Starting phenix.real_space_refine on Mon Dec 30 22:09:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j8f_36068/12_2024/8j8f_36068.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j8f_36068/12_2024/8j8f_36068.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j8f_36068/12_2024/8j8f_36068.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j8f_36068/12_2024/8j8f_36068.map" model { file = "/net/cci-nas-00/data/ceres_data/8j8f_36068/12_2024/8j8f_36068.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j8f_36068/12_2024/8j8f_36068.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 3 9.91 5 P 39 5.49 5 S 71 5.16 5 C 8957 2.51 5 N 2340 2.21 5 O 2749 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 14159 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1005, 8212 Classifications: {'peptide': 1005} Link IDs: {'PTRANS': 37, 'TRANS': 967} Chain: "B" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1762 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 2} Link IDs: {'PTRANS': 13, 'TRANS': 204} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 3418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3418 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 10, 'TRANS': 408} Chain breaks: 1 Chain: "P" Number of atoms: 291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 291 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "T" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 445 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 31 Unusual residues: {' CA': 3, 'DCP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 9.43, per 1000 atoms: 0.67 Number of scatterers: 14159 At special positions: 0 Unit cell: (95.76, 123.48, 146.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 3 19.99 S 71 16.00 P 39 15.00 O 2749 8.00 N 2340 7.00 C 8957 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.76 Conformation dependent library (CDL) restraints added in 1.9 seconds 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3140 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 20 sheets defined 39.5% alpha, 18.9% beta 10 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 5.09 Creating SS restraints... Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 108 through 118 Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 209 through 220 Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.595A pdb=" N GLU A 229 " --> pdb=" O SER A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 253 Processing helix chain 'A' and resid 267 through 280 Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 380 through 390 Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'A' and resid 448 through 474 removed outlier: 3.631A pdb=" N GLN A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 487 Processing helix chain 'A' and resid 497 through 502 removed outlier: 3.559A pdb=" N ILE A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 514 Processing helix chain 'A' and resid 552 through 562 Processing helix chain 'A' and resid 564 through 566 No H-bonds generated for 'chain 'A' and resid 564 through 566' Processing helix chain 'A' and resid 576 through 591 removed outlier: 3.902A pdb=" N GLN A 589 " --> pdb=" O GLN A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 642 Processing helix chain 'A' and resid 646 through 672 removed outlier: 3.528A pdb=" N GLY A 672 " --> pdb=" O TYR A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 703 Processing helix chain 'A' and resid 763 through 781 Processing helix chain 'A' and resid 837 through 857 Processing helix chain 'A' and resid 862 through 883 removed outlier: 3.509A pdb=" N ARG A 883 " --> pdb=" O GLU A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.977A pdb=" N MET A 891 " --> pdb=" O GLU A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 918 Processing helix chain 'A' and resid 967 through 981 removed outlier: 3.953A pdb=" N TYR A 971 " --> pdb=" O PHE A 967 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN A 981 " --> pdb=" O SER A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 997 removed outlier: 3.978A pdb=" N MET A 996 " --> pdb=" O PHE A 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 18 No H-bonds generated for 'chain 'B' and resid 16 through 18' Processing helix chain 'B' and resid 19 through 38 removed outlier: 4.094A pdb=" N MET B 23 " --> pdb=" O TRP B 19 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N SER B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N GLN B 25 " --> pdb=" O PRO