Starting phenix.real_space_refine on Wed Sep 17 10:12:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o4k_70104/09_2025/9o4k_70104.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o4k_70104/09_2025/9o4k_70104.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9o4k_70104/09_2025/9o4k_70104.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o4k_70104/09_2025/9o4k_70104.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o4k_70104/09_2025/9o4k_70104.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o4k_70104/09_2025/9o4k_70104.map" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.072 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 35 5.16 5 C 4942 2.51 5 N 1352 2.21 5 O 1409 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7738 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3270 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 17, 'TRANS': 416} Chain breaks: 2 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 72 Chain: "B" Number of atoms: 2560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2560 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 315} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 2, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "C" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 877 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 105} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 1006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1006 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain breaks: 1 Unresolved non-hydrogen bonds: 156 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 9, 'HIS:plan': 1, 'ASP:plan': 7, 'ASN:plan1': 3, 'ARG:plan': 2, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 91 Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'GA3': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.73, per 1000 atoms: 0.22 Number of scatterers: 7738 At special positions: 0 Unit cell: (77.0679, 98.2404, 123.647, 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 35 16.00 O 1409 8.00 N 1352 7.00 C 4942 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 410.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1926 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 4 sheets defined 56.8% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 44 through 51 Processing helix chain 'A' and resid 55 through 57 No H-bonds generated for 'chain 'A' and resid 55 through 57' Processing helix chain 'A' and resid 58 through 76 Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.858A pdb=" N LEU A 81 " --> pdb=" O GLN A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 108 Processing helix chain 'A' and resid 217 through 234 removed outlier: 3.708A pdb=" N LEU A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 253 removed outlier: 4.144A pdb=" N SER A 253 " --> pdb=" O CYS A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 275 removed outlier: 3.538A pdb=" N LYS A 260 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 299 Processing helix chain 'A' and resid 300 through 317 Processing helix chain 'A' and resid 335 through 345 removed outlier: 3.575A pdb=" N LEU A 339 " --> pdb=" O GLN A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 384 Processing helix chain 'A' and resid 396 through 400 removed outlier: 3.966A pdb=" N ASP A 399 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 400 " --> pdb=" O LEU A 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 396 through 400' Processing helix chain 'A' and resid 431 through 444 Processing helix chain 'A' and resid 461 through 479 Processing helix chain 'A' and resid 486 through 505 Processing helix chain 'A' and resid 507 through 511 removed outlier: 3.859A pdb=" N ASP A 510 " --> pdb=" O GLU A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 527 removed outlier: 3.590A pdb=" N TRP A 521 " --> pdb=" O THR A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 550 removed outlier: 3.821A pdb=" N PHE A 540 " --> pdb=" O GLY A 536 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE A 550 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 554 Processing helix chain 'B' and resid 11 through 15 removed outlier: 3.589A pdb=" N THR B 14 " --> pdb=" O GLU B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 33 Processing helix chain 'B' and resid 42 through 50 removed outlier: 3.624A pdb=" N ALA B 46 " --> pdb=" O ASN B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 139 Processing helix chain 'B' and resid 156 through 171 Processing helix chain 'B' and resid 191 through 206 removed outlier: 3.814A pdb=" N ASN B 195 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU B 206 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 233 removed outlier: 4.332A pdb=" N LYS B 231 " --> pdb=" O THR B 227 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N SER B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 252 Processing helix chain 'B' and resid 291 through 306 removed outlier: 3.658A pdb=" N GLY B 306 " --> pdb=" O LEU B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 342 removed outlier: 3.771A pdb=" N ASN B 332 " --> pdb=" O ASN B 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 46 removed outlier: 4.260A pdb=" N HIS C 46 " --> pdb=" O GLU C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 56 Processing helix chain 'C' and resid 59 through 