Starting phenix.real_space_refine on Thu Jun 12 17:00:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j8f_36068/06_2025/8j8f_36068.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j8f_36068/06_2025/8j8f_36068.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j8f_36068/06_2025/8j8f_36068.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j8f_36068/06_2025/8j8f_36068.map" model { file = "/net/cci-nas-00/data/ceres_data/8j8f_36068/06_2025/8j8f_36068.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j8f_36068/06_2025/8j8f_36068.cif" } resolution = 2.98 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= -0.000 sd= 0.027 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: 6 Type Number sf(0) Gaussians Ca 3 9.91 5 P 39 5.49 5 S 71 5.16 5 C 8957 2.51 5 N 2340 2.21 5 O 2749 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14159 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1005, 8212 Classifications: {'peptide': 1005} Link IDs: {'PTRANS': 37, 'TRANS': 967} Chain: "B" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1762 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 2} Link IDs: {'PTRANS': 13, 'TRANS': 204} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 3418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3418 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 10, 'TRANS': 408} Chain breaks: 1 Chain: "P" Number of atoms: 291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 291 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "T" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 445 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 31 Unusual residues: {' CA': 3, 'DCP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 9.16, per 1000 atoms: 0.65 Number of scatterers: 14159 At special positions: 0 Unit cell: (95.76, 123.48, 146.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 3 19.99 S 71 16.00 P 39 15.00 O 2749 8.00 N 2340 7.00 C 8957 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: 3.65 Conformation dependent library (CDL) restraints added in 1.7 seconds 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3140 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 20 sheets defined 39.5% alpha, 18.9% beta 10 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 4.87 Creating SS restraints... Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 108 through 118 Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 209 through 220 Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.595A pdb=" N GLU A 229 " --> pdb=" O SER A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 253 Processing helix chain 'A' and resid 267 through 280 Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 380 through 390 Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'A' and resid 448 through 474 removed outlier: 3.631A pdb=" N GLN A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 487 Processing helix chain 'A' and resid 497 through 502 removed outlier: 3.559A pdb=" N ILE A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 514 Processing helix chain 'A' and resid 552 through 562 Processing helix chain 'A' and resid 564 through 566 No H-bonds generated for 'chain 'A' and resid 564 through 566' Processing helix chain 'A' and resid 576 through 591 removed outlier: 3.902A pdb=" N GLN A 589 " --> pdb=" O GLN A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 642 Processing helix chain 'A' and resid 646 through 672 removed outlier: 3.528A pdb=" N GLY A 672 " --> pdb=" O TYR A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 703 Processing helix chain 'A' and resid 763 through 781 Processing helix chain 'A' and resid 837 through 857 Processing helix chain 'A' and resid 862 through 883 removed outlier: 3.509A pdb=" N ARG A 883 " --> pdb=" O GLU A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.977A pdb=" N MET A 891 " --> pdb=" O GLU A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 918 Processing helix chain 'A' and resid 967 through 981 removed outlier: 3.953A pdb=" N TYR A 971 " --> pdb=" O PHE A 967 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN A 981 " --> pdb=" O SER A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 997 removed outlier: 3.978A pdb=" N MET A 996 " --> pdb=" O PHE A 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 18 No H-bonds generated for 'chain 'B' and resid 16 through 18' Processing helix chain 'B' and resid 19 through 38 removed outlier: 4.094A pdb=" N MET B 23 " --> pdb=" O TRP B 19 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N SER B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N GLN B 25 " --> pdb=" O PRO B 21 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N GLU B 28 " --> pdb=" O SER B 24 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLU B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL B 33 " --> pdb=" O PHE B 29 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N SER B 35 " --> pdb=" O ASN B 31 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N TRP B 36 " --> pdb=" O GLU B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 101 removed outlier: 4.036A pdb=" N GLU B 91 " --> pdb=" O LYS B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 113 Processing helix chain 'B' and resid 133 through 151 removed outlier: 5.569A pdb=" N LYS B 139 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ILE B 140 " --> pdb=" O TYR B 136 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N HIS B 151 " --> pdb=" O HIS B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 170 removed outlier: 3.672A pdb=" N LEU B 170 " --> pdb=" O ILE B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 192 removed outlier: 3.692A pdb=" N GLU B 190 " --> pdb=" O HIS B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 205 Processing helix chain 'C' and resid 4 through 19 removed outlier: 3.571A pdb=" N SER C 19 " --> pdb=" O SER