Starting phenix.real_space_refine on Sat Sep 12 08:15:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rhg_24460/09_2026/7rhg_24460.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rhg_24460/09_2026/7rhg_24460.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rhg_24460/09_2026/7rhg_24460.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rhg_24460/09_2026/7rhg_24460.map" model { file = "/net/cci-nas-00/data/ceres_data/7rhg_24460/09_2026/7rhg_24460.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rhg_24460/09_2026/7rhg_24460.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7rhg_24460/09_2026/7rhg_24460.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rhg_24460/09_2026/7rhg_24460.cif" } resolution = 2.88 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= 0.005 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 82 5.16 5 C 9625 2.51 5 N 2405 2.21 5 O 2637 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14753 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 3689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3689 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Chain: "B" Number of atoms: 3542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3542 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 14, 'TRANS': 417} Chain breaks: 1 Chain: "A" Number of atoms: 3717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3717 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 14, 'TRANS': 439} Chain: "D" Number of atoms: 3717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3717 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 14, 'TRANS': 439} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNAv2': 1} Modifications used: {'rna3p': 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNAv2': 1} Modifications used: {'rna3p': 1} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNAv2': 1} Modifications used: {'rna3p': 1} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNAv2': 1} Modifications used: {'rna3p': 1} Time building chain proxies: 3.78, per 1000 atoms: 0.26 Number of scatterers: 14753 At special positions: 0 Unit cell: (97.556, 98.397, 119.422, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 82 16.00 P 4 15.00 O 2637 8.00 N 2405 7.00 C 9625 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: 1.28 Conformation dependent library (CDL) restraints added in 767.3 milliseconds 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3386 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 12 sheets defined 67.0% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'C' and resid 162 through 189 removed outlier: 3.569A pdb=" N TYR C 166 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Proline residue: C 175 - end of helix removed outlier: 3.599A pdb=" N VAL C 183 " --> pdb=" O ASN C 179 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ILE C 184 " --> pdb=" O TRP C 180 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA C 185 " --> pdb=" O THR C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 196 removed outlier: 3.684A pdb=" N TYR C 196 " --> pdb=" O LEU C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 219 removed outlier: 3.509A pdb=" N THR C 219 " --> pdb=" O MET C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 243 removed outlier: 3.581A pdb=" N ASN C 243 " --> pdb=" O LYS C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 252 removed outlier: 4.252A pdb=" N LYS C 247 " --> pdb=" O ASN C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 254 No H-bonds generated for 'chain 'C' and resid 253 through 254' Processing helix chain 'C' and resid 255 through 261 removed outlier: 3.628A pdb=" N LEU C 258 " --> pdb=" O PRO C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 276 removed outlier: 3.895A pdb=" N ILE C 270 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ASN C 273 " --> pdb=" O ILE C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 292 removed outlier: 3.874A pdb=" N MET C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR C 290 " --> pdb=" O GLN C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 326 Processing helix chain 'C' and resid 344 through 360 Processing helix chain 'C' and resid 371 through 404 Processing helix chain 'C' and resid 404 through 424 Processing helix chain 'C' and resid 427 through 444 Processing helix chain 'C' and resid 449 through 455 Processing helix chain 'C' and resid 458 through 477 removed outlier: 6.271A pdb=" N ASP C 472 " --> pdb=" O ASN C 468 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N THR C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS C 476 " --> pdb=" O ASP C 472 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL C 477 " --> pdb=" O THR C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 494 removed outlier: 3.840A pdb=" N VAL C 489 " --> pdb=" O ALA C 485 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLU C 490 " --> pdb=" O GLY C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 586 Processing helix chain 'C' and resid 588 through 605 Processing helix chain 'B' and resid 653 through 680 removed outlier: 3.701A pdb=" N VAL B 657 " --> pdb=" O ASN B 653 " (cutoff:3.500A) Proline residue: B 675 - end of helix Processing helix chain 'B' and resid 687 through 708 removed outlier: 3.570A pdb=" N TRP B 691 " --> pdb=" O ASN B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 735 removed outlier: 3.510A pdb=" N LEU B 733 " --> pdb=" O ARG B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 735 through 743 removed outlier: 3.715A pdb=" N LYS B 739 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 768 Proline residue: B 764 - end of helix removed outlier: 