Starting phenix.real_space_refine on Sat Oct 11 11:06:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j8f_36068/10_2025/8j8f_36068.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j8f_36068/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8j8f_36068/10_2025/8j8f_36068.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j8f_36068/10_2025/8j8f_36068.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j8f_36068/10_2025/8j8f_36068.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j8f_36068/10_2025/8j8f_36068.map" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 3.34, per 1000 atoms: 0.24 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: 1.21 Conformation dependent library (CDL) restraints added in 637.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.95 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: 2.68 Time building geometry restraints manager: 1.67 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: 7.290 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: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 15.970 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.650 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (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 ARG 0.001 0.000 ARG A 97 TYR 0.016 0.001 TYR A 668 PHE 0.012 0.001 PHE C 22 TRP 0.005 0.001 TRP C 136 HIS 0.005 0.001 HIS A 839 Details of bonding type rmsd covalent geometry : bond 0.00207 (14534) covalent geometry : angle 0.45673 (19800) hydrogen bonds : bond 0.16269 ( 585) hydrogen bonds : angle 5.92144 ( 1656) *********************** 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 : 0.471 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: 0.6997 (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: 0.4376 (mt) outliers start: 1 outliers final: 3 residues processed: 271 average time/residue: 0.6190 time to fit residues: 183.0429 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 : 0.533 ------------------------------------------------------------------------------- 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 98 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.0000 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 10.0000 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 964 GLN ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN C 134 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.210245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.167852 restraints weight = 17133.717| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 3.67 r_work: 0.3457 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14534 Z= 0.170 Angle : 0.574 8.218 19800 Z= 0.315 Chirality : 0.043 0.163 2191 Planarity : 0.004 0.083 2390 Dihedral : 14.088 87.252 2245 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.57 % Allowed : 11.68 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.21), residues: 1634 helix: 1.21 (0.22), residues: 583 sheet: -0.07 (0.28), residues: 357 loop : -1.01 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 713 TYR 0.016 0.001 TYR A 668 PHE 0.027 0.002 PHE C 104 TRP 0.010 0.001 TRP A 470 HIS 0.005 0.001 HIS B 133 Details of bonding type rmsd covalent geometry : bond 0.00393 (14534) covalent geometry : angle 0.57362 (19800) hydrogen bonds : bond 0.05249 ( 585) hydrogen bonds : angle 4.70712 ( 1656) *********************** 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 211 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 172 time to evaluate : 0.659 Fit side-chains revert: symmetry clash REVERT: A 174 LYS cc_start: 0.7009 (ptpt) cc_final: 0.6793 (mtmm) REVERT: A 837 LYS cc_start: 0.8263 (tppt) cc_final: 0.7927 (tppt) REVERT: A 853 MET cc_start: 0.5059 (OUTLIER) cc_final: 0.4450 (tpt) REVERT: A 859 MET cc_start: 0.3401 (mpp) cc_final: 0.2500 (tpt) REVERT: A 956 ARG cc_start: 0.7255 (OUTLIER) cc_final: 0.5909 (mmp-170) REVERT: B 8 HIS cc_start: 0.5077 (m90) cc_final: 0.4320 (m-70) REVERT: B 53 LEU cc_start: 0.7292 (mp) cc_final: 0.6440 (tt) REVERT: B 83 ASN cc_start: 0.7295 (m-40) cc_final: 0.6812 (m110) REVERT: C 53 VAL cc_start: 0.5707 (t) cc_final: 0.5256 (p) REVERT: C 63 GLU cc_start: 0.6751 (mm-30) cc_final: 0.6403 (pp20) REVERT: C 205 LEU cc_start: 0.5046 (mm) cc_final: 0.4612 (mt) outliers start: 39 outliers final: 16 residues processed: 190 average time/residue: 0.5800 time to fit residues: 121.8974 Evaluate side-chains 166 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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 83 CYS Chi-restraints excluded: chain A residue 207 MET 