlier: 3.566A pdb=" N TYR R 89 " --> pdb=" O GLY R 85 " (cutoff:3.500A) Proline residue: R 105 - end of helix Processing helix chain 'R' and resid 122 through 155 removed outlier: 3.543A pdb=" N GLY R 137 " --> pdb=" O VAL R 133 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR R 143 " --> pdb=" O ILE R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 164 through 183 Processing helix chain 'R' and resid 185 through 190 Processing helix chain 'R' and resid 210 through 226 removed outlier: 3.502A pdb=" N PHE R 226 " --> pdb=" O THR R 222 " (cutoff:3.500A) Processing helix chain 'R' and resid 226 through 246 Processing helix chain 'R' and resid 254 through 289 removed outlier: 4.231A pdb=" N SER R 258 " --> pdb=" O LEU R 254 " (cutoff:3.500A) Proline residue: R 275 - end of helix removed outlier: 3.566A pdb=" N THR R 281 " --> pdb=" O HIS R 277 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 315 removed outlier: 3.643A pdb=" N ASN R 299 " --> pdb=" O MET R 295 " (cutoff:3.500A) Processing helix chain 'R' and resid 315 through 325 Proline residue: R 321 - end of helix Processing helix chain 'R' and resid 328 through 335 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 210 Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 210 removed outlier: 6.218A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.303A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASN A 282 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL A 248 " --> pdb=" O ASN A 282 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N VAL A 277 " --> pdb=" O TYR A 350 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N HIS A 352 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N LEU A 279 " --> pdb=" O HIS A 352 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 52 removed outlier: 4.052A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.803A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.793A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.889A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.837A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 5.738A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.664A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 removed outlier: 4.218A pdb=" N GLN N 5 " --> pdb=" O ALA N 23 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU N 79 " --> pdb=" O CYS N 22 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.759A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ALA N 40 " --> pdb=" O GLY N 44 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N GLY N 44 " --> pdb=" O ALA N 40 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 192 through 194 407 hydrogen bonds defined for protein. 1164 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: 2.38 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2396 1.34 - 1.46: 1765 1.46 - 1.58: 3478 1.58 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 7709 Sorted by residual: bond pdb=" O5' ADP R 601 " pdb=" PA ADP R 601 " ideal model delta sigma weight residual 1.610 1.785 -0.175 2.00e-02 2.50e+03 7.69e+01 bond pdb=" O3A ADP R 601 " pdb=" PB ADP R 601 " ideal model delta sigma weight residual 1.610 1.728 -0.118 2.00e-02 2.50e+03 3.50e+01 bond pdb=" C5' ADP R 601 " pdb=" O5' ADP R 601 " ideal model delta sigma weight residual 1.426 1.333 0.093 2.00e-02 2.50e+03 2.16e+01 bond pdb=" C5 ADP R 601 " pdb=" C6 ADP R 601 " ideal model delta sigma weight residual 1.490 1.400 0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" O3A ADP R 601 " pdb=" PA ADP R 601 " ideal model delta sigma weight residual 1.610 1.542 0.068 2.00e-02 2.50e+03 1.16e+01 ... (remaining 7704 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 10431 2.56 - 5.12: 89 5.12 - 7.68: 12 7.68 - 10.24: 5 10.24 - 12.79: 3 Bond angle restraints: 10540 Sorted by residual: angle pdb=" O1A ADP R 601 " pdb=" PA ADP R 601 " pdb=" O5' ADP R 601 " ideal model delta sigma weight residual 108.20 95.41 12.79 3.00e+00 1.11e-01 1.82e+01 angle pdb=" C1' ADP R 601 " pdb=" C2' ADP R 601 " pdb=" C3' ADP R 601 " ideal model delta sigma weight residual 111.00 98.43 12.57 3.00e+00 1.11e-01 1.76e+01 angle pdb=" O1A ADP R 601 " pdb=" PA ADP R 601 " pdb=" O3A ADP R 601 " ideal