C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 42 Processing helix chain 'C' and resid 57 through 61 Processing helix chain 'C' and resid 107 through 117 Processing helix chain 'C' and resid 147 through 158 Processing helix chain 'C' and resid 177 through 188 Processing helix chain 'C' and resid 249 through 257 removed outlier: 3.544A pdb=" N LEU C 253 " --> pdb=" O ASP C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 287 No H-bonds generated for 'chain 'C' and resid 285 through 287' Processing helix chain 'C' and resid 288 through 298 Processing helix chain 'C' and resid 315 through 323 removed outlier: 3.516A pdb=" N LEU C 319 " --> pdb=" O GLY C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 341 removed outlier: 3.527A pdb=" N SER C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 351 Processing helix chain 'C' and resid 352 through 362 removed outlier: 3.628A pdb=" N LEU C 361 " --> pdb=" O SER C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 374 Processing helix chain 'C' and resid 391 through 395 removed outlier: 3.592A pdb=" N CYS C 394 " --> pdb=" O ASN C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 405 Processing helix chain 'C' and resid 406 through 425 removed outlier: 4.001A pdb=" N ARG C 423 " --> pdb=" O ASP C 419 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 127 removed outlier: 6.971A pdb=" N LYS A 21 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N TRP A 8 " --> pdb=" O TYR A 19 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N TYR A 19 " --> pdb=" O TRP A 8 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N GLU A 10 " --> pdb=" O PHE A 17 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N PHE A 17 " --> pdb=" O GLU A 10 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N TYR A 140 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N PHE A 31 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N CYS A 142 " --> pdb=" O PHE A 31 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ARG A 33 " --> pdb=" O CYS A 142 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N HIS A 141 " --> pdb=" O LYS A 134 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N LYS A 134 " --> pdb=" O HIS A 141 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 43 removed outlier: 3.647A pdb=" N GLY A 61 " --> pdb=" O MET A 88 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU A 90 " --> pdb=" O PRO A 59 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU A 92 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ALA A 57 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N ILE A 516 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ARG A 64 " --> pdb=" O ILE A 516 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL A 518 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ILE A 66 " --> pdb=" O VAL A 518 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 73 removed outlier: 6.256A pdb=" N LEU A 568 " --> pdb=" O ASP A 616 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASP A 616 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 570 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER A 574 " --> pdb=" O SER A 610 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 610 " --> pdb=" O SER A 574 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 223 removed outlier: 6.542A pdb=" N LEU A 222 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N SER A 184 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL A 259 " --> pdb=" O PHE A 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 285 through 287 Processing sheet with id=AA6, first strand: chain 'A' and resid 300 through 304 removed outlier: 3.600A pdb=" N ASN A 315 " --> pdb=" O GLN A 304 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 355 through 362 removed outlier: 6.814A pdb=" N THR A 369 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG A 407 " --> pdb=" O VAL A 418 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 533 through 534 removed outlier: 4.399A pdb=" N GLY A 750 " --> pdb=" O PHE A 534 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A 706 " --> pdb=" O ARG A 713 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 533 through 534 removed outlier: 4.399A pdb=" N GLY A 750 " --> pdb=" O PHE A 534 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N SER A 747 " --> pdb=" O GLU A 758 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLU A 758 " --> pdb=" O SER A 747 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR A 749 " --> pdb=" O PHE A 756 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA A 793 " --> pdb=" O ILE A 547 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASP A 549 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N PHE A 791 " --> pdb=" O ASP A 549 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU A 798 " --> pdb=" O THR A 807 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N THR A 807 " --> pdb=" O LEU A 798 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 892 through 895 Processing sheet with id=AB2, first strand: chain 'A' and resid 892 through 895 Processing sheet with id=AB3, first strand: chain 'B' and resid 116 through 120 removed outlier: 3.805A pdb=" N ILE B 117 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL B 64 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N CYS B 63 " --> pdb=" O TYR B 156 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU B 155 " --> pdb=" O ILE B 177 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 69 through 70 Processing sheet with id=AB5, first strand: chain 'C' and resid 77 through 82 removed outlier: 4.037A pdb=" N SER C 196 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR C 199 " --> pdb=" O GLN C 208 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLN C 208 " --> pdb=" O TYR C 199 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 85 through 87 removed outlier: 4.479A pdb=" N SER C 85 " --> pdb=" O LEU C 131 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU C 131 " --> pdb=" O SER C 85 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 124 through 126 removed outlier: 7.452A pdb=" N ILE C 142 " --> pdb=" O ASP C 125 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 222 through 227 removed outlier: 4.239A pdb=" N VAL C 237 " --> pdb=" O ILE C 245 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 266 through 268 Processing sheet with id=AC1, first strand: chain 'C' and resid 302 through 304 Processing sheet with id=AC2, first strand: chain 'C' and resid 375 through 380 removed outlier: 3.799A pdb=" N ASN C 386 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLU C 380 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL C 384 " --> pdb=" O GLU C 380 " (cutoff:3.500A) 569 hydrogen bonds defined for protein. 