67 removed outlier: 3.749A pdb=" N GLN C 67 " --> pdb=" O HIS C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 77 removed outlier: 3.899A pdb=" N TRP C 72 " --> pdb=" O ASP C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 98 Processing helix chain 'C' and resid 99 through 107 removed outlier: 3.665A pdb=" N LEU C 103 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR C 107 " --> pdb=" O LEU C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 113 Processing helix chain 'C' and resid 121 through 140 removed outlier: 3.586A pdb=" N LEU C 125 " --> pdb=" O GLY C 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 25 Processing helix chain 'D' and resid 26 through 35 Processing helix chain 'D' and resid 48 through 67 Processing helix chain 'D' and resid 80 through 91 removed outlier: 3.724A pdb=" N MET D 91 " --> pdb=" O ASP D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 109 removed outlier: 3.517A pdb=" N LEU D 98 " --> pdb=" O ASP D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 126 Processing helix chain 'D' and resid 131 through 138 removed outlier: 3.511A pdb=" N THR D 135 " --> pdb=" O GLU D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 155 Processing helix chain 'D' and resid 156 through 160 removed outlier: 3.684A pdb=" N GLU D 160 " --> pdb=" O TRP D 157 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 212 removed outlier: 3.571A pdb=" N PHE B 64 " --> pdb=" O ARG B 82 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG B 82 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU B 76 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU B 77 " --> pdb=" O ASN B 146 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N VAL B 143 " --> pdb=" O PRO B 107 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE B 109 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N VAL B 145 " --> pdb=" O ILE B 109 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N PHE B 111 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL B 108 " --> pdb=" O PHE B 186 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ALA B 188 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LEU B 110 " --> pdb=" O ALA B 188 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ASP B 190 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE B 112 " --> pdb=" O ASP B 190 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLY B 213 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASN B 214 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N VAL B 284 " --> pdb=" O ASN B 214 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU B 216 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ALA B 286 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N SER B 281 " --> pdb=" O LYS B 310 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N MET B 312 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL B 283 " --> pdb=" O MET B 312 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N LEU B 314 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL B 285 " --> pdb=" O LEU B 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 388 through 393 removed outlier: 6.839A pdb=" N VAL A 323 " --> pdb=" O ARG A 354 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N THR A 356 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL A 325 " --> pdb=" O THR A 356 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ILE A 358 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ASP A 327 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE A 447 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 451 " --> pdb=" O SER A 419 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 388 through 393 removed outlier: 6.839A pdb=" N VAL A 323 " --> pdb=" O ARG A 354 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N THR A 356 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL A 325 " --> pdb=" O THR A 356 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ILE A 358 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ASP A 327 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE A 447 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 451 " --> pdb=" O SER A 419 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N TRP A 569 " --> pdb=" O PRO A 573 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 15 through 18 removed outlier: 3.681A pdb=" N VAL D 42 " --> pdb=" O VAL D 7 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS D 9 " --> pdb=" O VAL D 42 " (cutoff:3.500A) 443 hydrogen bonds defined for protein. 1293 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: 1.23 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1359 1.32 - 1.44: 2042 1.44 - 1.57: 4459 1.57 - 1.69: 0 1.69 - 1.81: 53 Bond restraints: 7913 Sorted by residual: bond pdb=" CG ARG A 220 " pdb=" CD ARG A 220 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.76e+00 bond pdb=" CA LYS A 444 " pdb=" CB LYS A 444 " ideal model delta sigma weight residual 1.522 1.531 -0.008 7.00e-03 2.04e+04 1.42e+00 bond pdb=" C ILE B 105 " pdb=" N VAL B 106 " ideal model delta sigma weight residual 1.329 1.320 0.008 7.30e-03 1.88e+04 1.30e+00 bond pdb=" CB GLU A 61 " pdb=" CG GLU A 61 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.14e+00 bond pdb=" CB GLU A 560 " pdb=" CG GLU A 560 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.06e+00 ... (remaining 