B 21 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N GLU B 28 " --> pdb=" O SER B 24 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLU B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL B 33 " --> pdb=" O PHE B 29 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N SER B 35 " --> pdb=" O ASN B 31 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N TRP B 36 " --> pdb=" O GLU B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 101 removed outlier: 4.036A pdb=" N GLU B 91 " --> pdb=" O LYS B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 113 Processing helix chain 'B' and resid 133 through 151 removed outlier: 5.569A pdb=" N LYS B 139 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ILE B 140 " --> pdb=" O TYR B 136 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N HIS B 151 " --> pdb=" O HIS B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 170 removed outlier: 3.672A pdb=" N LEU B 170 " --> pdb=" O ILE B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 192 removed outlier: 3.692A pdb=" N GLU B 190 " --> pdb=" O HIS B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 205 Processing helix chain 'C' and resid 4 through 19 removed outlier: 3.571A pdb=" N SER C 19 " --> pdb=" O SER C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 42 Processing helix chain 'C' and resid 57 through 61 Processing helix chain 'C' and resid 107 through 117 Processing helix chain 'C' and resid 147 through 158 Processing helix chain 'C' and resid 177 through 188 Processing helix chain 'C' and resid 249 through 257 removed outlier: 3.544A pdb=" N LEU C 253 " --> pdb=" O ASP C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 287 No H-bonds generated for 'chain 'C' and resid 285 through 287' Processing helix chain 'C' and resid 288 through 298 Processing helix chain 'C' and resid 315 through 323 removed outlier: 3.516A pdb=" N LEU C 319 " --> pdb=" O GLY C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 341 removed outlier: 3.527A pdb=" N SER C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 351 Processing helix chain 'C' and resid 352 through 362 removed outlier: 3.628A pdb=" N LEU C 361 " --> pdb=" O SER C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 374 Processing helix chain 'C' and resid 391 through 395 removed outlier: 3.592A pdb=" N CYS C 394 " --> pdb=" O ASN C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 405 Processing helix chain 'C' and resid 406 through 425 removed outlier: 4.001A pdb=" N ARG C 423 " --> pdb=" O ASP C 419 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 127 removed outlier: 6.971A pdb=" N LYS A 21 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N TRP A 8 " --> pdb=" O TYR A 19 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N TYR A 19 " --> pdb=" O TRP A 8 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N GLU A 10 " --> pdb=" O PHE A 17 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N PHE A 17 " --> pdb=" O GLU A 10 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N TYR A 140 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N PHE A 31 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N CYS A 142 " --> pdb=" O PHE A 31 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ARG A 33 " --> pdb=" O CYS A 142 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N HIS A 141 " --> pdb=" O LYS A 134 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N LYS A 134 " --> pdb=" O HIS A 141 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 43 removed outlier: 3.647A pdb=" N GLY A 61 " --> pdb=" O MET A 88 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU A 90 " --> pdb=" O PRO A 59 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU A 92 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ALA A 57 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N ILE A 516 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ARG A 64 " --> pdb=" O ILE A 516 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL A 518 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ILE A 66 " --> pdb=" O VAL A 518 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 73 removed outlier: 6.256A pdb=" N LEU A 568 " --> pdb=" O ASP A 616 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASP A 616 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 570 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER A 574 " --> pdb=" O SER A 610 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 610 " --> pdb=" O SER A 574 