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 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 65 CYS Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 98 LEU 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 121 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 136 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 154 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 104 optimal weight: 0.0770 overall best weight: 1.1342 ------------------------------------------------------------------------------- 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 303 ASN A 907 ASN A 964 GLN B 109 ASN B 165 ASN C 134 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.208639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.159757 restraints weight = 17253.935| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 1.69 r_work: 0.3569 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3452 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14534 Z= 0.163 Angle : 0.557 6.731 19800 Z= 0.305 Chirality : 0.042 0.145 2191 Planarity : 0.004 0.082 2390 Dihedral : 14.111 87.714 2239 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.30 % Allowed : 14.84 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.21), residues: 1634 helix: 1.08 (0.22), residues: 588 sheet: -0.20 (0.28), residues: 348 loop : -1.11 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 713 TYR 0.016 0.001 TYR A 668 PHE 0.020 0.001 PHE C 104 TRP 0.008 0.001 TRP A 470 HIS 0.004 0.001 HIS B 147 Details of bonding type rmsd covalent geometry : bond 0.00379 (14534) covalent geometry : angle 0.55699 (19800) hydrogen bonds : bond 0.05013 ( 585) hydrogen bonds : angle 4.66397 ( 1656) *********************** 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 214 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 164 time to evaluate : 0.511 Fit side-chains REVERT: A 132 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7310 (mp) REVERT: A 744 ARG cc_start: 0.7129 (OUTLIER) cc_final: 0.6690 (mtm-85) REVERT: A 853 MET cc_start: 0.5016 (OUTLIER) cc_final: 0.4368 (tpt) REVERT: A 859 MET cc_start: 0.3507 (mpp) cc_final: 0.2497 (tpt) REVERT: A 917 ASN cc_start: 0.8408 (OUTLIER) cc_final: 0.7602 (t0) REVERT: A 942 LYS cc_start: 0.7529 (OUTLIER) cc_final: 0.6678 (mtpp) REVERT: A 956 ARG cc_start: 0.7262 (OUTLIER) cc_final: 0.5923 (mmp-170) REVERT: A 996 MET cc_start: 0.6747 (pmt) cc_final: 0.6218 (pmm) REVERT: B 8 HIS cc_start: 0.5145 (m90) cc_final: 0.4345 (m-70) REVERT: B 83 ASN cc_start: 0.7169 (m-40) cc_final: 0.6687 (m110) REVERT: C 11 LYS cc_start: 0.5027 (OUTLIER) cc_final: 0.4416 (mmtp) REVERT: C 53 VAL cc_start: 0.5509 (t) cc_final: 0.5086 (p) REVERT: C 63 GLU cc_start: 0.6643 (mm-30) cc_final: 0.6330 (pp20) REVERT: C 93 LYS cc_start: 0.4766 (pptt) cc_final: 0.3357 (mmtm) REVERT: C 95 MET cc_start: 0.4762 (mmp) cc_final: 0.3455 (mpt) REVERT: C 205 LEU cc_start: 0.4947 (mm) cc_final: 0.4465 (mt) REVERT: C 403 ILE cc_start: 0.7161 (mt) cc_final: 0.6416 (tt) outliers start: 50 outliers final: 18 residues processed: 194 average time/residue: 0.5900 time to fit residues: 126.5365 Evaluate side-chains 171 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 132 LEU Chi-restraints excluded: chain A residue 134 LYS 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 620 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 917 ASN 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 65 CYS 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 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 82 optimal weight: 0.7980 chunk 107 optimal weight: 0.0870 chunk 74 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 153 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 overall best weight: 0.8360 ------------------------------------------------------------------------------- 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 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN C 134 ASN C 304 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.209286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.166045 restraints weight = 17223.251| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 3.59 r_work: 0.3472 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2144 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= 0.139 Angle : 0.537 6.873 19800 Z= 0.294 Chirality : 0.041 0.231 2191 Planarity : 0.004 0.082 2390 Dihedral : 14.027 87.678 2239 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.10 % Allowed : 16.42 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.21), residues: 1634 helix: 