7908 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 10648 2.29 - 4.58: 121 4.58 - 6.87: 18 6.87 - 9.16: 2 9.16 - 11.45: 2 Bond angle restraints: 10791 Sorted by residual: angle pdb=" N SER B 191 " pdb=" CA SER B 191 " pdb=" CB SER B 191 " ideal model delta sigma weight residual 110.49 116.24 -5.75 1.69e+00 3.50e-01 1.16e+01 angle pdb=" CG ARG A 220 " pdb=" CD ARG A 220 " pdb=" NE ARG A 220 " ideal model delta sigma weight residual 112.00 119.45 -7.45 2.20e+00 2.07e-01 1.15e+01 angle pdb=" CA LEU B 34 " pdb=" CB LEU B 34 " pdb=" CG LEU B 34 " ideal model delta sigma weight residual 116.30 127.75 -11.45 3.50e+00 8.16e-02 1.07e+01 angle pdb=" CB ARG A 220 " pdb=" CG ARG A 220 " pdb=" CD ARG A 220 " ideal model delta sigma weight residual 111.30 117.88 -6.58 2.30e+00 1.89e-01 8.19e+00 angle pdb=" CB GLU A 61 " pdb=" CG GLU A 61 " pdb=" CD GLU A 61 " ideal model delta sigma weight residual 112.60 117.26 -4.66 1.70e+00 3.46e-01 7.52e+00 ... (remaining 10786 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4187 17.96 - 35.92: 420 35.92 - 53.88: 119 53.88 - 71.84: 16 71.84 - 89.80: 6 Dihedral angle restraints: 4748 sinusoidal: 1776 harmonic: 2972 Sorted by residual: dihedral pdb=" CA ASP B 128 " pdb=" CB ASP B 128 " pdb=" CG ASP B 128 " pdb=" OD1 ASP B 128 " ideal model delta sinusoidal sigma weight residual -30.00 -89.07 59.07 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASP B 190 " pdb=" CB ASP B 190 " pdb=" CG ASP B 190 " pdb=" OD1 ASP B 190 " ideal model delta sinusoidal sigma weight residual -30.00 -88.32 58.32 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CG ARG B 72 " pdb=" CD ARG B 72 " pdb=" NE ARG B 72 " pdb=" CZ ARG B 72 " ideal model delta sinusoidal sigma weight residual 90.00 133.88 -43.88 2 1.50e+01 4.44e-03 1.02e+01 ... (remaining 4745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 866 0.037 - 0.074: 265 0.074 - 0.110: 89 0.110 - 0.147: 16 0.147 - 0.184: 3 Chirality restraints: 1239 Sorted by residual: chirality pdb=" CG LEU A 470 " pdb=" CB LEU A 470 " pdb=" CD1 LEU A 470 " pdb=" CD2 LEU A 470 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.44e-01 chirality pdb=" CB ILE B 291 " pdb=" CA ILE B 291 " pdb=" CG1 ILE B 291 " pdb=" CG2 ILE B 291 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.35e-01 chirality pdb=" CA PHE B 117 " pdb=" N PHE B 117 " pdb=" C PHE B 117 " pdb=" CB PHE B 117 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.64e-01 ... (remaining 1236 not shown) Planarity restraints: 1389 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 106 " 0.043 5.00e-02 4.00e+02 6.58e-02 6.93e+00 pdb=" N PRO B 107 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 107 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 107 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 157 " -0.013 2.00e-02 2.50e+03 1.37e-02 4.70e+00 pdb=" CG TRP D 157 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP D 157 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP D 157 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 157 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 157 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 157 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 157 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 157 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 157 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 220 " -0.166 9.50e-02 1.11e+02 7.50e-02 4.63e+00 pdb=" NE ARG A 220 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 220 " -0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG A 220 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 220 " 0.000 2.00e-02 2.50e+03 ... (remaining 1386 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 2788 2.88 - 3.38: 7316 3.38 - 3.89: 12428 3.89 - 4.39: 13287 4.39 - 4.90: 23376 Nonbonded interactions: 59195 Sorted by model distance: nonbonded pdb=" O GLN A 233 " pdb=" NE2 GLN A 233 " model vdw 2.370 3.120 nonbonded pdb=" NE2 GLN A 499 " pdb=" OE2 GLU A 513 " model vdw 2.388 3.120 nonbonded pdb=" O SER A 519 " pdb=" OD1 ASN A 523 " model vdw 2.414 3.040 nonbonded pdb=" O LEU D 83 " pdb=" OD1 ASP D 87 " model vdw 2.533 3.040 nonbonded pdb=" O VAL B 241 " pdb=" OD1 ASP B 245 " model vdw 2.545 3.040 ... (remaining 59190 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: 2.140 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.350 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:9.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 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 : 0.002 0.040 7913 Z= 0.118 Angle : 0.600 11.446 10791 Z= 0.304 Chirality : 0.041 0.184 1239 Planarity : 0.005 0.075 1389 Dihedral : 15.818 89.799 2822 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.56 % Allowed : 28.91 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.26), residues: 1009 helix: 1.47 (0.23), residues: 536 sheet: 0.69 (0.52), residues: 116 loop : -1.09 (0.29), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 220 TYR 0.009 0.001 TYR B 81 PHE 0.024 0.001 PHE B 251 TRP 0.037 0.001 TRP D 157 HIS 0.007 0.001 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 7913) covalent geometry : angle 0.59958 (10791) hydrogen bonds : bond 0.12165 ( 423) hydrogen bonds : angle 5.09087 ( 1293) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 171 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 