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 223 removed outlier: 6.542A pdb=" N LEU A 222 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N SER A 184 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL A 259 " --> pdb=" O PHE A 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 285 through 287 Processing sheet with id=AA6, first strand: chain 'A' and resid 300 through 304 removed outlier: 3.600A pdb=" N ASN A 315 " --> pdb=" O GLN A 304 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 355 through 362 removed outlier: 6.814A pdb=" N THR A 369 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG A 407 " --> pdb=" O VAL A 418 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 533 through 534 removed outlier: 4.399A pdb=" N GLY A 750 " --> pdb=" O PHE A 534 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A 706 " --> pdb=" O ARG A 713 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 533 through 534 removed outlier: 4.399A pdb=" N GLY A 750 " --> pdb=" O PHE A 534 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N SER A 747 " --> pdb=" O GLU A 758 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLU A 758 " --> pdb=" O SER A 747 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR A 749 " --> pdb=" O PHE A 756 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA A 793 " --> pdb=" O ILE A 547 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASP A 549 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N PHE A 791 " --> pdb=" O ASP A 549 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU A 798 " --> pdb=" O THR A 807 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N THR A 807 " --> pdb=" O LEU A 798 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 892 through 895 Processing sheet with id=AB2, first strand: chain 'A' and resid 892 through 895 Processing sheet with id=AB3, first strand: chain 'B' and resid 116 through 120 removed outlier: 3.805A pdb=" N ILE B 117 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL B 64 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N CYS B 63 " --> pdb=" O TYR B 156 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU B 155 " --> pdb=" O ILE B 177 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 69 through 70 Processing sheet with id=AB5, first strand: chain 'C' and resid 77 through 82 removed outlier: 4.037A pdb=" N SER C 196 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR C 199 " --> pdb=" O GLN C 208 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLN C 208 " --> pdb=" O TYR C 199 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 85 through 87 removed outlier: 4.479A pdb=" N SER C 85 " --> pdb=" O LEU C 131 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU C 131 " --> pdb=" O SER C 85 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 124 through 126 removed outlier: 7.452A pdb=" N ILE C 142 " --> pdb=" O ASP C 125 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 222 through 227 removed outlier: 4.239A pdb=" N VAL C 237 " --> pdb=" O ILE C 245 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 266 through 268 Processing sheet with id=AC1, first strand: chain 'C' and resid 302 through 304 Processing sheet with id=AC2, first strand: chain 'C' and resid 375 through 380 removed outlier: 3.799A pdb=" N ASN C 386 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLU C 380 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL C 384 " --> pdb=" O GLU C 380 " (cutoff:3.500A) 569 hydrogen bonds defined for protein. 1614 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 21 hydrogen bonds 42 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 5.49 Time building geometry restraints manager: 4.09 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 38.220 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 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:11.