Starting phenix.real_space_refine on Sun Sep 13 06:57:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rol_54123/09_2026/9rol_54123_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rol_54123/09_2026/9rol_54123.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rol_54123/09_2026/9rol_54123.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rol_54123/09_2026/9rol_54123.map" model { file = "/net/cci-nas-00/data/ceres_data/9rol_54123/09_2026/9rol_54123_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rol_54123/09_2026/9rol_54123_trim.cif" } resolution = 3.54 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= -0.002 sd= 0.023 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 P 1 5.49 5 S 61 5.16 5 C 6606 2.51 5 N 1699 2.21 5 O 1931 1.98 5 H 10181 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s 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: 20479 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 15236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 15236 Classifications: {'peptide': 984} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 41, 'TRANS': 942} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 4574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4574 Classifications: {'peptide': 282} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 261} Chain: "C" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 543 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'CLR': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.04, per 1000 atoms: 0.20 Number of scatterers: 20479 At special positions: 0 Unit cell: (78.36, 90.114, 177.616, 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) S 61 16.00 P 1 15.00 O 1931 8.00 N 1699 7.00 C 6606 6.00 H 10181 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 175 " distance=2.04 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 276 " distance=2.03 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=1, symmetry=0 Links applied NAG-ASN " NAG B 401 " - " ASN B 158 " " NAG B 402 " - " ASN B 193 " " NAG B 403 " - " ASN B 265 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 605.8 milliseconds 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2396 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 9 sheets defined 49.5% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 37 through 46 Processing helix chain 'A' and resid 54 through 66 removed outlier: 3.531A pdb=" N ALA A 58 " --> pdb=" O THR A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 removed outlier: 3.789A pdb=" N PHE A 87 " --> pdb=" O CYS A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 112 removed outlier: 3.725A pdb=" N GLU A 112 " --> pdb=" O GLN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 149 removed outlier: 3.729A pdb=" N ILE A 147 " --> pdb=" O LYS A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 251 through 254 Processing helix chain 'A' and resid 255 through 265 Processing helix chain 'A' and resid 272 through 303 Processing helix chain 'A' and resid 306 through 322 Processing helix chain 'A' and resid 325 through 344 Processing helix chain 'A' and resid 352 through 359 removed outlier: 3.897A pdb=" N THR A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 357 " --> pdb=" O ALA A 353 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY A 358 " --> pdb=" O VAL A 354 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 352 through 359' Processing helix chain 'A' and resid 405 through 419 Processing helix chain 'A' and resid 440 through 455 Processing helix chain 'A' and resid 457 through 463 Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 521 through 537 Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.711A pdb=" N ALA A 592 " --> pdb=" O ALA A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 622 removed outlier: 3.582A pdb=" N ALA A 614 " --> pdb=" O HIS A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 639 Processing helix chain 'A' and resid 641 through 645 Processing helix chain 'A' and resid 664 through 675 removed outlier: 3.559A pdb=" N ILE A 668 " --> pdb=" O THR A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 698 removed outlier: 3.582A pdb=" N GLN A 698 " --> pdb=" O GLY A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 718 removed outlier: 4.380A pdb=" N ALA A 714 " --> pdb=" O ASN A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 736 Processing helix chain 'A' and resid 745 through 770 removed outlier: 4.015A pdb=" N VAL A 749 " --> pdb=" O PHE A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 774 removed outlier: 3.675A pdb=" N ILE A 774 " --> pdb=" O THR A 771 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 