3.694A pdb=" N LYS B 768 " --> pdb=" O ARG B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 783 removed outlier: 3.785A pdb=" N SER B 781 " --> pdb=" O SER B 777 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU B 783 " --> pdb=" O LEU B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 817 Processing helix chain 'B' and resid 832 through 844 Processing helix chain 'B' and resid 854 through 887 Processing helix chain 'B' and resid 887 through 907 Processing helix chain 'B' and resid 910 through 929 removed outlier: 3.565A pdb=" N ARG B 916 " --> pdb=" O SER B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 938 Processing helix chain 'B' and resid 941 through 958 removed outlier: 6.272A pdb=" N ASN B 955 " --> pdb=" O ASP B 951 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ILE B 956 " --> pdb=" O VAL B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 978 Processing helix chain 'B' and resid 1029 through 1035 removed outlier: 3.529A pdb=" N ALA B1035 " --> pdb=" O SER B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1059 through 1065 Processing helix chain 'B' and resid 1069 through 1082 Processing helix chain 'A' and resid 162 through 189 removed outlier: 3.545A pdb=" N TYR A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 174 " --> pdb=" O PHE A 170 " (cutoff:3.500A) Proline residue: A 175 - end of helix removed outlier: 3.702A pdb=" N VAL A 183 " --> pdb=" O ASN A 179 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N ILE A 184 " --> pdb=" O TRP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.671A pdb=" N TYR A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 220 Processing helix chain 'A' and resid 232 through 242 Processing helix chain 'A' and resid 243 through 252 removed outlier: 3.977A pdb=" N LYS A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 258 No H-bonds generated for 'chain 'A' and resid 256 through 258' Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'A' and resid 267 through 276 removed outlier: 4.017A pdb=" N ILE A 270 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASN A 273 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 292 removed outlier: 3.815A pdb=" N MET A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR A 290 " --> pdb=" O GLN A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 326 Processing helix chain 'A' and resid 344 through 361 Processing helix chain 'A' and resid 371 through 404 Processing helix chain 'A' and resid 404 through 425 Processing helix chain 'A' and resid 427 through 444 Processing helix chain 'A' and resid 449 through 455 Processing helix chain 'A' and resid 458 through 475 removed outlier: 6.110A pdb=" N ASP A 472 " --> pdb=" O ASN A 468 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N THR A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 494 Processing helix chain 'A' and resid 578 through 586 Processing helix chain 'A' and resid 588 through 606 Processing helix chain 'D' and resid 162 through 189 removed outlier: 3.711A pdb=" N TYR D 166 " --> pdb=" O GLY D 162 " (cutoff:3.500A) Proline residue: D 175 - end of helix removed outlier: 5.286A pdb=" N ILE D 184 " --> pdb=" O TRP D 180 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA D 185 " --> pdb=" O THR D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 196 removed outlier: 3.715A pdb=" N TYR D 196 " --> pdb=" O LEU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 220 Processing helix chain 'D' and resid 232 through 242 Processing helix chain 'D' and resid 243 through 253 removed outlier: 3.967A pdb=" N LYS D 247 " --> pdb=" O ASN D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 258 No H-bonds generated for 'chain 'D' and resid 256 through 258' Processing helix chain 'D' and resid 259 through 264 Processing helix chain 'D' and resid 267 through 276 removed outlier: 3.852A pdb=" N ILE D 270 " --> pdb=" O TYR D 267 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASN D 273 " --> pdb=" O ILE D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 292 removed outlier: 3.960A pdb=" N MET D 281 " --> pdb=" O ARG D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 326 Processing helix chain 'D' and resid 344 through 361 Processing helix chain 'D' and resid 371 through 404 Processing helix chain 'D' and resid 404 through 424 Processing helix chain 'D' and resid 427 through 444 Processing helix chain 'D' and resid 449 through 456 removed outlier: 3.883A pdb=" N TYR D 456 " --> pdb=" O GLU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 475 removed outlier: 5.858A pdb=" N ASP D 472 " --> pdb=" O ASN D 468 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N THR D 473 " --> pdb=" O VAL D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 494 Processing helix chain 'D' and resid 578 through 586 Processing helix chain 'D' and resid 588 through 606 Processing sheet with id=AA1, first strand: chain 'C' and resid 224 through 225 Processing sheet with id=AA2, first strand: chain 'C' and resid 496 through 499 Processing sheet with id=AA3, first strand: chain 'C' and resid 505 through 507 removed outlier: 6.684A pdb=" N ILE C 565 " --> pdb=" O ILE C 506 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASN C 564 " --> pdb=" O VAL C 527 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU C 524 " --> pdb=" O VAL C 537 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL C 537 " --> pdb=" O LEU C 524 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL C 526 " --> pdb=" O PHE C 535 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 715 through 717 removed outlier: 3.873A pdb=" N PHE B 715 " --> pdb=" O ILE B 722 