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.130 ------------------------------------------------------------------------------- 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= 0.129 Angle : 0.457 6.371 19800 Z= 0.254 Chirality : 0.039 0.143 2191 Planarity : 0.003 0.084 2390 Dihedral : 15.395 88.293 5564 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.07 % Allowed : 0.40 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.22), residues: 1634 helix: 1.31 (0.22), residues: 583 sheet: 0.24 (0.30), residues: 337 loop : -0.87 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 136 HIS 0.005 0.001 HIS A 839 PHE 0.012 0.001 PHE C 22 TYR 0.016 0.001 TYR A 668 ARG 0.001 0.000 ARG A 97 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 270 time to evaluate : 1.497 Fit side-chains REVERT: A 859 MET cc_start: 0.3607 (mpp) cc_final: 0.2867 (tpt) REVERT: B 8 HIS cc_start: 0.4994 (m90) cc_final: 0.4673 (m-70) REVERT: B 83 ASN cc_start: 0.7304 (m-40) cc_final: 0.6998 (m110) REVERT: C 53 VAL cc_start: 0.5731 (t) cc_final: 0.5339 (p) REVERT: C 205 LEU cc_start: 0.4724 (mm) cc_final: 0.4377 (mt) outliers start: 1 outliers final: 3 residues processed: 271 average time/residue: 1.3352 time to fit residues: 396.7698 Evaluate side-chains 159 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 156 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain B residue 68 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 20.0000 chunk 125 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 96 optimal weight: 0.0770 chunk 149 optimal weight: 10.0000 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN A 442 GLN A 907 ASN A 964 GLN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN C 134 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 14534 Z= 0.361 Angle : 0.643 8.227 19800 Z= 0.351 Chirality : 0.045 0.160 2191 Planarity : 0.005 0.085 2390 Dihedral : 14.347 87.812 2245 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.97 % Allowed : 12.14 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.21), residues: 1634 helix: 0.90 (0.22), residues: 588 sheet: -0.12 (0.29), residues: 339 loop : -1.19 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 470 HIS 0.005 0.001 HIS B 147 PHE 0.027 0.002 PHE C 104 TYR 0.019 0.002 TYR A 190 ARG 0.005 0.001 ARG A 823 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 172 time to evaluate : 1.657 Fit side-chains revert: symmetry clash REVERT: A 174 LYS cc_start: 0.6854 (ptpt) cc_final: 0.6640 (mtmm) REVERT: A 744 ARG cc_start: 0.6938 (OUTLIER) cc_final: 0.6461 (mtm-85) REVERT: A 837 LYS cc_start: 0.8423 (tppt) cc_final: 0.8093 (tppt) REVERT: A 853 MET cc_start: 0.5591 (OUTLIER) cc_final: 0.4760 (tpt) REVERT: A 859 MET cc_start: 0.3840 (mpp) cc_final: 0.2618 (tpt) REVERT: A 956 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.5830 (mmt180) REVERT: B 8 HIS cc_start: 0.5017 (m90) cc_final: 0.4402 (m-70) REVERT: B 83 ASN cc_start: 0.7326 (m-40) cc_final: 0.6938 (m110) REVERT: C 53 VAL cc_start: 0.6081 (t) cc_final: 0.5555 (p) REVERT: C 93 LYS cc_start: 0.4908 (mmtm) cc_final: 0.4618 (pptt) REVERT: C 205 LEU cc_start: 0.4735 (mm) cc_final: 0.4232 (mt) outliers start: 45 outliers final: 19 residues processed: 195 average time/residue: 1.2748 time to fit residues: 274.6514 Evaluate side-chains 165 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 744 ARG Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 956 ARG Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 308 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 chunk 41 optimal weight: 0.0970 chunk 150 optimal weight: 5.9990 chunk 162 optimal weight: 6.9990 chunk 133 optimal weight: 9.9990 chunk 148 optimal weight: 1.9990 chunk 51 optimal weight: 0.3980 chunk 120 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 964 GLN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2174 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= 0.266 Angle : 0.580 9.456 19800 Z= 0.316 Chirality : 0.043 0.184 2191 Planarity : 0.005 0.082 2390 Dihedral : 14.248 87.832 2239 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.30 % Allowed : 16.09 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.21), residues: 1634 helix: 0.94 (0.22), residues: 588 sheet: -0.23 (0.29), residues: 337 loop : -1.25 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 470 HIS 0.004 0.001 HIS B 147 PHE 0.020 0.002 PHE C 104 TYR 0.016 0.001 TYR A 668 ARG 0.006 0.000 ARG A 713 *********************** 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 219 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 169 time to evaluate : 1.868 Fit side-chains REVERT: A 132 LEU cc_start: 0.7617 (mp) cc_final: 0.7201 (mm) REVERT: A 398 ASP cc_start: 0.7501 (t0) cc_final: 0.7077 (t0) REVERT: A 688 THR cc_start: 0.8554 (OUTLIER) cc_final: 0.8117 (m) REVERT: A 853 MET cc_start: 0.5534 (OUTLIER) cc_final: 0.4628 (tpt) REVERT: A 859 MET cc_start: 0.3816 (mpp) cc_final: 0.2566 (tpt) REVERT: A 942 LYS cc_start: 0.7633 (OUTLIER) cc_final: 0.6868 (mtpp) REVERT: A 956 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.5871 (mmt180) REVERT: B 8 HIS