771 through 774' Processing helix chain 'A' and resid 777 through 787 Processing helix chain 'A' and resid 793 through 805 Processing helix chain 'A' and resid 806 through 812 removed outlier: 3.638A pdb=" N ILE A 810 " --> pdb=" O MET A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 815 No H-bonds generated for 'chain 'A' and resid 813 through 815' Processing helix chain 'A' and resid 820 through 824 removed outlier: 3.524A pdb=" N LYS A 823 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG A 824 " --> pdb=" O ILE A 821 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 820 through 824' Processing helix chain 'A' and resid 836 through 846 removed outlier: 3.895A pdb=" N GLN A 846 " --> pdb=" O MET A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 867 removed outlier: 3.843A pdb=" N ILE A 850 " --> pdb=" O GLN A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 873 Processing helix chain 'A' and resid 876 through 882 Processing helix chain 'A' and resid 897 through 927 removed outlier: 3.817A pdb=" N ALA A 922 " --> pdb=" O VAL A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 938 Processing helix chain 'A' and resid 941 through 961 removed outlier: 3.584A pdb=" N ILE A 945 " --> pdb=" O ASN A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 966 removed outlier: 4.396A pdb=" N ASP A 965 " --> pdb=" O PRO A 962 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A 966 " --> pdb=" O GLY A 963 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 962 through 966' Processing helix chain 'A' and resid 974 through 980 removed outlier: 4.094A pdb=" N TRP A 978 " --> pdb=" O LYS A 974 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE A 979 " --> pdb=" O PRO A 975 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS A 980 " --> pdb=" O SER A 976 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 974 through 980' Processing helix chain 'A' and resid 981 through 1002 removed outlier: 3.576A pdb=" N SER A 985 " --> pdb=" O ALA A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1012 Processing helix chain 'B' and resid 28 through 61 Processing helix chain 'B' and resid 94 through 97 Processing helix chain 'B' and resid 98 through 110 Processing helix chain 'B' and resid 111 through 117 removed outlier: 6.174A pdb=" N ASP B 114 " --> pdb=" O LYS B 111 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N SER B 115 " --> pdb=" O TYR B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 156 removed outlier: 3.811A pdb=" N TRP B 155 " --> pdb=" O LYS B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 208 Processing helix chain 'B' and resid 231 through 235 removed outlier: 3.834A pdb=" N ASN B 234 " --> pdb=" O GLY B 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 58 removed outlier: 3.503A pdb=" N LEU C 36 " --> pdb=" O ASP C 32 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG C 58 " --> pdb=" O ILE C 54 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 166 through 171 removed outlier: 4.863A pdb=" N LEU A 160 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU A 182 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU A 180 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N CYS A 239 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N LYS A 202 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLU A 241 " --> pdb=" O GLY A 200 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLY A 200 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR A 243 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ALA A 198 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ARG A 245 " --> pdb=" O ILE A 196 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 189 removed outlier: 4.012A pdb=" N THR A 237 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N CYS A 239 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N LYS A 202 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLU A 241 " --> pdb=" O GLY A 200 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLY A 200 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR A 243 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ALA A 198 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ARG A 245 " --> pdb=" O ILE A 196 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 602 through 604 removed outlier: 6.035A pdb=" N ILE A 363 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N THR A 362 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N THR A 705 " --> pdb=" O THR A 362 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N CYS A 364 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL A 702 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N