Starting phenix.real_space_refine on Thu Jul 2 11:17:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9z7b_73874/07_2026/9z7b_73874.cif Found real_map, /net/cci-nas-00/data/ceres_data/9z7b_73874/07_2026/9z7b_73874.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9z7b_73874/07_2026/9z7b_73874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9z7b_73874/07_2026/9z7b_73874.map" model { file = "/net/cci-nas-00/data/ceres_data/9z7b_73874/07_2026/9z7b_73874.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9z7b_73874/07_2026/9z7b_73874.cif" } resolution = 2.69 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= 0.017 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: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 5210 2.51 5 N 1455 2.21 5 O 1520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8203 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 828, 5739 Classifications: {'peptide': 828} Incomplete info: {'truncation_to_alanine': 158} Link IDs: {'PTRANS': 30, 'TRANS': 797} Chain breaks: 14 Unresolved non-hydrogen bonds: 454 Unresolved non-hydrogen angles: 569 Unresolved non-hydrogen dihedrals: 358 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'ASN:plan1': 12, 'ASP:plan': 23, 'ARG:plan': 5, 'PHE:plan': 3, 'HIS:plan': 3, 'GLN:plan1': 8, 'TRP:plan': 1, 'GLU:plan': 8} Unresolved non-hydrogen planarities: 236 Chain: "B" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1323 Classifications: {'peptide': 195} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 183} Chain breaks: 5 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 1141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1141 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 157} Chain breaks: 4 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASP:plan': 5, 'GLN:plan1': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 81 Time building chain proxies: 2.04, per 1000 atoms: 0.25 Number of scatterers: 8203 At special positions: 0 Unit cell: (74.102, 144.452, 128.506, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 1520 8.00 N 1455 7.00 C 5210 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 147 " - pdb=" SG CYS B 203 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 195 " 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=0, symmetry=0 Time building additional restraints: 0.61 Conformation dependent library (CDL) restraints added in 453.4 milliseconds 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2148 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 19 sheets defined 2.5% alpha, 26.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 8 through 18 removed outlier: 3.998A pdb=" N TYR A 12 " --> pdb=" O ALA A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 241 No H-bonds generated for 'chain 'A' and resid 240 through 241' Processing helix chain 'A' and resid 243 through 243 No H-bonds generated for 'chain 'A' and resid 243 through 243' Processing helix chain 'A' and resid 244 through 251 removed outlier: 3.899A pdb=" N ASP A 251 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 429 No H-bonds generated for 'chain 'A' and resid 427 through 429' Processing helix chain 'C' and resid 125 through 129 removed outlier: 3.688A pdb=" N GLY C 129 " --> pdb=" O GLN C 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 125 through 129' Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.627A pdb=" N ILE A 29 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY A 40 " --> pdb=" O VAL A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 61 Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 79 removed outlier: 6.626A pdb=" N ARG A 105 " --> pdb=" O VAL A 91 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 117 through 118 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 117 through 118 current: chain 'A' and resid 165 through 168 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 165 through 168 current: chain 'A' and resid 216 through 226 removed outlier: 7.133A pdb=" N TRP A 235 " --> pdb=" O ARG A 224 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 256 through 257 removed outlier: 6.146A pdb=" N LEU A 301 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE A 344 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU A 364 " --> pdb=" O LYS A 385 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU A 384 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL A 409 " --> pdb=" O SER A 432 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 265 through 270 removed outlier: 3.510A pdb=" N THR A 275 " --> pdb=" O ASP A 270 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 283 through 288 current: chain 'A' and resid 330 through 332 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 438 through 441 current: chain 'A' and resid 634 through 644 removed outlier: 4.378A pdb=" N ASP A 659 " --> pdb=" O MET A 638 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N THR A 640 " --> pdb=" O ASP A 659 