Starting phenix.real_space_refine on Tue Mar 3 21:19:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ydh_33747/03_2026/7ydh_33747_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ydh_33747/03_2026/7ydh_33747.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ydh_33747/03_2026/7ydh_33747_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ydh_33747/03_2026/7ydh_33747_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ydh_33747/03_2026/7ydh_33747.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ydh_33747/03_2026/7ydh_33747.map" } resolution = 3.1 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= 0.001 sd= 0.021 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 58 5.16 5 C 5589 2.51 5 N 1497 2.21 5 O 1620 1.98 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-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8764 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1779 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 3, 'TRANS': 211} Chain breaks: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "E" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1782 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2167 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 268} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 1.73, per 1000 atoms: 0.20 Number of scatterers: 8764 At special positions: 0 Unit cell: (93.5, 119.9, 133.1, 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 58 16.00 O 1620 8.00 N 1497 7.00 C 5589 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 230 " distance=2.05 Simple disulfide: pdb=" SG CYS R 612 " - pdb=" SG CYS R 684 " 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: 0.85 Conformation dependent library (CDL) restraints added in 328.3 milliseconds 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2076 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 12 sheets defined 36.5% alpha, 22.0% 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 25 Processing helix chain 'A' and resid 26 through 31 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 94 through 98 Processing helix chain 'A' and resid 114 through 129 removed outlier: 3.714A pdb=" N LEU A 118 " --> pdb=" O ASP A 114 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N THR A 119 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N GLU A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 127 " --> pdb=" O ASN A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 137 removed outlier: 4.335A pdb=" N ASN A 136 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL A 137 " --> pdb=" O PHE A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 152 Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.560A pdb=" N ASP A 160 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR A 161 " --> pdb=" O ILE A 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 157 through 161' Processing helix chain 'A' and resid 171 through 185 removed outlier: 3.723A pdb=" N VAL A 175 " --> pdb=" O CYS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 228 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.602A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.680A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 29 through 34' Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.683A pdb=" N PHE E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 4.060A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.625A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.709A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.521A pdb=" N GLU G 58 " --> pdb=" O PRO G 55 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 55 through 59' Processing helix chain 'R' and resid 544 through 572 removed outlier: 3.517A pdb=" N THR R 548 " --> pdb=" O ASP R 544 " (cutoff:3.500A) Processing helix chain 'R' and resid 577 through 601 Processing helix chain 'R' and resid 609 through 642 removed outlier: 3.761A pdb=" N ARG R 613 " --> pdb=" O GLY R 609 " (cutoff:3.500A) Processing