VAL A 722 " --> pdb=" O VAL A 702 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N VAL A 704 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N MET A 724 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N GLY A 706 " --> pdb=" O MET A 724 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 386 through 388 removed outlier: 6.923A pdb=" N SER A 580 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N MET A 381 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N LEU A 578 " --> pdb=" O MET A 381 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N PHE A 383 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 11.881A pdb=" N VAL A 576 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N PHE A 545 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU A 578 " --> pdb=" O LEU A 543 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU A 543 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLU A 484 " --> pdb=" O LYS A 466 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LYS A 466 " --> pdb=" O GLU A 484 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 386 through 388 removed outlier: 6.923A pdb=" N SER A 580 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N MET A 381 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N LEU A 578 " --> pdb=" O MET A 381 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N PHE A 383 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 11.881A pdb=" N VAL A 576 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLY A 577 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 653 through 656 Processing sheet with id=AA7, first strand: chain 'A' and resid 888 through 889 Processing sheet with id=AA8, first strand: chain 'B' and resid 78 through 79 Processing sheet with id=AA9, first strand: chain 'B' and resid 87 through 90 removed outlier: 6.428A pdb=" N ILE B 88 " --> pdb=" O GLU B 300 " (cutoff:3.500A) 512 hydrogen bonds defined for protein. 1446 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: 4.92 Time building geometry restraints manager: 3.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10156 1.03 - 1.23: 94 1.23 - 1.43: 4203 1.43 - 1.62: 6153 1.62 - 1.82: 91 Bond restraints: 20697 Sorted by residual: bond pdb=" N PHD A 366 " pdb=" H PHD A 366 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" C PHD A 366 " pdb=" O PHD A 366 " ideal model delta sigma weight residual 1.231 1.267 -0.036 2.00e-02 2.50e+03 3.26e+00 bond pdb=" CA PHD A 366 " pdb=" C PHD A 366 " ideal model delta sigma weight residual 1.525 1.558 -0.033 2.10e-02 2.27e+03 2.46e+00 bond pdb=" OD1 PHD A 366 " pdb=" P PHD A 366 " ideal model delta sigma weight residual 1.816 1.787 0.029 2.00e-02 2.50e+03 2.03e+00 bond pdb=" CG PHD A 366 " pdb=" OD2 PHD A 366 " ideal model delta sigma weight residual 1.218 1.243 -0.025 2.00e-02 2.50e+03 1.58e+00 ... (remaining 20692 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.27: 37456 7.27 - 14.54: 6 14.54 - 21.81: 0 21.81 - 29.08: 0 29.08 - 36.35: 3 Bond angle restraints: 37465 Sorted by residual: angle pdb=" C LYS B 192 " pdb=" CA LYS B 192 " pdb=" HA LYS B 192 " ideal model delta sigma weight residual 109.00 72.65 36.35 3.00e+00 1.11e-01 1.47e+02 angle pdb=" N LYS B 192 " pdb=" CA LYS B 192 " pdb=" HA LYS B 192 " ideal model delta sigma weight residual 110.00 75.61 34.39 3.00e+00 1.11e-01 1.31e+02 angle pdb=" CB LYS B 192 " pdb=" CA LYS B 192 " pdb=" HA LYS B 192 " ideal model delta sigma weight residual 109.00 77.88 31.12 3.00e+00 1.11e-01 1.08e+02 angle pdb=" N LYS B 192 " pdb=" CA LYS B 192 " pdb=" C LYS B 192 " ideal model delta sigma weight residual 108.63 116.11 -7.48 1.60e+00 3.91e-01 2.18e+01 angle pdb=" C SER A 365 " pdb=" N PHD A 366 " pdb=" H PHD A 366 " ideal model delta sigma weight residual 124.30 112.80 11.50 3.00e+00 1.11e-01 1.47e+01 ... (remaining 37460 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 8784 17.97 - 35.95: 791 35.95 - 53.92: 274 53.92 - 71.90: 57 71.90 - 89.87: 16 Dihedral angle restraints: 9922 sinusoidal: 5565 harmonic: 4357 Sorted by residual: dihedral pdb=" CA GLY B 161 " pdb=" C GLY B 161 " pdb=" N LEU B 162 " pdb=" CA LEU B 162 " ideal model delta harmonic sigma weight residual 180.00 155.35 24.65 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" C LYS B 192 " pdb=" N LYS B 192 " pdb=" CA LYS B 192 " pdb=" CB LYS B 192 " ideal model delta harmonic sigma weight residual -122.60 -132.35 9.75 0 2.50e+00 1.60e-01 1.52e+01 dihedral pdb=" N LYS B 192 " pdb=" C LYS B 192 " pdb=" CA LYS B 192 " pdb=" CB LYS B 192 " ideal model delta harmonic sigma weight residual 122.80 131.70 -8.90 0 2.50e+00 1.60e-01 1.27e+01 ... (remaining 9919 