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LYS A 661 " --> pdb=" O THR A 640 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N SER A 642 " --> pdb=" O LYS A 661 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA A 654 " --> pdb=" O GLN A 703 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N GLU A 705 " --> pdb=" O ALA A 654 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU A 656 " --> pdb=" O GLU A 705 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ASN A 707 " --> pdb=" O LEU A 656 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N SER A 658 " --> pdb=" O ASN A 707 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N THR A 709 " --> pdb=" O SER A 658 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE A 660 " --> pdb=" O THR A 709 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TYR A 704 " --> pdb=" O THR A 723 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N GLY A 725 " --> pdb=" O TYR A 704 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLY A 706 " --> pdb=" O GLY A 725 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N ASP A 727 " --> pdb=" O GLY A 706 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ILE A 708 " --> pdb=" O ASP A 727 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N TYR A 729 " --> pdb=" O ILE A 708 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU A 710 " --> pdb=" O TYR A 729 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N PHE A 722 " --> pdb=" O LEU A 741 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 740 through 742 current: chain 'A' and resid 912 through 921 removed outlier: 7.296A pdb=" N LYS A 917 " --> pdb=" O THR A 940 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LYS A 942 " --> pdb=" O LYS A 917 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ASP A 919 " --> pdb=" O LYS A 942 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N THR A 944 " --> pdb=" O ASP A 919 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N THR A 921 " --> pdb=" O THR A 944 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N SER A 946 " --> pdb=" O THR A 921 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 966 through 971 current: chain 'A' and resid 1005 through 1012 Processing sheet with id=AA7, first strand: chain 'A' and resid 316 through 317 removed outlier: 6.352A pdb=" N VAL A 316 " --> pdb=" O THR A 340 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 563 through 565 removed outlier: 6.547A pdb=" N VAL A 563 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE A 667 " --> pdb=" O ASP A 717 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU A 716 " --> pdb=" O SER A 734 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL A 733 " --> pdb=" O THR A 754 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU A 753 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE A 826 " --> pdb=" O THR A 871 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 611 through 612 removed outlier: 3.743A pdb=" N HIS A 611 " --> pdb=" O GLU A 632 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 673 through 677 removed outlier: 3.546A pdb=" N VAL A 676 " --> pdb=" O GLU A 689 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 786 through 787 Processing sheet with id=AB3, first strand: chain 'A' and resid 883 through 886 removed outlier: 6.749A pdb=" N ILE A 902 " --> pdb=" O VAL A 926 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N ARG A 928 " --> pdb=" O ILE A 902 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N SER A 904 " --> pdb=" O ARG A 928 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N PHE A 925 " --> pdb=" O ASN A 951 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N SER A 953 " --> pdb=" O PHE A 925 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N LEU A 927 " --> pdb=" O SER A 953 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.503A pdb=" N THR B 21 " --> pdb=" O SER B 7 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B 82 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 11 through 12 current: chain 'B' and resid 47 through 54 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 59 through 61 current: chain 'B' and resid 109 through 110 Processing sheet with id=AB6, first strand: chain 'B' and resid 127 through 130 removed outlier: 3.729A pdb=" N PHE B 129 " --> pdb=" O LEU B 148 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU B 145 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N TYR B 183 " --> pdb=" O ASP B 151 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 157 through 161 Processing sheet with id=AB8, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.571A pdb=" N SER C 7 " --> pdb=" O SER C 22 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASP C 70 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER C 67 " --> pdb=" O ASP C 70 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR C 72 " --> pdb=" O SER C 65 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 10 through 13 current: chain 'C' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 53 through 54 current: chain 'C' and resid 98 through 99 Processing sheet with id=AC1, first strand: chain 'C' and resid 117 through 119 removed outlier: 5.902A pdb=" N TYR C 174 " --> pdb=" O ASN C 139 " (cutoff:3.500A) 148 hydrogen bonds defined for protein. 