helix chain 'R' and resid 651 through 674 removed outlier: 3.802A pdb=" N VAL R 662 " --> pdb=" O ILE R 658 " (cutoff:3.500A) Proline residue: R 663 - end of helix Processing helix chain 'R' and resid 688 through 692 Processing helix chain 'R' and resid 693 through 720 removed outlier: 3.604A pdb=" N LEU R 697 " --> pdb=" O LEU R 693 " (cutoff:3.500A) Proline residue: R 699 - end of helix removed outlier: 3.568A pdb=" N PHE R 702 " --> pdb=" O GLY R 698 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N CYS R 706 " --> pdb=" O PHE R 702 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL R 709 " --> pdb=" O LEU R 705 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL R 712 " --> pdb=" O ALA R 708 " (cutoff:3.500A) Processing helix chain 'R' and resid 721 through 726 Processing helix chain 'R' and resid 730 through 747 removed outlier: 3.700A pdb=" N THR R 741 " --> pdb=" O ALA R 737 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALA R 742 " --> pdb=" O LEU R 738 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE R 743 " --> pdb=" O THR R 739 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA R 744 " --> pdb=" O ILE R 740 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE R 747 " --> pdb=" O ILE R 743 " (cutoff:3.500A) Processing helix chain 'R' and resid 750 through 759 removed outlier: 3.750A pdb=" N TRP R 753 " --> pdb=" O GLY R 750 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL R 754 " --> pdb=" O CYS R 751 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N PHE R 755 " --> pdb=" O THR R 752 " (cutoff:3.500A) Processing helix chain 'R' and resid 765 through 777 removed outlier: 3.994A pdb=" N LEU R 777 " --> pdb=" O ILE R 773 " (cutoff:3.500A) Processing helix chain 'R' and resid 777 through 787 Processing helix chain 'R' and resid 790 through 804 Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 76 removed outlier: 4.219A pdb=" N VAL A 86 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER A 105 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 143 " --> pdb=" O HIS A 198 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR A 200 " --> pdb=" O LEU A 143 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 7.097A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.395A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.881A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 7.093A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.657A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.617A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.712A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 7.122A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 142 through 143 Processing sheet with id=AB3, first strand: chain 'E' and resid 147 through 149 removed outlier: 6.117A pdb=" N VAL E 148 " --> pdb=" O GLU E 247 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TRP E 177 " --> pdb=" O LEU E 189 " (cutoff:3.500A) 397 hydrogen bonds defined for protein. 1098 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: 1.50 Time building geometry restraints manager: 1.13 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: 2838 1.34 - 1.47: 2187 1.47 - 1.59: 3841 1.59 - 1.71: 0 1.71 - 1.84: 79 Bond restraints: 8945 Sorted by residual: bond pdb=" N TYR E 236 " pdb=" CA TYR E 236 " ideal model delta sigma weight residual 1.454 1.488 -0.035 1.14e-02 7.69e+03 9.18e+00 bond pdb=" N VAL R 644 " pdb=" CA VAL R 644 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.21e-02 6.83e+03 8.08e+00 bond pdb=" N ILE R 740 " pdb=" CA ILE R 740 " ideal model delta sigma weight residual 1.459 1.494 -0.036 1.28e-02 6.10e+03 7.77e+00 bond pdb=" N VAL R 642 " pdb=" CA VAL R 642 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.61e+00 bond pdb=" N MET R 537 " pdb=" CA MET R 537 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.16e-02 7.43e+03 7.07e+00 ... (remaining 8940 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 11579 1.73 - 3.46: 453 3.46 - 5.19: 57 5.19 - 6.92: 12 6.92 - 8.64: 10 Bond angle restraints: 12111 Sorted by residual: angle pdb=" N ALA B 203 " pdb=" CA ALA B 203 " pdb=" C ALA B 203 " ideal model delta sigma weight residual 111.71 120.24 -8.53 1.34e+00 5.57e-01 4.05e+01 angle pdb=" N GLN A 191 " pdb=" CA GLN A 191 " pdb=" C GLN A 191 " ideal model delta sigma weight residual 108.13 115.64 -7.51 1.72e+00 3.38e-01 1.91e+01 angle pdb=" N ASP A 189 " pdb=" CA ASP A 189 " pdb=" C ASP A 189 " ideal model delta sigma weight residual 110.80 102.16 8.64 2.13e+00 2.20e-01 1.65e+01 angle pdb=" C TYR E 236 " pdb=" CA TYR E 236 " pdb=" CB TYR E 236 " ideal model delta sigma weight residual 109.56 116.19 -6.63 1.64e+00 3.72e-01 1.63e+01 angle pdb=" C ASN A 144 " pdb=" N LYS A 145 " pdb=" CA LYS A 145 " ideal model delta sigma weight residual 121.54 128.62 -7.08 1.91e+00 2.74e-01 1.37e+01 ... (remaining 12106 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 4938 17.71 - 35.42: 274 35.42 - 53.12: 60 53.12 - 70.83: 11 70.83 - 88.54: 4 Dihedral angle restraints: 5287 sinusoidal: 2065 harmonic: 3222 Sorted by residual: dihedral pdb=" CB CYS E 160 " pdb=" SG CYS E 160 " pdb=" SG CYS E 230 " pdb=" CB CYS E 230 " ideal model delta sinusoidal sigma weight residual 93.00 143.16 -50.16 1 1.00e+01 1.00e-02 3.45e+01 dihedral pdb=" CA LYS A 145 " pdb=" C LYS A 145 " pdb=" N THR A 146 " pdb=" CA THR A 146 " ideal model delta harmonic sigma weight residual 180.00 158.20 21.80 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CB CYS R 612 " pdb=" SG CYS R 612 " pdb=" SG CYS R 684 " pdb=" CB CYS R 684 " ideal model delta sinusoidal sigma weight residual -86.00 -119.89 33.89 1 1.00e+01 1.00e-02 1.63e+01 ... (remaining 5284 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1180 0.069 - 0.137: 169 0.137 - 0.206: 22 0.206 - 0.275: 3 0.275 - 0.344: 2 Chirality restraints: 1376 Sorted by residual: chirality pdb=" CA ALA B 203 " pdb=" N ALA B 203 " pdb=" C ALA B 203 " pdb=" CB ALA B 203 " both_signs ideal model delta sigma weight residual False 2.48 2.14 0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CA LYS A 145 " pdb=" N LYS A 145 " pdb=" C LYS A 145 " pdb=" CB LYS A 145 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" CA ASP B 291 " pdb=" N ASP B 291 " pdb=" C ASP B 291 " pdb=" CB ASP B 291 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 1373 not shown) Planarity restraints: 1530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 38 " 0.062 5.00e-02 4.00e+02 9.38e-02 1.41e+01 pdb=" N PRO B 39 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 783 " 0.006 2.00e-02 2.50e+03 1.65e-02 5.47e+00 pdb=" CG TYR R 783 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR R 783 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR R 783 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR R 783 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR R 783 " -0.012 2.00e-02 2.50e+03 pdb=" CZ TYR R 783 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR R 783 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS R 731 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.93e+00 pdb=" C LYS R 731 " -0.038 2.00e-02 2.50e+03 pdb=" O LYS R 731 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU R 732 " 0.013 2.00e-02 2.50e+03 ... (remaining 1527 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 247 2.70 - 3.25: 8190 3.25 - 3.80: 12811 3.80 - 4.35: 15830 4.35 - 4.90: 27805 Nonbonded interactions: 64883 Sorted by model distance: nonbonded pdb=" O ARG R 573 " pdb=" NE2 GLN R 576 " model vdw 2.153 3.120 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.273 3.040 nonbonded pdb=" O GLY E 210 " pdb=" OG1 THR E 211 " model vdw 2.273 3.040 nonbonded pdb=" OD1 ASP R 687 " pdb=" N PHE R 688 " model vdw 2.286 3.120 nonbonded pdb=" O SER A 44 " pdb=" ND2 ASN A 144 " model vdw 2.329 3.120 ... (remaining 64878 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.970 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 