Starting phenix.real_space_refine on Sun Dec 29 13:54:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cny_45766/12_2024/9cny_45766.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cny_45766/12_2024/9cny_45766.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cny_45766/12_2024/9cny_45766.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cny_45766/12_2024/9cny_45766.map" model { file = "/net/cci-nas-00/data/ceres_data/9cny_45766/12_2024/9cny_45766.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cny_45766/12_2024/9cny_45766.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 235 atoms to isotropic. 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 30 5.16 5 C 6562 2.51 5 N 1770 2.21 5 O 2048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 10410 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 5042 Classifications: {'peptide': 634} Link IDs: {'PTRANS': 25, 'TRANS': 608} Chain: "C" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 363 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 6, 'TRANS': 45} Chain: "D" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1732 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 11, 'TRANS': 202} Chain: "E" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 685 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 5, 'TRANS': 81} Chain: "B" Number of atoms: 2588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2588 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 11, 'TRANS': 334} Chain breaks: 2 Time building chain proxies: 6.30, per 1000 atoms: 0.61 Number of scatterers: 10410 At special positions: 0 Unit cell: (102.153, 115.373, 139.409, 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 30 16.00 O 2048 8.00 N 1770 7.00 C 6562 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.89 Conformation dependent library (CDL) restraints added in 1.3 seconds 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2432 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 15 sheets defined 24.5% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 189 through 195 Processing helix chain 'A' and resid 218 through 232 removed outlier: 3.831A pdb=" N ASP A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 288 Processing helix chain 'A' and resid 297 through 315 removed outlier: 3.696A pdb=" N TYR A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 332 No H-bonds generated for 'chain 'A' and resid 330 through 332' Processing helix chain 'A' and resid 361 through 367 Processing helix chain 'A' and resid 378 through 393 removed outlier: 3.554A pdb=" N LYS A 386 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 Processing helix chain 'A' and resid 542 through 553 removed outlier: 3.504A pdb=" N TRP A 546 " --> pdb=" O GLN A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 726 through 730 Processing helix chain 'A' and resid 750 through 754 removed outlier: 3.710A pdb=" N GLN A 753 " --> pdb=" O ASP A 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 44 removed outlier: 4.409A pdb=" N TYR C 41 " --> pdb=" O ASP C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 66 removed outlier: 3.963A pdb=" N TYR C 65 " --> pdb=" O SER C 62 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA C 66 " --> pdb=" O GLY C 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 66' Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.568A pdb=" N ALA C 79 " --> pdb=" O VAL C 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 46 Processing helix chain 'D' and resid 47 through 62 removed outlier: 4.065A pdb=" N ALA D 57 " --> pdb=" O THR D 53 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU D 58 " --> pdb=" O GLN D 54 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASP D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 Processing helix chain 'D' and resid 84 through 97 Processing helix chain 'D' and resid 104 through 118 Processing helix chain 'D' and resid 119 through 121 No H-bonds generated for 'chain 'D' and resid 119 through 121' Processing helix chain 'D' and resid 123 through 129 Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 removed outlier: 3.512A pdb=" N ASP D 172 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR D 177 " --> pdb=" O ARG D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 225 removed outlier: 3.735A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 227 through 241 removed outlier: 3.686A pdb=" N LYS D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 44 removed outlier: 3.586A pdb=" N SER E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 176 through 183 removed outlier: 6.428A pdb=" N ILE A 254 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN A 179 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE A 260 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 267 through 276 removed outlier: 7.300A pdb=" N LEU A 337 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL A 271 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL A 339 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL A 273 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL A 341 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLY A 275 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.110A pdb=" N TYR A 348 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL A 414 " --> pdb=" O TYR A 348 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ARG A 353 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N VAL A 418 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLU A 355 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N GLU A 420 " --> pdb=" O GLU A 355 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.110A pdb=" N TYR A 348 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL A 414 " --> pdb=" O TYR A 348 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLN A 403 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N THR A 397 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 424 through 430 removed outlier: 6.107A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A 738 " --> pdb=" O GLY A 771 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY A 771 " --> pdb=" O PHE A 738 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE A 791 " --> pdb=" O MET A 768 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 32 through 35 removed outlier: 3.846A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 32 through 35 removed outlier: 6.541A pdb=" N THR E 90 " --> pdb=" O ASN E 106 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ASN E 106 " --> pdb=" O THR E 90 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR E 92 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ILE E 104 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR E 94 " --> pdb=" O THR E 102 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.724A pdb=" N TRP B 48 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 66 through 68 removed outlier: 3.873A pdb=" N TRP B 93 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ASN B 85 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU B 91 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 111 through 118 removed outlier: 6.459A pdb=" N GLY B 114 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N TYR B 123 " --> pdb=" O GLY B 114 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N THR B 116 " --> pdb=" O HIS B 121 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N HIS B 121 " --> pdb=" O THR B 116 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N GLN B 130 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ASN B 135 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL B 141 " --> pdb=" O ASN B 135 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 156 through 158 removed outlier: 3.571A pdb=" N ALA B 173 " --> pdb=" O TRP B 183 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N TRP B 183 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASN B 175 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL B 181 " --> pdb=" O ASN B 175 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 201 through 203 removed outlier: 6.951A pdb=" N VAL B 216 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLN B 229 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ALA B 218 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 252 through 254 removed outlier: 4.276A pdb=" N TRP B 279 " --> pdb=" O ALA B 269 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ASP B 271 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE B 277 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 290 through 292 removed outlier: 3.659A pdb=" N TRP B 317 " --> pdb=" O ALA B 307 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N THR B 309 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR B 315 " --> pdb=" O THR B 309 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 331 through 333 removed outlier: 6.625A pdb=" N LEU B 346 " --> pdb=" O GLN B 359 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLN B 359 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TRP B 348 " --> pdb=" O VAL B 357 " (cutoff:3.500A) 467 hydrogen bonds defined for protein. 1278 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: 3.62 Time building geometry restraints manager: 3.