Starting phenix.real_space_refine on Sat Apr 6 06:12:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlo_36402/04_2024/8jlo_36402_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlo_36402/04_2024/8jlo_36402.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlo_36402/04_2024/8jlo_36402_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlo_36402/04_2024/8jlo_36402_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlo_36402/04_2024/8jlo_36402_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlo_36402/04_2024/8jlo_36402.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlo_36402/04_2024/8jlo_36402.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlo_36402/04_2024/8jlo_36402_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlo_36402/04_2024/8jlo_36402_updated.pdb" } resolution = 3.52 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= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 59 5.16 5 C 4690 2.51 5 N 1266 2.21 5 O 1328 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 15": "OE1" <-> "OE2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 314": "OE1" <-> "OE2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "R PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 22": "OE1" <-> "OE2" Residue "Y GLU 58": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 7343 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1972 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2593 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 2321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2321 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 11, 'TRANS': 274} Chain breaks: 1 Chain: "Y" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "R" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'UJL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.47, per 1000 atoms: 0.61 Number of scatterers: 7343 At special positions: 0 Unit cell: (74.8, 102.85, 131.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 59 16.00 O 1328 8.00 N 1266 7.00 C 4690 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 182 " 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: 2.97 Conformation dependent library (CDL) restraints added in 1.3 seconds 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1748 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 9 sheets defined 42.2% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 14 through 39 removed outlier: 3.505A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 233 through 236 removed outlier: 3.794A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 233 through 236' Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 316 removed outlier: 3.772A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 332 through 351 removed outlier: 3.796A pdb=" N ARG A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP A 343 " --> pdb=" O TYR A 339 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU A 344 " --> pdb=" O PHE A 340 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 removed outlier: 3.564A pdb=" N GLN A 390 " --> pdb=" O MET A 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.658A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 34 Processing helix chain 'R' and resid 22 through 50 Processing helix chain 'R' and resid 57 through 75 Processing helix chain 'R' and resid 77 through 86 Processing helix chain 'R' and resid 93 through 124 removed outlier: 3.808A pdb=" N SER R 110 " --> pdb=" O LEU R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 160 removed outlier: 3.715A pdb=" N VAL R 150 " --> pdb=" O ILE R 146 " (cutoff:3.500A) Proline residue: R 151 - end of helix Processing helix chain 'R' and resid 170 through 177 Processing helix chain 'R' and resid 188 through 198 removed outlier: 4.024A pdb=" N VAL R 192 " --> pdb=" O LYS R 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 200 through 232 Processing helix chain 'R' and resid 248 through 276 removed outlier: 3.953A pdb=" N ILE R 255 " --> pdb=" O LYS R 251 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL R 256 " --> pdb=" O THR R 252 " (cutoff:3.500A) Proline residue: R 266 - end of helix Proline residue: R 275 - end of helix Processing helix chain 'R' and resid 283 through 298 removed outlier: 4.112A pdb=" N VAL R 288 " --> pdb=" O THR R 284 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY R 293 " --> pdb=" O LEU R 289 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR R 294 " --> pdb=" O ILE R 290 " (cutoff:3.500A) Processing