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 : 0.006 0.052 8947 Z= 0.296 Angle : 0.799 8.645 12115 Z= 0.485 Chirality : 0.052 0.344 1376 Planarity : 0.005 0.094 1530 Dihedral : 12.108 88.540 3205 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.73 % Allowed : 0.94 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1102 helix: 1.41 (0.29), residues: 345 sheet: 0.51 (0.31), residues: 272 loop : -1.35 (0.24), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 46 TYR 0.035 0.003 TYR R 783 PHE 0.029 0.002 PHE B 234 TRP 0.029 0.003 TRP B 63 HIS 0.010 0.002 HIS R 620 Details of bonding type rmsd covalent geometry : bond 0.00575 ( 8945) covalent geometry : angle 0.79917 (12111) SS BOND : bond 0.01084 ( 2) SS BOND : angle 0.90314 ( 4) hydrogen bonds : bond 0.14525 ( 397) hydrogen bonds : angle 6.23108 ( 1098) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 192 time to evaluate : 0.276 Fit side-chains REVERT: E 220 LEU cc_start: 0.8286 (mt) cc_final: 0.8057 (mt) REVERT: G 21 MET cc_start: 0.7486 (mtm) cc_final: 0.6849 (mtm) REVERT: R 551 THR cc_start: 0.7448 (m) cc_final: 0.7206 (m) REVERT: R 796 GLU cc_start: 0.7216 (mm-30) cc_final: 0.6788 (mm-30) outliers start: 7 outliers final: 4 residues processed: 195 average time/residue: 0.0996 time to fit residues: 26.2616 Evaluate side-chains 179 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 175 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 536 LEU Chi-restraints excluded: chain R residue 537 MET Chi-restraints excluded: chain R residue 650 LEU Chi-restraints excluded: chain R residue 740 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.0570 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 0.3980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 ASN R 539 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.154179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.126179 restraints weight = 13014.628| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.76 r_work: 0.3509 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8947 Z= 0.144 Angle : 0.581 9.676 12115 Z= 0.314 Chirality : 0.043 0.158 1376 Planarity : 0.004 0.069 1530 Dihedral : 5.351 52.588 1217 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.90 % Favored : 97.01 % Rotamer: Outliers : 1.99 % Allowed : 6.07 % Favored : 91.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.53 (0.25), residues: 1102 helix: 2.16 (0.29), residues: 350 sheet: 0.60 (0.30), residues: 276 loop : -1.24 (0.25), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 304 TYR 0.021 0.002 TYR R 783 PHE 0.015 0.002 PHE B 253 TRP 0.023 0.002 TRP R 716 HIS 0.005 0.001 HIS R 786 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8945) covalent geometry : angle 0.58108 (12111) SS BOND : bond 0.00723 ( 2) SS BOND : angle 0.65269 ( 4) hydrogen bonds : bond 0.05723 ( 397) hydrogen bonds : angle 4.75848 ( 1098) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 214 ASP cc_start: 0.7880 (m-30) cc_final: 0.7573 (m-30) REVERT: B 63 TRP cc_start: 0.8183 (m100) cc_final: 0.7939 (m100) REVERT: B 75 GLN cc_start: 0.7011 (mt0) cc_final: 0.6446 (mt0) REVERT: B 293 ASN cc_start: 0.7727 (p0) cc_final: 0.7487 (p0) REVERT: E 83 MET cc_start: 0.6227 (ptp) cc_final: 0.5817 (ptp) REVERT: E 98 ARG cc_start: 0.7896 (ttp-170) cc_final: 0.7622 (tmm160) REVERT: E 220 LEU cc_start: 0.8447 (mt) cc_final: 0.8167 (mt) REVERT: G 21 MET cc_start: 0.7857 (mtm) cc_final: 0.7161 (mtm) REVERT: R 650 LEU cc_start: 0.6795 (OUTLIER) cc_final: 0.6454 (mp) REVERT: R 796 GLU cc_start: 0.7312 (mm-30) cc_final: 0.6801 (mm-30) outliers start: 19 outliers final: 8 residues processed: 185 average time/residue: 0.1003 time to fit residues: 24.9601 Evaluate side-chains 181 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 172 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain R residue 644 VAL Chi-restraints excluded: chain R residue 650 LEU Chi-restraints excluded: chain R residue 705 LEU Chi-restraints excluded: chain R residue 765 