399 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: 1.40 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2746 1.34 - 1.46: 1609 1.46 - 1.57: 3982 1.57 - 1.69: 1 1.69 - 1.81: 27 Bond restraints: 8365 Sorted by residual: bond pdb=" CA ASN A 234 " pdb=" CB ASN A 234 " ideal model delta sigma weight residual 1.536 1.585 -0.050 2.08e-02 2.31e+03 5.71e+00 bond pdb=" C LYS B 208 " pdb=" N PRO B 209 " ideal model delta sigma weight residual 1.334 1.389 -0.055 2.34e-02 1.83e+03 5.47e+00 bond pdb=" CB ASN A 234 " pdb=" CG ASN A 234 " ideal model delta sigma weight residual 1.516 1.561 -0.045 2.50e-02 1.60e+03 3.29e+00 bond pdb=" CB ASP A 589 " pdb=" CG ASP A 589 " ideal model delta sigma weight residual 1.516 1.557 -0.041 2.50e-02 1.60e+03 2.64e+00 bond pdb=" CA ASP A 589 " pdb=" CB ASP A 589 " ideal model delta sigma weight residual 1.530 1.553 -0.023 1.64e-02 3.72e+03 2.01e+00 ... (remaining 8360 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 11307 2.61 - 5.21: 128 5.21 - 7.82: 11 7.82 - 10.42: 1 10.42 - 13.03: 2 Bond angle restraints: 11449 Sorted by residual: angle pdb=" C ASN C 50 " pdb=" N THR C 51 " pdb=" CA THR C 51 " ideal model delta sigma weight residual 121.54 129.76 -8.22 1.91e+00 2.74e-01 1.85e+01 angle pdb=" C ILE A 687 " pdb=" CA ILE A 687 " pdb=" CB ILE A 687 " ideal model delta sigma weight residual 110.37 114.42 -4.05 1.07e+00 8.73e-01 1.44e+01 angle pdb=" CA LEU B 185 " pdb=" CB LEU B 185 " pdb=" CG LEU B 185 " ideal model delta sigma weight residual 116.30 129.33 -13.03 3.50e+00 8.16e-02 1.38e+01 angle pdb=" CA ASP A 589 " pdb=" CB ASP A 589 " pdb=" CG ASP A 589 " ideal model delta sigma weight residual 112.60 116.31 -3.71 1.00e+00 1.00e+00 1.37e+01 angle pdb=" CA LEU B 166 " pdb=" CB LEU B 166 " pdb=" CG LEU B 166 " ideal model delta sigma weight residual 116.30 128.10 -11.80 3.50e+00 8.16e-02 1.14e+01 ... (remaining 11444 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 4360 17.58 - 35.16: 303 35.16 - 52.73: 104 52.73 - 70.31: 25 70.31 - 87.89: 6 Dihedral angle restraints: 4798 sinusoidal: 1444 harmonic: 3354 Sorted by residual: dihedral pdb=" CB CYS B 147 " pdb=" SG CYS B 147 " pdb=" SG CYS B 203 " pdb=" CB CYS B 203 " ideal model delta sinusoidal sigma weight residual -86.00 -140.26 54.26 1 1.00e+01 1.00e-02 3.99e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 97 " pdb=" CB CYS B 97 " ideal model delta sinusoidal sigma weight residual 93.00 55.88 37.12 1 1.00e+01 1.00e-02 1.95e+01 dihedral pdb=" CB CYS C 135 " pdb=" SG CYS C 135 " pdb=" SG CYS C 195 " pdb=" CB CYS C 195 " ideal model delta sinusoidal sigma weight residual -86.00 -121.89 35.89 1 1.00e+01 1.00e-02 1.82e+01 ... (remaining 4795 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 907 0.041 - 0.083: 276 0.083 - 0.124: 129 0.124 - 0.165: 26 0.165 - 0.207: 4 Chirality restraints: 1342 Sorted by residual: chirality pdb=" CA ASP A 589 " pdb=" N ASP A 589 " pdb=" C ASP A 589 " pdb=" CB ASP A 589 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA VAL B 39 " pdb=" N VAL B 39 " pdb=" C VAL B 39 " pdb=" CB VAL B 39 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.17e-01 chirality pdb=" CB ILE A 687 " pdb=" CA ILE A 687 " pdb=" CG1 ILE A 687 " pdb=" CG2 ILE A 687 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.07e-01 ... (remaining 1339 not shown) Planarity restraints: 1506 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 687 " -0.043 5.00e-02 4.00e+02 6.49e-02 6.75e+00 pdb=" N PRO A 688 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 688 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 688 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 63 " -0.041 5.00e-02 4.00e+02 6.18e-02 6.12e+00 pdb=" N PRO A 64 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 64 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 64 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 589 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.84e+00 pdb=" CG ASP A 589 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASP A 589 " -0.016 2.00e-02 2.50e+03 pdb=" OD2 ASP A 589 " -0.014 2.00e-02 2.50e+03 ... (remaining 1503 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 4032 3.02 - 3.49: 7422 3.49 - 3.96: 13045 3.96 - 4.43: 14951 4.43 - 4.90: 25376 Nonbonded interactions: 64826 Sorted by model distance: nonbonded pdb=" C THR A 417 " pdb=" OG1 THR A 417 " model vdw 2.554 2.616 nonbonded pdb=" N SER A 63 " pdb=" O SER A 63 " model vdw 2.598 2.496 nonbonded pdb=" N SER A 69 " pdb=" O SER A 69 " model vdw 2.609 2.496 nonbonded pdb=" N THR A 399 " pdb=" OG1 THR A 399 " model vdw 2.634 2.496 nonbonded pdb=" N THR A 135 " pdb=" OG1 THR A 135 " model vdw 2.635 2.496 ... (remaining 64821 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.070 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.360 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:7.