1.15 (0.22), residues: 587 sheet: -0.28 (0.28), residues: 348 loop : -1.11 (0.24), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 146 TYR 0.014 0.001 TYR A 668 PHE 0.027 0.001 PHE A 992 TRP 0.010 0.001 TRP A 470 HIS 0.004 0.001 HIS A 839 Details of bonding type rmsd covalent geometry : bond 0.00313 (14534) covalent geometry : angle 0.53680 (19800) hydrogen bonds : bond 0.04493 ( 585) hydrogen bonds : angle 4.55968 ( 1656) *********************** 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 204 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 157 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: A 132 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7299 (mp) REVERT: A 398 ASP cc_start: 0.7626 (t0) cc_final: 0.7100 (t0) REVERT: A 608 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.6805 (mp) REVERT: A 688 THR cc_start: 0.8304 (OUTLIER) cc_final: 0.7806 (m) REVERT: A 744 ARG cc_start: 0.7047 (OUTLIER) cc_final: 0.6619 (mtm-85) REVERT: A 853 MET cc_start: 0.4946 (OUTLIER) cc_final: 0.4399 (tpt) REVERT: A 859 MET cc_start: 0.3471 (mpp) cc_final: 0.2470 (tpt) REVERT: B 8 HIS cc_start: 0.5191 (m90) cc_final: 0.4379 (m-70) REVERT: B 53 LEU cc_start: 0.7271 (mp) cc_final: 0.6445 (tt) REVERT: B 146 GLN cc_start: 0.6942 (mt0) cc_final: 0.6735 (mm-40) REVERT: C 11 LYS cc_start: 0.5121 (OUTLIER) cc_final: 0.4491 (mmtp) REVERT: C 53 VAL cc_start: 0.5468 (t) cc_final: 0.5056 (p) REVERT: C 95 MET cc_start: 0.4836 (mmp) cc_final: 0.3830 (mpt) REVERT: C 205 LEU cc_start: 0.5142 (mm) cc_final: 0.4640 (mt) REVERT: C 403 ILE cc_start: 0.7158 (mt) cc_final: 0.6488 (tt) outliers start: 47 outliers final: 20 residues processed: 189 average time/residue: 0.5725 time to fit residues: 120.2678 Evaluate side-chains 169 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL 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 132 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 449 LEU 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 744 ARG Chi-restraints excluded: chain A residue 800 MET 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 63 CYS Chi-restraints excluded: chain B residue 65 CYS 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 237 VAL Chi-restraints excluded: chain C residue 308 PHE Chi-restraints excluded: chain C residue 384 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 151 optimal weight: 2.9990 chunk 49 optimal weight: 0.0980 chunk 43 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 145 optimal weight: 0.5980 chunk 74 optimal weight: 0.0370 chunk 130 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.5060 ------------------------------------------------------------------------------- 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 C 134 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.210349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.162135 restraints weight = 17162.884| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 1.60 r_work: 0.3614 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2205 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= 0.115 Angle : 0.516 7.714 19800 Z= 0.283 Chirality : 0.040 0.161 2191 Planarity : 0.004 0.082 2390 Dihedral : 13.883 87.609 2239 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.17 % Allowed : 17.48 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.21), residues: 1634 helix: 1.28 (0.22), residues: 587 sheet: -0.24 (0.28), residues: 344 loop : -1.06 (0.24), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 713 TYR 0.014 0.001 TYR A 668 PHE 0.023 0.001 PHE A 55 TRP 0.011 0.001 TRP C 136 HIS 0.005 0.001 HIS A 839 Details of bonding type rmsd covalent geometry : bond 0.00253 (14534) covalent geometry : angle 0.51566 (19800) hydrogen bonds : bond 0.03999 ( 585) hydrogen bonds : angle 4.41125 ( 1656) *********************** 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 206 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 158 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: A 132 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7418 (mp) REVERT: A 540 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7780 (mtt) REVERT: A 596 TYR cc_start: 0.7985 (m-80) cc_final: 0.7694 (m-80) REVERT: A 608 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.6632 (mp) REVERT: A 688 THR cc_start: 0.8226 (OUTLIER) cc_final: 0.7700 (m) REVERT: A 706 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6045 (pp20) REVERT: A 713 ARG cc_start: 0.6173 (ttm110) cc_final: 0.5961 (tmt170) REVERT: A 744 ARG cc_start: 0.6788 (OUTLIER) cc_final: 0.6355 (mtm-85) REVERT: A 853 MET cc_start: 0.4922 (OUTLIER) cc_final: 0.4375 (tpt) REVERT: A 859 MET cc_start: 0.3420 (mpp) cc_final: 0.2464 (tpt) REVERT: A 916 LYS cc_start: 0.8563 (ptmt) cc_final: 0.7904 (mptm) REVERT: A 956 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.5937 (mmp-170) REVERT: B 8 HIS cc_start: 0.5011 (m90) cc_final: 0.4357 (m-70) REVERT: B 40 ASP cc_start: 0.5900 (t0) cc_final: 0.5648 (t0) REVERT: C 11 LYS cc_start: 0.5106 (OUTLIER) cc_final: 0.4466 (mmtp) REVERT: C 93 LYS cc_start: 0.4901 (pptt) cc_final: 0.3218 (mmtm) REVERT: C 95 MET cc_start: 0.4707 (mmp) cc_final: 0.3513 (mtt) REVERT: C 205 LEU cc_start: 0.5166 (mm) cc_final: 0.4663 (mt) REVERT: C 365 GLU cc_start: 0.6847 (tp30) cc_final: 0.5426 (mp0) REVERT: C 375 MET cc_start: 0.8130 (mtp) cc_final: 0.7764 (mtp) outliers start: 48 outliers final: 21 residues processed: 189 average time/residue: 0.5574 time to fit residues: 117.0032 Evaluate side-chains 172 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL 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 132 LEU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 371 ILE 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 800 MET 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 956 ARG Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain B residue 65 CYS 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 9 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 127 optimal weight: 7.9990 chunk 123 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 146 GLN C 134 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.206582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.157629 restraints weight = 17028.397| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 1.65 r_work: 0.3549 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14534 Z= 0.182 Angle : 0.587 8.650 19800 Z= 0.318 Chirality : 0.043 0.176 2191 Planarity : 0.005 0.083 2390 Dihedral : 14.223 88.012 2239 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.36 % Allowed : 18.14 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.21), residues: 1634 helix: 1.08 (0.22), residues: 581 sheet: -0.40 (0.28), residues: 354 loop : -1.18 (0.24), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 255 TYR 0.015 0.001 TYR A 190 PHE 0.023 0.002 PHE A 992 TRP 0.010 0.001 TRP C 136 HIS 0.005 0.001 HIS B 147 Details of bonding type rmsd covalent geometry : bond 0.00427 (14534) covalent geometry : angle 0.58670 (19800) hydrogen bonds : bond 0.05027 ( 585) hydrogen bonds : angle 4.63024 ( 1656) *********************** 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 203 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 152 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: A 132 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7470 (mt) REVERT: A 398 ASP cc_start: 0.7720 (t0) cc_final: 0.7145 (t0) REVERT: A 688 THR cc_start: 0.8365 (OUTLIER) cc_final: 0.7877 (m) REVERT: A 706 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.5995 (pp20) REVERT: A 744 ARG cc_start: 0.7024 (OUTLIER) cc_final: 0.6572 (mtm-85) REVERT: A 853 MET cc_start: 0.4890 (OUTLIER) cc_final: 0.4304 (tpt) REVERT: A 859 MET cc_start: 0.3594 (mpp) cc_final: 0.2372 (tpt) REVERT: A 956 ARG cc_start: 0.7210 (OUTLIER) cc_final: 0.6242 (mmp-170) REVERT: B 8 HIS cc_start: 0.5339 (m90) cc_final: 0.4574 (m-70) REVERT: C 63 GLU cc_start: 0.6854 (mm-30) cc_final: 0.6415 (pp20) REVERT: C 93 LYS cc_start: 0.4870 (pptt) cc_final: 0.3072 (mptp) REVERT: C 95 MET cc_start: 0.4861 (mmp) cc_final: 0.3642 (mtt) REVERT: C 205 LEU cc_start: 0.5294 (mm) cc_final: 0.4789 (mt) REVERT: C 255 ARG cc_start: 0.6258 (mmm160) cc_final: 0.5795 (mtm180) REVERT: C 304 ASN cc_start: 0.4662 (OUTLIER) cc_final: 0.4371 (p0) REVERT: C 375 MET cc_start: 0.8141 (mtp) cc_final: 0.7767 (mtp) outliers start: 51 outliers final: 20 residues processed: 185 average time/residue: 0.5813 time to fit residues: 118.5700 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 : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL 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 132 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 207 MET 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 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 956 ARG 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 177 ILE Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 304 ASN Chi-restraints excluded: chain C residue 308 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 126 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 135 optimal weight: 0.0470 