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1534 0.082 - 0.164: 95 0.164 - 0.247: 1 0.247 - 0.329: 0 0.329 - 0.411: 1 Chirality restraints: 1631 Sorted by residual: chirality pdb=" CA LYS B 192 " pdb=" N LYS B 192 " pdb=" C LYS B 192 " pdb=" CB LYS B 192 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" C1 NAG B 402 " pdb=" ND2 ASN B 193 " pdb=" C2 NAG B 402 " pdb=" O5 NAG B 402 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C1 NAG B 403 " pdb=" ND2 ASN B 265 " pdb=" C2 NAG B 403 " pdb=" O5 NAG B 403 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 4.68e-01 ... (remaining 1628 not shown) Planarity restraints: 3057 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 365 " -0.071 2.00e-02 2.50e+03 1.29e-01 1.67e+02 pdb=" N PHD A 366 " 0.223 2.00e-02 2.50e+03 pdb=" CA PHD A 366 " -0.062 2.00e-02 2.50e+03 pdb=" H PHD A 366 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHD A 366 " -0.033 2.00e-02 2.50e+03 6.85e-02 4.70e+01 pdb=" C PHD A 366 " 0.118 2.00e-02 2.50e+03 pdb=" O PHD A 366 " -0.044 2.00e-02 2.50e+03 pdb=" N LYS A 367 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 190 " -0.041 5.00e-02 4.00e+02 6.23e-02 6.22e+00 pdb=" N PRO B 191 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 191 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 191 " -0.035 5.00e-02 4.00e+02 ... (remaining 3054 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 597 2.12 - 2.74: 37754 2.74 - 3.36: 60047 3.36 - 3.98: 73805 3.98 - 4.60: 115438 Nonbonded interactions: 287641 Sorted by model distance: nonbonded pdb=" OP1 PHD A 366 " pdb=" H LEU A 371 " model vdw 1.505 2.450 nonbonded pdb=" H SER A 365 " pdb=" O ILE A 604 " model vdw 1.561 2.450 nonbonded pdb=" O VAL A 709 " pdb=" HG SER A 712 " model vdw 1.572 2.450 nonbonded pdb=" H VAL A 702 " pdb=" OD2 ASP A 719 " model vdw 1.609 2.450 nonbonded pdb=" HH TYR A 768 " pdb=" O THR A 804 " model vdw 1.609 2.450 ... (remaining 287636 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.750 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: 0.130 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.050 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 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 : 0.009 0.850 10523 Z= 0.842 Angle : 0.554 9.668 14287 Z= 0.274 Chirality : 0.040 0.411 1631 Planarity : 0.004 0.069 1820 Dihedral : 15.626 89.872 4104 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.09 % Allowed : 16.07 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.01 (0.24), residues: 1291 helix: 1.88 (0.23), residues: 552 sheet: -1.10 (0.47), residues: 124 loop : -1.57 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 586 TYR 0.017 0.001 TYR A 859 PHE 0.011 0.001 PHE A 297 TRP 0.004 0.001 TRP B 155 HIS 0.004 0.001 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (10516) covalent geometry : angle 0.55258 / 0.27 (14272) SS BOND : bond 0.00292 / 0.13 ( 3) SS BOND : angle 1.14398 / 0.55 ( 6) hydrogen bonds : bond 0.13217 / 9.06 ( 502) hydrogen bonds : angle 6.03158 / 4.55 ( 1446) Misc. bond : bond 0.85000 / 44.74 ( 1) link_NAG-ASN : bond 0.00254 / 0.13 ( 3) link_NAG-ASN : angle 1.30389 / 0.77 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 72 average time/residue: 0.2333 time to fit residues: 24.7791 Evaluate side-chains 70 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 69 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 797 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.0980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 518 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.151130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.100401 restraints weight = 76814.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.104818 restraints weight = 27921.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.107660 restraints weight = 16225.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.108954 restraints weight = 12135.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.108954 restraints weight = 10547.787| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.0451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10523 Z= 0.119 Angle : 0.516 6.397 14287 Z= 0.266 Chirality : 0.041 0.344 1631 Planarity : 0.004 0.049 1820 Dihedral : 6.621 57.854 1661 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.35 % Allowed : 14.81 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.06 (0.24), residues: 1291 helix: 1.97 (0.22), residues: 556 sheet: -1.13 (0.45), residues: 142 loop : -1.62 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 901 TYR 0.011 0.001 TYR A 859 PHE 0.016 0.001 PHE A 783 TRP 0.005 0.001 TRP A1006 HIS 0.004 0.001 