Starting phenix.real_space_refine on Sat Aug 3 19:24:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vy7_43647/08_2024/8vy7_43647.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vy7_43647/08_2024/8vy7_43647.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vy7_43647/08_2024/8vy7_43647.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vy7_43647/08_2024/8vy7_43647.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vy7_43647/08_2024/8vy7_43647.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vy7_43647/08_2024/8vy7_43647.cif" } resolution = 2.68 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= 0.021 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 5659 2.51 5 N 1488 2.21 5 O 1601 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8811 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1753 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 2564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2564 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 401 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1743 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "R" Number of atoms: 2299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2299 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 14 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: 5.27, per 1000 atoms: 0.60 Number of scatterers: 8811 At special positions: 0 Unit cell: (90.228, 120.888, 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 1601 8.00 N 1488 7.00 C 5659 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.99 Conformation dependent library (CDL) restraints added in 1.6 seconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 13 sheets defined 39.4% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.852A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.585A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.647A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.557A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'C' and resid 9 through 24 removed outlier: 3.739A 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 53 through 56 removed outlier: 4.366A pdb=" N GLY D 56 " --> pdb=" O SER D 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 53 through 56' Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.658A pdb=" N THR D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 37 Processing helix chain 'R' and resid 42 through 72 Processing helix chain 'R' and resid 72 through 77 Processing helix chain 'R' and resid 78 through 112 Processing helix chain 'R' and resid 116 through 124 Processing helix chain 'R' and resid 125 through 137 Processing helix chain 'R' and resid 137 through 158 removed outlier: 3.606A pdb=" N LEU R 141 " --> pdb=" O THR R 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 213 removed outlier: 4.214A pdb=" N LEU R 181 " --> pdb=" O SER R 177 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE R 189 " --> pdb=" O VAL R 185 " (cutoff:3.500A) Proline residue: R 190 - end of helix Processing helix chain 'R' and resid 228 through 257 removed outlier: 4.386A pdb=" N SER R 232 " --> pdb=" O ARG R 228 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU R 239 " --> pdb=" O THR R 235 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER R 246 " --> pdb=" O ILE R 242 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU R 257 " --> pdb=" O THR R 253 " (cutoff:3.500A) Processing helix chain 'R' and resid 260 through 270 removed outlier: 3.751A pdb=" N LEU R 264 " --> pdb=" O ASN R 260 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET R 270 " --> pdb=" O GLN R 266 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 282 removed outlier: 4.624A pdb=" N SER R 277 " --> pdb=" O PRO R 273 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N CYS R 278 " --> pdb=" O SER R 274 " (cutoff:3.500A) Processing helix chain 'R' and resid 284 through 302 removed outlier: 3.791A 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: 3.545A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.705A 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: 3.695A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.634A 