helix chain 'R' and resid 309 through 318 Processing helix chain 'Y' and resid 7 through 23 Processing helix chain 'Y' and resid 30 through 43 Processing sheet with id= A, first strand: chain 'A' and resid 40 through 44 removed outlier: 7.254A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 243 through 246 removed outlier: 7.347A pdb=" N SER A 286 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N PHE A 246 " --> pdb=" O SER A 286 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE A 288 " --> pdb=" O PHE A 246 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.764A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA B 328 " --> pdb=" O GLY B 319 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 60 through 63 removed outlier: 3.988A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ILE B 93 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 111 through 114 removed outlier: 3.647A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 178 through 180 removed outlier: 3.653A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 190 through 192 removed outlier: 3.528A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 250 through 254 removed outlier: 3.644A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 276 through 278 322 hydrogen bonds defined for protein. 948 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: 1.98 Time building geometry restraints manager: 3.22 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: 2362 1.34 - 1.46: 1549 1.46 - 1.58: 3505 1.58 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 7504 Sorted by residual: bond pdb=" C6 UJL R 401 " pdb=" C7 UJL R 401 " ideal model delta sigma weight residual 1.607 1.425 0.182 2.00e-02 2.50e+03 8.30e+01 bond pdb=" C8 UJL R 401 " pdb=" S1 UJL R 401 " ideal model delta sigma weight residual 1.546 1.715 -0.169 2.00e-02 2.50e+03 7.13e+01 bond pdb=" C9 UJL R 401 " pdb=" S1 UJL R 401 " ideal model delta sigma weight residual 1.566 1.727 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" C7 UJL R 401 " pdb=" C8 UJL R 401 " ideal model delta sigma weight residual 1.443 1.356 0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" C THR B 29 " pdb=" O THR B 29 " ideal model delta sigma weight residual 1.234 1.285 -0.051 1.26e-02 6.30e+03 1.62e+01 ... (remaining 7499 not shown) Histogram of bond angle deviations from ideal: 90.94 - 99.57: 1 99.57 - 108.20: 273 108.20 - 116.83: 4910 116.83 - 125.45: 4844 125.45 - 134.08: 126 Bond angle restraints: 10154 Sorted by residual: angle pdb=" C8 UJL R 401 " pdb=" S1 UJL R 401 " pdb=" C9 UJL R 401 " ideal model delta sigma weight residual 107.54 90.94 16.60 3.00e+00 1.11e-01 3.06e+01 angle pdb=" N GLU B 172 " pdb=" CA GLU B 172 " pdb=" C GLU B 172 " ideal model delta sigma weight residual 114.75 108.11 6.64 1.26e+00 6.30e-01 2.77e+01 angle pdb=" CB ARG B 19 " pdb=" CG ARG B 19 " pdb=" CD ARG B 19 " ideal model delta sigma weight residual 111.30 121.53 -10.23 2.30e+00 1.89e-01 1.98e+01 angle pdb=" N ILE B 171 " pdb=" CA ILE B 171 " pdb=" C ILE B 171 " ideal model delta sigma weight residual 106.21 110.52 -4.31 1.07e+00 8.73e-01 1.62e+01 angle pdb=" N TYR R 294 " pdb=" CA TYR R 294 " pdb=" C TYR R 294 " ideal model delta sigma weight residual 111.07 106.90 4.17 1.07e+00 8.73e-01 1.52e+01 ... (remaining 10149 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 4023 17.73 - 35.46: 351 35.46 - 53.19: 70 53.19 - 70.93: 19 70.93 - 88.66: 6 Dihedral angle restraints: 4469 sinusoidal: 1772 harmonic: 2697 Sorted by residual: dihedral pdb=" CA LEU R 75 " pdb=" C LEU R 75 " pdb=" N VAL R 76 " pdb=" CA VAL R 76 " ideal model delta harmonic sigma weight residual 180.00 -160.99 -19.01 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA ARG A 231 " pdb=" C ARG A 231 " pdb=" N ARG A 232 " pdb=" CA ARG A 232 " ideal model delta harmonic sigma weight residual 180.00 161.37 18.63 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA ILE B 171 " pdb=" C ILE B 171 " pdb=" N GLU B 172 " pdb=" CA GLU B 172 " ideal model delta harmonic sigma weight residual 180.00 161.62 18.38 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 4466 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 848 0.045 - 0.091: 246 0.091 - 0.136: 43 0.136 - 0.182: 1 0.182 - 0.227: 1 Chirality restraints: 1139 Sorted by residual: chirality pdb=" CA MET R 77 " pdb=" N MET R 77 " pdb=" C MET R 77 " pdb=" CB MET R 77 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB ILE B 338 " pdb=" CA ILE B 338 " pdb=" CG1 