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 979 through 983 removed outlier: 6.713A pdb=" N ASN B1053 " --> pdb=" O GLN B1003 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 988 through 990 removed outlier: 6.389A pdb=" N TYR B 988 " --> pdb=" O ALA B1048 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ALA B1048 " --> pdb=" O TYR B 988 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL B1020 " --> pdb=" O VAL B1009 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 224 through 225 Processing sheet with id=AA8, first strand: chain 'A' and resid 496 through 500 removed outlier: 6.720A pdb=" N ASP A 572 " --> pdb=" O LYS A 520 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 505 through 507 removed outlier: 6.386A pdb=" N TYR A 505 " --> pdb=" O SER A 567 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N SER A 567 " --> pdb=" O TYR A 505 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N CYS A 507 " --> pdb=" O ILE A 565 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN A 564 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL A 536 " --> pdb=" O VAL A 526 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 224 through 225 Processing sheet with id=AB2, first strand: chain 'D' and resid 496 through 500 removed outlier: 7.107A pdb=" N ASP D 572 " --> pdb=" O LYS D 520 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 505 through 507 removed outlier: 6.190A pdb=" N TYR D 505 " --> pdb=" O SER D 567 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N SER D 567 " --> pdb=" O TYR D 505 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN D 564 " --> pdb=" O VAL D 527 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL D 536 " --> pdb=" O VAL D 526 " (cutoff:3.500A) 930 hydrogen bonds defined for protein. 2670 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.87 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4540 1.34 - 1.46: 3203 1.46 - 1.58: 7221 1.58 - 1.69: 9 1.69 - 1.81: 138 Bond restraints: 15111 Sorted by residual: bond pdb=" N PRO B 685 " pdb=" CD PRO B 685 " ideal model delta sigma weight residual 1.473 1.520 -0.047 1.40e-02 5.10e+03 1.13e+01 bond pdb=" CB PRO B 685 " pdb=" CG PRO B 685 " ideal model delta sigma weight residual 1.492 1.589 -0.097 5.00e-02 4.00e+02 3.76e+00 bond pdb=" CB THR B 842 " pdb=" CG2 THR B 842 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.52e+00 bond pdb=" CB VAL A 492 " pdb=" CG1 VAL A 492 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.59e+00 bond pdb=" CB VAL A 350 " pdb=" CG1 VAL A 350 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.75e+00 ... (remaining 15106 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 20158 2.04 - 4.07: 271 4.07 - 6.11: 33 6.11 - 8.14: 16 8.14 - 10.18: 15 Bond angle restraints: 20493 Sorted by residual: angle pdb=" C1' CMP C 701 " pdb=" C2' CMP C 701 " pdb=" C3' CMP C 701 " ideal model delta sigma weight residual 111.00 100.82 10.18 3.00e+00 1.11e-01 1.15e+01 angle pdb=" C1' CMP D 701 " pdb=" C2' CMP D 701 " pdb=" C3' CMP D 701 " ideal model delta sigma weight residual 111.00 100.90 10.10 3.00e+00 1.11e-01 1.13e+01 angle pdb=" C1' CMP B1301 " pdb=" C2' CMP B1301 " pdb=" C3' CMP B1301 " ideal model delta sigma weight residual 111.00 101.00 10.00 3.00e+00 1.11e-01 1.11e+01 angle pdb=" C1' CMP A 701 " pdb=" C2' CMP A 701 " pdb=" C3' CMP A 701 " ideal model delta sigma weight residual 111.00 101.04 9.96 3.00e+00 1.11e-01 1.10e+01 angle pdb=" O1P CMP C 701 " pdb=" P CMP C 701 " pdb=" O2P CMP C 701 " ideal model delta sigma weight residual 109.50 118.94 -9.44 3.00e+00 1.11e-01 9.91e+00 ... (remaining 20488 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.48: 8813 34.48 - 68.96: 118 68.96 - 103.44: 20 103.44 - 137.92: 4 137.92 - 172.39: 4 Dihedral angle restraints: 8959 sinusoidal: 3675 harmonic: 5284 Sorted by residual: dihedral pdb=" C3' CMP C 701 " pdb=" O3' CMP C 701 " pdb=" P CMP C 701 " pdb=" O1P CMP C 701 " ideal model delta sinusoidal sigma weight residual -60.00 112.39 -172.39 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C3' CMP A 701 " pdb=" O3' CMP A 701 " pdb=" P CMP A 701 " pdb=" O1P CMP A 701 " ideal model delta sinusoidal sigma weight residual -60.00 112.38 -172.38 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C3' CMP D 701 " pdb=" O3' CMP D 701 " pdb=" P CMP D 701 " pdb=" O1P CMP D 701 " ideal model delta sinusoidal sigma weight residual -60.00 111.48 -171.48 1 2.00e+01 2.50e-03 4.77e+01 ... (remaining 8956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1871 0.053 - 0.107: 379 0.107 - 0.160: 33 0.160 - 0.214: 2 0.214 - 0.267: 4 Chirality restraints: 2289 Sorted by residual: chirality pdb=" C2' CMP B1301 " pdb=" C1' CMP B1301 " pdb=" C3' CMP B1301 " pdb=" O2' CMP B1301 " both_signs ideal model delta sigma weight residual False -2.51 -2.78 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" C2' CMP D 701 " pdb=" C1' CMP D 701 " pdb=" C3' CMP D 701 " pdb=" O2' CMP D 701 " both_signs ideal model delta sigma weight residual False -2.51 -2.78 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C2' CMP C 701 " pdb=" C1' CMP C 701 " pdb=" C3' CMP C 701 " pdb=" O2' CMP C 701 " both_signs ideal model delta sigma weight residual False -2.51 -2.77 0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 2286 not shown) Planarity restraints: 2524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 763 " -0.043 5.00e-02 4.00e+02 6.47e-02 6.70e+00 pdb=" N PRO B 764 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 764 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 764 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 339 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.74e+00 pdb=" N