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: 6.778A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.621A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.711A 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: 6.744A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.521A 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: 3.666A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.024A 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: 3.628A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.415A 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: 5.722A pdb=" N GLY D 10 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.610A 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: 5.722A pdb=" N GLY D 10 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N PHE D 110 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 128 through 129 removed outlier: 3.911A pdb=" N ALA D 199 " --> pdb=" O SER D 196 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 135 through 136 removed outlier: 6.704A pdb=" N TRP D 164 " --> pdb=" O LEU D 176 " (cutoff:3.500A) 471 hydrogen bonds defined for protein. 1338 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: 2.45 Time building geometry restraints manager: 3.32 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: 2778 1.34 - 1.46: 1822 1.46 - 1.57: 4307 1.57 - 1.69: 2 1.69 - 1.81: 90 Bond restraints: 8999 Sorted by residual: bond pdb=" C10 A1AEI R 501 " pdb=" N11 A1AEI R 501 " ideal model delta sigma weight residual 1.364 1.459 -0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" C13 A1AEI R 501 " pdb=" C14 A1AEI R 501 " ideal model delta sigma weight residual 1.461 1.529 -0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" N16 A1AEI R 501 " pdb=" N17 A1AEI R 501 " ideal model delta sigma weight residual 1.275 1.333 -0.058 2.00e-02 2.50e+03 8.56e+00 bond pdb=" C16 CLR R 502 " pdb=" C17 CLR R 502 " ideal model delta sigma weight residual 1.554 1.607 -0.053 2.00e-02 2.50e+03 7.07e+00 bond pdb=" C23 CLR R 502 " pdb=" C24 CLR R 502 " ideal model delta sigma weight residual 1.525 1.574 -0.049 2.00e-02 2.50e+03 5.94e+00 ... (remaining 8994 not shown) Histogram of bond angle deviations from ideal: 100.00 - 106.82: 189 106.82 - 113.64: 5043 113.64 - 120.46: 3376 120.46 - 127.28: 3504 127.28 - 134.10: 88 Bond angle restraints: 12200 Sorted by residual: angle pdb=" CA LEU A 227 " pdb=" CB LEU A 227 " pdb=" CG LEU A 227 " ideal model delta sigma weight residual 116.30 127.43 -11.13 3.50e+00 8.16e-02 1.01e+01 angle pdb=" N PRO D 224 " pdb=" CA PRO D 224 " pdb=" C PRO D 224 " ideal model delta sigma weight residual 112.10 120.32 -8.22 2.60e+00 1.48e-01 9.99e+00 angle pdb=" CA TYR D 178 " pdb=" CB TYR D 178 " pdb=" CG TYR D 178 " ideal model delta sigma weight residual 113.90 119.48 -5.58 1.80e+00 3.09e-01 9.62e+00 angle pdb=" C22 CLR R 502 " pdb=" C23 CLR R 502 " pdb=" C24 CLR R 502 " ideal model delta sigma weight residual 111.95 103.38 8.57 3.00e+00 1.11e-01 8.16e+00 angle pdb=" CA LEU R 51 " pdb=" CB LEU R 51 " pdb=" CG LEU R 51 " ideal model delta sigma weight residual 116.30 126.28 -9.98 3.50e+00 8.16e-02 8.14e+00 ... (remaining 12195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.47: 4972 22.47 - 44.95: 332 44.95 - 67.42: 23 67.42 - 89.90: 4 89.90 - 112.37: 3 Dihedral angle restraints: 5334 sinusoidal: 2046 harmonic: 3288 Sorted by residual: dihedral pdb=" CA LYS R 217 " pdb=" C LYS R 217 " pdb=" N ILE R 218 " pdb=" CA ILE R 218 " ideal model delta harmonic sigma weight residual 180.00 -148.99 -31.01 0 5.00e+00 4.00e-02 3.85e+01 dihedral pdb=" CA ASP B 290 " pdb=" C ASP B 290 " pdb=" N ASP B 291 " pdb=" CA ASP B 291 " ideal model delta harmonic sigma weight residual 180.00 158.38 21.62 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 159.38 20.62 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 5331 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1109 0.055 - 0.109: 240 0.109 - 0.164: 53 0.164 - 0.218: 6 0.218 - 0.273: 2 Chirality restraints: 1410 Sorted by residual: chirality pdb=" CB THR R 224 " pdb=" CA THR R 224 " pdb=" OG1 THR R 224 " pdb=" CG2 THR R 224 