1614 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 21 hydrogen bonds 42 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 5.39 Time building geometry restraints manager: 4.34 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: 3985 1.34 - 1.45: 2554 1.45 - 1.57: 7812 1.57 - 1.69: 75 1.69 - 1.81: 108 Bond restraints: 14534 Sorted by residual: bond pdb=" O1G DCP A1101 " pdb=" PG DCP A1101 " ideal model delta sigma weight residual 1.491 1.530 -0.039 2.20e-02 2.07e+03 3.16e+00 bond pdb=" O3G DCP A1101 " pdb=" PG DCP A1101 " ideal model delta sigma weight residual 1.533 1.489 0.044 2.80e-02 1.28e+03 2.46e+00 bond pdb=" C GLU B 20 " pdb=" N PRO B 21 " ideal model delta sigma weight residual 1.334 1.360 -0.026 2.34e-02 1.83e+03 1.26e+00 bond pdb=" C ALA B 9 " pdb=" N PRO B 10 " ideal model delta sigma weight residual 1.334 1.357 -0.023 2.34e-02 1.83e+03 1.01e+00 bond pdb=" CA THR B 85 " pdb=" CB THR B 85 " ideal model delta sigma weight residual 1.524 1.540 -0.016 1.62e-02 3.81e+03 9.78e-01 ... (remaining 14529 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 19369 1.27 - 2.55: 336 2.55 - 3.82: 70 3.82 - 5.10: 18 5.10 - 6.37: 7 Bond angle restraints: 19800 Sorted by residual: angle pdb=" O3B DCP A1101 " pdb=" PG DCP A1101 " pdb=" O3G DCP A1101 " ideal model delta sigma weight residual 104.48 110.61 -6.13 1.14e+00 7.76e-01 2.92e+01 angle pdb=" O1G DCP A1101 " pdb=" PG DCP A1101 " pdb=" O3B DCP A1101 " ideal model delta sigma weight residual 110.47 104.48 5.99 1.64e+00 3.70e-01 1.33e+01 angle pdb=" C ASP A 751 " pdb=" N THR A 752 " pdb=" CA THR A 752 " ideal model delta sigma weight residual 121.54 126.89 -5.35 1.91e+00 2.74e-01 7.85e+00 angle pdb=" CA VAL C 385 " pdb=" C VAL C 385 " pdb=" N ASN C 386 " ideal model delta sigma weight residual 116.60 120.47 -3.87 1.45e+00 4.76e-01 7.12e+00 angle pdb=" N SER C 100 " pdb=" CA SER C 100 " pdb=" C SER C 100 " ideal model delta sigma weight residual 114.04 110.76 3.28 1.24e+00 6.50e-01 7.02e+00 ... (remaining 19795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 7651 17.66 - 35.32: 811 35.32 - 52.98: 191 52.98 - 70.63: 41 70.63 - 88.29: 10 Dihedral angle restraints: 8704 sinusoidal: 3833 harmonic: 4871 Sorted by residual: dihedral pdb=" CA PRO A 593 " pdb=" C PRO A 593 " pdb=" N PRO A 594 " pdb=" CA PRO A 594 " ideal model delta harmonic sigma weight residual 180.00 148.94 31.06 0 5.00e+00 4.00e-02 3.86e+01 dihedral pdb=" CA ASP A 751 " pdb=" C ASP A 751 " pdb=" N THR A 752 " pdb=" CA THR A 752 " ideal model delta harmonic sigma weight residual 180.00 157.04 22.96 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA THR A 752 " pdb=" C THR A 752 " pdb=" N ASP A 753 " pdb=" CA ASP A 753 " ideal model delta harmonic sigma weight residual 180.00 159.95 20.05 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 8701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1395 0.029 - 0.057: 519 0.057 - 0.086: 146 0.086 - 0.114: 104 0.114 - 0.143: 27 Chirality restraints: 2191 Sorted by residual: chirality pdb=" CA GLU B 20 " pdb=" N GLU B 20 " pdb=" C GLU B 20 " pdb=" CB GLU B 20 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.11e-01 chirality pdb=" CA SER A 51 " pdb=" N SER A 51 " pdb=" C SER A 51 " pdb=" CB SER A 51 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" CA ILE B 45 " pdb=" N ILE B 45 " pdb=" C ILE B 45 " pdb=" CB ILE B 45 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 2188 not shown) Planarity restraints: 2390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 593 " -0.055 5.00e-02 4.00e+02 8.41e-02 1.13e+01 pdb=" N PRO A 594 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 594 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 594 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 751 " -0.009 2.00e-02 2.50e+03 1.74e-02 3.04e+00 pdb=" C ASP A 751 " 0.030 2.00e-02 2.50e+03 pdb=" O ASP A 751 " -0.012 2.00e-02 2.50e+03 pdb=" N THR A 752 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 273 " -0.009 2.00e-02 2.50e+03 1.71e-02 2.91e+00 pdb=" C THR A 273 " 0.030 2.00e-02 2.50e+03 pdb=" O THR A 273 " -0.011 2.00e-02 2.50e+03 pdb=" N ASN A 274 " -0.010 2.00e-02 2.50e+03 ... (remaining 2387 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 56 2.47 - 3.08: 9197 3.08 - 3.68: 21105 3.68 - 4.29: 31213 4.29 - 4.90: 51607 Nonbonded interactions: 113178 Sorted by model distance: nonbonded pdb="CA CA A1103 " pdb="CA CA A1104 " model vdw 1.861 1.980 nonbonded pdb=" O TRP A 112 " pdb=" OG SER A 116 " model vdw 2.195 3.040 nonbonded pdb=" OH TYR A 749 " pdb=" O LYS A 803 " model vdw 2.208 3.040 nonbonded pdb=" O ILE A 183 " pdb=" ND2 ASN A 204 " model vdw 2.244 3.120 nonbonded pdb=" O ASN A 181 " pdb=" OH TYR A 271 " model vdw 2.244 3.040 ... (remaining 113173 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: 6.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.700 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 38.420 Find NCS groups from input model: 0.130 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: 0.010 Load rotamer database and sin/cos tables:19.