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (10516) covalent geometry : angle 0.51469 / 0.27 (14272) SS BOND : bond 0.00298 / 0.14 ( 3) SS BOND : angle 0.94030 / 0.48 ( 6) hydrogen bonds : bond 0.04184 / 2.91 ( 502) hydrogen bonds : angle 4.92100 / 3.69 ( 1446) Misc. bond : bond 0.00679 / 0.36 ( 1) link_NAG-ASN : bond 0.00243 / 0.11 ( 3) link_NAG-ASN : angle 1.49815 / 0.96 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 80 average time/residue: 0.2071 time to fit residues: 25.2072 Evaluate side-chains 74 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 859 TYR Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 2 optimal weight: 7.9990 chunk 115 optimal weight: 0.7980 chunk 61 optimal weight: 10.0000 chunk 116 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 518 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.151474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.100462 restraints weight = 77272.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.104941 restraints weight = 28072.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.108016 restraints weight = 16388.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.109103 restraints weight = 12072.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.109103 restraints weight = 10605.477| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.0661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10523 Z= 0.115 Angle : 0.498 6.900 14287 Z= 0.253 Chirality : 0.040 0.351 1631 Planarity : 0.003 0.045 1820 Dihedral : 6.423 59.297 1659 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.44 % Allowed : 15.08 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.10 (0.24), residues: 1291 helix: 2.02 (0.22), residues: 555 sheet: -1.19 (0.47), residues: 131 loop : -1.59 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 901 TYR 0.011 0.001 TYR A 859 PHE 0.016 0.001 PHE A 783 TRP 0.004 0.001 TRP A1006 HIS 0.004 0.001 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (10516) covalent geometry : angle 0.49612 / 0.25 (14272) SS BOND : bond 0.00284 / 0.13 ( 3) SS BOND : angle 1.10437 / 0.52 ( 6) hydrogen bonds : bond 0.03695 / 2.55 ( 502) hydrogen bonds : angle 4.65251 / 3.47 ( 1446) Misc. bond : bond 0.00541 / 0.28 ( 1) link_NAG-ASN : bond 0.00207 / 0.10 ( 3) link_NAG-ASN : angle 1.48788 / 0.95 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 11 residues processed: 78 average time/residue: 0.2020 time to fit residues: 23.8821 Evaluate side-chains 77 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 859 TYR Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 7 optimal weight: 0.7980 chunk 13 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 45 optimal weight: 30.0000 chunk 69 optimal weight: 4.9990 chunk 112 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 44 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 473 ASN A 518 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.148085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.096022 restraints weight = 78445.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.100433 restraints weight = 29158.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.103212 restraints weight = 17245.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.104860 restraints weight = 13081.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.105521 restraints weight = 11267.524| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.0769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10523 Z= 0.143 Angle : 0.505 6.572 14287 Z= 0.258 Chirality : 0.041 0.345 1631 Planarity : 0.003 0.038 1820 Dihedral : 6.284 57.201 1659 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.53 % Allowed : 15.26 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.11 (0.24), residues: 1291 helix: 2.01 (0.22), residues: 558 sheet: -1.24 (0.47), residues: 131 loop : -1.56 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 901 TYR 0.013 0.001 TYR A 859 PHE 0.014 0.001 PHE A 783 TRP 0.004 0.001 TRP A1006 HIS 0.004 0.001 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (10516) covalent geometry : angle 0.50334 / 0.26 (14272) SS BOND : bond 0.00290 / 0.13 ( 3) SS BOND : angle 1.20087 / 0.56 ( 6) hydrogen bonds : bond 0.03543 / 2.45 ( 502) hydrogen bonds : angle 4.55105 / 3.39 ( 1446) Misc. bond : bond 0.00306 / 0.16 ( 1) link_NAG-ASN : bond 0.00216 / 0.10 ( 3) link_NAG-ASN : angle 1.54096 / 0.95 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 13 residues processed: 78 average time/residue: 0.2054 time to fit residues: 24.3062 Evaluate side-chains 79 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain A residue 859 TYR Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 52 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 104 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 51 optimal weight: 9.