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C17 CLR R 502 " pdb=" C13 CLR R 502 " pdb=" C16 CLR R 502 " pdb=" C20 CLR R 502 " both_signs ideal model delta sigma weight residual False 2.55 2.78 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB VAL A 233 " pdb=" CA VAL A 233 " pdb=" CG1 VAL A 233 " pdb=" CG2 VAL A 233 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1407 not shown) Planarity restraints: 1513 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR R 90 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.44e+00 pdb=" C THR R 90 " 0.032 2.00e-02 2.50e+03 pdb=" O THR R 90 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL R 91 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " -0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO B 194 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 240 " 0.020 2.00e-02 2.50e+03 1.29e-02 3.34e+00 pdb=" CG TYR R 240 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR R 240 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR R 240 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR R 240 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR R 240 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR R 240 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR R 240 " 0.006 2.00e-02 2.50e+03 ... (remaining 1510 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 1779 2.78 - 3.31: 7653 3.31 - 3.84: 15003 3.84 - 4.37: 17000 4.37 - 4.90: 30633 Nonbonded interactions: 72068 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.245 3.040 nonbonded pdb=" OD2 ASP B 83 " pdb=" OG1 THR B 86 " model vdw 2.287 3.040 nonbonded pdb=" OE2 GLU A 14 " pdb=" OG1 THR D 57 " model vdw 2.289 3.040 nonbonded pdb=" O LEU R 133 " pdb=" OG1 THR R 137 " model vdw 2.293 3.040 nonbonded pdb=" O ASN R 21 " pdb=" OG SER R 25 " model vdw 2.294 3.040 ... (remaining 72063 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: 2.100 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.810 Find NCS groups from input model: 0.100 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:11.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 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 0.095 8999 Z= 0.357 Angle : 0.708 11.125 12200 Z= 0.357 Chirality : 0.049 0.273 1410 Planarity : 0.004 0.046 1513 Dihedral : 14.098 112.369 3205 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.25 (0.24), residues: 1120 helix: 0.36 (0.22), residues: 414 sheet: 0.59 (0.32), residues: 286 loop : -1.15 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 297 HIS 0.005 0.001 HIS R 94 PHE 0.020 0.002 PHE A 267 TYR 0.030 0.002 TYR R 240 ARG 0.005 0.000 ARG D 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 1.107 Fit side-chains REVERT: A 26 ASP cc_start: 0.7783 (m-30) cc_final: 0.7396 (m-30) REVERT: A 240 MET cc_start: 0.4803 (pmm) cc_final: 0.4514 (pmm) REVERT: B 170 ASP cc_start: 0.7977 (t70) cc_final: 0.7591 (t0) REVERT: B 191 SER cc_start: 0.8600 (t) cc_final: 0.8381 (p) REVERT: D 144 SER cc_start: 0.8624 (m) cc_final: 0.8215 (t) REVERT: R 16 GLU cc_start: 0.7587 (pt0) cc_final: 0.7327 (pt0) REVERT: R 19 ILE cc_start: 0.8249 (mm) cc_final: 0.8025 (tp) REVERT: R 87 ASN cc_start: 0.8530 (m-40) cc_final: 0.8285 (m-40) REVERT: R 95 PHE cc_start: 0.7876 (m-10) cc_final: 0.7537 (m-80) REVERT: R 301 MET cc_start: 0.4282 (tpt) cc_final: 0.3934 (tpt) outliers start: 0 outliers final: 1 residues processed: 230 average time/residue: 0.9511 time to fit residues: 236.1739 Evaluate side-chains 202 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 201 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 261 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.5980 chunk 84 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7895 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8999 Z= 0.246 Angle : 0.564 10.568 12200 Z= 0.294 Chirality : 0.042 0.155 1410 Planarity : 0.004 0.037 1513 Dihedral : 5.230 58.483 1288 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.60 % Allowed : 10.55 % Favored : 87.85 % 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: 0.60 (0.25), residues: 1120 helix: 1.72 (0.24), residues: 416 sheet: 0.60 (0.30), residues: 