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 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 0.044 14534 Z= 0.100 Angle : 0.457 6.371 19800 Z= 0.254 Chirality : 0.039 0.143 2191 Planarity : 0.003 0.084 2390 Dihedral : 15.395 88.293 5564 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.07 % Allowed : 0.40 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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: 0.21 (0.22), residues: 1634 helix: 1.31 (0.22), residues: 583 sheet: 0.24 (0.30), residues: 337 loop : -0.87 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 136 HIS 0.005 0.001 HIS A 839 PHE 0.012 0.001 PHE C 22 TYR 0.016 0.001 TYR A 668 ARG 0.001 0.000 ARG A 97 Details of bonding type rmsd hydrogen bonds : bond 0.16269 ( 585) hydrogen bonds : angle 5.92144 ( 1656) covalent geometry : bond 0.00207 (14534) covalent geometry : angle 0.45673 (19800) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 270 time to evaluate : 1.778 Fit side-chains REVERT: A 859 MET cc_start: 0.3607 (mpp) cc_final: 0.2867 (tpt) REVERT: B 8 HIS cc_start: 0.4994 (m90) cc_final: 0.4673 (m-70) REVERT: B 83 ASN cc_start: 0.7304 (m-40) cc_final: 0.6998 (m110) REVERT: C 53 VAL cc_start: 0.5731 (t) cc_final: 0.5339 (p) REVERT: C 205 LEU cc_start: 0.4724 (mm) cc_final: 0.4377 (mt) outliers start: 1 outliers final: 3 residues processed: 271 average time/residue: 1.5306 time to fit residues: 455.2287 Evaluate side-chains 159 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 156 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain B residue 68 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 20.0000 chunk 125 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 96 optimal weight: 0.0770 chunk 149 optimal weight: 10.0000 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN A 442 GLN A 907 ASN A 964 GLN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN C 134 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.207230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.157933 restraints weight = 17144.089| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 1.70 r_work: 0.3544 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 14534 Z= 0.236 Angle : 0.643 8.226 19800 Z= 0.351 Chirality : 0.045 0.160 2191 Planarity : 0.005 0.085 2390 Dihedral : 14.347 87.812 2245 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.97 % Allowed : 12.14 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.21), residues: 1634 helix: 0.90 (0.22), residues: 588 sheet: -0.12 (0.29), residues: 339 loop : -1.19 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 470 HIS 0.005 0.001 HIS B 147 PHE 0.027 0.002 PHE C 104 TYR 0.019 0.002 TYR A 190 ARG 0.005 0.001 ARG A 823 Details of bonding type rmsd hydrogen bonds : bond 0.05933 ( 585) hydrogen bonds : angle 4.91409 ( 1656) covalent geometry : bond 0.00557 (14534) covalent geometry : angle 0.64311 (19800) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 172 time to evaluate : 1.622 Fit side-chains revert: symmetry clash REVERT: A 174 LYS cc_start: 0.6943 (ptpt) cc_final: 0.6740 (mtmm) REVERT: A 744 ARG cc_start: 0.7220 (OUTLIER) cc_final: 0.6747 (mtm-85) REVERT: A 837 LYS cc_start: 0.8421 (tppt) cc_final: 0.8084 (tppt) REVERT: A 853 MET cc_start: 0.5143 (OUTLIER) cc_final: 0.4491 (tpt) REVERT: A 859 MET cc_start: 0.3674 (mpp) cc_final: 0.2522 (tpt) REVERT: A 867 ASP cc_start: 0.6753 (t0) cc_final: 0.6551 (t0) REVERT: A 956 ARG cc_start: 0.7247 (OUTLIER) cc_final: 0.5857 (mmt180) REVERT: B 8 HIS cc_start: 0.5184 (m90) cc_final: 0.4369 (m-70) REVERT: B 83 ASN cc_start: 0.7264 (m-40) cc_final: 0.6792 (m110) REVERT: B 177 ILE cc_start: 0.7872 (mt) cc_final: 0.7671 (mm) REVERT: C 53 VAL cc_start: 0.5791 (t) cc_final: 0.5288 (p) REVERT: C 63 GLU cc_start: 0.6669 (mm-30) cc_final: 0.6379 (pp20) REVERT: C 205 LEU cc_start: 0.4965 (mm) cc_final: 0.4513 (mt) outliers start: 45 outliers final: 19 residues processed: 195 average time/residue: 1.1691 time to fit residues: 252.8314 Evaluate side-chains 168 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 744 ARG Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 956 ARG Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 308 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 10 optimal weight: 0.6980 chunk 96 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 chunk 79 optimal weight: 0.7980 chunk 159 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 964 GLN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.208640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.166966 restraints weight = 17196.628| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 3.65 r_work: 0.3437 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14534 Z= 0.150 Angle : 0.553 9.891 19800 Z= 0.303 Chirality : 0.042 0.186 2191 Planarity : 0.004 0.082 2390 Dihedral : 14.120 87.710 2239 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.90 % Allowed : 16.03 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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 (0.21), residues: 1634 helix: 1.06 (0.22), residues: 588 sheet: -0.21 (0.29), residues: 345 loop : -1.16 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 470 HIS 0.004 0.001 HIS A 839 PHE 0.020 0.001 PHE C 104 TYR 0.015 0.001 TYR A 668 ARG 0.006 0.000 ARG A 713 Details of bonding type rmsd hydrogen bonds : bond 0.04901 ( 585) hydrogen bonds : angle 4.68355 ( 1656) covalent geometry : bond 0.00343 (14534) covalent geometry : angle 0.55350 (19800) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 164 time to evaluate : 1.633 Fit side-chains REVERT: A 132 LEU cc_start: 0.7711 (mp) cc_final: 0.7246 (mm) REVERT: A 540 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.7989 (mtt) REVERT: A 688 THR cc_start: 0.8344 (OUTLIER) cc_final: 0.7859 (m) REVERT: A 853 MET cc_start: 0.4970 (OUTLIER) cc_final: 0.4335 (tpt) REVERT: A 859 MET cc_start: 0.3488 (mpp) cc_final: 0.2458 (tpt) REVERT: A 942 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.6712 (mtpp) REVERT: A 956 ARG cc_start: 0.7276 (OUTLIER) cc_final: 0.5908 (mmt180) REVERT: B 8 HIS cc_start: 0.5182 (m90) cc_final: 0.4329 (m-70) REVERT: B 53 LEU cc_start: 0.7245 (mp) cc_final: 0.6428 (tt) REVERT: B 83 ASN cc_start: 0.7142 (m-40) cc_final: 0.6635 (m110) REVERT: C 11 LYS cc_start: 0.4987 (OUTLIER) cc_final: 0.4436 (mmtp) REVERT: C 53 VAL cc_start: 0.5489 (t) cc_final: 0.5076 (p) REVERT: C 63 GLU cc_start: 0.6652 (mm-30) cc_final: 0.6326 (pp20) REVERT: C 93 LYS cc_start: 0.4845 (pptt) cc_final: 0.3384 (mmtm) REVERT: C 95 MET cc_start: 0.4821 (mmp) cc_final: 0.3506 (mpt) REVERT: C 205 LEU cc_start: 0.4993 (mm) cc_final: 0.4548 (mt) outliers start: 44 outliers final: 14 residues processed: 190 average time/residue: 1.1022 time to fit residues: 234.3853 Evaluate side-chains 165 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 956 ARG Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 308 PHE Chi-restraints excluded: chain C residue 311 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 54 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 110 optimal weight: 0.0970 chunk 91 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 118 optimal weight: 0.2980 chunk 142 optimal weight: 20.0000 chunk 16 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 899 ASN A 964 GLN B 55 GLN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.208949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.159911 restraints weight = 17050.423| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 1.61 r_work: 0.3580 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14534 Z= 0.139 Angle : 0.538 7.006 19800 Z= 0.295 Chirality : 0.041 0.230 2191 Planarity : 0.004 0.083 2390 Dihedral : 14.046 87.689 2239 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.03 % Allowed : 17.35 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.21), residues: 1634 helix: 1.12 (0.22), residues: 588 sheet: -0.25 (0.28), residues: 345 loop : -1.17 (0.24), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 136 HIS 0.005 0.001 HIS A 839 PHE 0.027 0.001 PHE A 992 TYR 0.014 0.001 TYR A 668 ARG 0.007 0.000 ARG A 713 Details of bonding type rmsd hydrogen bonds : bond 0.04558 ( 585) hydrogen bonds : angle 4.59001 ( 1656) covalent geometry : bond 0.00313 (14534) covalent geometry : angle 0.53826 (19800) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 159 time to evaluate : 1.457 Fit side-chains revert: symmetry clash REVERT: A 132 LEU cc_start: 0.7638 (mp) cc_final: 0.7200 (mm) REVERT: A 398 ASP cc_start: 0.7610 (t0) cc_final: 0.7089 (t0) REVERT: A 455 MET cc_start: 0.7685 (mtp) cc_final: 0.7468 (mtm) REVERT: A 540 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.7895 (mtt) REVERT: A 608 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.6816 (mp) REVERT: A 688 THR cc_start: 0.8306 (OUTLIER) cc_final: 0.7795 (m) REVERT: A 693 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7446 (mpp-170) REVERT: A 744 ARG cc_start: 0.7039 (OUTLIER) cc_final: 0.6601 (mtm-85) REVERT: A 853 MET cc_start: 0.4991 (OUTLIER) cc_final: 0.4428 (tpt) REVERT: A 859 MET cc_start: 0.3605 (mpp) cc_final: 0.2465 (tpt) REVERT: B 8 HIS cc_start: 0.5165 (m90) cc_final: 0.4416 (m-70) REVERT: C 11 LYS cc_start: 0.5001 (OUTLIER) cc_final: 0.4399 (mmtp) REVERT: C 63 GLU cc_start: 0.6748 (mm-30) cc_final: 0.6384 (pp20) REVERT: C 95 MET cc_start: 0.4928 (mmp) cc_final: 0.3869 (mpt) REVERT: C 205 LEU cc_start: 0.5250 (mm) cc_final: 0.4769 (mt) REVERT: C 375 MET cc_start: 0.8163 (mtp) cc_final: 0.7679 (mtp) REVERT: C 403 ILE cc_start: 0.7220 (mt) cc_final: 0.6500 (tt) outliers start: 46 outliers final: 20 residues processed: 191 average time/residue: 1.1307 time to fit residues: 241.0139 Evaluate side-chains 171 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 693 ARG Chi-restraints excluded: chain A residue 744 ARG Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 308 PHE Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 386 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 108 optimal weight: 4.9990 chunk 136 optimal weight: 8.9990 chunk 164 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 130 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 129 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 964 GLN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.206672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.157649 restraints weight = 17032.972| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 1.64 r_work: 0.3548 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14534 Z= 0.178 Angle : 0.580 7.251 19800 Z= 0.316 Chirality : 0.043 0.158 2191 Planarity : 0.005 0.082 2390 Dihedral : 14.242 87.941 2239 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.76 % Allowed : 18.14 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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: -0.35 (0.21), residues: 1634 helix: 1.06 (0.22), residues: 579 sheet: -0.35 (0.28), residues: 348 loop : -1.24 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 136 HIS 0.004 0.001 HIS A 839 PHE 0.021 0.002 PHE A 55 TYR 0.015 0.001 TYR A 668 ARG 0.009 0.000 ARG A 713 Details of bonding type rmsd hydrogen bonds : bond 0.05059 ( 585) hydrogen bonds : angle 4.69286 ( 1656) covalent geometry : bond 0.00414 (14534) covalent geometry : angle 0.57983 (19800) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 157 time to evaluate : 1.495 Fit side-chains revert: symmetry clash REVERT: A 132 LEU cc_start: 0.7748 (mp) cc_final: 0.7320 (mm) REVERT: A 398 ASP cc_start: 0.7672 (t0) cc_final: 0.7156 (t0) REVERT: A 608 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.6841 (mp) REVERT: A 688 THR cc_start: 0.8365 (OUTLIER) cc_final: 0.7902 (m) REVERT: A 706 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6019 (pp20) REVERT: A 713 ARG cc_start: 0.6292 (ttm110) cc_final: 0.5990 (tmt170) REVERT: A 744 ARG cc_start: 0.7053 (OUTLIER) cc_final: 0.6607 (mtm-85) REVERT: A 853 MET cc_start: 0.5048 (OUTLIER) cc_final: 0.4414 (tpt) REVERT: A 859 MET cc_start: 0.3752 (mpp) cc_final: 0.2447 (tpt) REVERT: A 916 LYS cc_start: 0.8610 (ptmt) cc_final: 0.7973 (mptm) REVERT: A 956 ARG cc_start: 0.7235 (OUTLIER) cc_final: 0.6251 (mmp-170) REVERT: B 8 HIS cc_start: 0.5258 (m90) cc_final: 0.4526 (m-70) REVERT: C 11 LYS cc_start: 0.5021 (OUTLIER) cc_final: 0.4426 (mmtp) REVERT: C 63 GLU cc_start: 0.6802 (mm-30) cc_final: 0.6418 (pp20) REVERT: C 93 LYS cc_start: 0.4768 (pptt) cc_final: 0.3030 (mptp) REVERT: C 95 MET cc_start: 0.4850 (mmp) cc_final: 0.3497 (mtt) REVERT: C 134 ASN cc_start: 0.7657 (t0) cc_final: 0.7254 (t0) REVERT: C 205 LEU cc_start: 0.5361 (mm) cc_final: 0.4875 (mt) outliers start: 57 outliers final: 28 residues processed: 195 average time/residue: 1.1322 time to fit residues: 246.2153 Evaluate side-chains 182 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 147 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 134 LYS Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 744 ARG Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 956 ARG Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 83 PHE Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 308 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 78 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 160 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 125 optimal weight: 0.4980 chunk 45 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 964 GLN B 55 GLN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.208165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.158472 restraints weight = 17191.835| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 1.64 r_work: 0.3576 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14534 Z= 0.132 Angle : 0.551 9.241 19800 Z= 0.298 Chirality : 0.041 0.159 2191 Planarity : 0.004 0.082 2390 Dihedral : 14.085 87.996 2239 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.20 % Favored : 94.74 % Rotamer: Outliers : 3.36 % Allowed : 19.53 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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: -0.27 (0.21), residues: 1634 helix: 1.17 (0.22), residues: 587 sheet: -0.39 (0.28), residues: 350 loop : -1.19 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 470 HIS 0.005 0.001 HIS A 839 PHE 0.012 0.001 PHE C 104 TYR 0.013 0.001 TYR A 668 ARG 0.011 0.000 ARG C 255 Details of bonding type rmsd hydrogen bonds : bond 0.04374 ( 585) hydrogen bonds : angle 4.54554 ( 1656) covalent geometry : bond 0.00296 (14534) covalent geometry : angle 0.55116 (19800) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 157 time to evaluate : 1.571 Fit side-chains revert: symmetry clash REVERT: A 132 LEU cc_start: 0.7727 (mp) cc_final: 0.7311 (mm) REVERT: A 398 ASP cc_start: 0.7636 (t0) cc_final: 0.7086 (t0) REVERT: A 455 MET cc_start: 0.7717 (mtp) cc_final: 0.7508 (mtm) REVERT: A 540 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.7917 (mtt) REVERT: A 608 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.6761 (mp) REVERT: A 688 THR cc_start: 0.8295 (OUTLIER) cc_final: 0.7797 (m) REVERT: A 693 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7451 (mpp-170) REVERT: A 706 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.5929 (pp20) REVERT: A 744 ARG cc_start: 0.6955 (OUTLIER) cc_final: 0.6517 (mtm-85) REVERT: A 853 MET cc_start: 0.5075 (OUTLIER) cc_final: 0.4454 (tpt) REVERT: A 859 MET cc_start: 0.3666 (mpp) cc_final: 0.2420 (tpt) REVERT: A 956 ARG cc_start: 0.7233 (OUTLIER) cc_final: 0.5932 (mmp-170) REVERT: B 8 HIS cc_start: 0.5100 (m90) cc_final: 0.4387 (m-70) REVERT: C 63 GLU cc_start: 0.6794 (mm-30) cc_final: 0.6394 (pp20) REVERT: C 93 LYS cc_start: 0.4726 (pptt) cc_final: 0.3062 (mptp) REVERT: C 95 MET cc_start: 0.4860 (mmp) cc_final: 0.3650 (mtt) REVERT: C 133 ASN cc_start: 0.6343 (m-40) cc_final: 0.5569 (p0) REVERT: C 205 LEU cc_start: 0.5287 (mm) cc_final: 0.4812 (mt) REVERT: C 255 ARG cc_start: 0.6286 (mmm160) cc_final: 0.5852 (mtm180) outliers start: 51 outliers final: 26 residues processed: 191 average time/residue: 1.1114 time to fit residues: 236.7785 Evaluate side-chains 178 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 693 ARG Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 744 ARG Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 956 ARG Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 83 PHE Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 308 PHE Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 384 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 147 optimal weight: 30.0000 chunk 19 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 chunk 120 optimal weight: 4.9990 chunk 161 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 164 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 143 optimal weight: 0.5980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 964 GLN B 55 GLN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.206093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.157221 restraints weight = 17113.612| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 1.67 r_work: 0.3542 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14534 Z= 0.178 Angle : 0.594 7.979 19800 Z= 0.321 Chirality : 0.043 0.193 2191 Planarity : 0.005 0.083 2390 Dihedral : 14.246 88.352 2239 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.69 % Favored : 94.25 % Rotamer: Outliers : 3.56 % Allowed : 19.99 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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: -0.38 (0.21), residues: 1634 helix: 1.08 (0.22), residues: 579 sheet: -0.44 (0.28), residues: 346 loop : -1.25 (0.24), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 