PRO D 340 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 340 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 340 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 382 " -0.016 2.00e-02 2.50e+03 1.48e-02 3.81e+00 pdb=" CG PHE A 382 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE A 382 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 382 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 382 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 382 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 382 " -0.002 2.00e-02 2.50e+03 ... (remaining 2521 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 804 2.74 - 3.28: 15197 3.28 - 3.82: 26734 3.82 - 4.36: 31293 4.36 - 4.90: 52896 Nonbonded interactions: 126924 Sorted by model distance: nonbonded pdb=" O THR C 357 " pdb=" OG1 THR C 361 " model vdw 2.196 3.040 nonbonded pdb=" O LEU C 169 " pdb=" OG1 THR C 173 " model vdw 2.221 3.040 nonbonded pdb=" O LEU D 169 " pdb=" OG1 THR D 173 " model vdw 2.241 3.040 nonbonded pdb=" O THR A 357 " pdb=" OG1 THR A 361 " model vdw 2.269 3.040 nonbonded pdb=" OE2 GLU A 515 " pdb=" OH TYR A 517 " model vdw 2.272 3.040 ... (remaining 126919 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 156 through 605 or resid 701)) selection = chain 'C' selection = (chain 'D' and (resid 156 through 605 or resid 701)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.750 Find NCS groups from input model: 0.300 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: 0.000 Load rotamer database and sin/cos tables:6.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 15111 Z= 0.142 Angle : 0.635 10.181 20493 Z= 0.309 Chirality : 0.042 0.267 2289 Planarity : 0.004 0.065 2524 Dihedral : 14.888 172.395 5573 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.19), residues: 1780 helix: 0.77 (0.14), residues: 1141 sheet: 0.38 (0.72), residues: 44 loop : 0.20 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 407 TYR 0.017 0.001 TYR B 787 PHE 0.034 0.001 PHE A 382 TRP 0.021 0.002 TRP D 168 HIS 0.004 0.001 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (15111) covalent geometry : angle 0.63519 / 0.31 (20493) hydrogen bonds : bond 0.14670 / 9.57 ( 930) hydrogen bonds : angle 5.65655 / 4.20 ( 2670) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.573 Fit side-chains REVERT: C 296 ASN cc_start: 0.8505 (m-40) cc_final: 0.8270 (m-40) REVERT: B 1061 ASP cc_start: 0.7803 (m-30) cc_final: 0.7512 (m-30) REVERT: A 281 MET cc_start: 0.8450 (ttp) cc_final: 0.8242 (ttm) REVERT: D 237 ILE cc_start: 0.8421 (mm) cc_final: 0.8182 (mm) REVERT: D 411 GLN cc_start: 0.8169 (tp-100) cc_final: 0.7827 (mm-40) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.6790 time to fit residues: 142.4156 Evaluate side-chains 138 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 758 ASN B 805 ASN B 864 ASN B1068 HIS A 411 GLN A 559 ASN D 243 ASN D 498 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.118153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.095638 restraints weight = 18381.801| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 1.24 r_work: 0.2901 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15111 Z= 0.151 Angle : 0.555 9.600 20493 Z= 0.276 Chirality : 0.041 0.173 2289 Planarity : 0.004 0.051 2524 Dihedral : 11.584 179.653 2033 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.24 % Allowed : 6.96 % Favored : 91.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.20), residues: 1780 helix: 1.63 (0.15), residues: 1122 sheet: 0.67 (0.66), residues: 44 loop : 0.47 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 514 TYR 0.017 0.001 TYR D 349 PHE 0.019 0.001 PHE A 382 TRP 0.018 0.002 TRP D 168 HIS 0.005 0.001 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (15111) covalent geometry : angle 0.55518 / 0.28 (20493) hydrogen bonds : bond 0.03962 / 2.59 ( 930) hydrogen bonds : angle 4.28937 / 3.17 ( 2670) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 0.657 Fit side-chains REVERT: B 1061 ASP cc_start: 0.8148 (m-30) cc_final: 0.7846 (m-30) REVERT: D 411 GLN cc_start: 0.8510 (tp-100) cc_final: 0.8213 (mm-40) REVERT: D 455 LYS cc_start: 0.8317 (mmtm) cc_final: 0.7827 (ptpt) REVERT: D 540 ASP cc_start: 0.7899 (p0) cc_final: 0.7685 (p0) outliers start: 20 outliers final: 8 residues processed: 174 average time/residue: 0.6210 time to fit residues: 119.2348 Evaluate side-chains 153 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 145 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain B residue 720 ASP Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 47 optimal weight: 0.0970 chunk 71 optimal weight: 0.5980 chunk 121 optimal weight: 4.9990 chunk 109 optimal weight: 0.0970 chunk 53 optimal weight: 10.0000 chunk 126 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 170 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1053 ASN A 411 GLN A 559 ASN D 498 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.114972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.091295 restraints weight = 18768.261| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.35 r_work: 0.2875 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15111 Z= 0.138 Angle : 0.534 9.480 20493 Z= 0.262 Chirality : 0.040 0.156 2289 Planarity : 0.004 0.044 2524 Dihedral : 11.063 176.847 2033 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.30 % Allowed : 9.75 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.20), residues: 1780 helix: 1.89 (0.15), residues: 1122 sheet: 1.05 (0.65), residues: 44 loop : 0.52 (0.27), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 778 TYR 0.023 0.001 TYR B 732 PHE 0.016 0.001 PHE C 298 TRP 0.018 