cc_start: 0.5081 (m90) cc_final: 0.4489 (m-70) REVERT: B 53 LEU cc_start: 0.7601 (mp) cc_final: 0.7106 (tt) REVERT: B 83 ASN cc_start: 0.7252 (m-40) cc_final: 0.6837 (m110) REVERT: C 11 LYS cc_start: 0.4876 (OUTLIER) cc_final: 0.4164 (mmtp) REVERT: C 53 VAL cc_start: 0.6028 (t) cc_final: 0.5501 (p) REVERT: C 95 MET cc_start: 0.4492 (mmp) cc_final: 0.3944 (mpt) REVERT: C 205 LEU cc_start: 0.4838 (mm) cc_final: 0.4307 (mt) outliers start: 50 outliers final: 18 residues processed: 198 average time/residue: 1.1893 time to fit residues: 261.8369 Evaluate side-chains 172 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 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 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 148 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 chunk 159 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 142 optimal weight: 20.0000 chunk 42 optimal weight: 0.0170 overall best weight: 1.5824 ------------------------------------------------------------------------------- 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 899 ASN A 964 GLN B 55 GLN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14534 Z= 0.310 Angle : 0.607 8.430 19800 Z= 0.331 Chirality : 0.044 0.200 2191 Planarity : 0.005 0.083 2390 Dihedral : 14.355 87.944 2239 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 3.89 % Allowed : 17.94 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.21), residues: 1634 helix: 0.89 (0.22), residues: 580 sheet: -0.37 (0.28), residues: 347 loop : -1.35 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 470 HIS 0.004 0.001 HIS A 839 PHE 0.027 0.002 PHE A 992 TYR 0.016 0.002 TYR A 637 ARG 0.006 0.000 ARG A 713 *********************** 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 214 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 155 time to evaluate : 1.855 Fit side-chains revert: symmetry clash REVERT: A 115 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7640 (mp) REVERT: A 132 LEU cc_start: 0.7692 (mp) cc_final: 0.7289 (mm) REVERT: A 398 ASP cc_start: 0.7540 (t0) cc_final: 0.7117 (t0) REVERT: A 608 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7087 (mp) REVERT: A 688 THR cc_start: 0.8547 (OUTLIER) cc_final: 0.8119 (m) REVERT: A 744 ARG cc_start: 0.6923 (OUTLIER) cc_final: 0.6465 (mtm-85) REVERT: A 853 MET cc_start: 0.5616 (OUTLIER) cc_final: 0.4675 (tpt) REVERT: A 859 MET cc_start: 0.4031 (mpp) cc_final: 0.2577 (tpt) REVERT: A 956 ARG cc_start: 0.7166 (OUTLIER) cc_final: 0.6004 (mmt180) REVERT: C 11 LYS cc_start: 0.4898 (OUTLIER) cc_final: 0.4138 (mmtp) REVERT: C 95 MET cc_start: 0.4455 (mmp) cc_final: 0.3880 (mpt) REVERT: C 205 LEU cc_start: 0.5129 (mm) cc_final: 0.4559 (mt) outliers start: 59 outliers final: 27 residues processed: 195 average time/residue: 1.1983 time to fit residues: 258.8044 Evaluate side-chains 179 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 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 748 VAL Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 956 ARG Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain 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 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 Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 386 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 118 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 136 optimal weight: 0.6980 chunk 110 optimal weight: 9.9990 chunk 0 optimal weight: 1.9990 chunk 81 optimal weight: 0.0970 chunk 143 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2594 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= 0.235 Angle : 0.573 6.771 19800 Z= 0.312 Chirality : 0.042 0.155 2191 Planarity : 0.005 0.081 2390 Dihedral : 14.226 88.059 2239 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.63 % Allowed : 19.20 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.21), residues: 1634 helix: 0.98 (0.22), residues: 587 sheet: -0.39 (0.28), residues: 348 loop : -1.33 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 136 HIS 0.009 0.001 HIS B 8 PHE 0.024 0.001 PHE A 55 TYR 0.013 0.001 TYR A 668 ARG 0.012 0.001 ARG C 255 *********************** 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 207 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 152 time to evaluate : 1.715 Fit side-chains revert: symmetry clash REVERT: A 115 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7631 (mp) REVERT: A 132 LEU cc_start: 0.7670 (mp) cc_final: 0.7289 (mm) REVERT: A 398 ASP cc_start: 