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 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 0.055 8369 Z= 0.172 Angle : 0.698 13.025 11457 Z= 0.386 Chirality : 0.050 0.207 1342 Planarity : 0.007 0.083 1506 Dihedral : 14.959 87.890 2638 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.90 % Allowed : 18.72 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.62 % 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: -1.83 (0.24), residues: 1140 helix: -3.38 (0.63), residues: 16 sheet: -1.13 (0.22), residues: 549 loop : -1.11 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 54 TYR 0.017 0.002 TYR A 12 PHE 0.028 0.002 PHE A 648 TRP 0.009 0.001 TRP A 631 HIS 0.005 0.001 HIS B 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.17 ( 8365) covalent geometry : angle 0.69792 / 0.39 (11449) SS BOND : bond 0.00118 / 0.05 ( 4) SS BOND : angle 0.79538 / 0.40 ( 8) hydrogen bonds : bond 0.22035 / 13.68 ( 148) hydrogen bonds : angle 9.93588 / 6.92 ( 399) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.295 Fit side-chains REVERT: A 11 ILE cc_start: 0.6192 (mt) cc_final: 0.5893 (mp) REVERT: A 705 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8339 (mt-10) REVERT: A 712 HIS cc_start: 0.7448 (m90) cc_final: 0.5889 (t-170) REVERT: A 803 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.7763 (m-30) REVERT: A 811 ASN cc_start: 0.7076 (m-40) cc_final: 0.6612 (t0) REVERT: A 892 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7811 (pt) REVERT: A 941 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6138 (mp0) REVERT: A 1008 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7746 (pt) REVERT: B 155 GLU cc_start: 0.6916 (mt-10) cc_final: 0.6661 (tt0) outliers start: 20 outliers final: 10 residues processed: 92 average time/residue: 0.4207 time to fit residues: 41.9982 Evaluate side-chains 91 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 941 GLU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain C residue 85 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.0970 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.0370 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 overall best weight: 1.4262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 GLN A 425 GLN A 572 ASN A 713 ASN A 867 ASN B 5 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.150572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.123776 restraints weight = 10166.958| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.89 r_work: 0.3455 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8369 Z= 0.146 Angle : 0.513 9.261 11457 Z= 0.273 Chirality : 0.045 0.135 1342 Planarity : 0.005 0.048 1506 Dihedral : 5.955 61.095 1257 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 5.22 % Allowed : 16.11 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.62 % 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: -1.60 (0.24), residues: 1140 helix: -0.23 (1.13), residues: 17 sheet: -1.08 (0.22), residues: 539 loop : -0.94 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 104 TYR 0.015 0.002 TYR B 96 PHE 0.022 0.002 PHE A 648 TRP 0.014 0.002 TRP A 354 HIS 0.005 0.001 HIS B 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 ( 8365) covalent geometry : angle 0.51279 / 0.27 (11449) SS BOND : bond 0.00183 / 0.07 ( 4) SS BOND : angle 0.77808 / 0.44 ( 8) hydrogen bonds : bond 0.03240 / 2.02 ( 148) hydrogen bonds : angle 6.47556 / 4.51 ( 399) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 82 time to evaluate : 0.293 Fit side-chains REVERT: A 9 TYR cc_start: 0.6010 (t80) cc_final: 0.5587 (t80) REVERT: A 85 LYS cc_start: 0.6351 (OUTLIER) cc_final: 0.4986 (mmtm) REVERT: A 324 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8315 (tt0) REVERT: A 472 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7899 (tt) REVERT: A 705 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8267 (mt-10) REVERT: A 811 ASN cc_start: 0.7100 (m-40) cc_final: 0.6616 (t0) REVERT: B 206 ASN cc_start: 0.7585 (OUTLIER) cc_final: 0.7356 (m110) REVERT: C 107 ILE cc_start: 0.6524 (OUTLIER) cc_final: 0.6319 (mm) outliers start: 36 outliers final: 14 residues processed: 102 average time/residue: 0.3962 time to fit residues: 43.8908 Evaluate side-chains 95 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 107 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 74 optimal weight: 8.9990 chunk 62 optimal weight: 0.5980 chunk 4 optimal weight: 0.0030 chunk 83 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 112 optimal weight: 9.9990 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 713 ASN A 867 ASN B 5 GLN B 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.151266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.124514 restraints weight = 