0.001 TRP D 168 HIS 0.004 0.001 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (15111) covalent geometry : angle 0.53437 / 0.26 (20493) hydrogen bonds : bond 0.03637 / 2.37 ( 930) hydrogen bonds : angle 4.03598 / 2.98 ( 2670) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.506 Fit side-chains REVERT: C 475 LYS cc_start: 0.8480 (mmtt) cc_final: 0.8236 (mmmt) REVERT: B 770 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8316 (mtp) REVERT: B 1061 ASP cc_start: 0.8171 (m-30) cc_final: 0.7860 (m-30) REVERT: B 1081 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7294 (ppt-90) REVERT: A 243 ASN cc_start: 0.7415 (t0) cc_final: 0.7051 (m-40) REVERT: A 409 GLU cc_start: 0.8021 (pt0) cc_final: 0.7621 (pp20) REVERT: D 411 GLN cc_start: 0.8552 (tp-100) cc_final: 0.8266 (mm-40) REVERT: D 455 LYS cc_start: 0.8239 (mmtm) cc_final: 0.7713 (ptpt) REVERT: D 540 ASP cc_start: 0.7951 (p0) cc_final: 0.7739 (p0) outliers start: 21 outliers final: 10 residues processed: 165 average time/residue: 0.5993 time to fit residues: 109.3231 Evaluate side-chains 151 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain B residue 720 ASP Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 770 MET Chi-restraints excluded: chain B residue 1081 ARG Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 482 ASP Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 132 optimal weight: 8.9990 chunk 157 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 98 optimal weight: 0.0470 chunk 11 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 18 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 overall best weight: 2.1882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 714 GLN A 411 GLN D 243 ASN D 496 GLN D 498 GLN D 559 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.113332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.089684 restraints weight = 18553.324| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.35 r_work: 0.2837 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15111 Z= 0.185 Angle : 0.561 8.484 20493 Z= 0.276 Chirality : 0.041 0.162 2289 Planarity : 0.004 0.040 2524 Dihedral : 10.402 173.547 2033 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.55 % Allowed : 10.87 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.20), residues: 1780 helix: 1.94 (0.15), residues: 1108 sheet: 1.16 (0.65), residues: 43 loop : 0.53 (0.26), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 514 TYR 0.018 0.002 TYR D 349 PHE 0.017 0.002 PHE D 298 TRP 0.019 0.002 TRP C 168 HIS 0.005 0.001 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (15111) covalent geometry : angle 0.56080 / 0.28 (20493) hydrogen bonds : bond 0.03776 / 2.44 ( 930) hydrogen bonds : angle 4.08791 / 3.02 ( 2670) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.554 Fit side-chains REVERT: C 415 ASP cc_start: 0.8440 (m-30) cc_final: 0.8166 (m-30) REVERT: C 475 LYS cc_start: 0.8463 (mmtt) cc_final: 0.8192 (mmmt) REVERT: B 770 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8296 (mtp) REVERT: B 1061 ASP cc_start: 0.8204 (m-30) cc_final: 0.7869 (m-30) REVERT: B 1081 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7343 (ppt-90) REVERT: A 243 ASN cc_start: 0.7503 (t0) cc_final: 0.7102 (m-40) REVERT: A 409 GLU cc_start: 0.8046 (pt0) cc_final: 0.7631 (pp20) REVERT: A 556 LYS cc_start: 0.7100 (mttm) cc_final: 0.6784 (ttmm) REVERT: A 594 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.7542 (tmm) REVERT: D 411 GLN cc_start: 0.8557 (tp-100) cc_final: 0.8259 (mm-40) REVERT: D 455 LYS cc_start: 0.8152 (mmtm) cc_final: 0.7633 (ptpt) REVERT: D 540 ASP cc_start: 0.8017 (p0) cc_final: 0.7800 (p0) outliers start: 25 outliers final: 12 residues processed: 166 average time/residue: 0.6242 time to fit residues: 114.3989 Evaluate side-chains 154 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain B residue 720 ASP Chi-restraints excluded: chain B residue 770 MET Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1081 ARG Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 482 ASP Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 575 CYS Chi-restraints excluded: chain D residue 609 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 124 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 169 optimal weight: 7.9990 chunk 65 optimal weight: 0.7980 chunk 96 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 714 GLN A 411 GLN D 243 ASN D 496 GLN D 498 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.113115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.089584 restraints weight = 18454.551| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 1.34 r_work: 0.2840 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15111 Z= 0.179 Angle : 0.567 8.817 20493 Z= 0.277 Chirality : 0.041 0.169 2289 Planarity : 0.004 0.040 2524 Dihedral : 9.817 177.335 2033 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.93 % Allowed : 10.81 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.20), residues: 1780 helix: 1.95 (0.15), residues: 1108 sheet: 1.33 (0.64), residues: 44 loop : 0.55 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 514 TYR 0.017 0.002 TYR D 349 PHE 0.017 0.002 PHE D 298 TRP 0.021 0.002 TRP C 168 HIS 0.005 0.001 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (15111) covalent geometry : angle 0.56689 / 0.28 (20493) hydrogen bonds : bond 0.03776 / 2.45 ( 930) hydrogen bonds : angle 4.06153 / 3.00 ( 2670) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 0.650 Fit side-chains revert: symmetry clash REVERT: C 415 ASP cc_start: 0.8407 (m-30) cc_final: 0.8149 (m-30) REVERT: C 451 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.7930 (mppt) REVERT: C 475 LYS cc_start: 0.8547 (mmtt) cc_final: 0.8275 (mmmt) REVERT: C 564 ASN cc_start: 0.8842 (OUTLIER) cc_final: 0.8457 (m-40) REVERT: B 1060 LYS cc_start: 0.8659 (tppt) cc_final: 0.8025 (ttpp) REVERT: B 1081 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7410 (ppt-90) REVERT: A 243 ASN cc_start: 0.7524 (t0) cc_final: 0.7170 (m-40) REVERT: A 409 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7631 (pp20) REVERT: A 553 LYS cc_start: 0.7461 (pttt) cc_final: 0.6767 (pptt) REVERT: A 594 MET cc_start: 0.7657 (OUTLIER) cc_final: 0.7437 (tmm) REVERT: D 411 GLN cc_start: 0.8564 (tp-100) cc_final: 0.8246 (mm-40) REVERT: D 455 LYS cc_start: 0.8188 (mmtm) cc_final: 0.7652 (ptpt) REVERT: D 540 ASP cc_start: 0.8009 (p0) cc_final: 0.7792 (p0) outliers start: 31 outliers final: 12 residues processed: 169 average time/residue: 0.6429 time to fit residues: 119.5741 Evaluate side-chains 156 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 564 ASN Chi-restraints excluded: chain B residue 720 ASP Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1081 ARG Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 482 ASP Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 575 CYS Chi-restraints excluded: chain D residue 609 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 57 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 165 optimal weight: 0.0070 chunk 163 optimal weight: 0.4980 chunk 142 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 714 GLN A 411 GLN D 243 ASN D 498 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.117680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.095263 restraints weight = 18411.638| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.23 r_work: 0.2942 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15111 Z= 0.103 Angle : 0.522 8.562 20493 Z= 0.250 Chirality : 0.039 0.156 2289 Planarity : 0.003 0.044 2524 Dihedral : 9.336 150.251 2033 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.99 % Allowed : 12.36 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.20), residues: 1780 helix: 2.11 (0.15), residues: 1125 sheet: 1.44 (0.64), residues: 50 loop : 0.59 (0.27), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 514 TYR 0.014 0.001 TYR B 732 PHE 0.014 0.001 PHE C 298 TRP 0.020 0.001 TRP C 168 HIS 0.002 0.001 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (15111) covalent geometry : angle 0.52245 / 0.25 (20493) hydrogen bonds : bond 0.03301 / 2.14 ( 930) hydrogen bonds : angle 3.82633 / 2.83 ( 2670) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: C 415 ASP cc_start: 0.8331 (m-30) cc_final: 0.8108 (m-30) REVERT: C 451 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.7942 (mppt) REVERT: C 475 LYS cc_start: 0.8479 (mmtt) cc_final: 0.8223 (mttt) REVERT: B 897 MET cc_start: 0.8783 (ttt) cc_final: 0.8569 (ttt) REVERT: B 1060 LYS cc_start: 0.8665 (tppt) cc_final: 0.8121 (ttpp) REVERT: B 1081 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7433 (ppt-90) REVERT: A 212 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8165 (mp) REVERT: A 409 GLU cc_start: 0.8003 (pt0) cc_final: 0.7572 (pp20) REVERT: A 553 LYS cc_start: 0.7357 (pttt) cc_final: 0.6732 (pptt) REVERT: A 556 LYS cc_start: 0.6998 (mttm) cc_final: 0.6610 (ttmm) REVERT: A 608 LEU cc_start: 0.8550 (mp) cc_final: 0.8276 (mm) REVERT: D 411 GLN cc_start: 0.8561 (tp-100) cc_final: 0.8279 (mm-40) REVERT: D 455 LYS cc_start: 0.8189 (mmtm) cc_final: 0.7748 (ptpt) REVERT: D 540 ASP cc_start: 0.7921 (p0) cc_final: 0.7718 (p0) REVERT: D 594 MET cc_start: 0.7858 (tpp) cc_final: 0.7548 (tpp) outliers start: 16 outliers final: 3 residues processed: 160 average time/residue: 0.6035 time to fit residues: 106.7861 Evaluate side-chains 149 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 143 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 521 GLU Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 1081 ARG Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain D residue 482 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 53 optimal weight: 0.7980 chunk 173 optimal weight: 0.0050 chunk 40 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 158 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 overall best weight: 1.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 564 ASN B 714 GLN A 411 GLN D 243 ASN D 496 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.116425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.093941 restraints weight = 18265.899| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.22 r_work: 0.2879 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15111 Z= 0.148 Angle : 0.549 9.004 20493 Z= 0.266 Chirality : 0.040 0.167 2289 Planarity : 0.004 0.043 2524 Dihedral : 9.152 137.474 2033 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.06 % Allowed : 12.80 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.20), residues: 1780 helix: 2.23 (0.15), residues: 1101 sheet: 1.36 (0.66), residues: 45 loop : 0.65 (0.26), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 514 TYR 0.017 0.001 TYR D 349 PHE 0.017 0.001 PHE B 870 TRP 0.017 0.002 TRP D 168 HIS 0.005 0.001 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (15111) covalent geometry : angle 0.54859 / 0.27 (20493) hydrogen bonds : bond 0.03540 / 2.30 ( 930) hydrogen bonds : angle 3.90845 / 2.89 ( 2670) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.607 Fit side-chains REVERT: C 415 ASP cc_start: 0.8345 (m-30) cc_final: 0.8122 (m-30) REVERT: C 451 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.7965 (mppt) REVERT: C 564 ASN cc_start: 0.8778 (OUTLIER) cc_final: 0.8375 (m-40) REVERT: B 1061 