LEU cc_start: 0.8458 (mp) cc_final: 0.8169 (tt) REVERT: A 219 VAL cc_start: 0.8826 (t) cc_final: 0.8434 (m) REVERT: A 383 ILE cc_start: 0.7617 (OUTLIER) cc_final: 0.7235 (mp) REVERT: A 488 ASP cc_start: 0.8191 (m-30) cc_final: 0.7696 (t0) REVERT: B 98 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7756 (tm-30) REVERT: C 102 ARG cc_start: 0.6798 (mtt180) cc_final: 0.6142 (mpt-90) REVERT: D 83 LEU cc_start: 0.7855 (mp) cc_final: 0.7517 (pp) REVERT: D 111 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7593 (ptpp) REVERT: D 144 THR cc_start: 0.5742 (p) cc_final: 0.5220 (t) outliers start: 12 outliers final: 3 residues processed: 179 average time/residue: 0.4874 time to fit residues: 93.0772 Evaluate side-chains 122 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 117 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain D residue 111 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.2980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.2980 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 GLN A 331 ASN A 456 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.117306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.096348 restraints weight = 17380.360| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 3.78 r_work: 0.3561 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 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 0.040 7913 Z= 0.146 Angle : 0.585 9.136 10791 Z= 0.298 Chirality : 0.042 0.153 1239 Planarity : 0.005 0.063 1389 Dihedral : 4.503 53.994 1187 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.95 % Allowed : 24.09 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.27), residues: 1009 helix: 1.70 (0.23), residues: 539 sheet: 0.64 (0.51), residues: 119 loop : -0.89 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 220 TYR 0.015 0.002 TYR A 264 PHE 0.016 0.002 PHE B 117 TRP 0.027 0.002 TRP C 80 HIS 0.009 0.001 HIS A 223 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 7913) covalent geometry : angle 0.58499 (10791) hydrogen bonds : bond 0.04063 ( 423) hydrogen bonds : angle 4.10483 ( 1293) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 116 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LEU cc_start: 0.6520 (OUTLIER) cc_final: 0.6076 (mp) REVERT: A 234 GLN cc_start: 0.9128 (mm-40) cc_final: 0.8869 (mm-40) REVERT: A 383 ILE cc_start: 0.7407 (OUTLIER) cc_final: 0.7068 (mp) REVERT: A 488 ASP cc_start: 0.8427 (m-30) cc_final: 0.8222 (m-30) REVERT: A 491 MET cc_start: 0.7467 (tpt) cc_final: 0.7109 (tpt) REVERT: A 566 MET cc_start: 0.8442 (mpt) cc_final: 0.8182 (mpt) REVERT: B 98 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7606 (tm-30) REVERT: B 182 LYS cc_start: 0.7252 (mppt) cc_final: 0.6831 (mmtt) REVERT: B 212 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8260 (mp) REVERT: C 45 LYS cc_start: 0.7937 (tttt) cc_final: 0.7725 (tptp) REVERT: C 81 THR cc_start: 0.9015 (m) cc_final: 0.8664 (p) REVERT: C 102 ARG cc_start: 0.6973 (mtt180) cc_final: 0.5769 (mpt-90) REVERT: D 119 GLN cc_start: 0.8125 (tp40) cc_final: 0.7859 (mm110) outliers start: 38 outliers final: 15 residues processed: 137 average time/residue: 0.4040 time to fit residues: 60.0884 Evaluate side-chains 125 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 80 TRP Chi-restraints excluded: chain D residue 22 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 42 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 50 optimal weight: 0.2980 chunk 60 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.115952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.094943 restraints weight = 17225.591| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 3.76 r_work: 0.3568 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7913 Z= 0.112 Angle : 0.531 8.469 10791 Z= 0.267 Chirality : 0.041 0.141 1239 Planarity : 0.005 0.066 1389 Dihedral : 4.070 58.571 1180 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 5.73 % Allowed : 23.44 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.27), residues: 1009 helix: 1.88 (0.23), residues: 539 sheet: 0.70 (0.51), residues: 122 loop : -0.79 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 429 TYR 0.016 0.001 TYR A 472 PHE 0.020 0.001 PHE B 117 TRP 0.014 0.001 TRP D 157 HIS 0.007 0.001 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 7913) covalent geometry : angle 0.53142 (10791) hydrogen bonds : bond 0.03518 ( 423) hydrogen bonds : angle 3.91138 ( 1293) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 124 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LEU cc_start: 0.6394 (OUTLIER) cc_final: 0.5992 (mp) REVERT: A 221 LEU cc_start: 0.9125 (mm) cc_final: 0.8893 (tm) REVERT: A 223 HIS cc_start: 0.8780 (m-70) cc_final: 0.8442 (m-70) REVERT: A 226 MET cc_start: 0.8770 (mmm) cc_final: 0.8472 (mmm) REVERT: A 488 ASP cc_start: 0.8421 (m-30) cc_final: 0.8192 (m-30) REVERT: A 491 MET cc_start: 0.7441 (tpt) cc_final: 0.7020 (tpt) REVERT: B 27 PHE cc_start: 0.8184 (OUTLIER) cc_final: 0.7743 (t80) REVERT: B 98 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7626 (tm-30) REVERT: B 176 LYS cc_start: 0.6851 (mtpp) cc_final: 0.6645 (mtpp) REVERT: B 212 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8246 (mp) REVERT: C 45 LYS cc_start: 0.7981 (tttt) cc_final: 0.7701 (tptp) REVERT: C 67 GLN cc_start: 0.9439 (OUTLIER) cc_final: 