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3479 1.34 - 1.46: 2170 1.46 - 1.58: 4938 1.58 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 10645 Sorted by residual: bond pdb=" N SER C 36 " pdb=" CA SER C 36 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 bond pdb=" N GLU E 24 " pdb=" CA GLU E 24 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.90e+00 bond pdb=" N ASP D 29 " pdb=" CA ASP D 29 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.86e+00 bond pdb=" N VAL A 173 " pdb=" CA VAL A 173 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.83e+00 bond pdb=" N VAL B 30 " pdb=" CA VAL B 30 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.74e+00 ... (remaining 10640 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 14150 1.77 - 3.54: 263 3.54 - 5.30: 65 5.30 - 7.07: 1 7.07 - 8.84: 1 Bond angle restraints: 14480 Sorted by residual: angle pdb=" CB MET B 189 " pdb=" CG MET B 189 " pdb=" SD MET B 189 " ideal model delta sigma weight residual 112.70 121.54 -8.84 3.00e+00 1.11e-01 8.68e+00 angle pdb=" C GLY A 184 " pdb=" N ASN A 185 " pdb=" CA ASN A 185 " ideal model delta sigma weight residual 121.54 126.53 -4.99 1.91e+00 2.74e-01 6.83e+00 angle pdb=" CA LYS B 31 " pdb=" CB LYS B 31 " pdb=" CG LYS B 31 " ideal model delta sigma weight residual 114.10 119.05 -4.95 2.00e+00 2.50e-01 6.12e+00 angle pdb=" N VAL A 208 " pdb=" CA VAL A 208 " pdb=" C VAL A 208 " ideal model delta sigma weight residual 113.71 111.40 2.31 9.50e-01 1.11e+00 5.93e+00 angle pdb=" CA ILE C 67 " pdb=" C ILE C 67 " pdb=" N PRO C 68 " ideal model delta sigma weight residual 118.12 120.05 -1.93 8.10e-01 1.52e+00 5.65e+00 ... (remaining 14475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 5770 17.98 - 35.96: 398 35.96 - 53.94: 60 53.94 - 71.93: 16 71.93 - 89.91: 21 Dihedral angle restraints: 6265 sinusoidal: 2433 harmonic: 3832 Sorted by residual: dihedral pdb=" CB CYS A 690 " pdb=" SG CYS A 690 " pdb=" SG CYS A 700 " pdb=" CB CYS A 700 " ideal model delta sinusoidal sigma weight residual -86.00 -136.72 50.72 1 1.00e+01 1.00e-02 3.52e+01 dihedral pdb=" CA GLU B 127 " pdb=" C GLU B 127 " pdb=" N LYS B 128 " pdb=" CA LYS B 128 " ideal model delta harmonic sigma weight residual 180.00 155.62 24.38 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA ASN B 266 " pdb=" C ASN B 266 " pdb=" N LEU B 267 " pdb=" CA LEU B 267 " ideal model delta harmonic sigma weight residual 180.00 156.66 23.34 0 5.00e+00 4.00e-02 2.18e+01 ... (remaining 6262 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 996 0.033 - 0.066: 381 0.066 - 0.100: 110 0.100 - 0.133: 74 0.133 - 0.166: 8 Chirality restraints: 1569 Sorted by residual: chirality pdb=" CA TRP A 546 " pdb=" N TRP A 546 " pdb=" C TRP A 546 " pdb=" CB TRP A 546 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.90e-01 chirality pdb=" CA ILE B 296 " pdb=" N ILE B 296 " pdb=" C ILE B 296 " pdb=" CB ILE B 296 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CB THR D 53 " pdb=" CA THR D 53 " pdb=" OG1 THR D 53 " pdb=" CG2 THR D 53 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.14e-01 ... (remaining 1566 not shown) Planarity restraints: 1911 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 546 " 0.038 2.00e-02 2.50e+03 2.88e-02 2.07e+01 pdb=" CG TRP A 546 " -0.078 2.00e-02 2.50e+03 pdb=" CD1 TRP A 546 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP A 546 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 546 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 546 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 546 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 546 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 546 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 546 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 586 " -0.042 5.00e-02 4.00e+02 6.25e-02 6.24e+00 pdb=" N PRO A 587 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 587 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 587 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 227 " -0.181 9.50e-02 1.11e+02 8.14e-02 4.42e+00 pdb=" NE ARG A 227 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 227 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 227 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 227 " -0.003 2.00e-02 2.50e+03 ... (remaining 1908 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 113 2.58 - 3.16: 9190 3.16 - 3.74: 15953 3.74 - 4.32: 21581 4.32 - 4.90: 36260 Nonbonded interactions: 83097 Sorted by model distance: nonbonded pdb=" O TYR A 548 " pdb=" OG SER A 551 " model vdw 2.003 3.040 nonbonded pdb=" OG SER A 715 " pdb=" OD1 ASP A 740 " model vdw 2.049 3.040 nonbonded pdb=" OG1 THR A 423 " pdb=" OE1 GLN A 446 " model vdw 2.065 3.040 nonbonded pdb=" OD1 ASP B 363 " pdb=" OH TYR B 388 " model vdw 2.130 3.040 nonbonded pdb=" OD1 ASP A 362 " pdb=" NH1 ARG A 366 " model vdw 2.133 3.120 ... (remaining 83092 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 25.990 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 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 : 0.003 0.054 10645 Z= 0.230 Angle : 0.629 8.838 14480 Z= 0.336 Chirality : 0.044 0.166 1569 Planarity : 0.005 0.081 1911 Dihedral : 13.796 89.908 3830 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.23), residues: 1319 helix: 0.43 (0.30), residues: 269 sheet: 0.21 (0.26), residues: 387 loop : -0.08 (0.25), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.002 TRP A 546 