ILE B 338 " pdb=" CG2 ILE B 338 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 ... (remaining 1136 not shown) Planarity restraints: 1282 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 28 " -0.018 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C ALA B 28 " 0.063 2.00e-02 2.50e+03 pdb=" O ALA B 28 " -0.024 2.00e-02 2.50e+03 pdb=" N THR B 29 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 220 " 0.011 2.00e-02 2.50e+03 1.63e-02 3.97e+00 pdb=" CG HIS A 220 " -0.034 2.00e-02 2.50e+03 pdb=" ND1 HIS A 220 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 HIS A 220 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 HIS A 220 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS A 220 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 99 " 0.018 2.00e-02 2.50e+03 1.25e-02 3.92e+00 pdb=" CG TRP B 99 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP B 99 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP B 99 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 99 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 99 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 99 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 99 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 99 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 99 " 0.006 2.00e-02 2.50e+03 ... (remaining 1279 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1631 2.79 - 3.31: 7046 3.31 - 3.84: 11197 3.84 - 4.37: 12746 4.37 - 4.90: 22588 Nonbonded interactions: 55208 Sorted by model distance: nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASN B 110 " model vdw 2.257 2.440 nonbonded pdb=" OD1 ASP A 274 " pdb=" ND2 ASN A 278 " model vdw 2.336 2.520 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.348 2.440 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.356 2.440 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.365 2.440 ... (remaining 55203 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.340 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: 3.880 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 23.870 Find NCS groups from input model: 0.170 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: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 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 0.182 7504 Z= 0.348 Angle : 0.735 16.597 10154 Z= 0.431 Chirality : 0.042 0.227 1139 Planarity : 0.004 0.037 1282 Dihedral : 14.262 88.658 2718 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.25 % Allowed : 0.75 % Favored : 98.99 % 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: -0.64 (0.28), residues: 910 helix: 1.96 (0.26), residues: 394 sheet: -2.04 (0.42), residues: 162 loop : -2.47 (0.28), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 99 HIS 0.021 0.001 HIS A 220 PHE 0.020 0.001 PHE A 315 TYR 0.016 0.001 TYR A 253 ARG 0.018 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 132 time to evaluate : 0.821 Fit side-chains REVERT: A 215 ASP cc_start: 0.7936 (t70) cc_final: 0.7588 (t0) REVERT: B 29 THR cc_start: 0.8233 (OUTLIER) cc_final: 0.7911 (p) REVERT: B 325 MET cc_start: 0.8455 (mtt) cc_final: 0.8169 (mtm) REVERT: R 162 GLU cc_start: 0.8875 (pt0) cc_final: 0.8674 (pm20) REVERT: R 302 MET cc_start: 0.8018 (mtm) cc_final: 0.7401 (tmm) outliers start: 2 outliers final: 0 residues processed: 134 average time/residue: 0.1791 time to fit residues: 32.7546 Evaluate side-chains 114 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 0.9990 chunk 68 optimal weight: 0.0870 chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 46 optimal weight: 9.9990 chunk 36 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.0922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7504 Z= 0.174 Angle : 0.554 8.477 10154 Z= 0.291 Chirality : 0.041 0.168 1139 Planarity : 0.004 0.047 1282 Dihedral : 4.206 42.861 1012 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.01 % Allowed : 10.55 % Favored : 88.44 % 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: -0.28 (0.29), residues: 910 helix: 2.22 (0.26), residues: 394 sheet: -1.79 (0.42), residues: 161 loop : -2.27 (0.29), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.014 0.001 HIS A 220 PHE 0.026 0.001 PHE R 154 TYR 0.011 0.001 TYR B 264 ARG 0.002 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 118 time to evaluate : 0.822 Fit side-chains REVERT: B 118 ASP cc_start: 0.7184 (t0) cc_final: 0.6981 (t0) REVERT: B 325 MET cc_start: 0.8468 (mtt) cc_final: 0.8178 (mtm) REVERT: R 27 TYR