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 518 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.148507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.095889 restraints weight = 78382.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.100385 restraints weight = 29407.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 74)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.103276 restraints weight = 17433.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.104879 restraints weight = 13222.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.105569 restraints weight = 11451.524| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.0871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10523 Z= 0.133 Angle : 0.499 6.131 14287 Z= 0.255 Chirality : 0.041 0.348 1631 Planarity : 0.003 0.040 1820 Dihedral : 6.151 56.810 1659 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.71 % Allowed : 15.44 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.15 (0.24), residues: 1291 helix: 2.01 (0.22), residues: 565 sheet: -1.25 (0.47), residues: 131 loop : -1.55 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 901 TYR 0.012 0.001 TYR A 859 PHE 0.014 0.001 PHE A 783 TRP 0.004 0.001 TRP A1006 HIS 0.004 0.001 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (10516) covalent geometry : angle 0.49757 / 0.25 (14272) SS BOND : bond 0.00298 / 0.13 ( 3) SS BOND : angle 1.20300 / 0.56 ( 6) hydrogen bonds : bond 0.03460 / 2.38 ( 502) hydrogen bonds : angle 4.40968 / 3.28 ( 1446) Misc. bond : bond 0.00297 / 0.16 ( 1) link_NAG-ASN : bond 0.00198 / 0.09 ( 3) link_NAG-ASN : angle 1.55665 / 0.97 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 16 residues processed: 82 average time/residue: 0.2049 time to fit residues: 25.6227 Evaluate side-chains 82 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain A residue 859 TYR Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 81 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 49 optimal weight: 20.0000 chunk 12 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 126 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 39 optimal weight: 30.0000 chunk 21 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 937 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.146778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.094022 restraints weight = 78100.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.098346 restraints weight = 29219.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.101086 restraints weight = 17408.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.102659 restraints weight = 13271.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.103301 restraints weight = 11485.896| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10523 Z= 0.197 Angle : 0.537 6.474 14287 Z= 0.277 Chirality : 0.041 0.343 1631 Planarity : 0.003 0.037 1820 Dihedral : 6.164 58.488 1659 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.06 % Allowed : 15.35 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.08 (0.24), residues: 1291 helix: 1.95 (0.22), residues: 565 sheet: -1.14 (0.48), residues: 125 loop : -1.62 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 901 TYR 0.014 0.001 TYR A 859 PHE 0.015 0.001 PHE A 783 TRP 0.005 0.001 TRP A1006 HIS 0.004 0.001 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.20 (10516) covalent geometry : angle 0.53513 / 0.28 (14272) SS BOND : bond 0.00359 / 0.16 ( 3) SS BOND : angle 1.42260 / 0.66 ( 6) hydrogen bonds : bond 0.03576 / 2.47 ( 502) hydrogen bonds : angle 4.47104 / 3.33 ( 1446) Misc. bond : bond 0.00280 / 0.15 ( 1) link_NAG-ASN : bond 0.00310 / 0.14 ( 3) link_NAG-ASN : angle 1.64557 / 0.95 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 67 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 17 residues processed: 83 average time/residue: 0.2025 time to fit residues: 25.6296 Evaluate side-chains 82 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain A residue 859 TYR Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 85 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 30.0000 chunk 112 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 518 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.147897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.096109 restraints weight = 77656.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.100500 restraints weight = 28830.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.103212 restraints weight = 16958.