model delta sigma weight residual 108.20 119.65 -11.45 3.00e+00 1.11e-01 1.46e+01 angle pdb=" N THR N 114 " pdb=" CA THR N 114 " pdb=" C THR N 114 " ideal model delta sigma weight residual 114.64 109.31 5.33 1.52e+00 4.33e-01 1.23e+01 angle pdb=" O3A ADP R 601 " pdb=" PA ADP R 601 " pdb=" O5' ADP R 601 " ideal model delta sigma weight residual 102.60 92.56 10.04 3.00e+00 1.11e-01 1.12e+01 ... (remaining 10535 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.50: 4404 31.50 - 63.01: 99 63.01 - 94.51: 5 94.51 - 126.02: 2 126.02 - 157.52: 1 Dihedral angle restraints: 4511 sinusoidal: 1500 harmonic: 3011 Sorted by residual: dihedral pdb=" CB CYS R 42 " pdb=" SG CYS R 42 " pdb=" SG CYS R 296 " pdb=" CB CYS R 296 " ideal model delta sinusoidal sigma weight residual 93.00 162.18 -69.18 1 1.00e+01 1.00e-02 6.19e+01 dihedral pdb=" O1B ADP R 601 " pdb=" O3A ADP R 601 " pdb=" PB ADP R 601 " pdb=" PA ADP R 601 " ideal model delta sinusoidal sigma weight residual 300.00 142.48 157.52 1 2.00e+01 2.50e-03 4.62e+01 dihedral pdb=" CA SER N 112 " pdb=" C SER N 112 " pdb=" N THR N 113 " pdb=" CA THR N 113 " ideal model delta harmonic sigma weight residual 180.00 -149.40 -30.60 0 5.00e+00 4.00e-02 3.75e+01 ... (remaining 4508 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 997 0.051 - 0.102: 211 0.102 - 0.154: 30 0.154 - 0.205: 3 0.205 - 0.256: 3 Chirality restraints: 1244 Sorted by residual: chirality pdb=" C2' ADP R 601 " pdb=" C1' ADP R 601 " pdb=" C3' ADP R 601 " pdb=" O2' ADP R 601 " both_signs ideal model delta sigma weight residual False -2.51 -2.77 0.26 2.00e-01 2.50e+01 1.64e+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 -2.70 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" C4' ADP R 601 " pdb=" C3' ADP R 601 " pdb=" C5' ADP R 601 " pdb=" O4' ADP R 601 " both_signs ideal model delta sigma weight residual False -2.50 -2.71 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 1241 not shown) Planarity restraints: 1319 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 280 " -0.012 2.00e-02 2.50e+03 2.50e-02 6.26e+00 pdb=" C PHE A 280 " 0.043 2.00e-02 2.50e+03 pdb=" O PHE A 280 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU A 281 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS R 81 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.76e+00 pdb=" N PRO R 82 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO R 82 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO R 82 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 317 " -0.030 5.00e-02 4.00e+02 4.63e-02 3.44e+00 pdb=" N PRO A 318 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 318 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 318 " -0.026 5.00e-02 4.00e+02 ... (remaining 1316 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 191 2.70 - 3.25: 7637 3.25 - 3.80: 12732 3.80 - 4.35: 16476 4.35 - 4.90: 27869 Nonbonded interactions: 64905 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.148 3.040 nonbonded pdb=" OG1 THR N 104 " pdb=" OD1 ASP N 106 " model vdw 2.185 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.239 3.040 nonbonded pdb=" NE2 HIS B 54 " pdb=" OG SER B 72 " model vdw 2.269 3.120 nonbonded pdb=" O VAL R 268 " pdb=" OG SER R 272 " model vdw 2.272 3.040 ... (remaining 64900 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: 1.430 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.080 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 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 0.175 7709 Z= 0.338 Angle : 0.694 12.795 10540 Z= 0.364 Chirality : 0.044 0.256 1244 Planarity : 0.004 0.048 1319 Dihedral : 14.063 157.520 2567 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.87 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 11.84 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.19 (0.27), residues: 1022 helix: 1.31 (0.28), residues: 369 sheet: -0.69 (0.34), residues: 201 loop : -1.03 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 234 HIS 0.003 0.001 HIS A 347 PHE 0.017 0.001 PHE R 131 TYR 0.015 0.001 TYR B 105 ARG 0.003 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.737 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7262 (mm-30) cc_final: 0.6947 (mm-30) REVERT: A 38 ARG cc_start: 0.7449 (mtp180) cc_final: 0.6645 (mmt180) REVERT: A 222 PHE cc_start: 0.8251 (p90) cc_final: 0.7732 (p90) REVERT: A 236 GLN cc_start: 0.8284 (mt0) cc_final: 0.7619 (mp10) REVERT: A 323 ARG cc_start: 0.7844 (mtp85) cc_final: 0.7613 (mtp180) REVERT: A 329 TYR cc_start: 0.7611 (m-80) cc_final: 0.7183 (m-80) REVERT: R 164 LYS cc_start: 0.5777 (mttm) cc_final: 0.5524 (mmmt) REVERT: R 178 ILE cc_start: 0.7508 (mt) cc_final: 0.7186 (mt) REVERT: R 226 PHE cc_start: 0.7923 (t80) cc_final: 0.7565 (t80) REVERT: R 314 SER cc_start: 0.7882 (p) cc_final: 0.7673 (p) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.2140 time to fit residues: 41.2487 Evaluate side-chains 111 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 chunk 25 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.199449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.161022 restraints weight = 7556.800| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 2.18 r_work: 0.3749 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 7709 Z= 0.314 Angle : 0.637 7.814 10540 Z= 0.326 Chirality : 0.045 0.164 1244 Planarity : 0.005 0.052 1319 Dihedral : 7.931 138.965 1193 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.97 % Favored : 93.84 % Rotamer: Outliers : 3.36 % Allowed : 14.91 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.10 (0.26), residues: 1022 helix: 1.66 (0.27), residues: 363 sheet: -0.78 (0.34), residues: 197 loop : -1.14 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP N 47 HIS 0.003 0.001 HIS B 91 PHE 0.023 0.002 PHE N 108 TYR 0.018 0.002 TYR B 105 ARG 0.008 0.001 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.707 Fit side-chains REVERT: A 27 GLU cc_start: 0.7434 (mm-30) cc_final: 0.7070 (mm-30) REVERT: A 38 ARG cc_start: 0.7793 (mtp180) cc_final: 0.7549 (mtm110) REVERT: A 235 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8519 (tp) REVERT: A 236 GLN cc_start: 0.8508 (mt0) cc_final: 0.7842 (mp10) REVERT: A 329 TYR cc_start: 0.7929 (m-80) cc_final: 0.7476 (m-80) REVERT: B 61 MET cc_start: 0.7794 (tmm) cc_final: 0.6814 (ttp) REVERT: B 275 SER cc_start: 0.8461 (m) cc_final: 0.8059 (m) REVERT: R 219 MET cc_start: 0.7463 (mmt) cc_final: 0.7161 (mmt) REVERT: R 225 MET cc_start: 0.7882 (mmm) cc_final: 0.7559 (mtt) REVERT: R 226 PHE cc_start: 0.8000 (t80) cc_final: 0.7583 (t80) outliers start: 23 outliers final: 13 residues processed: 135 average time/residue: 0.1768 time to fit residues: 33.2528 Evaluate side-chains 117 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain R residue 210 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 98 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 92 optimal weight: 0.3980 chunk 33 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.201086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.163668 restraints weight = 7630.787| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 2.13 r_work: 0.3781 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7709 Z= 0.214 Angle : 0.577 6.977 10540 Z= 0.295 Chirality : 0.042 0.149 1244 Planarity : 0.004 0.051 1319 Dihedral : 7.768 142.982 1193 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.34 % Allowed : 17.40 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.01 (0.27), residues: 1022 helix: 1.80 (0.27), residues: 365 sheet: -0.73 (0.35), residues: 197 loop : -1.12 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP N 47 HIS 0.003 0.001 HIS A 347 PHE 0.013 0.001 PHE R 226 TYR 0.022 0.002 TYR R 214 ARG 0.006 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.733 Fit side-chains REVERT: A 27 GLU cc_start: 0.7392 (mm-30) cc_final: 0.7072 (mm-30) REVERT: A 236 GLN cc_start: 0.8466 (mt0) cc_final: 0.7829 (mp10) REVERT: B 61 MET cc_start: 0.7813 (tmm) cc_final: 0.6819 (ttp) REVERT: B 290 ASP cc_start: 0.7621 (m-30) cc_final: 0.7309 (m-30) REVERT: N 95 TYR cc_start: 0.8785 (m-80) cc_final: 0.8546 (m-80) REVERT: R 159 SER cc_start: 0.8720 (p) cc_final: 0.8444 (p) REVERT: R 219 MET cc_start: 0.7438 (mmt) cc_final: 0.7199 (mmt) REVERT: R 225 MET cc_start: 0.7815 (mmm) cc_final: 0.7573 (mtt) REVERT: R 226 PHE cc_start: 0.7898 (t80) cc_final: 0.7590 (t80) REVERT: R 332 ARG cc_start: 0.7105 (mtm180) cc_final: 0.6898 (mtm180) outliers start: 16 outliers final: 12 residues processed: 125 average time/residue: 0.1510 time to fit residues: 27.2772 Evaluate side-chains 109 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain R residue 210 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 24 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 chunk 77 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 55 optimal weight: 0.0770 overall best weight: 1.1540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.198979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.159966 restraints weight = 7613.382| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 2.21 r_work: 0.3729 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 7709 Z= 0.301 Angle : 0.607 6.786 10540 Z= 0.313 Chirality : 0.044 0.155 1244 Planarity : 0.004 0.050 1319 Dihedral : 7.840 145.248 1193 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 4.24 % Allowed : 18.13 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.17 (0.26), residues: 1022 helix: 1.64 (0.27), residues: 364 sheet: -0.78 (0.35), residues: 196 loop : -1.24 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP N 47 HIS 0.003 0.001 HIS R 277 PHE 0.020 0.002 PHE N 108 TYR 0.017 0.002 TYR N 60 ARG 0.004 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 106 time to evaluate : 0.756 Fit side-chains REVERT: A 27 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7077 (mm-30) REVERT: A 213 GLN cc_start: 0.8056 (tt0) cc_final: 0.7443 (tt0) REVERT: A 222 PHE cc_start: 0.8309 (OUTLIER) cc_final: 0.7746 (p90) REVERT: A 280 PHE cc_start: 0.9061 (OUTLIER) cc_final: 0.8476 (t80) REVERT: B 105 TYR cc_start: 0.8567 (OUTLIER) cc_final: 0.6699 (m-80) REVERT: R 126 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7286 (tm) REVERT: R 219 MET cc_start: 0.7563 (mmt) cc_final: 0.7348 (mmt) REVERT: R 226 PHE cc_start: 0.7894 (t80) cc_final: 0.7572 (t80) outliers start: 29 outliers final: 17 residues processed: 128 average time/residue: 0.1560 time to fit residues: 28.8517 Evaluate side-chains 124 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 280 PHE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 201 THR Chi-restraints excluded: chain R residue 210 TYR Chi-restraints excluded: chain R residue 271 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 7 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 17 optimal weight: 0.0030 chunk 57 optimal weight: 0.0170 chunk 24 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.4628 ------------------------------------------------------------------------------- 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 = 0.4341 r_free = 0.4341 target = 0.204347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.165755 restraints weight = 7609.238| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 2.21 r_work: 0.3794 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7709 Z= 0.178 Angle : 0.545 6.845 10540 Z= 0.279 Chirality : 0.042 0.139 1244 Planarity : 0.004 0.049 1319 Dihedral : 7.680 151.285 1193 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.09 % Allowed : 19.30 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.08 (0.27), residues: 1022 helix: 1.90 (0.27), residues: 366 sheet: -0.67 (0.35), residues: 200 loop : -1.14 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP N 47 HIS 0.003 0.001 HIS A 41 PHE 0.014 0.001 PHE R 226 TYR 0.020 0.002 TYR N 60 ARG 0.004 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.798 Fit side-chains REVERT: A 27 GLU cc_start: 0.7391 (mm-30) cc_final: 0.7096 (mm-30) REVERT: A 213 GLN cc_start: 0.8056 (tt0) cc_final: 0.7429 (tt0) REVERT: A 222 PHE cc_start: 0.8175 (OUTLIER) cc_final: 0.7593 (p90) REVERT: A 280 PHE cc_start: 0.8969 (OUTLIER) cc_final: 0.8399 (t80) REVERT: A 329 TYR cc_start: 0.7791 (m-80) cc_final: 0.7353 (m-80) REVERT: B 105 TYR cc_start: 0.8546 (OUTLIER) cc_final: 0.6535 (m-80) REVERT: B 290 ASP cc_start: 0.7662 (m-30) cc_final: 0.7369 (m-30) REVERT: R 126 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7283 (tp) REVERT: R 204 ASP cc_start: 0.7921 (t70) cc_final: 0.7706 (t0) REVERT: R 226 PHE cc_start: 0.7689 (t80) cc_final: 0.7434 (t80) REVERT: R 279 MET cc_start: 0.8772 (mmp) cc_final: 