cc_start: 0.8650 (m-80) cc_final: 0.8301 (m-80) REVERT: R 302 MET cc_start: 0.8073 (mtm) cc_final: 0.7446 (tmm) outliers start: 8 outliers final: 5 residues processed: 122 average time/residue: 0.1754 time to fit residues: 30.0189 Evaluate side-chains 106 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 101 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain R residue 295 LEU Chi-restraints excluded: chain R residue 303 VAL Chi-restraints excluded: chain Y residue 42 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 27 optimal weight: 0.4980 chunk 65 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7504 Z= 0.179 Angle : 0.527 8.374 10154 Z= 0.277 Chirality : 0.041 0.157 1139 Planarity : 0.003 0.036 1282 Dihedral : 3.856 21.255 1011 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.88 % Allowed : 12.81 % Favored : 85.30 % 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: -0.16 (0.29), residues: 910 helix: 2.28 (0.26), residues: 392 sheet: -1.84 (0.40), residues: 163 loop : -2.08 (0.29), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.013 0.001 HIS A 220 PHE 0.026 0.001 PHE R 165 TYR 0.010 0.001 TYR A 311 ARG 0.006 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 114 time to evaluate : 0.740 Fit side-chains REVERT: B 118 ASP cc_start: 0.7263 (t0) cc_final: 0.6936 (t0) REVERT: B 325 MET cc_start: 0.8474 (mtt) cc_final: 0.8178 (mtm) REVERT: R 27 TYR cc_start: 0.8730 (m-80) cc_final: 0.8397 (m-80) REVERT: R 302 MET cc_start: 0.8062 (mtm) cc_final: 0.7455 (tmm) outliers start: 15 outliers final: 12 residues processed: 122 average time/residue: 0.1898 time to fit residues: 31.3969 Evaluate side-chains 115 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain R residue 158 MET Chi-restraints excluded: chain R residue 274 ASP Chi-restraints excluded: chain R residue 295 LEU Chi-restraints excluded: chain R residue 303 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 7504 Z= 0.154 Angle : 0.516 12.008 10154 Z= 0.265 Chirality : 0.041 0.151 1139 Planarity : 0.003 0.035 1282 Dihedral : 3.769 21.463 1011 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.76 % Allowed : 14.57 % Favored : 83.67 % 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: -0.00 (0.29), residues: 910 helix: 2.41 (0.26), residues: 392 sheet: -1.74 (0.40), residues: 167 loop : -1.98 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.008 0.001 HIS A 220 PHE 0.029 0.001 PHE R 154 TYR 0.008 0.001 TYR R 90 ARG 0.008 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 108 time to evaluate : 0.823 Fit side-chains REVERT: B 118 ASP cc_start: 0.7224 (t0) cc_final: 0.6848 (t0) REVERT: B 234 PHE cc_start: 0.8152 (OUTLIER) cc_final: 0.7656 (m-80) REVERT: B 325 MET cc_start: 0.8449 (mtt) cc_final: 0.8188 (mtm) REVERT: R 27 TYR cc_start: 0.8871 (m-80) cc_final: 0.8354 (m-80) REVERT: R 302 MET cc_start: 0.8095 (mtm) cc_final: 0.7494 (tmm) outliers start: 14 outliers final: 10 residues processed: 115 average time/residue: 0.1940 time to fit residues: 30.4065 Evaluate side-chains 115 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 149 SER Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 295 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 44 optimal weight: 4.9990 chunk 78 optimal weight: 0.5980 chunk 21 optimal weight: 0.1980 chunk 29 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 7504 Z= 0.214 Angle : 0.530 10.244 10154 Z= 0.276 Chirality : 0.041 0.156 1139 Planarity : 0.003 0.035 1282 Dihedral : 3.785 20.886 1011 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.39 % Allowed : 15.70 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.29), residues: 910 helix: 2.35 (0.26), residues: 393 sheet: -1.82 (0.39), residues: 167 loop : -1.96 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.007 0.001 HIS A 220 PHE 0.031 0.002 PHE R 165 TYR 0.010 0.001 TYR A 311 ARG 0.003 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 108 time to evaluate : 0.855 Fit side-chains REVERT: A 221 MET cc_start: 0.8208 (ttp) cc_final: 0.7925 (ttp) REVERT: B 118 ASP cc_start: 0.7245 (t0) cc_final: 0.6855 (t0) REVERT: B 234 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.7846 (m-80) REVERT: B 339 TRP cc_start: 0.8252 (m100) cc_final: 0.7978 (m-10) REVERT: R 27 TYR cc_start: 0.8823 (m-80) cc_final: 0.8329 (m-80) REVERT: R 302 MET cc_start: 0.8097 (mtm) cc_final: 0.7485 (tmm) outliers start: 19 outliers final: 11 residues processed: 120 average time/residue: 0.1791 time to fit residues: 29.9975 