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.104810 restraints weight = 12860.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.105489 restraints weight = 11124.304| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10523 Z= 0.133 Angle : 0.508 6.531 14287 Z= 0.259 Chirality : 0.041 0.348 1631 Planarity : 0.003 0.039 1820 Dihedral : 6.051 55.884 1659 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.97 % Allowed : 15.62 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.15 (0.24), residues: 1291 helix: 2.01 (0.22), residues: 565 sheet: -1.08 (0.48), residues: 125 loop : -1.58 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 901 TYR 0.012 0.001 TYR A 859 PHE 0.014 0.001 PHE A 783 TRP 0.004 0.001 TRP A1006 HIS 0.004 0.001 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (10516) covalent geometry : angle 0.50640 / 0.26 (14272) SS BOND : bond 0.00321 / 0.15 ( 3) SS BOND : angle 1.23579 / 0.59 ( 6) hydrogen bonds : bond 0.03440 / 2.36 ( 502) hydrogen bonds : angle 4.32595 / 3.22 ( 1446) Misc. bond : bond 0.00261 / 0.14 ( 1) link_NAG-ASN : bond 0.00205 / 0.10 ( 3) link_NAG-ASN : angle 1.55151 / 0.97 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 19 residues processed: 82 average time/residue: 0.1952 time to fit residues: 24.0983 Evaluate side-chains 85 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain A residue 859 TYR Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 24 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 30.0000 chunk 15 optimal weight: 6.9990 chunk 108 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 29 optimal weight: 0.4980 chunk 80 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.150963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.099692 restraints weight = 77530.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.104265 restraints weight = 28054.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.107198 restraints weight = 16186.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.108244 restraints weight = 12032.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.108244 restraints weight = 10604.396| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10523 Z= 0.126 Angle : 0.501 6.743 14287 Z= 0.254 Chirality : 0.040 0.343 1631 Planarity : 0.003 0.036 1820 Dihedral : 5.908 54.930 1659 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.06 % Allowed : 15.71 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.20 (0.24), residues: 1291 helix: 2.06 (0.22), residues: 566 sheet: -1.07 (0.48), residues: 125 loop : -1.57 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 901 TYR 0.012 0.001 TYR A 859 PHE 0.013 0.001 PHE A 783 TRP 0.004 0.001 TRP A1006 HIS 0.004 0.001 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (10516) covalent geometry : angle 0.49929 / 0.25 (14272) SS BOND : bond 0.00306 / 0.14 ( 3) SS BOND : angle 1.20863 / 0.57 ( 6) hydrogen bonds : bond 0.03317 / 2.28 ( 502) hydrogen bonds : angle 4.26468 / 3.18 ( 1446) Misc. bond : bond 0.00258 / 0.14 ( 1) link_NAG-ASN : bond 0.00212 / 0.10 ( 3) link_NAG-ASN : angle 1.58623 / 0.99 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 18 residues processed: 84 average time/residue: 0.1988 time to fit residues: 25.3141 Evaluate side-chains 86 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain A residue 859 TYR Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 0.0370 chunk 123 optimal weight: 0.7980 chunk 36 optimal weight: 10.0000 chunk 115 optimal weight: 0.2980 chunk 99 optimal weight: 0.2980 chunk 39 optimal weight: 30.0000 chunk 73 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 1 optimal weight: 9.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.151942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.100956 restraints weight = 76952.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.105529 restraints weight = 27726.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.108372 restraints weight = 15959.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.109571 restraints weight = 11930.