0.7515 (t0) cc_final: 0.7110 (t0) REVERT: A 688 THR cc_start: 0.8520 (OUTLIER) cc_final: 0.8087 (m) REVERT: A 693 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7581 (mmp80) REVERT: A 744 ARG cc_start: 0.6836 (OUTLIER) cc_final: 0.6381 (mtm-85) REVERT: A 853 MET cc_start: 0.5564 (OUTLIER) cc_final: 0.4729 (tpt) REVERT: A 859 MET cc_start: 0.3949 (mpp) cc_final: 0.2505 (tpt) REVERT: A 916 LYS cc_start: 0.8498 (ptmt) cc_final: 0.8031 (mptm) REVERT: A 956 ARG cc_start: 0.7139 (OUTLIER) cc_final: 0.5936 (mmt180) REVERT: C 95 MET cc_start: 0.4450 (mmp) cc_final: 0.4242 (mtt) REVERT: C 205 LEU cc_start: 0.5165 (mm) cc_final: 0.4582 (mt) REVERT: C 403 ILE cc_start: 0.6651 (mt) cc_final: 0.5968 (tt) outliers start: 55 outliers final: 28 residues processed: 190 average time/residue: 1.1506 time to fit residues: 243.9694 Evaluate side-chains 181 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 1.580 ------------------------------------------------------------------------------- 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 115 ILE Chi-restraints excluded: chain A residue 134 LYS Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 693 ARG Chi-restraints excluded: chain A residue 744 ARG Chi-restraints excluded: chain A residue 763 ASP Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 956 ARG Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 83 PHE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 308 PHE Chi-restraints excluded: chain C residue 311 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 0.8980 chunk 143 optimal weight: 6.9990 chunk 31 optimal weight: 0.3980 chunk 93 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 73 optimal weight: 0.4980 chunk 13 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN A 964 GLN B 55 GLN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2590 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= 0.180 Angle : 0.542 8.579 19800 Z= 0.295 Chirality : 0.041 0.156 2191 Planarity : 0.004 0.082 2390 Dihedral : 14.031 88.172 2239 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.97 % Allowed : 20.38 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.21), residues: 1634 helix: 1.13 (0.22), residues: 587 sheet: -0.41 (0.28), residues: 356 loop : -1.25 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 470 HIS 0.009 0.001 HIS B 8 PHE 0.013 0.001 PHE C 83 TYR 0.013 0.001 TYR A 668 ARG 0.009 0.000 ARG A 713 *********************** 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 204 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 159 time to evaluate : 1.618 Fit side-chains revert: symmetry clash REVERT: A 132 LEU cc_start: 0.7647 (mp) cc_final: 0.7288 (mm) REVERT: A 398 ASP cc_start: 0.7458 (t0) cc_final: 0.7066 (t0) REVERT: A 512 GLU cc_start: 0.7267 (tm-30) cc_final: 0.7067 (tm-30) REVERT: A 688 THR cc_start: 0.8451 (OUTLIER) cc_final: 0.7967 (m) REVERT: A 693 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7599 (mmp80) REVERT: A 744 ARG cc_start: 0.6777 (OUTLIER) cc_final: 0.6351 (mtm-85) REVERT: A 853 MET cc_start: 0.5540 (OUTLIER) cc_final: 0.4719 (tpt) REVERT: A 859 MET cc_start: 0.3881 (mpp) cc_final: 0.2522 (tpt) REVERT: A 916 LYS cc_start: 0.8474 (ptmt) cc_final: 0.7993 (mptm) REVERT: C 205 LEU cc_start: 0.5165 (mm) cc_final: 0.4577 (mt) outliers start: 45 outliers final: 23 residues processed: 189 average time/residue: 1.1769 time to fit residues: 249.1697 Evaluate side-chains 177 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 1.715 ------------------------------------------------------------------------------- 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 199 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 693 ARG Chi-restraints excluded: chain A residue 744 ARG Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 116 optimal weight: 0.4980 chunk 134 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 99 optimal weight: 0.2980 chunk 96 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 964 GLN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14534 Z= 0.218 Angle : 0.564 8.103 19800 Z= 0.306 Chirality : 0.042 0.160 2191 Planarity : 0.004 0.082 2390 Dihedral : 14.111 88.429 2239 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.03 % Allowed : 20.84 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.21), residues: 1634 helix: 1.07 (0.22), residues: 587 sheet: -0.44 (0.28), residues: 356 loop : -1.23 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 470 HIS 0.007 0.001 HIS B 8 PHE 