Evaluate side-chains 119 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 107 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain R residue 149 SER Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 295 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 83 optimal weight: 0.0980 chunk 9 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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: 0.7671 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7504 Z= 0.187 Angle : 0.522 11.526 10154 Z= 0.269 Chirality : 0.041 0.159 1139 Planarity : 0.003 0.035 1282 Dihedral : 3.778 21.043 1011 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.01 % Allowed : 17.46 % Favored : 80.53 % 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: -0.01 (0.28), residues: 910 helix: 2.38 (0.26), residues: 393 sheet: -1.77 (0.39), residues: 167 loop : -1.95 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.007 0.001 HIS A 220 PHE 0.035 0.001 PHE R 154 TYR 0.009 0.001 TYR A 311 ARG 0.005 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 116 time to evaluate : 0.857 Fit side-chains REVERT: A 221 MET cc_start: 0.8257 (ttp) cc_final: 0.7975 (ttp) REVERT: B 118 ASP cc_start: 0.7176 (t0) cc_final: 0.6778 (t0) REVERT: R 27 TYR cc_start: 0.8993 (m-80) cc_final: 0.8378 (m-80) REVERT: R 302 MET cc_start: 0.8087 (mtm) cc_final: 0.7477 (tmm) outliers start: 16 outliers final: 10 residues processed: 125 average time/residue: 0.1843 time to fit residues: 32.1160 Evaluate side-chains 119 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 149 SER Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 295 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 6.9990 chunk 49 optimal weight: 0.0370 chunk 73 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 overall best weight: 1.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 286 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 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 : 0.004 0.045 7504 Z= 0.283 Angle : 0.563 10.475 10154 Z= 0.294 Chirality : 0.043 0.179 1139 Planarity : 0.004 0.035 1282 Dihedral : 3.908 20.830 1011 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.39 % Allowed : 17.96 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.28), residues: 910 helix: 2.27 (0.26), residues: 393 sheet: -1.77 (0.40), residues: 167 loop : -1.93 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 339 HIS 0.006 0.001 HIS A 220 PHE 0.032 0.002 PHE R 165 TYR 0.016 0.001 TYR A 253 ARG 0.004 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 112 time to evaluate : 0.858 Fit side-chains REVERT: A 35 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7306 (tp40) REVERT: A 221 MET cc_start: 0.8237 (ttp) cc_final: 0.8003 (ttp) REVERT: B 118 ASP cc_start: 0.7303 (t0) cc_final: 0.6947 (t0) REVERT: R 27 TYR cc_start: 0.8981 (m-80) cc_final: 0.8388 (m-80) REVERT: R 302 MET cc_start: 0.8079 (mtm) cc_final: 0.7439 (tmm) outliers start: 19 outliers final: 14 residues processed: 122 average time/residue: 0.1785 time to fit residues: 30.5337 Evaluate side-chains 119 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 104 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 149 SER Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 274 ASP Chi-restraints excluded: chain R residue 295 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 16 optimal weight: 0.3980 chunk 55 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 68 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 7504 Z= 0.152 Angle : 0.523 11.326 10154 Z= 0.268 Chirality : 0.041 0.186 1139 Planarity : 0.003 0.036 1282 Dihedral : 3.803 21.229 1011 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.76 % Allowed : 18.84 % Favored : 79.40 % 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: 0.23 (0.29), residues: 910 helix: 2.48 (0.26), residues: 393 sheet: -1.51 (0.41), residues: 165 loop : -1.78 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.006 0.001 HIS A 220 PHE 0.036 0.001 PHE R 154 TYR 0.017 0.001 TYR A 253 ARG 0.005 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 0.807 Fit side-chains REVERT: A 221 MET cc_start: 0.8194 (ttp) cc_final: 0.7983 (ttp) REVERT: B 118 ASP cc_start: 0.7194 (t0) cc_final: 0.6904 (t0) REVERT: R 27 TYR cc_start: 0.8962 (m-80) cc_final: 0.8355 (m-80) REVERT: R 302 MET cc_start: 0.8072 (mtm) cc_final: 0.7461 (tmm) outliers start: 14 outliers final: 12 residues processed: 120 average time/residue: 0.1775 time to fit residues: 29.5821 