0.8518 (mmp) outliers start: 28 outliers final: 18 residues processed: 131 average time/residue: 0.1607 time to fit residues: 30.3040 Evaluate side-chains 120 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 280 PHE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 201 THR Chi-restraints excluded: chain R residue 210 TYR Chi-restraints excluded: chain R residue 271 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4318 r_free = 0.4318 target = 0.201728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.162909 restraints weight = 7608.177| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 2.21 r_work: 0.3744 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7709 Z= 0.244 Angle : 0.573 7.286 10540 Z= 0.294 Chirality : 0.042 0.147 1244 Planarity : 0.004 0.049 1319 Dihedral : 7.683 149.510 1193 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.68 % Allowed : 19.59 % Favored : 75.73 % 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: 0.02 (0.27), residues: 1022 helix: 1.76 (0.27), residues: 368 sheet: -0.57 (0.35), residues: 195 loop : -1.17 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP N 47 HIS 0.002 0.001 HIS B 91 PHE 0.014 0.002 PHE N 108 TYR 0.020 0.002 TYR N 60 ARG 0.003 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 0.828 Fit side-chains REVERT: A 27 GLU cc_start: 0.7422 (mm-30) cc_final: 0.7119 (mm-30) REVERT: A 222 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7670 (p90) REVERT: A 280 PHE cc_start: 0.9015 (OUTLIER) cc_final: 0.8458 (t80) REVERT: B 105 TYR cc_start: 0.8588 (OUTLIER) cc_final: 0.6560 (m-80) REVERT: B 245 SER cc_start: 0.8397 (OUTLIER) cc_final: 0.7938 (m) REVERT: R 126 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7260 (tm) REVERT: R 219 MET cc_start: 0.7379 (OUTLIER) cc_final: 0.6968 (tpp) REVERT: R 226 PHE cc_start: 0.7616 (t80) cc_final: 0.7314 (t80) REVERT: R 279 MET cc_start: 0.8790 (mmp) cc_final: 0.8508 (mmp) outliers start: 32 outliers final: 19 residues processed: 128 average time/residue: 0.1568 time to fit residues: 29.1790 Evaluate side-chains 125 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 280 PHE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 201 THR Chi-restraints excluded: chain R residue 210 TYR Chi-restraints excluded: chain R residue 219 MET Chi-restraints excluded: chain R residue 271 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 59 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 0.1980 chunk 15 optimal weight: 0.8980 chunk 60 optimal weight: 8.9990 chunk 81 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 82 optimal weight: 0.0970 chunk 6 optimal weight: 0.0270 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN B 88 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.207044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.168525 restraints weight = 7499.664| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 2.19 r_work: 0.3805 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7709 Z= 0.158 Angle : 0.539 7.271 10540 Z= 0.276 Chirality : 0.041 0.138 1244 Planarity : 0.004 0.049 1319 Dihedral : 7.606 150.732 1193 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.36 % Allowed : 21.49 % Favored : 75.15 % 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: 0.33 (0.27), residues: 1022 helix: 2.18 (0.28), residues: 362 sheet: -0.55 (0.35), residues: 202 loop : -1.04 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP N 47 HIS 0.003 0.001 HIS A 41 PHE 0.013 0.001 PHE R 131 TYR 0.022 0.001 TYR N 60 ARG 0.003 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.823 Fit side-chains REVERT: A 27 GLU cc_start: 0.7378 (mm-30) cc_final: 0.7146 (mm-30) REVERT: A 222 PHE cc_start: 0.8046 (OUTLIER) cc_final: 0.7497 (p90) REVERT: A 280 PHE cc_start: 0.8939 (OUTLIER) cc_final: 0.8372 (t80) REVERT: A 329 TYR cc_start: 0.7756 (m-80) cc_final: 0.7307 (m-80) REVERT: B 105 TYR cc_start: 0.8542 (OUTLIER) cc_final: 0.6543 (m-80) REVERT: B 245 SER cc_start: 0.8288 (OUTLIER) cc_final: 0.7892 (m) REVERT: N 46 GLU cc_start: 0.7285 (pt0) cc_final: 0.7055 (pm20) REVERT: R 126 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7310 (tp) REVERT: R 159 SER cc_start: 0.8598 (p) cc_final: 0.8354 (p) REVERT: R 