0.026 0.001 PHE A 992 TYR 0.013 0.001 TYR A 668 ARG 0.007 0.000 ARG C 135 *********************** 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 194 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 148 time to evaluate : 1.645 Fit side-chains revert: symmetry clash REVERT: A 132 LEU cc_start: 0.7746 (mp) cc_final: 0.7348 (mm) REVERT: A 398 ASP cc_start: 0.7485 (t0) cc_final: 0.7089 (t0) REVERT: A 688 THR cc_start: 0.8470 (OUTLIER) cc_final: 0.8029 (m) REVERT: A 706 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6300 (pp20) REVERT: A 744 ARG cc_start: 0.6782 (OUTLIER) cc_final: 0.6353 (mtm-85) REVERT: A 853 MET cc_start: 0.5476 (OUTLIER) cc_final: 0.4653 (tpt) REVERT: A 859 MET cc_start: 0.3879 (mpp) cc_final: 0.2481 (tpt) REVERT: A 916 LYS cc_start: 0.8512 (ptmt) cc_final: 0.8017 (mptm) REVERT: B 1 MET cc_start: 0.5746 (mmm) cc_final: 0.5289 (mmp) REVERT: C 205 LEU cc_start: 0.5213 (mm) cc_final: 0.4611 (mt) outliers start: 46 outliers final: 26 residues processed: 182 average time/residue: 1.1691 time to fit residues: 236.5687 Evaluate side-chains 174 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 744 ARG Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 83 PHE Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 308 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 964 GLN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14534 Z= 0.246 Angle : 0.585 8.834 19800 Z= 0.316 Chirality : 0.043 0.213 2191 Planarity : 0.004 0.082 2390 Dihedral : 14.197 88.627 2239 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.75 % Favored : 94.19 % Rotamer: Outliers : 3.23 % Allowed : 21.57 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.21), residues: 1634 helix: 1.03 (0.22), residues: 585 sheet: -0.46 (0.28), residues: 354 loop : -1.30 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 136 HIS 0.006 0.001 HIS A 839 PHE 0.025 0.001 PHE A 992 TYR 0.014 0.001 TYR A 637 ARG 0.008 0.000 ARG C 135 *********************** 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 194 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 145 time to evaluate : 1.547 Fit side-chains revert: symmetry clash REVERT: A 132 LEU cc_start: 0.7754 (mp) cc_final: 0.7379 (mm) REVERT: A 398 ASP cc_start: 0.7550 (t0) cc_final: 0.7144 (t0) REVERT: A 688 THR cc_start: 0.8504 (OUTLIER) cc_final: 0.8064 (m) REVERT: A 706 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6212 (pp20) REVERT: A 744 ARG cc_start: 0.6825 (OUTLIER) cc_final: 0.6388 (mtm-85) REVERT: A 853 MET cc_start: 0.5418 (OUTLIER) cc_final: 0.4560 (tpt) REVERT: A 859 MET cc_start: 0.3846 (mpp) cc_final: 0.2339 (tpt) REVERT: A 916 LYS cc_start: 0.8520 (ptmt) cc_final: 0.8020 (mptm) REVERT: B 1 MET cc_start: 0.5736 (mmm) cc_final: 0.5305 (mmp) REVERT: C 205 LEU cc_start: 0.5262 (mm) cc_final: 0.4674 (mt) outliers start: 49 outliers final: 29 residues processed: 179 average time/residue: 1.1409 time to fit residues: 227.8592 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 : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 744 ARG Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 83 PHE 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 311 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 0.9990 chunk 139 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 133 optimal weight: 9.9990 chunk 140 optimal weight: 7.9990 chunk 147 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 ASN B 211 ASN C 304 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 14534 Z= 0.537 Angle : 0.768 9.150 19800 Z= 0.411 Chirality : 0.050 0.193 2191 Planarity : 0.006 0.086 2390 Dihedral : 14.886 88.652 2239 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 3.63 % Allowed : 21.57 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.21), residues: 1634 helix: 0.37 (0.22), residues: 583 sheet: -0.65 (0.28), residues: 345 loop : -1.65 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP C 136 HIS 0.005 0.001 HIS B 147 PHE 0.026 0.003 PHE A 370 TYR 0.026 0.002 TYR A 637 ARG 0.007 0.001 ARG A 927 *********************** 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 210 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 155 time to evaluate : 1.682 Fit side-chains revert: symmetry clash REVERT: A 132 LEU cc_start: 0.7905 (mp) cc_final: 0.7547 (mm) REVERT: A 398 ASP cc_start: 0.7763 (t0) cc_final: 0.7390 (t0) REVERT: A 512 GLU cc_start: 0.7438 (tm-30) cc_final: 0.7141 (tm-30) REVERT: A 642 LYS cc_start: 0.7276 (tppt) cc_final: 0.6864 (tppt) REVERT: A 688 THR cc_start: 0.8643 (OUTLIER) cc_final: 0.8374 (m) REVERT: A 706 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6305 (pp20) REVERT: A 744 ARG cc_start: 0.7025 (OUTLIER) cc_final: 0.6575 (mtm-85) REVERT: A 844 LYS cc_start: 0.7893 (tttt) cc_final: 0.7662 (tttp) REVERT: A 853 MET cc_start: 0.5540 (OUTLIER) cc_final: 0.4652 (tpt) REVERT: A 916 LYS cc_start: 0.8426 (ptmt) cc_final: 0.7926 (mptm) REVERT: B 1 MET cc_start: 0.5623 (mmm) cc_final: 0.5220 (mmp) REVERT: C 205 LEU cc_start: 0.5312 (mm) cc_final: 0.4711 (mt) outliers start: 55 outliers final: 29 residues processed: 190 average time/residue: 1.2594 time to fit residues: 266.0636 Evaluate side-chains 177 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 609 ILE 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 853 MET Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain 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 86 VAL Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 308 PHE Chi-restraints excluded: chain C residue 311 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 74 optimal weight: 0.0170 chunk 108 optimal weight: 6.9990 chunk 164 optimal weight: 1.9990 chunk 151 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 964 GLN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 ASN B 211 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 14534 Z= 0.237 Angle : 0.620 9.842 19800 Z= 0.336 Chirality : 0.043 0.211 2191 Planarity : 0.005 0.081 2390 Dihedral : 14.342 88.683 2239 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.57 % Favored : 94.37 % Rotamer: Outliers : 2.11 % Allowed : 23.88 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.21), residues: 1634 helix: 0.67 (0.22), residues: 586 sheet: -0.55 (0.28), residues: 340 loop : -1.51 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 136 HIS 0.006 0.001 HIS A 839 PHE 0.015 0.001 PHE A 992 TYR 0.013 0.001 TYR C 307 ARG 0.009 0.000 ARG C 135 ********************** 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 184 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 1.649 Fit side-chains revert: symmetry clash REVERT: A 132 LEU cc_start: 0.7731 (mp) cc_final: 0.7418 (mm) REVERT: A 398 ASP cc_start: 0.7667 (t0) cc_final: 0.7252 (t0) REVERT: A 512 GLU cc_start: 0.7333 (tm-30) cc_final: 0.7021 (tm-30) REVERT: A 688 THR cc_start: 0.8528 (OUTLIER) cc_final: 0.8100 (m) REVERT: A 706 GLU cc_start: 0.7103 (pp20) cc_final: 0.6252 (pp20) REVERT: A 744 ARG cc_start: 0.6887 (OUTLIER) cc_final: 0.6432 (mtm-85) REVERT: A 844 LYS cc_start: 0.7690 (tttt) cc_final: 0.7438 (tttp) REVERT: A 853 MET cc_start: 0.5319 (OUTLIER) cc_final: 0.4518 (tpt) REVERT: A 859 MET cc_start: 0.3537 (mpt) cc_final: 0.1624 (tpt) REVERT: A 916 LYS cc_start: 0.8479 (ptmt) cc_final: 0.7995 (mptm) REVERT: B 1 MET cc_start: 0.5381 (mmm) cc_final: 0.5012 (mmp) REVERT: B 23 MET cc_start: 0.6895 (mmp) cc_final: 0.6668 (mmm) REVERT: C 205 LEU cc_start: 0.5285 (mm) cc_final: 0.4741 (mt) outliers start: 32 outliers final: 23 residues processed: 173 average time/residue: 1.2815 time to fit residues: 244.2255 Evaluate side-chains 167 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 688 THR 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 942 LYS 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 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 139 optimal weight: 0.5980 chunk 40 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 134 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 964 GLN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.204849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.161858 restraints weight = 16947.412| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 3.60 r_work: 0.3421 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 14534 Z= 0.305 Angle : 0.656 9.208 19800 Z= 0.354 Chirality : 0.045 0.317 2191 Planarity : 0.005 0.083 2390 Dihedral : 14.408 88.882 2239 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.61 % Favored : 93.33 % Rotamer: Outliers : 2.51 % Allowed : 23.68 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.21), residues: 1634 helix: 0.63 (0.22), residues: 584 sheet: -0.58 (0.28), residues: 340 loop : -1.53 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 470 HIS 0.006 0.001 HIS A 839 PHE 0.035 0.002 PHE A 992 TYR 0.016 0.002 TYR A 637 ARG 0.005 0.000 ARG A 146 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4696.76 seconds wall clock time: 85 minutes 49.27 seconds (5149.27 seconds total)