0.8713 (mp10) REVERT: C 81 THR cc_start: 0.9056 (m) cc_final: 0.8715 (p) REVERT: C 102 ARG cc_start: 0.6969 (mtt180) cc_final: 0.5904 (mpt-90) REVERT: C 138 LYS cc_start: 0.7567 (ttpt) cc_final: 0.7315 (tmmt) REVERT: D 83 LEU cc_start: 0.8492 (mp) cc_final: 0.8110 (pp) REVERT: D 119 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7838 (mm110) outliers start: 44 outliers final: 18 residues processed: 149 average time/residue: 0.4007 time to fit residues: 64.7579 Evaluate side-chains 139 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 80 TRP Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 119 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 30 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 90 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 HIS ** A 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 GLN A 384 HIS A 523 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.109592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.088727 restraints weight = 17886.748| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 3.76 r_work: 0.3457 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7913 Z= 0.200 Angle : 0.623 10.756 10791 Z= 0.320 Chirality : 0.044 0.209 1239 Planarity : 0.005 0.052 1389 Dihedral : 4.207 34.575 1178 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 7.16 % Allowed : 23.70 % Favored : 69.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.26), residues: 1009 helix: 1.44 (0.23), residues: 539 sheet: 0.63 (0.51), residues: 118 loop : -0.89 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 429 TYR 0.015 0.002 TYR B 81 PHE 0.022 0.002 PHE B 117 TRP 0.015 0.002 TRP C 80 HIS 0.008 0.002 HIS A 384 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 7913) covalent geometry : angle 0.62343 (10791) hydrogen bonds : bond 0.04872 ( 423) hydrogen bonds : angle 4.18454 ( 1293) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 119 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LEU cc_start: 0.6502 (OUTLIER) cc_final: 0.6035 (mp) REVERT: A 219 VAL cc_start: 0.8894 (m) cc_final: 0.8217 (p) REVERT: A 221 LEU cc_start: 0.9159 (mm) cc_final: 0.8941 (tm) REVERT: A 223 HIS cc_start: 0.8813 (m-70) cc_final: 0.8342 (m-70) REVERT: A 371 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7165 (pp20) REVERT: A 401 ASP cc_start: 0.7331 (t0) cc_final: 0.7104 (t0) REVERT: A 488 ASP cc_start: 0.8502 (m-30) cc_final: 0.8279 (m-30) REVERT: A 491 MET cc_start: 0.7541 (tpt) cc_final: 0.7098 (tpt) REVERT: A 507 GLU cc_start: 0.7037 (pm20) cc_final: 0.6815 (mp0) REVERT: B 27 PHE cc_start: 0.8242 (OUTLIER) cc_final: 0.7694 (t80) REVERT: B 152 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7630 (pm20) REVERT: B 181 SER cc_start: 0.8059 (m) cc_final: 0.7734 (p) REVERT: B 212 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8291 (mp) REVERT: B 308 GLU cc_start: 0.8777 (tp30) cc_final: 0.8554 (tm-30) REVERT: B 310 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8336 (tttm) REVERT: C 45 LYS cc_start: 0.8146 (tttt) cc_final: 0.7889 (tptp) REVERT: C 67 GLN cc_start: 0.9470 (OUTLIER) cc_final: 0.8674 (mp10) REVERT: C 102 ARG cc_start: 0.7184 (mtt180) cc_final: 0.6068 (mpt-90) REVERT: C 138 LYS cc_start: 0.7732 (ttpt) cc_final: 0.7475 (tmmt) REVERT: D 83 LEU cc_start: 0.8513 (mp) cc_final: 0.8223 (pp) REVERT: D 119 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7857 (mm110) outliers start: 55 outliers final: 21 residues processed: 151 average time/residue: 0.4232 time to fit residues: 68.7052 Evaluate side-chains 143 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 151 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 74 optimal weight: 0.5980 chunk 86 optimal weight: 5.9990 chunk 54 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 6 optimal weight: 7.9990 chunk 95 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 43 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4035 r_free = 0.4035 target = 0.112251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.091381 restraints weight = 17592.283| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 3.75 r_work: 0.3508 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7913 Z= 0.114 Angle : 0.539 9.387 10791 Z= 0.274 Chirality : 0.041 0.143 1239 Planarity : 0.004 0.046 1389 Dihedral : 3.829 34.068 1178 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.17 % Allowed : 26.56 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.27), residues: 1009 helix: 1.79 (0.23), residues: 539 sheet: 0.58 (0.51), residues: 122 loop : -0.62 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 429 TYR 0.015 0.001 TYR A 472 PHE 0.019 0.001 PHE B 117 TRP 0.012 0.001 TRP D 86 HIS 0.006 0.001 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 7913) covalent geometry : angle 0.53948 (10791) hydrogen bonds : bond 0.03525 ( 423) hydrogen bonds : angle 3.89856 ( 1293) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LEU cc_start: 0.6472 (OUTLIER) cc_final: 0.6046 (mp) REVERT: A 213 ASP cc_start: 0.8176 (t0) cc_final: 0.6755 (m-30) REVERT: A 219 VAL cc_start: 0.8929 (m) cc_final: 0.8306 (p) REVERT: A 223 HIS cc_start: 0.8849 (m-70) cc_final: 0.8379 (m-70) REVERT: A 383 ILE cc_start: 0.7334 (OUTLIER) cc_final: 0.7012 (mp) REVERT: A 401 ASP cc_start: 0.7342 (t0) cc_final: 0.7098 (t0) REVERT: A 488 ASP cc_start: 0.8445 (m-30) cc_final: 