Evaluate side-chains 121 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 109 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 149 SER Chi-restraints excluded: chain R residue 295 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 85 optimal weight: 0.0170 chunk 52 optimal weight: 0.9980 overall best weight: 0.9020 ------------------------------------------------------------------------------- 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: 0.7665 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7504 Z= 0.167 Angle : 0.530 11.453 10154 Z= 0.272 Chirality : 0.041 0.191 1139 Planarity : 0.003 0.036 1282 Dihedral : 3.741 20.700 1011 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.51 % Allowed : 19.60 % Favored : 78.89 % 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: 0.29 (0.29), residues: 910 helix: 2.51 (0.26), residues: 393 sheet: -1.43 (0.41), residues: 165 loop : -1.75 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 339 HIS 0.006 0.001 HIS A 220 PHE 0.033 0.001 PHE R 165 TYR 0.016 0.001 TYR A 253 ARG 0.005 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 108 time to evaluate : 0.630 Fit side-chains REVERT: A 221 MET cc_start: 0.8180 (ttp) cc_final: 0.7970 (ttp) REVERT: B 118 ASP cc_start: 0.7161 (t0) cc_final: 0.6891 (t0) REVERT: R 27 TYR cc_start: 0.8955 (m-80) cc_final: 0.8301 (m-80) REVERT: R 302 MET cc_start: 0.8063 (mtm) cc_final: 0.7447 (tmm) outliers start: 12 outliers final: 11 residues processed: 115 average time/residue: 0.1734 time to fit residues: 27.4555 Evaluate side-chains 117 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 106 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 149 SER Chi-restraints excluded: chain R residue 295 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 89 optimal weight: 0.1980 chunk 82 optimal weight: 0.4980 chunk 71 optimal weight: 0.0370 chunk 7 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- 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: 0.7645 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7504 Z= 0.148 Angle : 0.527 12.015 10154 Z= 0.270 Chirality : 0.041 0.201 1139 Planarity : 0.003 0.036 1282 Dihedral : 3.711 20.772 1011 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.38 % Allowed : 19.47 % Favored : 79.15 % 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: 0.37 (0.29), residues: 910 helix: 2.56 (0.26), residues: 393 sheet: -1.34 (0.42), residues: 165 loop : -1.72 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.006 0.001 HIS A 220 PHE 0.035 0.001 PHE R 154 TYR 0.017 0.001 TYR A 253 ARG 0.006 0.000 ARG B 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 116 time to evaluate : 0.840 Fit side-chains REVERT: A 221 MET cc_start: 0.8141 (ttp) cc_final: 0.7934 (ttp) REVERT: B 118 ASP cc_start: 0.7135 (t0) cc_final: 0.6879 (t0) REVERT: B 175 GLN cc_start: 0.8463 (mt0) cc_final: 0.7864 (mm-40) REVERT: B 259 GLN cc_start: 0.8589 (tt0) cc_final: 0.8388 (tt0) REVERT: R 27 TYR cc_start: 0.8953 (m-80) cc_final: 0.8328 (m-80) REVERT: R 302 MET cc_start: 0.8056 (mtm) cc_final: 0.7450 (tmm) outliers start: 11 outliers final: 11 residues processed: 123 average time/residue: 0.1902 time to fit residues: 32.1034 Evaluate side-chains 119 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 108 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 149 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 73 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.4050 r_free = 0.4050 target = 0.184638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.141946 restraints weight = 8923.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.140089 restraints weight = 6841.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.141592 restraints weight = 8603.040| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7504 Z= 0.167 Angle : 0.537 12.039 10154 Z= 0.273 Chirality : 0.041 0.207 1139 Planarity : 0.003 0.036 1282 Dihedral : 3.717 20.559 1011 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.63 % Allowed : 19.60 % Favored : 78.77 % 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: 0.36 (0.29), residues: 910 helix: 2.54 (0.26), residues: 393 sheet: -1.28 (0.42), residues: 164 loop : -1.74 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 339 HIS 0.006 0.001 HIS A 220 PHE 0.033 0.001 PHE R 165 TYR 0.016 0.001 TYR A 253 ARG 0.006 0.000 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1640.02 seconds wall clock time: 31 minutes 5.33 seconds (1865.33 seconds total)