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.110835 restraints weight = 10435.920| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 10523 Z= 0.095 Angle : 0.497 7.499 14287 Z= 0.250 Chirality : 0.040 0.350 1631 Planarity : 0.003 0.038 1820 Dihedral : 5.776 55.515 1659 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.35 % Allowed : 16.52 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.29 (0.24), residues: 1291 helix: 2.11 (0.22), residues: 568 sheet: -1.05 (0.48), residues: 125 loop : -1.51 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 586 TYR 0.010 0.001 TYR A 859 PHE 0.012 0.001 PHE A 783 TRP 0.004 0.001 TRP A 977 HIS 0.003 0.001 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.09 (10516) covalent geometry : angle 0.49505 / 0.25 (14272) SS BOND : bond 0.00267 / 0.13 ( 3) SS BOND : angle 1.03380 / 0.50 ( 6) hydrogen bonds : bond 0.03195 / 2.19 ( 502) hydrogen bonds : angle 4.13974 / 3.09 ( 1446) Misc. bond : bond 0.00242 / 0.13 ( 1) link_NAG-ASN : bond 0.00199 / 0.10 ( 3) link_NAG-ASN : angle 1.63285 / 1.05 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 630 THR cc_start: 0.8437 (OUTLIER) cc_final: 0.7974 (p) REVERT: B 145 GLU cc_start: 0.8336 (tt0) cc_final: 0.8042 (tt0) outliers start: 15 outliers final: 14 residues processed: 82 average time/residue: 0.1980 time to fit residues: 24.7427 Evaluate side-chains 85 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 859 TYR Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 27 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 52 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 24 optimal weight: 0.2980 chunk 20 optimal weight: 1.9990 chunk 103 optimal weight: 0.0770 chunk 120 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 overall best weight: 0.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.151787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.100738 restraints weight = 77064.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.105367 restraints weight = 27804.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.107971 restraints weight = 16032.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.109782 restraints weight = 12061.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.110529 restraints weight = 10299.223| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10523 Z= 0.099 Angle : 0.495 6.810 14287 Z= 0.248 Chirality : 0.040 0.349 1631 Planarity : 0.003 0.036 1820 Dihedral : 5.645 55.006 1659 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.35 % Allowed : 16.61 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.31 (0.24), residues: 1291 helix: 2.17 (0.22), residues: 568 sheet: -1.22 (0.47), residues: 131 loop : -1.50 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 586 TYR 0.011 0.001 TYR A 859 PHE 0.011 0.001 PHE A 783 TRP 0.004 0.001 TRP A 977 HIS 0.003 0.000 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (10516) covalent geometry : angle 0.49312 / 0.25 (14272) SS BOND : bond 0.00261 / 0.12 ( 3) SS BOND : angle 1.03711 / 0.49 ( 6) hydrogen bonds : bond 0.03096 / 2.13 ( 502) hydrogen bonds : angle 4.08841 / 3.05 ( 1446) Misc. bond : bond 0.00309 / 0.16 ( 1) link_NAG-ASN : bond 0.00210 / 0.10 ( 3) link_NAG-ASN : angle 1.64724 / 1.05 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 630 THR cc_start: 0.8427 (OUTLIER) cc_final: 0.8009 (p) REVERT: B 145 GLU cc_start: 0.8310 (tt0) cc_final: 0.8024 (tt0) outliers start: 15 outliers final: 13 residues processed: 79 average time/residue: 0.1985 time to fit residues: 23.9005 Evaluate side-chains 83 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 859 TYR Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 21 optimal weight: 20.0000 chunk 98 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.151224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.100069 restraints weight = 77217.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.104460 restraints weight = 27990.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.107488 restraints weight = 16301.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.108896 restraints weight = 12071.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.109715 restraints weight = 10405.539| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10523 Z= 0.135 Angle : 0.507 6.796 14287 Z= 0.256 Chirality : 0.041 0.349 1631 Planarity : 0.003 0.036 1820 Dihedral : 5.596 54.599 1659 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.44 % Allowed : 16.61 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.32 (0.24), residues: 1291 helix: 2.17 (0.22), residues: 567 sheet: -1.07 (0.48), residues: 126 loop : -1.51 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 901 TYR 0.013 0.001 TYR A 859 PHE 0.012 0.001 PHE A 783 TRP 0.004 0.001 TRP A 977 HIS 0.003 0.001 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (10516) covalent geometry : angle 0.50504 / 0.26 (14272) SS BOND : bond 0.00281 / 0.13 ( 3) SS BOND : angle 1.18027 / 0.55 ( 6) hydrogen bonds : bond 0.03169 / 2.18 ( 502) hydrogen bonds : angle 4.12520 / 3.08 ( 1446) Misc. bond : bond 0.00275 / 0.14 ( 1) link_NAG-ASN : bond 0.00222 / 0.10 ( 3) link_NAG-ASN : angle 1.63124 / 0.99 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3967.40 seconds wall clock time: 68 minutes 24.45 seconds (4104.45 seconds total)