280 loop : -1.09 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS R 151 PHE 0.024 0.001 PHE R 82 TYR 0.020 0.001 TYR D 178 ARG 0.006 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 204 time to evaluate : 0.993 Fit side-chains REVERT: A 26 ASP cc_start: 0.7788 (m-30) cc_final: 0.7399 (m-30) REVERT: A 240 MET cc_start: 0.4677 (pmm) cc_final: 0.4426 (pmm) REVERT: A 270 LYS cc_start: 0.8761 (mttm) cc_final: 0.8531 (mttp) REVERT: A 312 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8157 (mttm) REVERT: A 345 LYS cc_start: 0.8258 (mmtt) cc_final: 0.8015 (mttp) REVERT: B 52 ARG cc_start: 0.8260 (mtm-85) cc_final: 0.7984 (mtt-85) REVERT: D 67 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8191 (ptm160) REVERT: D 144 SER cc_start: 0.8620 (m) cc_final: 0.8288 (t) REVERT: D 226 THR cc_start: 0.8612 (OUTLIER) cc_final: 0.8392 (p) REVERT: R 19 ILE cc_start: 0.8228 (mm) cc_final: 0.7999 (tp) REVERT: R 24 ASN cc_start: 0.7937 (m-40) cc_final: 0.7658 (m-40) REVERT: R 31 ASN cc_start: 0.7323 (m110) cc_final: 0.7039 (m110) REVERT: R 87 ASN cc_start: 0.8504 (m-40) cc_final: 0.8302 (m-40) REVERT: R 95 PHE cc_start: 0.7884 (m-10) cc_final: 0.7542 (m-80) REVERT: R 116 ASN cc_start: 0.7657 (t0) cc_final: 0.7409 (t0) REVERT: R 144 ASN cc_start: 0.8489 (t0) cc_final: 0.8233 (t0) REVERT: R 212 MET cc_start: 0.8412 (mmm) cc_final: 0.8169 (mmm) REVERT: R 270 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.8108 (ttm) REVERT: R 301 MET cc_start: 0.4350 (tpt) cc_final: 0.4021 (tpt) outliers start: 15 outliers final: 4 residues processed: 205 average time/residue: 0.9752 time to fit residues: 215.5469 Evaluate side-chains 198 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 190 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain R residue 188 PHE Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 270 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 0.4980 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 109 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.7909 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8999 Z= 0.282 Angle : 0.553 9.797 12200 Z= 0.290 Chirality : 0.043 0.204 1410 Planarity : 0.003 0.036 1513 Dihedral : 5.117 55.237 1288 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.67 % Allowed : 14.29 % Favored : 83.05 % 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: 0.87 (0.25), residues: 1120 helix: 2.10 (0.25), residues: 417 sheet: 0.59 (0.30), residues: 281 loop : -1.01 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.006 0.001 HIS R 151 PHE 0.025 0.002 PHE R 26 TYR 0.023 0.002 TYR D 178 ARG 0.006 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 199 time to evaluate : 0.984 Fit side-chains REVERT: A 26 ASP cc_start: 0.7796 (m-30) cc_final: 0.7406 (m-30) REVERT: A 240 MET cc_start: 0.4653 (pmm) cc_final: 0.4407 (pmm) REVERT: A 312 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8161 (mttm) REVERT: B 136 SER cc_start: 0.8432 (m) cc_final: 0.8179 (p) REVERT: B 170 ASP cc_start: 0.7975 (t70) cc_final: 0.7565 (t0) REVERT: B 197 ARG cc_start: 0.7156 (mtt-85) cc_final: 0.6868 (mtt-85) REVERT: B 217 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.8044 (pmm) REVERT: D 144 SER cc_start: 0.8599 (m) cc_final: 0.8288 (t) REVERT: D 226 THR cc_start: 0.8617 (OUTLIER) cc_final: 0.8381 (p) REVERT: R 31 ASN cc_start: 0.7461 (m110) cc_final: 0.7136 (m110) REVERT: R 95 PHE cc_start: 0.7888 (m-10) cc_final: 0.7548 (m-80) REVERT: R 212 MET cc_start: 0.8375 (mmm) cc_final: 0.8121 (mmm) REVERT: R 247 PHE cc_start: 0.6269 (OUTLIER) cc_final: 0.6011 (m-10) REVERT: R 301 MET cc_start: 0.4400 (tpt) cc_final: 0.4083 (tpt) outliers start: 25 outliers final: 9 residues processed: 208 average time/residue: 0.9679 time to fit residues: 217.0608 Evaluate side-chains 200 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 187 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 188 PHE Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 247 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7907 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8999 Z= 0.265 Angle : 0.548 9.170 12200 Z= 0.286 Chirality : 0.042 0.159 1410 Planarity : 0.003 0.035 1513 Dihedral : 5.083 55.199 1286 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.45 % Allowed : 15.46 % Favored : 82.09 % 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: 0.92 (0.25), residues: 1120 helix: 2.19 (0.25), residues: 418 sheet: 0.60 (0.30), residues: 281 loop : -1.03 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS R 151 PHE 0.022 0.002 PHE R 72 TYR 0.024 0.001 TYR D 178 ARG 0.004 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 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: 23 poor density : 193 time to evaluate : 0.961 Fit side-chains REVERT: A 26 ASP cc_start: 0.7797 (m-30) cc_final: 0.7399 (m-30) REVERT: A 240 MET cc_start: 0.4617 (pmm) cc_final: 0.4385 (pmm) REVERT: B 136 SER cc_start: 0.8408 (m) cc_final: 0.8185 (p) REVERT: B 170 ASP cc_start: 0.7985 (t70) cc_final: 0.7568 (t0) REVERT: B 217 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.8079 (pmm) REVERT: D 144 SER cc_start: 0.8591 (m) cc_final: 0.8301 (t) REVERT: R 19 ILE cc_start: 0.8303 (mt) cc_final: 0.8008 (tp) REVERT: R 31 ASN cc_start: 0.7434 (m110) cc_final: 0.7108 (m110) REVERT: R 95 PHE cc_start: 0.7891 (m-10) cc_final: 0.7572 (m-80) REVERT: R 247 PHE cc_start: 0.6392 (OUTLIER) cc_final: 0.6170 (m-10) REVERT: R 301 MET cc_start: 0.4393 (tpt) cc_final: 0.4080 (tpt) outliers start: 23 outliers final: 13 residues processed: 200 average time/residue: 0.9973 time to fit residues: 215.4985 Evaluate side-chains 199 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 184 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 188 PHE Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 247 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.9990 chunk 79 optimal weight: 0.3980 chunk 44 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 96 optimal weight: 0.0010 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- 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: 0.7894 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8999 Z= 0.211 Angle : 0.521 8.357 12200 Z= 0.272 Chirality : 0.041 0.145 1410 Planarity : 0.003 0.033 1513 Dihedral : 4.981 55.330 1286 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.35 % Allowed : 17.06 % Favored : 80.60 % 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: 1.02 (0.25), residues: 1120 helix: 2.32 (0.25), residues: 420 sheet: 0.65 (0.30), residues: 277 loop : -1.03 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS R 94 PHE 0.017 0.001 PHE R 82 TYR 0.022 0.001 TYR D 178 ARG 0.004 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 192 time to evaluate : 0.954 Fit side-chains REVERT: A 8 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7522 (mt-10) REVERT: A 26 ASP cc_start: 0.7793 (m-30) cc_final: 0.7388 (m-30) REVERT: A 240 MET cc_start: 0.4597 (pmm) cc_final: 0.4366 (pmm) REVERT: B 136 SER cc_start: 0.8381 (m) cc_final: 0.8172 (p) REVERT: B 150 ARG cc_start: 0.8905 (mmt-90) cc_final: 0.8682 (mmt-90) REVERT: B 217 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.8094 (pmm) REVERT: D 144 SER cc_start: 0.8574 (m) cc_final: 0.8284 (t) REVERT: D 226 THR cc_start: 0.8578 (m) cc_final: 0.8282 (p) REVERT: R 95 PHE cc_start: 0.7887 (m-10) cc_final: 0.7560 (m-80) REVERT: R 120 LEU cc_start: 0.8623 (mp) cc_final: 0.8336 (mm) REVERT: R 247 PHE cc_start: 0.6419 (OUTLIER) cc_final: 0.6199 (m-10) REVERT: R 301 MET cc_start: 0.4383 (tpt) cc_final: 0.4081 (tpt) outliers start: 22 outliers final: 10 residues processed: 197 average time/residue: 0.9391 time to fit residues: 199.8998 Evaluate side-chains 197 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 184 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 188 PHE Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 247 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 107 optimal weight: 0.0980 chunk 89 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 0.2980 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 0.0770 chunk 103 optimal weight: 0.0980 chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 overall best weight: 0.2738 ------------------------------------------------------------------------------- 