HIS 0.003 0.001 HIS B 165 PHE 0.028 0.002 PHE A 197 TYR 0.023 0.002 TYR D 205 ARG 0.010 0.001 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 1.189 Fit side-chains revert: symmetry clash REVERT: A 369 MET cc_start: 0.7678 (mmt) cc_final: 0.7062 (mmt) REVERT: A 489 LEU cc_start: 0.8514 (mm) cc_final: 0.8290 (mm) REVERT: A 711 MET cc_start: 0.8933 (ppp) cc_final: 0.8542 (ttp) REVERT: C 78 LYS cc_start: 0.8512 (mmtm) cc_final: 0.8041 (mmtt) REVERT: D 134 ASP cc_start: 0.8335 (p0) cc_final: 0.8109 (p0) REVERT: D 183 GLU cc_start: 0.8152 (tp30) cc_final: 0.7917 (tp30) REVERT: E 41 ASN cc_start: 0.8794 (t0) cc_final: 0.8427 (p0) REVERT: B 82 LYS cc_start: 0.7664 (mtpt) cc_final: 0.6980 (mtmt) REVERT: B 223 GLN cc_start: 0.8066 (tt0) cc_final: 0.7682 (tm-30) REVERT: B 266 ASN cc_start: 0.7176 (m110) cc_final: 0.6674 (t0) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.2250 time to fit residues: 71.0373 Evaluate side-chains 165 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 55 optimal weight: 0.0670 chunk 33 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 overall best weight: 1.3722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN A 390 ASN A 538 ASN A 573 ASN A 606 ASN ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 GLN B 334 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10645 Z= 0.295 Angle : 0.652 8.044 14480 Z= 0.348 Chirality : 0.047 0.191 1569 Planarity : 0.004 0.043 1911 Dihedral : 5.184 26.376 1460 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.07 % Allowed : 9.37 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.23), residues: 1319 helix: 0.72 (0.31), residues: 279 sheet: 0.00 (0.25), residues: 382 loop : -0.14 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP A 546 HIS 0.009 0.001 HIS A 677 PHE 0.018 0.002 PHE A 197 TYR 0.021 0.002 TYR A 618 ARG 0.005 0.001 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 1.161 Fit side-chains revert: symmetry clash REVERT: A 286 GLN cc_start: 0.7986 (tp40) cc_final: 0.7260 (tm-30) REVERT: A 369 MET cc_start: 0.7739 (mmt) cc_final: 0.7097 (mmt) REVERT: A 483 VAL cc_start: 0.8547 (t) cc_final: 0.8091 (p) REVERT: A 630 LEU cc_start: 0.8894 (tt) cc_final: 0.8584 (tp) REVERT: A 711 MET cc_start: 0.8745 (ppp) cc_final: 0.8289 (ttp) REVERT: A 768 MET cc_start: 0.6557 (mtm) cc_final: 0.5962 (ttm) REVERT: A 777 MET cc_start: 0.9352 (tpp) cc_final: 0.8865 (tpt) REVERT: C 39 GLU cc_start: 0.8392 (mp0) cc_final: 0.7863 (mp0) REVERT: C 78 LYS cc_start: 0.8337 (mmtm) cc_final: 0.7986 (mmtt) REVERT: D 42 LYS cc_start: 0.8664 (tptm) cc_final: 0.8344 (tptt) REVERT: D 134 ASP cc_start: 0.8671 (p0) cc_final: 0.8240 (p0) REVERT: D 232 GLU cc_start: 0.8185 (tp30) cc_final: 0.7927 (tp30) REVERT: E 53 GLN cc_start: 0.7952 (tp40) cc_final: 0.7693 (tp40) REVERT: B 59 PHE cc_start: 0.9044 (m-80) cc_final: 0.8815 (m-80) REVERT: B 82 LYS cc_start: 0.7962 (mtpt) cc_final: 0.7109 (mtmt) REVERT: B 168 ASN cc_start: 0.7872 (p0) cc_final: 0.7601 (p0) REVERT: B 223 GLN cc_start: 0.8245 (tt0) cc_final: 0.8042 (tp40) REVERT: B 329 SER cc_start: 0.9413 (m) cc_final: 0.9183 (m) outliers start: 23 outliers final: 14 residues processed: 193 average time/residue: 0.2392 time to fit residues: 65.4047 Evaluate side-chains 176 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 301 GLN Chi-restraints excluded: chain B residue 349 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 99 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 32 optimal weight: 30.0000 chunk 119 optimal weight: 6.9990 chunk 128 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 52 GLN E 96 ASN B 64 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10645 Z= 0.334 Angle : 0.635 6.998 14480 Z= 0.337 Chirality : 0.046 0.170 1569 Planarity : 0.004 0.049 1911 Dihedral : 5.060 26.704 1460 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.70 % Allowed : 13.42 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.23), residues: 1319 helix: 0.70 (0.31), residues: 280 sheet: -0.11 (0.25), residues: 378 loop : -0.28 (0.25), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 546 HIS 0.006 0.001 HIS A 677 PHE 0.021 0.002 PHE A 197 TYR 0.019 0.002 TYR D 184 ARG 0.008 0.001 ARG A 391 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 176 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 GLN cc_start: 0.7971 (tp40) cc_final: 0.7255 (tm-30) REVERT: A 287 LEU cc_start: 0.8453 (mm) cc_final: 0.8165 (tp) REVERT: A 369 MET cc_start: 0.7775 (mmt) cc_final: 0.7218 (mmt) REVERT: A 483 VAL cc_start: 0.8572 (t) cc_final: 0.8135 (p) REVERT: A 617 THR cc_start: 0.9005 (m) cc_final: 0.8401 (p) REVERT: A 646 MET cc_start: 0.7877 (tmm) cc_final: 0.6910 (tmm) REVERT: A 650 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7788 (tm-30) REVERT: A 711 MET cc_start: 0.8867 (ppp) cc_final: 0.8344 (ttp) REVERT: C 39 GLU cc_start: 0.8472 (mp0) cc_final: 0.7972 (mp0) REVERT: C 78 LYS