ASP cc_start: 0.8195 (m-30) cc_final: 0.7907 (m-30) REVERT: B 1081 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7456 (ppt-90) REVERT: A 212 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8246 (mp) REVERT: A 553 LYS cc_start: 0.7400 (pttt) cc_final: 0.6808 (pptt) REVERT: A 556 LYS cc_start: 0.7028 (mttm) cc_final: 0.6696 (ttmm) REVERT: D 411 GLN cc_start: 0.8557 (tp-100) cc_final: 0.8266 (mm-40) REVERT: D 455 LYS cc_start: 0.8228 (mmtm) cc_final: 0.7751 (ptpt) REVERT: D 484 GLU cc_start: 0.7357 (mt-10) cc_final: 0.6982 (mp0) REVERT: D 540 ASP cc_start: 0.7945 (p0) cc_final: 0.7729 (p0) REVERT: D 594 MET cc_start: 0.7888 (tpp) cc_final: 0.7602 (tpp) outliers start: 17 outliers final: 6 residues processed: 155 average time/residue: 0.6343 time to fit residues: 108.2831 Evaluate side-chains 147 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 521 GLU Chi-restraints excluded: chain C residue 564 ASN Chi-restraints excluded: chain B residue 720 ASP Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 1081 ARG Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain D residue 482 ASP Chi-restraints excluded: chain D residue 575 CYS Chi-restraints excluded: chain D residue 609 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 55 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 0.1980 chunk 147 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 143 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 564 ASN B 714 GLN A 411 GLN D 243 ASN D 498 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.115854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.093145 restraints weight = 18478.008| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.24 r_work: 0.2881 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15111 Z= 0.141 Angle : 0.545 8.903 20493 Z= 0.264 Chirality : 0.040 0.166 2289 Planarity : 0.004 0.044 2524 Dihedral : 9.122 135.501 2033 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.06 % Allowed : 13.35 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.20), residues: 1780 helix: 2.23 (0.15), residues: 1101 sheet: 1.32 (0.66), residues: 45 loop : 0.65 (0.26), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 514 TYR 0.015 0.001 TYR D 349 PHE 0.016 0.001 PHE C 298 TRP 0.018 0.002 TRP C 168 HIS 0.004 0.001 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (15111) covalent geometry : angle 0.54503 / 0.26 (20493) hydrogen bonds : bond 0.03509 / 2.28 ( 930) hydrogen bonds : angle 3.89276 / 2.88 ( 2670) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.615 Fit side-chains REVERT: C 415 ASP cc_start: 0.8340 (m-30) cc_final: 0.8119 (m-30) REVERT: C 451 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.7969 (mppt) REVERT: C 564 ASN cc_start: 0.8874 (OUTLIER) cc_final: 0.8507 (m-40) REVERT: B 665 MET cc_start: 0.8527 (mmp) cc_final: 0.8091 (mmp) REVERT: B 1061 ASP cc_start: 0.8180 (m-30) cc_final: 0.7895 (m-30) REVERT: B 1081 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7458 (ppt-90) REVERT: A 212 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8238 (mp) REVERT: A 243 ASN cc_start: 0.7374 (t0) cc_final: 0.7112 (m-40) REVERT: A 553 LYS cc_start: 0.7401 (pttt) cc_final: 0.6807 (pptt) REVERT: A 556 LYS cc_start: 0.7028 (mttm) cc_final: 0.6697 (ttmm) REVERT: D 411 GLN cc_start: 0.8550 (tp-100) cc_final: 0.8270 (mm-40) REVERT: D 455 LYS cc_start: 0.8223 (mmtm) cc_final: 0.7750 (ptpt) REVERT: D 484 GLU cc_start: 0.7308 (mt-10) cc_final: 0.6971 (mp0) REVERT: D 540 ASP cc_start: 0.7957 (p0) cc_final: 0.7734 (p0) REVERT: D 594 MET cc_start: 0.7848 (tpp) cc_final: 0.7577 (tpp) outliers start: 17 outliers final: 6 residues processed: 147 average time/residue: 0.6471 time to fit residues: 104.6874 Evaluate side-chains 146 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 521 GLU Chi-restraints excluded: chain C residue 564 ASN Chi-restraints excluded: chain B residue 720 ASP Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 1081 ARG Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain D residue 482 ASP Chi-restraints excluded: chain D residue 609 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 32 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 176 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 175 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 99 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 58.7836 > 50:) chunk 170 optimal weight: 8.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 564 ASN B 714 GLN A 411 GLN D 243 ASN D 498 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.114448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.091176 restraints weight = 18469.520| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.33 r_work: 0.2843 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15111 Z= 0.146 Angle : 0.549 8.945 20493 Z= 0.265 Chirality : 0.040 0.167 2289 Planarity : 0.004 0.044 2524 Dihedral : 9.109 134.410 2033 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.93 % Allowed : 13.66 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.20), residues: 1780 helix: 2.23 (0.15), residues: 1101 sheet: 1.34 (0.66), residues: 45 loop : 0.66 (0.26), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 514 TYR 0.016 0.001 TYR D 349 PHE 0.016 0.001 PHE C 298 TRP 0.018 0.002 TRP C 168 HIS 0.004 0.001 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (15111) covalent geometry : angle 0.54878 / 0.27 (20493) hydrogen bonds : bond 0.03530 / 2.29 ( 930) hydrogen bonds : angle 3.90127 / 2.88 ( 2670) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.606 Fit side-chains revert: symmetry clash REVERT: C 415 ASP cc_start: 0.8401 (m-30) cc_final: 