10084.507| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.90 r_work: 0.3464 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8369 Z= 0.103 Angle : 0.457 7.870 11457 Z= 0.242 Chirality : 0.044 0.138 1342 Planarity : 0.004 0.046 1506 Dihedral : 4.376 51.733 1240 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.50 % Allowed : 16.69 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.62 % 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: -1.30 (0.25), residues: 1140 helix: 1.31 (1.37), residues: 17 sheet: -0.87 (0.22), residues: 549 loop : -0.79 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 104 TYR 0.011 0.001 TYR A 138 PHE 0.018 0.001 PHE B 80 TRP 0.010 0.001 TRP A 354 HIS 0.004 0.001 HIS B 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 ( 8365) covalent geometry : angle 0.45693 / 0.24 (11449) SS BOND : bond 0.00169 / 0.07 ( 4) SS BOND : angle 0.55190 / 0.31 ( 8) hydrogen bonds : bond 0.02540 / 1.62 ( 148) hydrogen bonds : angle 5.61599 / 3.92 ( 399) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 79 time to evaluate : 0.308 Fit side-chains REVERT: A 85 LYS cc_start: 0.6290 (OUTLIER) cc_final: 0.4960 (mmtm) REVERT: A 472 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7932 (tt) REVERT: A 632 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7995 (mt-10) REVERT: A 679 ASN cc_start: 0.6537 (m110) cc_final: 0.6248 (m110) REVERT: A 705 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8208 (mt-10) REVERT: A 803 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.7912 (m-30) REVERT: A 941 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.6802 (mp0) REVERT: B 206 ASN cc_start: 0.7679 (t0) cc_final: 0.7286 (m-40) outliers start: 31 outliers final: 16 residues processed: 100 average time/residue: 0.4099 time to fit residues: 44.6677 Evaluate side-chains 97 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 941 GLU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain C residue 85 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 0.0980 chunk 46 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 108 optimal weight: 7.9990 chunk 4 optimal weight: 0.0980 chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 68 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 GLN A 713 ASN B 5 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.150765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.123822 restraints weight = 10292.764| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 1.93 r_work: 0.3578 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8369 Z= 0.105 Angle : 0.458 8.277 11457 Z= 0.241 Chirality : 0.044 0.140 1342 Planarity : 0.004 0.043 1506 Dihedral : 4.238 40.578 1240 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.79 % Allowed : 16.69 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.62 % 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: -1.13 (0.25), residues: 1140 helix: 1.75 (1.37), residues: 17 sheet: -0.66 (0.23), residues: 527 loop : -0.80 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 104 TYR 0.011 0.001 TYR A 138 PHE 0.016 0.001 PHE A 648 TRP 0.010 0.001 TRP A 354 HIS 0.003 0.001 HIS B 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 8365) covalent geometry : angle 0.45766 / 0.24 (11449) SS BOND : bond 0.00150 / 0.06 ( 4) SS BOND : angle 0.49939 / 0.28 ( 8) hydrogen bonds : bond 0.02324 / 1.49 ( 148) hydrogen bonds : angle 5.29453 / 3.69 ( 399) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 79 time to evaluate : 0.329 Fit side-chains REVERT: A 85 LYS cc_start: 0.6408 (OUTLIER) cc_final: 0.5032 (mmtm) REVERT: A 472 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7893 (tt) REVERT: A 632 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8019 (mt-10) REVERT: A 705 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8320 (mt-10) REVERT: A 941 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7016 (mp0) REVERT: B 206 ASN cc_start: 0.7710 (t0) cc_final: 0.7306 (m-40) outliers start: 33 outliers final: 20 residues processed: 101 average time/residue: 0.4197 time to fit residues: 46.1331 Evaluate side-chains 97 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 573 MET Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 941 GLU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain C residue 85 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 114 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 16 optimal weight: 0.2980 chunk 80 optimal weight: 0.0010 chunk 51 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 37 optimal weight: 0.2980 chunk 90 optimal weight: 5.9990 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 713 ASN A 772 HIS B 5 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.152893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.126226 restraints weight = 10158.378| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 1.85 r_work: 0.3593 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8369 Z= 0.072 Angle : 