cc_start: 0.8465 (mmtm) cc_final: 0.8076 (mmtt) REVERT: D 134 ASP cc_start: 0.8809 (p0) cc_final: 0.8312 (p0) REVERT: D 136 ASP cc_start: 0.8377 (m-30) cc_final: 0.7899 (m-30) REVERT: D 188 ARG cc_start: 0.9061 (tpp80) cc_final: 0.8573 (tpp80) REVERT: D 232 GLU cc_start: 0.8137 (tp30) cc_final: 0.7892 (tp30) REVERT: B 182 LYS cc_start: 0.8988 (mmtm) cc_final: 0.8782 (mmmm) REVERT: B 221 MET cc_start: 0.8714 (mpp) cc_final: 0.8310 (mpp) REVERT: B 280 LYS cc_start: 0.8590 (ptmm) cc_final: 0.8198 (ptmm) REVERT: B 329 SER cc_start: 0.9442 (m) cc_final: 0.9222 (m) outliers start: 30 outliers final: 22 residues processed: 195 average time/residue: 0.2369 time to fit residues: 65.1092 Evaluate side-chains 184 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 349 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 61 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 80 optimal weight: 0.0570 chunk 119 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.5304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 234 GLN B 266 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10645 Z= 0.306 Angle : 0.605 6.819 14480 Z= 0.320 Chirality : 0.044 0.164 1569 Planarity : 0.004 0.048 1911 Dihedral : 4.899 26.646 1460 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.33 % Allowed : 16.13 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.23), residues: 1319 helix: 0.88 (0.32), residues: 274 sheet: -0.16 (0.26), residues: 370 loop : -0.28 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 546 HIS 0.005 0.001 HIS A 677 PHE 0.021 0.002 PHE A 197 TYR 0.037 0.002 TYR A 609 ARG 0.006 0.000 ARG A 391 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 173 time to evaluate : 1.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 286 GLN cc_start: 0.8000 (tp40) cc_final: 0.7312 (tm-30) REVERT: A 287 LEU cc_start: 0.8441 (mm) cc_final: 0.8174 (tp) REVERT: A 369 MET cc_start: 0.7715 (mmt) cc_final: 0.7242 (mmt) REVERT: A 412 VAL cc_start: 0.9087 (OUTLIER) cc_final: 0.8885 (p) REVERT: A 617 THR cc_start: 0.8997 (m) cc_final: 0.8360 (p) REVERT: A 711 MET cc_start: 0.8905 (ppp) cc_final: 0.8386 (ttp) REVERT: A 768 MET cc_start: 0.6788 (mtm) cc_final: 0.6021 (ttm) REVERT: C 39 GLU cc_start: 0.8648 (mp0) cc_final: 0.8074 (mp0) REVERT: C 78 LYS cc_start: 0.8525 (mmtm) cc_final: 0.8077 (mmtt) REVERT: D 134 ASP cc_start: 0.8813 (p0) cc_final: 0.8421 (p0) REVERT: D 188 ARG cc_start: 0.9019 (tpp80) cc_final: 0.8808 (tpp80) REVERT: D 207 ASP cc_start: 0.7916 (t70) cc_final: 0.7569 (t70) REVERT: D 232 GLU cc_start: 0.8057 (tp30) cc_final: 0.7847 (tp30) REVERT: E 87 THR cc_start: 0.8907 (t) cc_final: 0.8630 (p) REVERT: B 87 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8146 (m-30) REVERT: B 168 ASN cc_start: 0.8153 (p0) cc_final: 0.7747 (p0) REVERT: B 221 MET cc_start: 0.8754 (mpp) cc_final: 0.8057 (mpp) REVERT: B 280 LYS cc_start: 0.8657 (ptmm) cc_final: 0.8386 (ptmm) REVERT: B 329 SER cc_start: 0.9449 (m) cc_final: 0.9216 (m) outliers start: 37 outliers final: 29 residues processed: 195 average time/residue: 0.2264 time to fit residues: 62.9233 Evaluate side-chains 193 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 564 SER Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 349 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 4.9990 chunk 71 optimal weight: 0.0050 chunk 1 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 108 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 113 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 ASN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10645 Z= 0.215 Angle : 0.568 7.376 14480 Z= 0.299 Chirality : 0.043 0.163 1569 Planarity : 0.004 0.043 1911 Dihedral : 4.672 25.542 1460 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.06 % Allowed : 17.75 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.23), residues: 1319 helix: 0.96 (0.32), residues: 274 sheet: -0.13 (0.25), residues: 373 loop : -0.16 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 317 HIS 0.003 0.001 HIS A 677 PHE 0.021 0.001 PHE A 197 TYR 0.026 0.002 TYR A 609 ARG 0.005 0.000 ARG A 391 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 177 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 286 GLN cc_start: 0.7996 (tp40) cc_final: 0.7299 (tm-30) REVERT: A 287 LEU cc_start: 0.8393 (mm) cc_final: 0.8181 (tp) REVERT: A 413 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.8145 (p0) REVERT: A 483 VAL cc_start: 0.8451 (t) cc_final: 0.8071 (p) REVERT: A 617 THR cc_start: 0.8999 (m) cc_final: 0.8393 (p) REVERT: A 646 MET cc_start: 0.7953 (tmm) cc_final: 0.7623 (tmm) REVERT: A 650 GLU cc_start: 0.8194 (tp30) cc_final: 0.7914 (tm-30) REVERT: A 711 MET cc_start: 0.8915 (ppp) cc_final: 0.8401 (ttp) REVERT: A 768 MET cc_start: 0.6509 (mtm) cc_final: 0.5984 (ttm) REVERT: C 39 GLU cc_start: 0.8696 (mp0) cc_final: 0.8411 (mp0) REVERT: C 78 LYS cc_start: 0.8546 (mmtm) cc_final: 