0.8153 (m-30) REVERT: C 451 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.7917 (mppt) REVERT: C 564 ASN cc_start: 0.8848 (OUTLIER) cc_final: 0.8488 (m-40) REVERT: B 665 MET cc_start: 0.8530 (mmp) cc_final: 0.8087 (mmp) REVERT: B 1060 LYS cc_start: 0.8626 (tppt) cc_final: 0.7985 (ttpp) REVERT: B 1081 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7421 (ppt-90) REVERT: A 212 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8231 (mp) REVERT: A 243 ASN cc_start: 0.7369 (t0) cc_final: 0.7014 (m-40) REVERT: A 553 LYS cc_start: 0.7433 (pttt) cc_final: 0.6800 (pptt) REVERT: A 556 LYS cc_start: 0.6982 (mttm) cc_final: 0.6657 (ttmm) REVERT: D 411 GLN cc_start: 0.8553 (tp-100) cc_final: 0.8259 (mm-40) REVERT: D 455 LYS cc_start: 0.8163 (mmtm) cc_final: 0.7651 (ptpt) REVERT: D 484 GLU cc_start: 0.7355 (mt-10) cc_final: 0.6980 (mp0) REVERT: D 540 ASP cc_start: 0.8001 (p0) cc_final: 0.7775 (p0) outliers start: 15 outliers final: 6 residues processed: 148 average time/residue: 0.6360 time to fit residues: 103.7441 Evaluate side-chains 145 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 521 GLU Chi-restraints excluded: chain C residue 564 ASN Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 1081 ARG Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain D residue 482 ASP Chi-restraints excluded: chain D residue 575 CYS Chi-restraints excluded: chain D residue 609 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 138 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 564 ASN B 714 GLN A 411 GLN D 243 ASN D 496 GLN D 498 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.116211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.093550 restraints weight = 18372.984| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.23 r_work: 0.2886 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15111 Z= 0.129 Angle : 0.545 8.871 20493 Z= 0.262 Chirality : 0.039 0.164 2289 Planarity : 0.004 0.044 2524 Dihedral : 9.098 134.011 2033 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.75 % Allowed : 13.73 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.49 (0.20), residues: 1780 helix: 2.28 (0.15), residues: 1101 sheet: 1.29 (0.65), residues: 45 loop : 0.68 (0.26), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 514 TYR 0.014 0.001 TYR D 349 PHE 0.015 0.001 PHE C 298 TRP 0.019 0.002 TRP C 168 HIS 0.004 0.001 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (15111) covalent geometry : angle 0.54526 / 0.26 (20493) hydrogen bonds : bond 0.03466 / 2.25 ( 930) hydrogen bonds : angle 3.87101 / 2.86 ( 2670) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 0.618 Fit side-chains revert: symmetry clash REVERT: C 415 ASP cc_start: 0.8356 (m-30) cc_final: 0.8136 (m-30) REVERT: C 451 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.7967 (mppt) REVERT: C 564 ASN cc_start: 0.8852 (OUTLIER) cc_final: 0.8527 (m-40) REVERT: B 665 MET cc_start: 0.8531 (mmp) cc_final: 0.8080 (mmp) REVERT: B 1060 LYS cc_start: 0.8693 (tppt) cc_final: 0.8141 (ttpp) REVERT: B 1081 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7474 (ppt-90) REVERT: A 212 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8231 (mp) REVERT: A 243 ASN cc_start: 0.7416 (t0) cc_final: 0.7071 (m-40) REVERT: A 553 LYS cc_start: 0.7390 (pttt) cc_final: 0.6800 (pptt) REVERT: A 556 LYS cc_start: 0.7034 (mttm) cc_final: 0.6703 (ttmm) REVERT: D 411 GLN cc_start: 0.8551 (tp-100) cc_final: 0.8274 (mm-40) REVERT: D 455 LYS cc_start: 0.8199 (mmtm) cc_final: 0.7736 (ptpt) REVERT: D 484 GLU cc_start: 0.7313 (mt-10) cc_final: 0.6971 (mp0) REVERT: D 540 ASP cc_start: 0.7937 (p0) cc_final: 0.7711 (p0) outliers start: 12 outliers final: 6 residues processed: 149 average time/residue: 0.6338 time to fit residues: 103.9135 Evaluate side-chains 148 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 138 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 521 GLU Chi-restraints excluded: chain C residue 564 ASN Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 1081 ARG Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain D residue 482 ASP Chi-restraints excluded: chain D residue 575 CYS Chi-restraints excluded: chain D residue 609 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 69 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 154 optimal weight: 0.0000 chunk 111 optimal weight: 0.6980 chunk 37 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 148 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 564 ASN B 714 GLN A 411 GLN D 243 ASN D 498 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.117246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.095057 restraints weight = 18249.047| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.22 r_work: 0.2923 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15111 Z= 0.113 Angle : 0.535 9.130 20493 Z= 0.257 Chirality : 0.039 0.161 2289 Planarity : 0.003 0.044 2524 Dihedral : 9.082 133.657 2033 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.75 % Allowed : 13.73 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.59 (0.20), residues: 1780 helix: 2.35 (0.15), residues: 1101 sheet: 1.43 (0.63), residues: 50 loop : 0.70 (0.26), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 514 TYR 0.013 0.001 TYR B 732 PHE 0.015 0.001 PHE C 285 TRP 0.019 0.001 TRP C 168 HIS 0.003 0.001 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (15111) covalent geometry : angle 0.53475 / 0.26 (20493) hydrogen bonds : bond 0.03367 / 2.19 ( 930) hydrogen bonds : angle 3.82444 / 2.83 ( 2670) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4360.57 seconds wall clock time: 75 minutes 22.38 seconds (4522.38 seconds total)