219 MET cc_start: 0.7354 (OUTLIER) cc_final: 0.6872 (tpp) REVERT: R 332 ARG cc_start: 0.7050 (mtm180) cc_final: 0.6797 (mtm180) outliers start: 23 outliers final: 15 residues processed: 114 average time/residue: 0.1429 time to fit residues: 24.3735 Evaluate side-chains 113 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 280 PHE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 201 THR Chi-restraints excluded: chain R residue 210 TYR Chi-restraints excluded: chain R residue 219 MET Chi-restraints excluded: chain R residue 271 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 89 optimal weight: 0.7980 chunk 48 optimal weight: 0.0370 chunk 69 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 83 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 55 optimal weight: 20.0000 chunk 66 optimal weight: 1.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN B 88 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.205534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.166590 restraints weight = 7646.819| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 2.23 r_work: 0.3784 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7709 Z= 0.190 Angle : 0.547 7.192 10540 Z= 0.280 Chirality : 0.042 0.141 1244 Planarity : 0.004 0.050 1319 Dihedral : 7.497 142.347 1193 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.51 % Allowed : 22.08 % Favored : 74.42 % 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: 0.31 (0.27), residues: 1022 helix: 2.18 (0.27), residues: 361 sheet: -0.55 (0.35), residues: 202 loop : -1.07 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.003 0.001 HIS R 277 PHE 0.029 0.001 PHE R 226 TYR 0.017 0.001 TYR N 60 ARG 0.003 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.744 Fit side-chains REVERT: A 213 GLN cc_start: 0.8016 (tt0) cc_final: 0.7369 (tt0) REVERT: A 222 PHE cc_start: 0.8116 (OUTLIER) cc_final: 0.7593 (p90) REVERT: A 236 GLN cc_start: 0.8424 (mt0) cc_final: 0.7815 (mp10) REVERT: A 280 PHE cc_start: 0.8968 (OUTLIER) cc_final: 0.8408 (t80) REVERT: B 105 TYR cc_start: 0.8576 (OUTLIER) cc_final: 0.6513 (m-80) REVERT: B 245 SER cc_start: 0.8346 (OUTLIER) cc_final: 0.7876 (m) REVERT: B 283 ARG cc_start: 0.7648 (tpt-90) cc_final: 0.7026 (tpp-160) REVERT: N 46 GLU cc_start: 0.7330 (pt0) cc_final: 0.7085 (pm20) REVERT: R 126 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7361 (tm) REVERT: R 226 PHE cc_start: 0.7756 (t80) cc_final: 0.7429 (t80) outliers start: 24 outliers final: 17 residues processed: 120 average time/residue: 0.1561 time to fit residues: 26.8979 Evaluate side-chains 119 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 234 TRP Chi-restraints excluded: chain A residue 280 PHE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 201 THR Chi-restraints excluded: chain R residue 210 TYR Chi-restraints excluded: chain R residue 219 MET Chi-restraints excluded: chain R residue 271 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 93 optimal weight: 0.4980 chunk 17 optimal weight: 0.0000 chunk 20 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 73 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- 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 = 0.4350 r_free = 0.4350 target = 0.205050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.166572 restraints weight = 7696.163| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 2.23 r_work: 0.3792 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7709 Z= 0.193 Angle : 0.544 7.027 10540 Z= 0.279 Chirality : 0.042 0.141 1244 Planarity : 0.004 0.050 1319 Dihedral : 7.322 136.325 1193 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.65 % Allowed : 21.64 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.27), residues: 1022 helix: 2.20 (0.27), residues: 361 sheet: -0.50 (0.35), residues: 202 loop : -1.08 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.002 0.001 HIS A 41 PHE 0.032 0.001 PHE R 226 TYR 0.016 0.001 TYR R 214 ARG 0.003 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.923 Fit side-chains REVERT: A 222 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.7601 (p90) REVERT: A 280 PHE cc_start: 0.8978 (OUTLIER) cc_final: 0.8443 (t80) REVERT: B 105 TYR cc_start: 0.8550 (OUTLIER) cc_final: 0.6529 (m-80) REVERT: B 245 SER cc_start: 0.8354 (OUTLIER) cc_final: 0.7926 (m) REVERT: B 283 ARG cc_start: 0.7690 (tpt-90) cc_final: 0.7097 (tpp-160) REVERT: N 46 GLU cc_start: 0.7320 (pt0) cc_final: 0.7119 (pm20) REVERT: R 126 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7493 (tm) REVERT: R 226 PHE cc_start: 0.7637 (t80) cc_final: 0.7269 (t80) outliers start: 25 outliers final: 18 residues processed: 114 average time/residue: 0.1671 time to fit residues: 27.2618 Evaluate side-chains 117 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 234 TRP Chi-restraints excluded: chain A residue 280 PHE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 201 THR Chi-restraints excluded: chain R residue 210 TYR Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain R residue 316 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 88 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 71 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 8 optimal weight: 0.3980 chunk 97 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 27 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.204939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.165943 restraints weight = 7692.853| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 2.23 r_work: 0.3780 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7709 Z= 0.198 Angle : 0.548 7.233 10540 Z= 0.280 Chirality : 0.042 0.142 1244 Planarity : 0.004 0.050 1319 Dihedral : 7.146 129.610 1193 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.36 % Allowed : 21.64 % Favored : 75.00 % 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: 0.31 (0.27), residues: 1022 helix: 2.16 (0.27), residues: 362 sheet: -0.48 (0.35), residues: 202 loop : -1.09 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP N 47 HIS 0.002 0.001 HIS A 41 PHE 0.027 0.001 PHE R 226 TYR 0.017 0.001 TYR R 214 ARG 0.003 0.000 ARG N 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.740 Fit side-chains REVERT: A 213 GLN cc_start: 0.8056 (tt0) cc_final: 0.7607 (tt0) REVERT: A 222 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7667 (p90) REVERT: A 280 PHE cc_start: 0.8965 (OUTLIER) cc_final: 0.8424 (t80) REVERT: B 105 TYR cc_start: 0.8573 (OUTLIER) cc_final: 0.6443 (m-80) REVERT: B 245 SER cc_start: 0.8364 (OUTLIER) cc_final: 0.7916 (m) REVERT: B 283 ARG cc_start: 0.7665 (tpt-90) cc_final: 0.7032 (tpp-160) REVERT: N 46 GLU cc_start: 0.7363 (pt0) cc_final: 0.7110 (pm20) REVERT: R 126 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7368 (tm) REVERT: R 226 PHE cc_start: 0.7501 (t80) cc_final: 0.7124 (t80) outliers start: 23 outliers final: 17 residues processed: 107 average time/residue: 0.1596 time to fit residues: 25.0504 Evaluate side-chains 113 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 234 TRP Chi-restraints excluded: chain A residue 280 PHE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 210 TYR Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain R residue 316 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 47 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 17 optimal weight: 0.0770 chunk 6 optimal weight: 0.7980 chunk 51 optimal weight: 0.3980 chunk 72 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN B 88 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.204602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.166265 restraints weight = 7567.236| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 2.18 r_work: 0.3783 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7709 Z= 0.200 Angle : 0.547 7.047 10540 Z= 0.280 Chirality : 0.042 0.142 1244 Planarity : 0.004 0.050 1319 Dihedral : 7.019 125.322 1193 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.36 % Allowed : 21.78 % Favored : 74.85 % 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: 0.34 (0.27), residues: 1022 helix: 2.17 (0.27), residues: 362 sheet: -0.38 (0.36), residues: 200 loop : -1.10 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.002 0.001 HIS A 41 PHE 0.024 0.001 PHE R 226 TYR 0.018 0.001 TYR R 214 ARG 0.003 0.000 ARG A 270 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3677.35 seconds wall clock time: 63 minutes 56.78 seconds (3836.78 seconds total)