0.8229 (mmtt) REVERT: D 134 ASP cc_start: 0.8771 (p0) cc_final: 0.8240 (p0) REVERT: D 188 ARG cc_start: 0.8966 (tpp80) cc_final: 0.8738 (tpp80) REVERT: D 207 ASP cc_start: 0.7888 (t70) cc_final: 0.7566 (t70) REVERT: D 232 GLU cc_start: 0.8007 (tp30) cc_final: 0.7741 (tp30) REVERT: E 87 THR cc_start: 0.8887 (t) cc_final: 0.8602 (p) REVERT: B 32 MET cc_start: 0.9243 (OUTLIER) cc_final: 0.8853 (ppp) REVERT: B 87 ASP cc_start: 0.8558 (OUTLIER) cc_final: 0.8238 (m-30) REVERT: B 221 MET cc_start: 0.8748 (mpp) cc_final: 0.7911 (mpp) REVERT: B 223 GLN cc_start: 0.7621 (tp40) cc_final: 0.7373 (tp-100) REVERT: B 329 SER cc_start: 0.9434 (m) cc_final: 0.9206 (m) outliers start: 34 outliers final: 24 residues processed: 198 average time/residue: 0.2361 time to fit residues: 66.8826 Evaluate side-chains 190 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 349 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 74 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 chunk 41 optimal weight: 0.0870 chunk 66 optimal weight: 0.0770 overall best weight: 0.5916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10645 Z= 0.180 Angle : 0.562 6.969 14480 Z= 0.294 Chirality : 0.042 0.166 1569 Planarity : 0.004 0.043 1911 Dihedral : 4.489 24.129 1460 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.88 % Allowed : 18.92 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.23), residues: 1319 helix: 1.03 (0.32), residues: 276 sheet: -0.08 (0.25), residues: 380 loop : -0.11 (0.25), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 317 HIS 0.003 0.001 HIS A 677 PHE 0.019 0.001 PHE A 197 TYR 0.025 0.001 TYR A 609 ARG 0.007 0.001 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 177 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 286 GLN cc_start: 0.8022 (tp40) cc_final: 0.7328 (tm-30) REVERT: A 617 THR cc_start: 0.8985 (m) cc_final: 0.8409 (p) REVERT: A 646 MET cc_start: 0.7850 (tmm) cc_final: 0.6585 (tmm) REVERT: A 650 GLU cc_start: 0.8155 (tp30) cc_final: 0.7740 (tm-30) REVERT: A 768 MET cc_start: 0.6630 (mtm) cc_final: 0.6050 (ttm) REVERT: C 39 GLU cc_start: 0.8724 (mp0) cc_final: 0.8402 (mp0) REVERT: C 78 LYS cc_start: 0.8549 (mmtm) cc_final: 0.8328 (mmtt) REVERT: D 42 LYS cc_start: 0.8718 (tptp) cc_final: 0.8486 (tttm) REVERT: D 183 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7664 (tt0) REVERT: D 188 ARG cc_start: 0.8861 (tpp80) cc_final: 0.8633 (tpp80) REVERT: D 207 ASP cc_start: 0.7905 (t70) cc_final: 0.7623 (t70) REVERT: D 232 GLU cc_start: 0.8012 (tp30) cc_final: 0.7730 (tp30) REVERT: E 45 LYS cc_start: 0.8756 (mtmm) cc_final: 0.8427 (ttpp) REVERT: E 87 THR cc_start: 0.8892 (t) cc_final: 0.8599 (p) REVERT: B 31 LYS cc_start: 0.8874 (tmtt) cc_final: 0.8669 (tmtt) REVERT: B 32 MET cc_start: 0.9172 (OUTLIER) cc_final: 0.8566 (ppp) REVERT: B 87 ASP cc_start: 0.8546 (OUTLIER) cc_final: 0.8195 (m-30) REVERT: B 221 MET cc_start: 0.8739 (mpp) cc_final: 0.7829 (mpp) REVERT: B 223 GLN cc_start: 0.7503 (tp40) cc_final: 0.7179 (tp-100) REVERT: B 329 SER cc_start: 0.9430 (m) cc_final: 0.9188 (m) outliers start: 32 outliers final: 26 residues processed: 195 average time/residue: 0.2221 time to fit residues: 61.9462 Evaluate side-chains 198 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 564 SER Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 349 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 0.7980 chunk 14 optimal weight: 0.0050 chunk 72 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 70 optimal weight: 0.0470 chunk 126 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 overall best weight: 0.4892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 99 ASN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10645 Z= 0.163 Angle : 0.548 7.331 14480 Z= 0.284 Chirality : 0.042 0.163 1569 Planarity : 0.004 0.040 1911 Dihedral : 4.317 22.994 1460 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.15 % Allowed : 19.37 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.23), residues: 1319 helix: 1.04 (0.32), residues: 276 sheet: -0.01 (0.25), residues: 376 loop : -0.06 (0.25), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 317 HIS 0.003 0.001 HIS A 533 PHE 0.019 0.001 PHE A 197 TYR 0.023 0.001 TYR D 107 ARG 0.008 0.000 ARG A 321 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 179 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 286 GLN cc_start: 0.7923 (tp40) cc_final: 0.7288 (tm-30) REVERT: A 287 LEU cc_start: 0.7948 (tp) cc_final: 0.7457 (tp) REVERT: A 325 MET cc_start: 0.7967 (mmm) cc_final: 0.7688 (mmp) REVERT: A 369 MET cc_start: 0.8051 (mmm) cc_final: 0.6975 (mmt) REVERT: A 617 THR cc_start: 0.8956 (m) cc_final: 0.8461 (p) REVERT: A 646 MET cc_start: 0.7880 (tmm) cc_final: 0.6791 (tmm) REVERT: A 650 GLU cc_start: 0.8086 (tp30) cc_final: 0.7829 (tm-30) REVERT: A 768 MET cc_start: 0.6601 (mtm) cc_final: 0.5983 (ttm) REVERT: C 39 GLU cc_start: 0.8757 (mp0) cc_final: 0.8219 (mp0) REVERT: C 78 LYS cc_start: 0.8565 (mmtm) cc_final: 0.8199 (mmtt) REVERT: D 42 LYS cc_start: 0.8793 (tptp) cc_final: 0.8553 (tttm) REVERT: D 99 ASN cc_start: 0.8442 (OUTLIER) cc_final: 0.7825 (p0) REVERT: D 207 ASP cc_start: 0.7893 (t70) cc_final: 0.7632 (t70) REVERT: D 232 GLU cc_start: 0.7980 (tp30) cc_final: 0.7661 (tp30) REVERT: E 87 THR cc_start: 0.8949 (t) cc_final: 0.8623 (p) REVERT: B 32 MET cc_start: 0.9174 (OUTLIER) cc_final: 0.8718 (ppp) REVERT: B 87 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.8143 (m-30) REVERT: B 221 MET cc_start: 0.8787 (mpp) cc_final: 0.7735 (mpp) REVERT: B 223 GLN cc_start: 0.7526 (tp40) cc_final: 0.7277 (tp-100) REVERT: B 246 ASP cc_start: 0.8404 (p0) cc_final: 0.8081 (p0) REVERT: B 316 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8967 (mp) REVERT: B 329 SER cc_start: 0.9422 (m) cc_final: 0.9166 (m) outliers start: 35 outliers final: 28 residues processed: 199 average time/residue: 0.2222 time to fit residues: 63.4013 Evaluate side-chains 199 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 351 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 11 optimal weight: 0.2980 chunk 99 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10645 Z= 0.184 Angle : 0.562 8.142 14480 Z= 0.292 Chirality : 0.042 0.159 1569 Planarity : 0.004 0.043 1911 Dihedral : 4.285 22.474 1460 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.97 % Allowed : 19.28 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.23), residues: 1319 helix: 1.03 (0.32), residues: 276 sheet: -0.01 (0.25), residues: 383 loop : -0.05 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 317 HIS 0.003 0.001 HIS A 533 PHE 0.020 0.001 PHE A 197 TYR 0.020 0.001 TYR A 609 ARG 0.008 0.001 ARG A 321 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 286 GLN cc_start: 0.7922 (tp40) cc_final: 0.7271 (tm-30) REVERT: A 287 LEU cc_start: 0.7944 (tp) cc_final: 0.7430 (tp) REVERT: A 617 THR cc_start: 0.8958 (m) cc_final: 0.8472 (p) REVERT: A 646 MET cc_start: 0.7864 (tmm) cc_final: 0.6730 (tmm) REVERT: A 650 GLU cc_start: 0.7978 (tp30) cc_final: 0.7731 (tm-30) REVERT: A 768 MET cc_start: 0.6601 (mtm) cc_final: 0.6021 (ttm) REVERT: C 39 GLU cc_start: 0.8752 (mp0) cc_final: 0.8418 (mp0) REVERT: D 42 LYS cc_start: 0.8847 (tptp) cc_final: 0.8616 (tttm) REVERT: D 183 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7671 (tt0) REVERT: D 207 ASP cc_start: 0.7890 (t0) cc_final: 0.7635 (t70) REVERT: D 232 GLU cc_start: 0.8009 (tp30) cc_final: 0.7699 (tp30) REVERT: E 87 THR cc_start: 0.8942 (t) cc_final: 0.8637 (p) REVERT: B 31 LYS cc_start: 0.8941 (tmtt) cc_final: 0.8723 (tmtt) REVERT: B 32 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.8572 (ppp) REVERT: B 87 ASP cc_start: 0.8522 (OUTLIER) cc_final: 0.8072 (m-30) REVERT: B 221 MET cc_start: 0.8767 (mpp) cc_final: 0.7710 (mpp) REVERT: B 223 GLN cc_start: 0.7641 (tp40) cc_final: 0.7393 (tp-100) REVERT: B 316 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8956 (mp) REVERT: B 329 SER cc_start: 0.9432 (m) cc_final: 0.9204 (m) outliers start: 33 outliers final: 27 residues processed: 186 average time/residue: 0.2211 time to fit residues: 59.2441 Evaluate side-chains 198 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 316 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 0.7980 chunk 110 optimal weight: 6.9990 chunk 117 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 36 optimal weight: 7.9990 chunk 106 optimal weight: 0.1980 chunk 111 optimal weight: 0.9980 chunk 77 optimal weight: 8.9990 chunk 124 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10645 Z= 0.180 Angle : 0.565 10.285 14480 Z= 0.291 Chirality : 0.042 0.156 1569 Planarity : 0.004 0.042 1911 Dihedral : 4.240 22.515 1460 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.24 % Allowed : 19.64 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.23), residues: 1319 helix: 1.05 (0.32), residues: 275 sheet: 0.09 (0.24), residues: 386 loop : -0.05 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 317 HIS 0.003 0.001 HIS A 533 PHE 0.019 0.001 PHE A 197 TYR 0.019 0.001 TYR A 609 ARG 0.007 0.000 ARG A 321 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 286 GLN cc_start: 0.7987 (tp40) cc_final: 0.7280 (tm-30) REVERT: A 287 LEU cc_start: 0.7969 (tp) cc_final: 0.7320 (tp) REVERT: A 617 THR cc_start: 0.8971 (m) cc_final: 0.8477 (p) REVERT: A 646 MET cc_start: 0.7853 (tmm) cc_final: 0.6686 (tmm) REVERT: A 650 GLU cc_start: 0.7927 (tp30) cc_final: 0.7662 (tm-30) REVERT: A 768 MET cc_start: 0.6534 (mtm) cc_final: 0.5995 (ttm) REVERT: C 39 GLU cc_start: 0.8760 (mp0) cc_final: 0.8426 (mp0) REVERT: C 78 LYS cc_start: 0.8030 (mmtt) cc_final: 0.7536 (mmtt) REVERT: D 183 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7667 (tt0) REVERT: D 207 ASP cc_start: 0.7874 (t0) cc_final: 0.7570 (t0) REVERT: D 232 GLU cc_start: 0.8024 (tp30) cc_final: 