chunk 96 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 139 optimal weight: 10.0000 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 964 GLN B 55 GLN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN B 211 ASN C 134 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.208791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.160167 restraints weight = 17004.605| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 1.68 r_work: 0.3583 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2550 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= 0.134 Angle : 0.546 7.963 19800 Z= 0.298 Chirality : 0.041 0.161 2191 Planarity : 0.004 0.081 2390 Dihedral : 14.052 88.007 2239 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.14 % Favored : 94.80 % Rotamer: Outliers : 3.03 % Allowed : 19.59 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.21), residues: 1634 helix: 1.13 (0.22), residues: 587 sheet: -0.38 (0.28), residues: 356 loop : -1.16 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 255 TYR 0.013 0.001 TYR A 668 PHE 0.037 0.001 PHE A 992 TRP 0.011 0.001 TRP A 470 HIS 0.005 0.001 HIS A 839 Details of bonding type rmsd covalent geometry : bond 0.00303 (14534) covalent geometry : angle 0.54632 (19800) hydrogen bonds : bond 0.04268 ( 585) hydrogen bonds : angle 4.48960 ( 1656) *********************** 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 197 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 151 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: A 132 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7463 (mp) REVERT: A 398 ASP cc_start: 0.7656 (t0) cc_final: 0.7136 (t0) REVERT: A 688 THR cc_start: 0.8288 (OUTLIER) cc_final: 0.7757 (m) REVERT: A 706 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.5986 (pp20) REVERT: A 744 ARG cc_start: 0.6910 (OUTLIER) cc_final: 0.6475 (mtm-85) REVERT: A 853 MET cc_start: 0.5065 (OUTLIER) cc_final: 0.4443 (tpt) REVERT: A 859 MET cc_start: 0.3583 (mpp) cc_final: 0.2430 (tpt) REVERT: A 956 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.5949 (mmp-170) REVERT: B 8 HIS cc_start: 0.5028 (m90) cc_final: 0.4366 (m-70) REVERT: B 110 LEU cc_start: 0.3942 (OUTLIER) cc_final: 0.3722 (tt) REVERT: C 95 MET cc_start: 0.4804 (mmp) cc_final: 0.3902 (mtt) REVERT: C 133 ASN cc_start: 0.6376 (m-40) cc_final: 0.5747 (p0) REVERT: C 205 LEU cc_start: 0.5260 (mm) cc_final: 0.4764 (mt) REVERT: C 255 ARG cc_start: 0.6227 (mmm160) cc_final: 0.5828 (mtm180) REVERT: C 365 GLU cc_start: 0.6759 (tp30) cc_final: 0.5322 (mp0) REVERT: C 375 MET cc_start: 0.8163 (mtp) cc_final: 0.7771 (mtp) outliers start: 46 outliers final: 24 residues processed: 178 average time/residue: 0.5532 time to fit residues: 109.0692 Evaluate side-chains 173 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 132 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 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 800 MET 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 956 ARG Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 110 LEU 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 83 PHE 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 Chi-restraints excluded: chain C residue 384 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 122 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 151 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 128 optimal weight: 30.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 211 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.204273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.155202 restraints weight = 17068.502| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 1.77 r_work: 0.3498 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 14534 Z= 0.244 Angle : 0.656 7.420 19800 Z= 0.355 Chirality : 0.045 0.173 2191 Planarity : 0.005 0.085 2390 Dihedral : 14.489 88.430 2239 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.43 % Favored : 93.51 % Rotamer: Outliers : 3.50 % Allowed : 19.