0.8202 (m-30) REVERT: A 491 MET cc_start: 0.7528 (tpt) cc_final: 0.7157 (tpt) REVERT: A 507 GLU cc_start: 0.7086 (pm20) cc_final: 0.6833 (mp0) REVERT: B 98 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7718 (tm-30) REVERT: B 181 SER cc_start: 0.8054 (m) cc_final: 0.7691 (p) REVERT: B 212 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8247 (mp) REVERT: C 45 LYS cc_start: 0.8129 (tttt) cc_final: 0.7865 (tptp) REVERT: C 67 GLN cc_start: 0.9462 (OUTLIER) cc_final: 0.8680 (mp10) REVERT: C 102 ARG cc_start: 0.7147 (mtt180) cc_final: 0.6030 (mpt-90) REVERT: D 83 LEU cc_start: 0.8540 (mp) cc_final: 0.8295 (pp) REVERT: D 119 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7832 (mm110) REVERT: D 126 LYS cc_start: 0.7440 (tttt) cc_final: 0.7111 (mmpt) outliers start: 32 outliers final: 17 residues processed: 140 average time/residue: 0.3635 time to fit residues: 55.6026 Evaluate side-chains 138 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 119 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 64 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.111999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.090935 restraints weight = 17808.848| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 3.88 r_work: 0.3521 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7913 Z= 0.125 Angle : 0.562 8.248 10791 Z= 0.284 Chirality : 0.041 0.145 1239 Planarity : 0.004 0.046 1389 Dihedral : 3.795 33.536 1178 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.69 % Allowed : 26.56 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.27), residues: 1009 helix: 1.78 (0.23), residues: 540 sheet: 0.59 (0.50), residues: 122 loop : -0.63 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 429 TYR 0.018 0.001 TYR A 472 PHE 0.021 0.002 PHE B 117 TRP 0.014 0.001 TRP D 86 HIS 0.005 0.001 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 7913) covalent geometry : angle 0.56173 (10791) hydrogen bonds : bond 0.03636 ( 423) hydrogen bonds : angle 3.86745 ( 1293) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 123 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LEU cc_start: 0.6363 (OUTLIER) cc_final: 0.5976 (mp) REVERT: A 213 ASP cc_start: 0.8139 (t0) cc_final: 0.6723 (m-30) REVERT: A 219 VAL cc_start: 0.8976 (m) cc_final: 0.8361 (p) REVERT: A 223 HIS cc_start: 0.8933 (m-70) cc_final: 0.8470 (m-70) REVERT: A 371 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7315 (pp20) REVERT: A 383 ILE cc_start: 0.7261 (OUTLIER) cc_final: 0.6948 (mp) REVERT: A 401 ASP cc_start: 0.7314 (t0) cc_final: 0.7056 (t0) REVERT: A 488 ASP cc_start: 0.8446 (m-30) cc_final: 0.8184 (m-30) REVERT: A 491 MET cc_start: 0.7538 (tpt) cc_final: 0.7150 (tpt) REVERT: A 507 GLU cc_start: 0.7124 (pm20) cc_final: 0.6893 (mp0) REVERT: B 98 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7685 (tm-30) REVERT: B 181 SER cc_start: 0.8030 (m) cc_final: 0.7677 (p) REVERT: B 212 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8200 (mp) REVERT: B 308 GLU cc_start: 0.8611 (tp30) cc_final: 0.8329 (tm-30) REVERT: B 310 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8310 (tttm) REVERT: C 45 LYS cc_start: 0.8103 (tttt) cc_final: 0.7820 (tptp) REVERT: C 67 GLN cc_start: 0.9474 (OUTLIER) cc_final: 0.8641 (mp10) REVERT: C 102 ARG cc_start: 0.7070 (mtt180) cc_final: 0.5968 (mpt-90) REVERT: D 119 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7854 (mm110) REVERT: D 126 LYS cc_start: 0.7399 (tttt) cc_final: 0.7075 (mmpt) outliers start: 36 outliers final: 26 residues processed: 144 average time/residue: 0.3729 time to fit residues: 58.6665 Evaluate side-chains 148 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 12 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.109814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.088796 restraints weight = 17876.565| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 3.86 r_work: 0.3478 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7913 Z= 0.171 Angle : 0.604 8.643 10791 Z= 0.310 Chirality : 0.043 0.170 1239 Planarity : 0.005 0.046 1389 Dihedral : 3.995 32.978 1178 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 5.86 % Allowed : 26.43 % Favored : 67.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.27), residues: 1009 helix: 1.59 (0.23), residues: 539 sheet: 0.48 (0.50), residues: 119 loop : -0.81 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 346 TYR 0.016 0.002 TYR A 472 PHE 0.022 0.002 PHE B 117 TRP 0.012 0.002 TRP C 80 HIS 0.006 0.001 HIS A 424 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 7913) covalent geometry : angle 0.60376 (10791) hydrogen bonds : bond 0.04295 ( 423) hydrogen bonds : angle 4.02967 ( 1293) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 113 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LEU cc_start: 0.6476 (OUTLIER) cc_final: 0.6043 (mp) REVERT: A 219 VAL cc_start: 0.9006 (m) cc_final: 0.8396 (p) REVERT: A 223 HIS cc_start: 0.8965 (m-70) cc_final: 0.8513 (m-70) REVERT: A 371 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7271 (pp20) REVERT: A 383 ILE cc_start: 0.7478 (OUTLIER) cc_final: 0.7091 (mp) REVERT: A 401 ASP cc_start: 0.7207 (t0) cc_final: 0.6771 (t70) REVERT: A 488 ASP cc_start: 0.8490 (m-30) cc_final: 0.8231 (m-30) REVERT: A 491 MET cc_start: 0.7571 (tpt) cc_final: 0.7185 (tpt) REVERT: A 507 GLU cc_start: 0.7138 (pm20) cc_final: 