0.414 7.415 11457 Z= 0.219 Chirality : 0.043 0.136 1342 Planarity : 0.004 0.043 1506 Dihedral : 3.855 38.633 1240 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.19 % Allowed : 18.87 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.62 % 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: -0.92 (0.25), residues: 1140 helix: 1.71 (1.34), residues: 17 sheet: -0.55 (0.22), residues: 538 loop : -0.62 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 104 TYR 0.008 0.001 TYR B 96 PHE 0.015 0.001 PHE B 80 TRP 0.006 0.001 TRP B 110 HIS 0.002 0.000 HIS B 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00164 / 0.07 ( 8365) covalent geometry : angle 0.41421 / 0.22 (11449) SS BOND : bond 0.00130 / 0.05 ( 4) SS BOND : angle 0.39113 / 0.22 ( 8) hydrogen bonds : bond 0.01976 / 1.25 ( 148) hydrogen bonds : angle 4.87194 / 3.39 ( 399) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.319 Fit side-chains REVERT: A 85 LYS cc_start: 0.6321 (OUTLIER) cc_final: 0.4949 (mmtm) REVERT: A 472 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7929 (tt) REVERT: A 632 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8007 (mt-10) REVERT: A 833 THR cc_start: 0.7984 (m) cc_final: 0.7746 (p) REVERT: A 941 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7303 (mm-30) REVERT: B 206 ASN cc_start: 0.7696 (t0) cc_final: 0.7313 (m-40) REVERT: C 82 ASP cc_start: 0.7376 (p0) cc_final: 0.6924 (p0) outliers start: 22 outliers final: 11 residues processed: 94 average time/residue: 0.4322 time to fit residues: 44.0557 Evaluate side-chains 90 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 941 GLU Chi-restraints excluded: chain B residue 189 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 112 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 106 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 10 GLN ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 GLN A 572 ASN A 713 ASN A 867 ASN B 5 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.149664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.122881 restraints weight = 10157.799| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.90 r_work: 0.3441 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8369 Z= 0.136 Angle : 0.486 9.409 11457 Z= 0.257 Chirality : 0.045 0.176 1342 Planarity : 0.004 0.049 1506 Dihedral : 4.204 35.136 1238 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.50 % Allowed : 17.71 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.62 % 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: -0.96 (0.25), residues: 1140 helix: 1.78 (1.34), residues: 17 sheet: -0.51 (0.24), residues: 503 loop : -0.74 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 104 TYR 0.014 0.001 TYR B 96 PHE 0.020 0.002 PHE A 648 TRP 0.011 0.001 TRP A 354 HIS 0.004 0.001 HIS C 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 8365) covalent geometry : angle 0.48589 / 0.26 (11449) SS BOND : bond 0.00156 / 0.07 ( 4) SS BOND : angle 0.44081 / 0.25 ( 8) hydrogen bonds : bond 0.02454 / 1.57 ( 148) hydrogen bonds : angle 5.15240 / 3.59 ( 399) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 69 time to evaluate : 0.313 Fit side-chains REVERT: A 85 LYS cc_start: 0.6464 (OUTLIER) cc_final: 0.5049 (mmtm) REVERT: A 324 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8288 (tt0) REVERT: A 472 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7872 (tt) REVERT: A 632 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8065 (mt-10) REVERT: A 705 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8302 (mt-10) REVERT: A 803 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.7980 (m-30) REVERT: A 941 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.6937 (mp0) REVERT: B 206 ASN cc_start: 0.7748 (OUTLIER) cc_final: 0.7335 (m-40) outliers start: 31 outliers final: 19 residues processed: 87 average time/residue: 0.4619 time to fit residues: 43.5082 Evaluate side-chains 94 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 68 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 573 MET Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 941 GLU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain C residue 69 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 62 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 113 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 713 ASN A 867 ASN B 5 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.145743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.118001 restraints weight = 10343.092| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.99 r_work: 0.3402 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8369 Z= 0.199 Angle : 0.559 9.729 11457 Z= 0.297 Chirality : 0.046 0.164 1342 Planarity : 0.004 0.051 1506 Dihedral : 4.730 33.748 1238 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 5.52 % Allowed : 16.98 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.62 % 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: -1.19 (0.25), residues: 1140 helix: 1.26 (1.23), residues: 17 sheet: -0.69 (0.24), residues: 482 loop : -0.86 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 104 TYR 0.025 0.002 TYR A 138 PHE 0.025 0.002 PHE A 648 TRP 0.016 0.002 TRP A 354 HIS 0.005 0.001 HIS C 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 ( 8365) covalent geometry : angle 0.55947 / 0.30 (11449) SS BOND : bond 0.00251 / 0.12 ( 4) SS BOND : angle 0.58526 / 0.33 ( 8) hydrogen bonds : bond 0.02865 / 1.83 ( 148) hydrogen bonds : angle 5.57279 / 3.90 ( 399) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 64 time to evaluate : 0.312 Fit side-chains REVERT: A 85 LYS cc_start: 0.6626 (OUTLIER) cc_final: 0.5087 (mmtm) REVERT: A 472 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7851 (tt) REVERT: A 705 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8338 (mt-10) REVERT: A 803 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.8053 (m-30) REVERT: A 941 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.6933 (mp0) REVERT: B 206 ASN cc_start: 0.7680 (OUTLIER) cc_final: 0.7339 (m-40) REVERT: C 54 ARG cc_start: 0.8371 (mtm180) cc_final: 0.8157 (mtt90) outliers start: 38 outliers final: 22 residues processed: 87 average time/residue: 0.4506 time to fit residues: 42.5102 Evaluate side-chains 89 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 62 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 573 MET Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 941 GLU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 85 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 8 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 chunk 15 optimal weight: 0.0270 chunk 1 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 GLN A 713 ASN B 5 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.150912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.124237 restraints weight = 10255.942| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 1.92 r_work: 0.3577 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8369 Z= 0.085 Angle : 0.445 9.314 11457 Z= 0.236 Chirality : 0.043 0.148 1342 Planarity : 0.004 0.048 1506 Dihedral : 3.997 35.130 1238 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.77 % Allowed : 18.58 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.62 % 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: -1.01 (0.25), residues: 1140 helix: 1.74 (1.40), residues: 17 sheet: -0.58 (0.24), residues: 489 loop : -0.73 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 104 TYR 0.012 0.001 TYR A 138 PHE 0.017 0.001 PHE B 80 TRP 0.009 0.001 TRP A 354 HIS 0.002 0.001 HIS B 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.09 ( 8365) covalent geometry : angle 0.44457 / 0.24 (11449) SS BOND : bond 0.00153 / 0.06 ( 4) SS BOND : angle 0.43956 / 0.23 ( 8) hydrogen bonds : bond 0.02042 / 1.30 ( 148) hydrogen bonds : angle 4.94030 / 3.47 ( 399) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 0.317 Fit side-chains REVERT: A 85 LYS cc_start: 0.6303 (OUTLIER) cc_final: 0.4969 (mmtm) REVERT: A 472 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7885 (tt) REVERT: A 705 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8315 (mt-10) REVERT: A 941 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7328 (mm-30) REVERT: B 206 ASN cc_start: 0.7727 (t0) cc_final: 0.7283 (m-40) outliers start: 26 outliers final: 17 residues processed: 95 average time/residue: 0.4500 time to fit residues: 46.3471 Evaluate side-chains 92 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 941 GLU Chi-restraints excluded: chain C residue 85 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 63 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 18 optimal weight: 0.1980 chunk 1 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 81 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 112 optimal weight: 0.7980 chunk 22 optimal weight: 7.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 ASN A 572 ASN A 713 ASN B 5 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.146152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.118511 restraints weight = 10337.066| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.00 r_work: 0.3408 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8369 Z= 0.181 Angle : 0.539 9.588 11457 Z= 0.286 Chirality : 0.046 0.155 1342 Planarity : 0.004 0.053 1506 Dihedral : 4.533 33.182 1237 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.06 % Allowed : 18.43 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.62 % 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: -1.19 (0.25), residues: 1140 helix: 1.17 (1.27), residues: 17 sheet: -0.58 (0.24), residues: 479 loop : -0.96 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 104 TYR 0.022 0.002 TYR A 138 PHE 0.025 0.002 PHE A 648 TRP 0.015 0.002 TRP A 354 HIS 0.004 0.001 HIS C 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 ( 8365) covalent geometry : angle 0.53875 / 0.29 (11449) SS