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.21), residues: 1634 helix: 0.78 (0.22), residues: 579 sheet: -0.45 (0.28), residues: 348 loop : -1.34 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 255 TYR 0.019 0.002 TYR A 637 PHE 0.022 0.002 PHE A 992 TRP 0.010 0.002 TRP A 940 HIS 0.004 0.001 HIS B 8 Details of bonding type rmsd covalent geometry : bond 0.00581 (14534) covalent geometry : angle 0.65606 (19800) hydrogen bonds : bond 0.05648 ( 585) hydrogen bonds : angle 4.86160 ( 1656) *********************** 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 201 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 148 time to evaluate : 0.522 Fit side-chains revert: symmetry clash REVERT: A 398 ASP cc_start: 0.7822 (t0) cc_final: 0.7311 (t0) REVERT: A 688 THR cc_start: 0.8411 (OUTLIER) cc_final: 0.7974 (m) REVERT: A 706 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6436 (pp20) REVERT: A 744 ARG cc_start: 0.7161 (OUTLIER) cc_final: 0.6690 (mtm-85) REVERT: A 853 MET cc_start: 0.4956 (OUTLIER) cc_final: 0.4279 (tpt) REVERT: A 859 MET cc_start: 0.3775 (mpp) cc_final: 0.2324 (tpt) REVERT: A 916 LYS cc_start: 0.8652 (ptmt) cc_final: 0.8012 (mptm) REVERT: A 956 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.6358 (mmp-170) REVERT: A 986 LYS cc_start: 0.7019 (tppt) cc_final: 0.6306 (tppp) REVERT: B 1 MET cc_start: 0.5332 (mmm) cc_final: 0.4938 (mmp) REVERT: C 95 MET cc_start: 0.4963 (mmp) cc_final: 0.3999 (mtt) REVERT: C 133 ASN cc_start: 0.6402 (m-40) cc_final: 0.5838 (p0) REVERT: C 205 LEU cc_start: 0.5383 (mm) cc_final: 0.4867 (mt) REVERT: C 255 ARG cc_start: 0.5993 (mmm160) cc_final: 0.5604 (mtm180) REVERT: C 375 MET cc_start: 0.8147 (mtp) cc_final: 0.7786 (mtp) outliers start: 53 outliers final: 28 residues processed: 184 average time/residue: 0.5910 time to fit residues: 120.1698 Evaluate side-chains 173 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL 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 199 LEU Chi-restraints excluded: chain A residue 207 MET 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 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 800 MET 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 36 GLU Chi-restraints excluded: chain C residue 112 SER 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 163 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 161 optimal weight: 2.9990 chunk 138 optimal weight: 20.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 109 ASN B 111 ASN B 211 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.206577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.157714 restraints weight = 17125.420| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 1.70 r_work: 0.3544 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2854 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= 0.159 Angle : 0.594 9.665 19800 Z= 0.322 Chirality : 0.042 0.161 2191 Planarity : 0.004 0.080 2390 Dihedral : 14.261 88.420 2239 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.20 % Favored : 94.74 % Rotamer: Outliers : 2.31 % Allowed : 21.64 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.21), residues: 1634 helix: 0.88 (0.22), residues: 587 sheet: -0.48 (0.28), residues: 340 loop : -1.32 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 135 TYR 0.013 0.001 TYR A 668 PHE 0.013 0.001 PHE A 560 TRP 0.009 0.001 TRP A 470 HIS 0.009 0.001 HIS B 8 Details of bonding type rmsd covalent geometry : bond 0.00367 (14534) covalent geometry : angle 0.59393 (19800) hydrogen bonds : bond 0.04660 ( 585) hydrogen bonds : angle 4.64591 ( 1656) *********************** 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 181 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 132 LEU cc_start: 0.7745 (mp) cc_final: 0.7244 (mm) REVERT: A 398 ASP cc_start: 0.7749 (t0) cc_final: 0.7174 (t0) REVERT: A 512 GLU cc_start: 0.7244 (tm-30) cc_final: 0.7022 (tm-30) REVERT: A 688 THR cc_start: 0.8367 (OUTLIER) cc_final: 0.7884 (m) REVERT: A 706 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6248 (pp20) REVERT: A 744 ARG cc_start: 0.7031 (OUTLIER) cc_final: 0.6573 (mtm-85) REVERT: A 853 MET cc_start: 0.4975 (OUTLIER) cc_final: 0.4286 (tpt) REVERT: A 859 MET cc_start: 0.3662 (mpp) cc_final: 0.2289 (tpt) REVERT: A 956 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.6083 (mmt180) REVERT: B 1 MET cc_start: 0.5201 (mmm) cc_final: 0.4828 (mmp) REVERT: C 93 LYS cc_start: 0.4600 (pptt) cc_final: 0.3106 (mptp) REVERT: C 95 MET cc_start: 0.4946 (mmp) cc_final: 0.3876 (mtt) REVERT: C 133 ASN cc_start: 0.6404 (m-40) cc_final: 0.5872 (p0) REVERT: C 205 LEU cc_start: 0.5304 (mm) cc_final: 0.4829 (mt) REVERT: C 255 ARG cc_start: 0.5985 (mmm160) cc_final: 0.5629 (mtm180) REVERT: C 365 GLU cc_start: 0.6869 (tp30) cc_final: 0.6588 (mm-30) REVERT: C 375 MET cc_start: 0.8135 (mtp) cc_final: 0.7715 (mtp) outliers start: 35 outliers final: 21 residues processed: 169 average time/residue: 0.5458 time to fit residues: 101.5485 Evaluate side-chains 159 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 207 MET Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 391 THR 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 