0.7687 (tp30) REVERT: E 50 MET cc_start: 0.7441 (tpp) cc_final: 0.6792 (tpp) REVERT: E 87 THR cc_start: 0.8945 (OUTLIER) cc_final: 0.8646 (p) REVERT: B 31 LYS cc_start: 0.8928 (tmtt) cc_final: 0.8705 (tmtt) REVERT: B 32 MET cc_start: 0.9125 (OUTLIER) cc_final: 0.8519 (ppp) REVERT: B 87 ASP cc_start: 0.8502 (OUTLIER) cc_final: 0.8055 (m-30) REVERT: B 221 MET cc_start: 0.8754 (mpp) cc_final: 0.7670 (mpp) REVERT: B 261 LEU cc_start: 0.8915 (tt) cc_final: 0.8615 (tt) REVERT: B 316 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8917 (mp) REVERT: B 329 SER cc_start: 0.9435 (m) cc_final: 0.9205 (m) outliers start: 36 outliers final: 28 residues processed: 194 average time/residue: 0.2181 time to fit residues: 60.4048 Evaluate side-chains 203 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 170 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 576 TRP Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 316 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 86 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 120 optimal weight: 0.3980 chunk 103 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 80 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 110 optimal weight: 6.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 223 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10645 Z= 0.184 Angle : 0.590 11.497 14480 Z= 0.302 Chirality : 0.043 0.157 1569 Planarity : 0.004 0.048 1911 Dihedral : 4.230 22.530 1460 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.24 % Allowed : 19.82 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.23), residues: 1319 helix: 1.06 (0.32), residues: 275 sheet: 0.13 (0.25), residues: 388 loop : -0.07 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 317 HIS 0.003 0.001 HIS A 533 PHE 0.020 0.001 PHE A 197 TYR 0.034 0.001 TYR A 609 ARG 0.008 0.000 ARG A 321 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 170 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 286 GLN cc_start: 0.7987 (tp40) cc_final: 0.7567 (tm-30) REVERT: A 287 LEU cc_start: 0.7964 (tp) cc_final: 0.7647 (tp) REVERT: A 617 THR cc_start: 0.8973 (m) cc_final: 0.8485 (p) REVERT: A 626 LYS cc_start: 0.8625 (mptt) cc_final: 0.8347 (mmtm) REVERT: A 646 MET cc_start: 0.7871 (tmm) cc_final: 0.6683 (tmm) REVERT: A 650 GLU cc_start: 0.7921 (tp30) cc_final: 0.7535 (tm-30) REVERT: A 768 MET cc_start: 0.6538 (mtm) cc_final: 0.5999 (ttm) REVERT: C 39 GLU cc_start: 0.8752 (mp0) cc_final: 0.8375 (mp0) REVERT: C 78 LYS cc_start: 0.7984 (mmtt) cc_final: 0.7627 (mmtt) REVERT: D 183 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7663 (tt0) REVERT: D 207 ASP cc_start: 0.7871 (t0) cc_final: 0.7574 (t0) REVERT: D 232 GLU cc_start: 0.8043 (tp30) cc_final: 0.7716 (tp30) REVERT: E 50 MET cc_start: 0.7338 (tpp) cc_final: 0.7038 (tpp) REVERT: E 87 THR cc_start: 0.8942 (OUTLIER) cc_final: 0.8645 (p) REVERT: B 31 LYS cc_start: 0.8920 (tmtt) cc_final: 0.8694 (tmtt) REVERT: B 32 MET cc_start: 0.9130 (OUTLIER) cc_final: 0.8532 (ppp) REVERT: B 87 ASP cc_start: 0.8499 (OUTLIER) cc_final: 0.8048 (m-30) REVERT: B 188 ASP cc_start: 0.7759 (t0) cc_final: 0.7437 (m-30) REVERT: B 221 MET cc_start: 0.8801 (mpp) cc_final: 0.7742 (mpp) REVERT: B 261 LEU cc_start: 0.8911 (tt) cc_final: 0.8614 (tt) REVERT: B 316 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8902 (mp) REVERT: B 329 SER cc_start: 0.9431 (m) cc_final: 0.9205 (m) outliers start: 36 outliers final: 30 residues processed: 190 average time/residue: 0.2320 time to fit residues: 63.6899 Evaluate side-chains 202 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 167 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 316 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 91 optimal weight: 0.0050 chunk 5 optimal weight: 3.9990 overall best weight: 1.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 GLN B 301 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.134761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.101372 restraints weight = 19829.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.102473 restraints weight = 15010.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.102494 restraints weight = 12461.234| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10645 Z= 0.274 Angle : 0.617 11.249 14480 Z= 0.321 Chirality : 0.043 0.155 1569 Planarity : 0.004 0.047 1911 Dihedral : 4.427 22.473 1460 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.42 % Allowed : 20.00 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.23), residues: 1319 helix: 0.95 (0.32), residues: 276 sheet: -0.03 (0.25), residues: 387 loop : -0.17 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 317 HIS 0.003 0.001 HIS B 347 PHE 0.021 0.001 PHE A 197 TYR 0.034 0.002 TYR A 609 ARG 0.008 0.001 ARG A 321 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2249.55 seconds wall clock time: 42 minutes 40.28 seconds (2560.28 seconds total)