BOND : bond 0.00243 / 0.11 ( 4) SS BOND : angle 0.55703 / 0.31 ( 8) hydrogen bonds : bond 0.02713 / 1.74 ( 148) hydrogen bonds : angle 5.41439 / 3.80 ( 399) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 65 time to evaluate : 0.365 Fit side-chains REVERT: A 85 LYS cc_start: 0.6614 (OUTLIER) cc_final: 0.5063 (mmtm) REVERT: A 472 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7846 (tt) REVERT: A 705 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8328 (mt-10) REVERT: A 803 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.8039 (m-30) REVERT: A 941 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.6951 (mp0) REVERT: B 206 ASN cc_start: 0.7679 (t0) cc_final: 0.7311 (m-40) outliers start: 28 outliers final: 20 residues processed: 82 average time/residue: 0.4594 time to fit residues: 40.8707 Evaluate side-chains 87 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 573 MET Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 941 GLU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain C residue 85 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 5 optimal weight: 0.0270 chunk 68 optimal weight: 0.0020 chunk 46 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 99 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.7850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 GLN A 601 GLN A 713 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.149104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.122450 restraints weight = 10234.624| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.85 r_work: 0.3570 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3473 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8369 Z= 0.100 Angle : 0.464 9.312 11457 Z= 0.247 Chirality : 0.044 0.143 1342 Planarity : 0.004 0.051 1506 Dihedral : 4.113 33.861 1237 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.77 % Allowed : 19.01 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.62 % 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: -1.02 (0.25), residues: 1140 helix: 1.55 (1.39), residues: 17 sheet: -0.58 (0.24), residues: 486 loop : -0.75 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 104 TYR 0.015 0.001 TYR A 138 PHE 0.018 0.001 PHE A 648 TRP 0.011 0.001 TRP A 354 HIS 0.003 0.001 HIS C 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 ( 8365) covalent geometry : angle 0.46381 / 0.25 (11449) SS BOND : bond 0.00159 / 0.06 ( 4) SS BOND : angle 0.43027 / 0.23 ( 8) hydrogen bonds : bond 0.02175 / 1.39 ( 148) hydrogen bonds : angle 5.02988 / 3.54 ( 399) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 0.452 Fit side-chains REVERT: A 85 LYS cc_start: 0.6423 (OUTLIER) cc_final: 0.5074 (mmtm) REVERT: A 472 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7911 (tt) REVERT: A 705 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8340 (mt-10) REVERT: A 941 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7316 (mm-30) REVERT: A 979 MET cc_start: 0.7502 (ttt) cc_final: 0.7258 (ttt) REVERT: B 206 ASN cc_start: 0.7763 (t0) cc_final: 0.7318 (m-40) outliers start: 26 outliers final: 20 residues processed: 87 average time/residue: 0.4670 time to fit residues: 43.9833 Evaluate side-chains 93 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 573 MET Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 941 GLU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain C residue 85 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 66 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 111 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 0.0980 chunk 42 optimal weight: 0.0870 overall best weight: 1.8364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 GLN A 601 GLN A 713 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.146385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.118759 restraints weight = 10294.878| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.98 r_work: 0.3415 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8369 Z= 0.175 Angle : 0.534 9.663 11457 Z= 0.284 Chirality : 0.046 0.150 1342 Planarity : 0.004 0.054 1506 Dihedral : 4.502 33.212 1237 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.50 % Allowed : 18.43 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.62 % 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: -1.17 (0.25), residues: 1140 helix: 1.19 (1.28), residues: 17 sheet: -0.63 (0.24), residues: 476 loop : -0.88 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 104 TYR 0.021 0.002 TYR A 138 PHE 0.026 0.002 PHE A 648 TRP 0.015 0.001 TRP A 354 HIS 0.004 0.001 HIS C 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 ( 8365) covalent geometry : angle 0.53387 / 0.28 (11449) SS BOND : bond 0.00236 / 0.11 ( 4) SS BOND : angle 0.53519 / 0.30 ( 8) hydrogen bonds : bond 0.02655 / 1.69 ( 148) hydrogen bonds : angle 5.39101 / 3.79 ( 399) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2791.13 seconds wall clock time: 48 minutes 15.81 seconds (2895.81 seconds total)