838 PHE Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 933 ILE 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 176 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 112 SER 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 71 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 1 optimal weight: 0.0970 chunk 51 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 964 GLN B 109 ASN B 111 ASN ** 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 = 0.4330 r_free = 0.4330 target = 0.207467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.158954 restraints weight = 17093.788| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 1.63 r_work: 0.3564 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2871 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= 0.141 Angle : 0.583 9.257 19800 Z= 0.315 Chirality : 0.042 0.199 2191 Planarity : 0.004 0.083 2390 Dihedral : 14.100 88.505 2239 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.63 % Favored : 94.31 % Rotamer: Outliers : 2.24 % Allowed : 21.97 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.21), residues: 1634 helix: 0.99 (0.22), residues: 587 sheet: -0.48 (0.28), residues: 348 loop : -1.29 (0.24), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 146 TYR 0.013 0.001 TYR A 668 PHE 0.042 0.001 PHE A 992 TRP 0.010 0.001 TRP A 470 HIS 0.008 0.001 HIS B 8 Details of bonding type rmsd covalent geometry : bond 0.00319 (14534) covalent geometry : angle 0.58289 (19800) hydrogen bonds : bond 0.04304 ( 585) hydrogen bonds : angle 4.53929 ( 1656) ********************** 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 187 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: A 132 LEU cc_start: 0.7720 (mp) cc_final: 0.7245 (mm) REVERT: A 398 ASP cc_start: 0.7701 (t0) cc_final: 0.7172 (t0) REVERT: A 512 GLU cc_start: 0.7260 (tm-30) cc_final: 0.7044 (tm-30) REVERT: A 688 THR cc_start: 0.8282 (OUTLIER) cc_final: 0.7798 (m) REVERT: A 706 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6298 (pp20) REVERT: A 744 ARG cc_start: 0.7010 (OUTLIER) cc_final: 0.6569 (mtm-85) REVERT: A 853 MET cc_start: 0.5020 (OUTLIER) cc_final: 0.4341 (tpt) REVERT: A 859 MET cc_start: 0.3574 (mpp) cc_final: 0.2232 (tpt) REVERT: B 1 MET cc_start: 0.5257 (mmm) cc_final: 0.4875 (mmp) REVERT: C 93 LYS cc_start: 0.4536 (pptt) cc_final: 0.3106 (mptp) REVERT: C 95 MET cc_start: 0.4797 (mmp) cc_final: 0.3779 (mtt) REVERT: C 133 ASN cc_start: 0.6339 (m-40) cc_final: 0.5940 (p0) REVERT: C 205 LEU cc_start: 0.5252 (mm) cc_final: 0.4780 (mt) REVERT: C 375 MET cc_start: 0.8150 (mtp) cc_final: 0.7734 (mtp) outliers start: 34 outliers final: 22 residues processed: 175 average time/residue: 0.5854 time to fit residues: 113.3717 Evaluate side-chains 166 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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 207 MET 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 620 GLU Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 707 LEU 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 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 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 53 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 136 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 112 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 964 GLN ** 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 = 0.4315 r_free = 0.4315 target = 0.205877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.156943 restraints weight = 17151.081| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 1.68 r_work: 0.3538 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14534 Z= 0.180 Angle : 0.629 9.426 19800 Z= 0.338 Chirality : 0.044 0.209 2191 Planarity : 0.005 0.081 2390 Dihedral : 14.272 88.754 2239 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.30 % Favored : 93.64 % Rotamer: Outliers : 2.04 % Allowed : 22.82 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.21), residues: 1634 helix: 0.87 (0.22), residues: 585 sheet: -0.44 (0.28), residues: 340 loop : -1.33 (0.24), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 135 TYR 0.015 0.001 TYR A 637 PHE 0.016 0.002 PHE A 370 TRP 0.008 0.001 TRP C 136 HIS 0.004 0.001 HIS A 839 Details of bonding type rmsd covalent geometry : bond 0.00422 (14534) covalent geometry : angle 0.62924 (19800) hydrogen bonds : bond 0.04871 ( 585) hydrogen bonds : angle 4.69795 ( 1656) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5801.67 seconds wall clock time: 99 minutes 37.62 seconds (5977.62 seconds total)