0.6909 (mp0) REVERT: B 98 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7727 (tm-30) REVERT: B 152 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7570 (pm20) REVERT: B 181 SER cc_start: 0.8022 (m) cc_final: 0.7228 (p) REVERT: B 182 LYS cc_start: 0.7287 (mppt) cc_final: 0.6492 (mppt) REVERT: B 212 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8230 (mp) REVERT: C 45 LYS cc_start: 0.8151 (tttt) cc_final: 0.7877 (tptp) REVERT: C 67 GLN cc_start: 0.9484 (OUTLIER) cc_final: 0.8636 (mp10) REVERT: C 83 ILE cc_start: 0.5159 (OUTLIER) cc_final: 0.4910 (mp) REVERT: C 102 ARG cc_start: 0.7187 (mtt180) cc_final: 0.5998 (mmt-90) REVERT: D 83 LEU cc_start: 0.8698 (mp) cc_final: 0.8497 (pp) REVERT: D 119 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7898 (mm110) outliers start: 45 outliers final: 24 residues processed: 144 average time/residue: 0.3581 time to fit residues: 56.4234 Evaluate side-chains 140 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 108 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 60 optimal weight: 0.0980 chunk 31 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4044 r_free = 0.4044 target = 0.112150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.091314 restraints weight = 17739.309| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 3.84 r_work: 0.3518 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7913 Z= 0.118 Angle : 0.591 10.912 10791 Z= 0.295 Chirality : 0.042 0.256 1239 Planarity : 0.004 0.045 1389 Dihedral : 3.798 32.760 1178 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 5.08 % Allowed : 27.34 % Favored : 67.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.27), residues: 1009 helix: 1.76 (0.23), residues: 539 sheet: 0.52 (0.50), residues: 122 loop : -0.63 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 429 TYR 0.019 0.001 TYR A 472 PHE 0.024 0.001 PHE B 117 TRP 0.014 0.001 TRP D 86 HIS 0.004 0.001 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 7913) covalent geometry : angle 0.59090 (10791) hydrogen bonds : bond 0.03596 ( 423) hydrogen bonds : angle 3.90243 ( 1293) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 117 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LEU cc_start: 0.6405 (OUTLIER) cc_final: 0.5987 (mp) REVERT: A 210 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.8115 (mt) REVERT: A 213 ASP cc_start: 0.8183 (t0) cc_final: 0.6735 (m-30) REVERT: A 219 VAL cc_start: 0.8991 (m) cc_final: 0.8409 (p) REVERT: A 223 HIS cc_start: 0.8975 (m-70) cc_final: 0.8539 (m-70) REVERT: A 371 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7276 (pp20) REVERT: A 383 ILE cc_start: 0.7249 (OUTLIER) cc_final: 0.6966 (mp) REVERT: A 401 ASP cc_start: 0.7204 (t0) cc_final: 0.6763 (t70) REVERT: A 488 ASP cc_start: 0.8442 (m-30) cc_final: 0.8187 (m-30) REVERT: A 491 MET cc_start: 0.7514 (tpt) cc_final: 0.7139 (tpt) REVERT: A 507 GLU cc_start: 0.7140 (pm20) cc_final: 0.6910 (mp0) REVERT: B 98 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7721 (tm-30) REVERT: B 152 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7587 (pm20) REVERT: B 212 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8185 (mp) REVERT: B 308 GLU cc_start: 0.8578 (tp30) cc_final: 0.8256 (tm-30) REVERT: C 45 LYS cc_start: 0.8123 (tttt) cc_final: 0.7848 (tptp) REVERT: C 67 GLN cc_start: 0.9472 (OUTLIER) cc_final: 0.8626 (mp10) REVERT: C 102 ARG cc_start: 0.6976 (mtt180) cc_final: 0.5880 (mmm-85) REVERT: D 119 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7890 (mm110) outliers start: 39 outliers final: 23 residues processed: 143 average time/residue: 0.3539 time to fit residues: 55.2732 Evaluate side-chains 137 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 106 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 129 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 76 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.111038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.090005 restraints weight = 17856.076| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 3.87 r_work: 0.3508 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7913 Z= 0.132 Angle : 0.625 12.055 10791 Z= 0.309 Chirality : 0.043 0.226 1239 Planarity : 0.004 0.045 1389 Dihedral : 3.850 32.425 1178 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.95 % Allowed : 27.99 % Favored : 67.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.27), residues: 1009 helix: 1.71 (0.23), residues: 538 sheet: 0.48 (0.50), residues: 122 loop : -0.63 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 429 TYR 0.019 0.001 TYR A 472 PHE 0.029 0.002 PHE B 117 TRP 0.016 0.001 TRP D 86 HIS 0.004 0.001 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 7913) covalent geometry : angle 0.62501 (10791) hydrogen bonds : bond 0.03789 ( 423) hydrogen bonds : angle 3.94292 ( 1293) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 115 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 LEU cc_start: 0.6425 (OUTLIER) cc_final: 0.6016 (mp) REVERT: A 210 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8163 (mt) REVERT: A 213 ASP cc_start: 0.8204 (t0) cc_final: 0.6784 (m-30) REVERT: A 219 VAL cc_start: 0.9012 (m) cc_final: 0.8380 (p) REVERT: A 223 HIS cc_start: 0.8981 (m-70) cc_final: 0.8496 (m-70) REVERT: A 371 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7234 (pp20) REVERT: A 383 ILE cc_start: 0.7276 (OUTLIER) cc_final: 0.6968 (mp) REVERT: A 401 ASP cc_start: 0.7198 (t0) cc_final: 0.6738 (t70) REVERT: A 488 ASP cc_start: 0.8459 (m-30) cc_final: 0.8196 (m-30) REVERT: A 491 MET cc_start: 0.7510 (tpt) cc_final: 0.6990 (tpp) REVERT: A 507 GLU cc_start: 0.7154 (pm20) cc_final: 0.6908 (mp0) REVERT: B 98 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7763 (tm-30) REVERT: B 152 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7661 (pm20) REVERT: B 181 SER cc_start: 0.7977 (m) cc_final: 0.7160 (p) REVERT: B 182 LYS cc_start: 0.7391 (mppt) cc_final: 0.6643 (mppt) REVERT: B 212 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8182 (mp) REVERT: B 308 GLU cc_start: 0.8585 (tp30) cc_final: 0.8280 (tm-30) REVERT: C 45 LYS cc_start: 0.8099 (tttt) cc_final: 0.7830 (tptp) REVERT: C 55 SER cc_start: 0.8273 (m) cc_final: 0.7894 (p) REVERT: C 67 GLN cc_start: 0.9478 (OUTLIER) cc_final: 0.8600 (mp10) REVERT: C 102 ARG cc_start: 0.7080 (mtt180) cc_final: 0.5879 (mmm-85) REVERT: D 124 MET cc_start: 0.7380 (ptp) cc_final: 0.6827 (pmm) outliers start: 38 outliers final: 27 residues processed: 141 average time/residue: 0.3523 time to fit residues: 54.3813 Evaluate side-chains 142 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 108 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 70 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.4036 r_free = 0.4036 target = 0.111357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.090310 restraints weight = 17625.997| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 3.84 r_work: 0.3511 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7913 Z= 0.129 Angle : 0.643 13.470 10791 Z= 0.321 Chirality : 0.043 0.235 1239 Planarity : 0.004 0.045 1389 Dihedral : 3.815 32.193 1178 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.82 % Allowed : 28.52 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.27), residues: 1009 helix: 1.77 (0.23), residues: 538 sheet: 0.50 (0.49), residues: 122 loop : -0.65 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 429 TYR 0.019 0.001 TYR A 472 PHE 0.028 0.002 PHE B 117 TRP 0.017 0.001 TRP D 86 HIS 0.004 0.001 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 7913) covalent geometry : angle 0.64321 (10791) hydrogen bonds : bond 0.03776 ( 423) hydrogen bonds : angle 3.99842 ( 1293) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 112 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 LEU cc_start: 0.6418 (OUTLIER) cc_final: 0.6008 (mp) REVERT: A 210 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8153 (mt) REVERT: A 213 ASP cc_start: 0.8159 (t0) cc_final: 0.6737 (m-30) REVERT: A 219 VAL cc_start: 0.9033 (m) cc_final: 0.8401 (p) REVERT: A 223 HIS cc_start: 0.8955 (m-70) cc_final: 0.8467 (m-70) REVERT: A 371 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7124 (pp20) REVERT: A 383 ILE cc_start: 0.7247 (OUTLIER) cc_final: 0.6937 (mp) REVERT: A 401 ASP cc_start: 0.7211 (t0) cc_final: 0.6737 (t70) REVERT: A 488 ASP cc_start: 0.8464 (m-30) cc_final: 0.8201 (m-30) REVERT: A 491 MET cc_start: 0.7507 (tpt) cc_final: 0.6989 (tpp) REVERT: A 507 GLU cc_start: 0.7169 (pm20) cc_final: 0.6918 (mp0) REVERT: B 98 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7763 (tm-30) REVERT: B 152 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7709 (pm20) REVERT: B 181 SER cc_start: 0.7928 (m) cc_final: 0.7117 (p) REVERT: B 182 LYS cc_start: 0.7393 (mppt) cc_final: 0.6682 (mppt) REVERT: B 212 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8202 (mp) REVERT: B 308 GLU cc_start: 0.8577 (tp30) cc_final: 0.8261 (tm-30) REVERT: C 45 LYS cc_start: 0.8150 (tttt) cc_final: 0.7810 (tptp) REVERT: C 55 SER cc_start: 0.8270 (m) cc_final: 0.7896 (p) REVERT: C 67 GLN cc_start: 0.9472 (OUTLIER) cc_final: 0.8593 (mp10) REVERT: C 102 ARG cc_start: 0.7081 (mtt180) cc_final: 0.5882 (mmm-85) REVERT: D 124 MET cc_start: 0.7338 (ptp) cc_final: 0.6835 (pmm) outliers start: 37 outliers final: 26 residues processed: 139 average time/residue: 0.3545 time to fit residues: 53.8154 Evaluate side-chains 145 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 72 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 59 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.4017 r_free = 0.4017 target = 0.110403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.089570 restraints weight = 17816.957| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 3.86 r_work: 0.3488 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7913 Z= 0.151 Angle : 0.661 13.365 10791 Z= 0.335 Chirality : 0.044 0.229 1239 Planarity : 0.004 0.046 1389 Dihedral : 3.952 32.021 1178 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.95 % Allowed : 28.65 % Favored : 66.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.27), residues: 1009 helix: 1.69 (0.23), residues: 536 sheet: 0.56 (0.49), residues: 120 loop : -0.73 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 346 TYR 0.018 0.002 TYR A 472 PHE 0.027 0.002 PHE B 117 TRP 0.015 0.001 TRP D 86 HIS 0.005 0.001 HIS A 424 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 7913) covalent geometry : angle 0.66089 (10791) hydrogen bonds : bond 0.04212 ( 423) hydrogen bonds : angle 4.10042 ( 1293) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2725.60 seconds wall clock time: 47 minutes 7.48 seconds (2827.48 seconds total)