136 HIS 0.005 0.001 HIS A 839 PHE 0.026 0.002 PHE A 992 TYR 0.016 0.001 TYR A 637 ARG 0.009 0.001 ARG C 255 Details of bonding type rmsd hydrogen bonds : bond 0.05001 ( 585) hydrogen bonds : angle 4.69033 ( 1656) covalent geometry : bond 0.00417 (14534) covalent geometry : angle 0.59414 (19800) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 146 time to evaluate : 2.110 Fit side-chains revert: symmetry clash REVERT: A 132 LEU cc_start: 0.7827 (mp) cc_final: 0.7388 (mm) REVERT: A 398 ASP cc_start: 0.7698 (t0) cc_final: 0.7153 (t0) REVERT: A 455 MET cc_start: 0.7858 (mtp) cc_final: 0.7625 (mtm) REVERT: A 688 THR cc_start: 0.8357 (OUTLIER) cc_final: 0.7914 (m) REVERT: A 693 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7432 (mpp-170) REVERT: A 744 ARG cc_start: 0.7058 (OUTLIER) cc_final: 0.6602 (mtm-85) REVERT: A 853 MET cc_start: 0.4956 (OUTLIER) cc_final: 0.4317 (tpt) REVERT: A 859 MET cc_start: 0.3635 (mpp) cc_final: 0.2384 (tpt) REVERT: A 916 LYS cc_start: 0.8618 (ptmt) cc_final: 0.7954 (mptm) REVERT: A 956 ARG cc_start: 0.7225 (OUTLIER) cc_final: 0.6293 (mmp-170) REVERT: C 95 MET cc_start: 0.4916 (mmp) cc_final: 0.3929 (mtt) REVERT: C 133 ASN cc_start: 0.6385 (m-40) cc_final: 0.5775 (p0) REVERT: C 205 LEU cc_start: 0.5336 (mm) cc_final: 0.4860 (mt) REVERT: C 255 ARG cc_start: 0.6244 (mmm160) cc_final: 0.5804 (mtm180) outliers start: 54 outliers final: 29 residues processed: 181 average time/residue: 1.4313 time to fit residues: 288.8517 Evaluate side-chains 174 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 140 time to evaluate : 2.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 693 ARG Chi-restraints excluded: chain A residue 744 ARG Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 956 ARG Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 308 PHE Chi-restraints excluded: chain C residue 311 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 8 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 60 optimal weight: 0.0030 chunk 86 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 102 optimal weight: 0.0070 chunk 127 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.5612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN A 964 GLN B 55 GLN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.208629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.163083 restraints weight = 17111.532| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 1.84 r_work: 0.3570 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14534 Z= 0.123 Angle : 0.548 9.051 19800 Z= 0.296 Chirality : 0.041 0.165 2191 Planarity : 0.004 0.081 2390 Dihedral : 14.025 88.340 2239 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.08 % Favored : 94.86 % Rotamer: Outliers : 2.57 % Allowed : 20.91 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.21), residues: 1634 helix: 1.13 (0.22), residues: 587 sheet: -0.49 (0.28), residues: 356 loop : -1.18 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 470 HIS 0.008 0.001 HIS B 8 PHE 0.014 0.001 PHE A 992 TYR 0.014 0.001 TYR B 121 ARG 0.011 0.000 ARG A 713 Details of bonding type rmsd hydrogen bonds : bond 0.04077 ( 585) hydrogen bonds : angle 4.49329 ( 1656) covalent geometry : bond 0.00272 (14534) covalent geometry : angle 0.54752 (19800) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 146 time to evaluate : 1.672 Fit side-chains revert: symmetry clash REVERT: A 132 LEU cc_start: 0.7691 (mp) cc_final: 0.7332 (mm) REVERT: A 398 ASP cc_start: 0.7695 (t0) cc_final: 0.7189 (t0) REVERT: A 688 THR cc_start: 0.8265 (OUTLIER) cc_final: 0.7775 (m) REVERT: A 713 ARG cc_start: 0.6265 (ttm110) cc_final: 0.5961 (tmt170) REVERT: A 853 MET cc_start: 0.5065 (OUTLIER) cc_final: 0.4426 (tpt) REVERT: A 859 MET cc_start: 0.3549 (mpp) cc_final: 0.2379 (tpt) REVERT: B 1 MET cc_start: 0.5537 (mmm) cc_final: 0.5172 (mmp) REVERT: C 95 MET cc_start: 0.4853 (mmp) cc_final: 0.3968 (mtt) REVERT: C 133 ASN cc_start: 0.6334 (m-40) cc_final: 0.5808 (p0) REVERT: C 205 LEU cc_start: 0.5282 (mm) cc_final: 0.4809 (mt) REVERT: C 255 ARG cc_start: 0.6172 (mmm160) cc_final: 0.5817 (mtm180) outliers start: 39 outliers final: 23 residues processed: 173 average time/residue: 1.7405 time to fit residues: 340.9224 Evaluate side-chains 167 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 763 ASP Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 83 PHE Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 308 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 17 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 150 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 157 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 ASN A 964 GLN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN C 304 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.207983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.158576 restraints weight = 17004.867| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 1.67 r_work: 0.3571 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14534 Z= 0.145 Angle : 0.578 11.384 19800 Z= 0.311 Chirality : 0.042 0.170 2191 Planarity : 0.004 0.082 2390 Dihedral : 14.089 88.511 2239 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.63 % Favored : 94.31 % Rotamer: Outliers : 2.24 % Allowed : 21.64 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.21), residues: 1634 helix: 1.06 (0.22), residues: 587 sheet: -0.51 (0.28), residues: 356 loop : -1.19 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 470 HIS 0.008 0.001 HIS B 8 PHE 0.025 0.001 PHE A 55 TYR 0.014 0.001 TYR B 121 ARG 0.009 0.000 ARG A 713 Details of bonding type rmsd hydrogen bonds : bond 0.04435 ( 585) hydrogen bonds : angle 4.54280 ( 1656) covalent geometry : bond 0.00332 (14534) covalent geometry : angle 0.57821 (19800) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 148 time to evaluate : 2.026 Fit side-chains revert: symmetry clash REVERT: A 132 LEU cc_start: 0.7797 (mp) cc_final: 0.7378 (mm) REVERT: A 398 ASP cc_start: 0.7613 (t0) cc_final: 0.7110 (t0) REVERT: A 512 GLU cc_start: 0.7242 (tm-30) cc_final: 0.6999 (tm-30) REVERT: A 688 THR cc_start: 0.8295 (OUTLIER) cc_final: 0.7784 (m) REVERT: A 706 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6101 (pp20) REVERT: A 713 ARG cc_start: 0.6294 (ttm110) cc_final: 0.5853 (tmt170) REVERT: A 744 ARG cc_start: 0.6950 (OUTLIER) cc_final: 0.6513 (mtm-85) REVERT: A 853 MET cc_start: 0.4944 (OUTLIER) cc_final: 0.4324 (tpt) REVERT: A 859 MET cc_start: 0.3475 (mpp) cc_final: 0.2252 (tpt) REVERT: B 1 MET cc_start: 0.5401 (mmm) cc_final: 0.5028 (mmp) REVERT: C 95 MET cc_start: 0.4847 (mmp) cc_final: 0.3947 (mtt) REVERT: C 133 ASN cc_start: 0.6268 (m-40) cc_final: 0.5769 (p0) REVERT: C 205 LEU cc_start: 0.5328 (mm) cc_final: 0.4861 (mt) REVERT: C 255 ARG cc_start: 0.6049 (mmm160) cc_final: 0.5694 (mtm180) REVERT: C 365 GLU cc_start: 0.6565 (mm-30) cc_final: 0.5275 (mp0) outliers start: 34 outliers final: 21 residues processed: 174 average time/residue: 1.6289 time to fit residues: 316.2664 Evaluate side-chains 162 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 744 ARG Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 83 PHE Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 308 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 7 optimal weight: 4.9990 chunk 92 optimal weight: 0.0980 chunk 140 optimal weight: 7.9990 chunk 139 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 149 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN A 964 GLN B 55 GLN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.204412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.155171 restraints weight = 17018.013| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 1.68 r_work: 0.3517 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14534 Z= 0.229 Angle : 0.664 7.961 19800 Z= 0.357 Chirality : 0.045 0.209 2191 Planarity : 0.005 0.083 2390 Dihedral : 14.466 88.771 2239 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.36 % Favored : 93.57 % Rotamer: Outliers : 2.31 % Allowed : 22.03 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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: -0.70 (0.21), residues: 1634 helix: 0.68 (0.22), residues: 585 sheet: -0.56 (0.28), residues: 346 loop : -1.35 (0.24), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 940 HIS 0.004 0.001 HIS A 839 PHE 0.019 0.002 PHE A 370 TYR 0.020 0.002 TYR A 637 ARG 0.009 0.001 ARG C 135 Details of bonding type rmsd hydrogen bonds : bond 0.05560 ( 585) hydrogen bonds : angle 4.88607 ( 1656) covalent geometry : bond 0.00543 (14534) covalent geometry : angle 0.66427 (19800) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 150 time to evaluate : 1.470 Fit side-chains revert: symmetry clash REVERT: A 132 LEU cc_start: 0.7843 (mp) cc_final: 0.7439 (mm) REVERT: A 398 ASP cc_start: 0.7799 (t0) cc_final: 0.7286 (t0) REVERT: A 512 GLU cc_start: 0.7333 (tm-30) cc_final: 0.7090 (tm-30) REVERT: A 540 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.7955 (mtt) REVERT: A 579 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7412 (mm-30) REVERT: A 688 THR cc_start: 0.8405 (OUTLIER) cc_final: 0.8031 (m) REVERT: A 706 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6071 (pp20) REVERT: A 744 ARG cc_start: 0.7097 (OUTLIER) cc_final: 0.6633 (mtm-85) REVERT: A 853 MET cc_start: 0.5053 (OUTLIER) cc_final: 0.4379 (tpt) REVERT: A 859 MET cc_start: 0.3768 (mpp) cc_final: 0.2341 (tpt) REVERT: A 986 LYS cc_start: 0.7055 (tppt) cc_final: 0.6338 (tppp) REVERT: B 1 MET cc_start: 0.5309 (mmm) cc_final: 0.4938 (mmp) REVERT: C 93 LYS cc_start: 0.4559 (pptt) cc_final: 0.3067 (mptp) REVERT: C 95 MET cc_start: 0.5034 (mmp) cc_final: 0.3885 (mtt) REVERT: C 133 ASN cc_start: 0.6394 (m-40) cc_final: 0.5907 (p0) REVERT: C 205 LEU cc_start: 0.5375 (mm) cc_final: 0.4889 (mt) outliers start: 35 outliers final: 23 residues processed: 177 average time/residue: 1.1870 time to fit residues: 232.4835 Evaluate side-chains 170 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 579 GLU Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 744 ARG Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 152 PHE Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 308 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 45 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 126 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 140 optimal weight: 9.9990 chunk 47 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 163 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 964 GLN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.205483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.156461 restraints weight = 17293.243| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 1.76 r_work: 0.3527 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14534 Z= 0.186 Angle : 0.642 9.841 19800 Z= 0.343 Chirality : 0.044 0.193 2191 Planarity : 0.005 0.083 2390 Dihedral : 14.343 88.768 2239 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.12 % Favored : 93.82 % Rotamer: Outliers : 2.04 % Allowed : 23.02 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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: -0.66 (0.21), residues: 1634 helix: 0.74 (0.22), residues: 586 sheet: -0.52 (0.28), residues: 340 loop : -1.36 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 136 HIS 0.005 0.001 HIS A 839 PHE 0.033 0.002 PHE A 992 TYR 0.020 0.002 TYR B 121 ARG 0.011 0.001 ARG A 713 Details of bonding type rmsd hydrogen bonds : bond 0.04992 ( 585) hydrogen bonds : angle 4.79508 ( 1656) covalent geometry : bond 0.00438 (14534) covalent geometry : angle 0.64188 (19800) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12099.05 seconds wall clock time: 212 minutes 34.11 seconds (12754.11 seconds total)