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: 0.7861 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8999 Z= 0.144 Angle : 0.497 7.914 12200 Z= 0.259 Chirality : 0.040 0.179 1410 Planarity : 0.003 0.031 1513 Dihedral : 4.864 59.957 1286 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.13 % Allowed : 18.23 % Favored : 79.64 % 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: 1.25 (0.25), residues: 1120 helix: 2.58 (0.25), residues: 420 sheet: 0.75 (0.31), residues: 270 loop : -0.95 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS R 94 PHE 0.015 0.001 PHE R 82 TYR 0.017 0.001 TYR D 178 ARG 0.004 0.000 ARG R 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 186 time to evaluate : 0.996 Fit side-chains REVERT: A 8 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7469 (mt-10) REVERT: A 26 ASP cc_start: 0.7785 (m-30) cc_final: 0.7388 (m-30) REVERT: A 240 MET cc_start: 0.4528 (pmm) cc_final: 0.4314 (pmm) REVERT: A 312 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8087 (mptm) REVERT: A 345 LYS cc_start: 0.8226 (mmtt) cc_final: 0.7984 (mttp) REVERT: B 52 ARG cc_start: 0.8246 (mtm-85) cc_final: 0.7927 (mtt-85) REVERT: B 197 ARG cc_start: 0.7141 (mtt-85) cc_final: 0.6641 (mtt-85) REVERT: B 214 ARG cc_start: 0.8041 (mmt90) cc_final: 0.7537 (mpt-90) REVERT: B 217 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.8066 (pmm) REVERT: B 254 ASP cc_start: 0.7583 (t70) cc_final: 0.7329 (t70) REVERT: D 144 SER cc_start: 0.8558 (m) cc_final: 0.8263 (t) REVERT: D 226 THR cc_start: 0.8587 (m) cc_final: 0.8317 (p) REVERT: R 19 ILE cc_start: 0.8263 (mt) cc_final: 0.7975 (tp) REVERT: R 95 PHE cc_start: 0.7837 (m-10) cc_final: 0.7558 (m-80) REVERT: R 120 LEU cc_start: 0.8623 (mp) cc_final: 0.8347 (mm) REVERT: R 301 MET cc_start: 0.4358 (tpt) cc_final: 0.4078 (tpt) outliers start: 20 outliers final: 7 residues processed: 191 average time/residue: 0.9055 time to fit residues: 187.7817 Evaluate side-chains 192 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 182 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 188 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.0070 chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 66 optimal weight: 0.0010 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 0.1980 chunk 42 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.3604 ------------------------------------------------------------------------------- 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: 0.7864 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8999 Z= 0.164 Angle : 0.517 9.404 12200 Z= 0.265 Chirality : 0.041 0.200 1410 Planarity : 0.003 0.031 1513 Dihedral : 4.823 58.982 1286 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.71 % Allowed : 19.51 % Favored : 78.78 % 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: 1.34 (0.26), residues: 1120 helix: 2.70 (0.25), residues: 420 sheet: 0.81 (0.31), residues: 268 loop : -0.94 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS R 94 PHE 0.023 0.001 PHE R 72 TYR 0.018 0.001 TYR D 178 ARG 0.004 0.000 ARG R 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 184 time to evaluate : 0.926 Fit side-chains REVERT: A 8 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7490 (mt-10) REVERT: A 26 ASP cc_start: 0.7786 (m-30) cc_final: 0.7389 (m-30) REVERT: A 240 MET cc_start: 0.4549 (pmm) cc_final: 0.4316 (pmm) REVERT: A 312 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8093 (mptm) REVERT: A 345 LYS cc_start: 0.8233 (mmtt) cc_final: 0.7983 (mttp) REVERT: B 52 ARG cc_start: 0.8248 (mtm-85) cc_final: 0.7904 (mtt-85) REVERT: B 197 ARG cc_start: 0.7097 (mtt-85) cc_final: 0.6668 (mtt-85) REVERT: B 214 ARG cc_start: 0.8048 (mmt90) cc_final: 0.7567 (mpt-90) REVERT: B 217 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.8118 (pmm) REVERT: B 254 ASP cc_start: 0.7573 (t70) cc_final: 0.7325 (t70) REVERT: D 144 SER cc_start: 0.8539 (m) cc_final: 0.8259 (t) REVERT: D 226 THR cc_start: 0.8591 (m) cc_final: 0.8323 (p) REVERT: R 19 ILE cc_start: 0.8272 (mt) cc_final: 0.7989 (tp) REVERT: R 95 PHE cc_start: 0.7841 (m-10) cc_final: 0.7557 (m-80) REVERT: R 120 LEU cc_start: 0.8600 (mp) cc_final: 0.8335 (mm) REVERT: R 301 MET cc_start: 0.4348 (tpt) cc_final: 0.4076 (tpt) outliers start: 16 outliers final: 8 residues processed: 187 average time/residue: 0.9656 time to fit residues: 195.8210 Evaluate side-chains 194 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 183 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 204 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 9 optimal weight: 0.4980 chunk 84 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 102 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7889 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8999 Z= 0.231 Angle : 0.548 11.526 12200 Z= 0.279 Chirality : 0.042 0.191 1410 Planarity : 0.003 0.031 1513 Dihedral : 4.863 57.145 1286 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.71 % Allowed : 19.40 % Favored : 78.89 % 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: 1.27 (0.25), residues: 1120 helix: 2.62 (0.25), residues: 420 sheet: 0.72 (0.31), residues: 271 loop : -0.93 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS R 94 PHE 0.015 0.001 PHE R 82 TYR 0.023 0.001 TYR D 178 ARG 0.003 0.000 ARG R 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 186 time to evaluate : 0.887 Fit side-chains REVERT: A 8 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7543 (mt-10) REVERT: A 26 ASP cc_start: 0.7792 (m-30) cc_final: 0.7383 (m-30) REVERT: A 240 MET cc_start: 0.4597 (pmm) cc_final: 0.4364 (pmm) REVERT: A 312 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8114 (mptm) REVERT: B 52 ARG cc_start: 0.8281 (mtm-85) cc_final: 0.7948 (mtt-85) REVERT: B 197 ARG cc_start: 0.7157 (mtt-85) cc_final: 0.6954 (mtt-85) REVERT: B 217 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8112 (pmm) REVERT: B 254 ASP cc_start: 0.7621 (t70) cc_final: 0.7336 (t70) REVERT: D 144 SER cc_start: 0.8554 (m) cc_final: 0.8268 (t) REVERT: D 226 THR cc_start: 0.8574 (m) cc_final: 0.8280 (p) REVERT: R 19 ILE cc_start: 0.8273 (mt) cc_final: 0.7997 (tp) REVERT: R 95 PHE cc_start: 0.7859 (m-10) cc_final: 0.7530 (m-80) REVERT: R 120 LEU cc_start: 0.8620 (mp) cc_final: 0.8350 (mm) REVERT: R 301 MET cc_start: 0.4344 (tpt) cc_final: 0.4080 (tpt) outliers start: 16 outliers final: 7 residues processed: 190 average time/residue: 0.8933 time to fit residues: 184.2211 Evaluate side-chains 197 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 187 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 188 PHE Chi-restraints excluded: chain R residue 204 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 43 optimal weight: 0.0970 chunk 78 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 99 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 64 optimal weight: 0.0770 overall best weight: 0.4336 ------------------------------------------------------------------------------- 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: 0.7874 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8999 Z= 0.181 Angle : 0.529 11.008 12200 Z= 0.270 Chirality : 0.041 0.192 1410 Planarity : 0.003 0.030 1513 Dihedral : 4.835 59.776 1286 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.71 % Allowed : 19.62 % Favored : 78.68 % 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: 1.33 (0.25), residues: 1120 helix: 2.69 (0.25), residues: 420 sheet: 0.77 (0.31), residues: 269 loop : -0.93 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS R 94 PHE 0.025 0.001 PHE R 72 TYR 0.019 0.001 TYR D 178 ARG 0.007 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 191 time to evaluate : 0.887 Fit side-chains REVERT: A 8 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7502 (mt-10) REVERT: A 26 ASP cc_start: 0.7787 (m-30) cc_final: 0.7386 (m-30) REVERT: A 240 MET cc_start: 0.4596 (pmm) cc_final: 0.4340 (pmm) REVERT: B 52 ARG cc_start: 0.8260 (mtm-85) cc_final: 0.7939 (mtt-85) REVERT: B 197 ARG cc_start: 0.7181 (mtt-85) cc_final: 0.6871 (mtt-85) REVERT: B 214 ARG cc_start: 0.8052 (mmt90) cc_final: 0.7677 (mpt-90) REVERT: B 217 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.8090 (pmm) REVERT: B 254 ASP cc_start: 0.7621 (t70) cc_final: 0.7354 (t70) REVERT: D 144 SER cc_start: 0.8551 (m) cc_final: 0.8264 (t) REVERT: D 226 THR cc_start: 0.8572 (m) cc_final: 0.8282 (p) REVERT: R 19 ILE cc_start: 0.8273 (mt) cc_final: 0.7996 (tp) REVERT: R 95 PHE cc_start: 0.7852 (m-10) cc_final: 0.7528 (m-80) REVERT: R 120 LEU cc_start: 0.8606 (mp) cc_final: 0.8330 (mm) REVERT: R 212 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8170 (mtm) REVERT: R 301 MET cc_start: 0.4325 (tpt) cc_final: 0.4050 (tpt) outliers start: 16 outliers final: 8 residues processed: 194 average time/residue: 0.9886 time to fit residues: 207.5352 Evaluate side-chains 199 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 188 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 188 PHE Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 212 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 0.0870 chunk 69 optimal weight: 0.8980 chunk 93 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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: 0.7890 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8999 Z= 0.238 Angle : 0.557 10.489 12200 Z= 0.285 Chirality : 0.043 0.286 1410 Planarity : 0.003 0.032 1513 Dihedral : 4.894 58.653 1286 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.71 % Allowed : 20.04 % Favored : 78.25 % 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: 1.24 (0.26), residues: 1120 helix: 2.62 (0.25), residues: 420 sheet: 0.65 (0.31), residues: 276 loop : -0.95 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS R 94 PHE 0.015 0.001 PHE R 82 TYR 0.023 0.001 TYR D 178 ARG 0.006 0.000 ARG B 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 199 time to evaluate : 0.903 Fit side-chains REVERT: A 8 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7534 (mt-10) REVERT: A 26 ASP cc_start: 0.7794 (m-30) cc_final: 0.7382 (m-30) REVERT: A 240 MET cc_start: 0.4667 (pmm) cc_final: 0.4387 (pmm) REVERT: B 52 ARG cc_start: 0.8266 (mtm-85) cc_final: 0.7946 (mtt-85) REVERT: B 197 ARG cc_start: 0.7143 (mtt-85) cc_final: 0.6834 (mtt-85) REVERT: B 214 ARG cc_start: 0.8063 (mmt90) cc_final: 0.7699 (mpt-90) REVERT: B 217 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.8080 (pmm) REVERT: B 254 ASP cc_start: 0.7629 (t70) cc_final: 0.7339 (t70) REVERT: D 144 SER cc_start: 0.8554 (m) cc_final: 0.8270 (t) REVERT: D 226 THR cc_start: 0.8592 (m) cc_final: 0.8294 (p) REVERT: R 19 ILE cc_start: 0.8268 (mt) cc_final: 0.7996 (tp) REVERT: R 95 PHE cc_start: 0.7865 (m-10) cc_final: 0.7537 (m-80) REVERT: R 120 LEU cc_start: 0.8627 (mp) cc_final: 0.8338 (mm) REVERT: R 212 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.8144 (mtm) REVERT: R 301 MET cc_start: 0.4320 (tpt) cc_final: 0.4053 (tpt) outliers start: 16 outliers final: 8 residues processed: 202 average time/residue: 0.9921 time to fit residues: 215.6650 Evaluate side-chains 209 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 198 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain R residue 188 PHE Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 212 MET Chi-restraints excluded: chain R residue 297 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 36 optimal weight: 0.1980 chunk 90 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 77 optimal weight: 0.0970 chunk 5 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 = 0.3744 r_free = 0.3744 target = 0.128330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.112188 restraints weight = 12912.488| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.73 r_work: 0.3414 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8999 Z= 0.215 Angle : 0.560 11.062 12200 Z= 0.285 Chirality : 0.043 0.274 1410 Planarity : 0.003 0.031 1513 Dihedral : 4.896 58.430 1286 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.71 % Allowed : 20.36 % Favored : 77.93 % 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: 1.29 (0.26), residues: 1120 helix: 2.67 (0.25), residues: 420 sheet: 0.73 (0.31), residues: 269 loop : -0.96 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS R 94 PHE 0.025 0.001 PHE R 72 TYR 0.021 0.001 TYR D 178 ARG 0.007 0.000 ARG B 214 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 3912.91 seconds wall clock time: 68 minutes 17.67 seconds (4097.67 seconds total)