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 25 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 26 optimal weight: 0.4980 chunk 42 optimal weight: 0.4980 chunk 55 optimal weight: 0.1980 chunk 13 optimal weight: 0.0570 chunk 5 optimal weight: 0.3980 chunk 92 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 overall best weight: 0.3298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.156446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.128666 restraints weight = 12979.146| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.76 r_work: 0.3548 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8947 Z= 0.110 Angle : 0.523 8.890 12115 Z= 0.280 Chirality : 0.042 0.169 1376 Planarity : 0.004 0.059 1530 Dihedral : 4.619 52.837 1210 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.63 % Favored : 97.28 % Rotamer: Outliers : 2.09 % Allowed : 8.37 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.80 (0.25), residues: 1102 helix: 2.38 (0.29), residues: 356 sheet: 0.72 (0.30), residues: 282 loop : -1.10 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 96 TYR 0.018 0.001 TYR E 95 PHE 0.017 0.001 PHE A 74 TRP 0.019 0.002 TRP B 82 HIS 0.004 0.001 HIS R 786 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 8945) covalent geometry : angle 0.52339 (12111) SS BOND : bond 0.00604 ( 2) SS BOND : angle 0.69090 ( 4) hydrogen bonds : bond 0.04588 ( 397) hydrogen bonds : angle 4.31115 ( 1098) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 174 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.6756 (mmm) cc_final: 0.6264 (tmm) REVERT: A 214 ASP cc_start: 0.7836 (m-30) cc_final: 0.7480 (m-30) REVERT: B 46 ARG cc_start: 0.7953 (ttm110) cc_final: 0.7606 (ttp80) REVERT: B 292 PHE cc_start: 0.7677 (m-80) cc_final: 0.7429 (m-80) REVERT: B 293 ASN cc_start: 0.7676 (p0) cc_final: 0.7361 (p0) REVERT: E 83 MET cc_start: 0.6140 (ptp) cc_final: 0.5769 (ptp) REVERT: E 220 LEU cc_start: 0.8438 (mt) cc_final: 0.8183 (mt) REVERT: E 231 MET cc_start: 0.6930 (ttp) cc_final: 0.6225 (ttt) REVERT: G 21 MET cc_start: 0.7794 (mtm) cc_final: 0.7087 (mtm) REVERT: R 575 ILE cc_start: 0.7614 (OUTLIER) cc_final: 0.7098 (pt) REVERT: R 796 GLU cc_start: 0.7311 (mm-30) cc_final: 0.6775 (mm-30) outliers start: 20 outliers final: 10 residues processed: 180 average time/residue: 0.0989 time to fit residues: 24.1533 Evaluate side-chains 180 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 169 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain R residue 537 MET Chi-restraints excluded: chain R residue 575 ILE Chi-restraints excluded: chain R residue 576 GLN Chi-restraints excluded: chain R residue 644 VAL Chi-restraints excluded: chain R residue 765 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 60 optimal weight: 2.9990 chunk 6 optimal weight: 0.2980 chunk 102 optimal weight: 0.0030 chunk 71 optimal weight: 0.2980 chunk 88 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 31 optimal weight: 0.0670 chunk 32 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 overall best weight: 0.2528 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 110 ASN R 539 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.157711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.129761 restraints weight = 13118.194| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.76 r_work: 0.3571 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8947 Z= 0.099 Angle : 0.505 8.550 12115 Z= 0.268 Chirality : 0.041 0.150 1376 Planarity : 0.003 0.052 1530 Dihedral : 4.172 27.976 1208 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.27 % Favored : 97.64 % Rotamer: Outliers : 1.99 % Allowed : 9.31 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.93 (0.25), residues: 1102 helix: 2.47 (0.29), residues: 357 sheet: 0.91 (0.32), residues: 257 loop : -1.00 (0.25), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 304 TYR 0.029 0.001 TYR R 783 PHE 0.013 0.001 PHE A 74 TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS R 786 Details of bonding type rmsd covalent geometry : bond 0.00203 ( 8945) covalent geometry : angle 0.50501 (12111) SS BOND : bond 0.00524 ( 2) SS BOND : angle 0.61443 ( 4) hydrogen bonds : bond 0.04180 ( 397) hydrogen bonds : angle 4.14233 ( 1098) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.6762 (mmm) cc_final: 0.6270 (tmm) REVERT: A 214 ASP cc_start: 0.7744 (m-30) cc_final: 0.7371 (m-30) REVERT: B 46 ARG cc_start: 0.7965 (ttm110) cc_final: 0.7599 (ttp80) REVERT: B 75 GLN cc_start: 0.7260 (OUTLIER) cc_final: 0.6739 (mt0) REVERT: B 262 MET cc_start: 0.6042 (tpp) cc_final: 0.5801 (tpp) REVERT: B 292 PHE cc_start: 0.7649 (m-80) cc_final: 0.7394 (m-80) REVERT: B 293 ASN cc_start: 0.7639 (p0) cc_final: 0.7301 (p0) REVERT: E 220 LEU cc_start: 0.8416 (mt) cc_final: 0.8160 (mt) REVERT: E 231 MET cc_start: 0.6870 (ttp) cc_final: 0.6165 (ttt) REVERT: G 21 MET cc_start: 0.7763 (mtm) cc_final: 0.7052 (mtm) REVERT: R 551 THR cc_start: 0.7371 (m) cc_final: 0.7008 (m) REVERT: R 796 GLU cc_start: 0.7288 (mm-30) cc_final: 0.6718 (mm-30) outliers start: 19 outliers final: 11 residues processed: 179 average time/residue: 0.0965 time to fit residues: 23.6585 Evaluate side-chains 174 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 162 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain R residue 537 MET Chi-restraints excluded: chain R residue 576 GLN Chi-restraints excluded: chain R residue 705 LEU Chi-restraints excluded: chain R residue 765 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 90 optimal weight: 0.6980 chunk 7 optimal weight: 0.2980 chunk 4 optimal weight: 0.9980 chunk 85 optimal weight: 0.1980 chunk 48 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 0.0970 chunk 45 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN B 132 ASN R 539 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.155763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.127785 restraints weight = 13057.439| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.76 r_work: 0.3549 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8947 Z= 0.120 Angle : 0.516 8.146 12115 Z= 0.276 Chirality : 0.041 0.169 1376 Planarity : 0.003 0.049 1530 Dihedral : 4.192 28.320 1208 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.54 % Favored : 97.37 % Rotamer: Outliers : 1.99 % Allowed : 9.62 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1102 helix: 2.66 (0.29), residues: 351 sheet: 0.89 (0.31), residues: 274 loop : -1.04 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 96 TYR 0.018 0.001 TYR R 783 PHE 0.014 0.001 PHE B 253 TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 8945) covalent geometry : angle 0.51559 (12111) SS BOND : bond 0.00656 ( 2) SS BOND : angle 0.51631 ( 4) hydrogen bonds : bond 0.04617 ( 397) hydrogen bonds : angle 4.15530 ( 1098) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.6771 (mmm) cc_final: 0.6271 (tmm) REVERT: A 214 ASP cc_start: 0.7759 (m-30) cc_final: 0.7392 (m-30) REVERT: A 222 ASP cc_start: 0.7620 (t0) cc_final: 0.7344 (t0) REVERT: B 46 ARG cc_start: 0.7954 (ttm110) cc_final: 0.7581 (ttp80) REVERT: B 292 PHE cc_start: 0.7660 (m-80) cc_final: 0.7417 (m-80) REVERT: B 293 ASN cc_start: 0.7635 (p0) cc_final: 0.7301 (p0) REVERT: E 220 LEU cc_start: 0.8393 (mt) cc_final: 0.8148 (mt) REVERT: E 231 MET cc_start: 0.6936 (ttp) cc_final: 0.6225 (ttt) REVERT: G 21 MET cc_start: 0.7786 (mtm) cc_final: 0.7100 (mtm) REVERT: R 551 THR cc_start: 0.7439 (m) cc_final: 0.7076 (m) REVERT: R 575 ILE cc_start: 0.7564 (OUTLIER) cc_final: 0.6990 (pt) REVERT: R 796 GLU cc_start: 0.7317 (mm-30) cc_final: 0.6861 (mm-30) outliers start: 19 outliers final: 14 residues processed: 178 average time/residue: 0.1032 time to fit residues: 24.7408 Evaluate side-chains 178 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 163 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain R residue 537 MET Chi-restraints excluded: chain R residue 575 ILE Chi-restraints excluded: chain R residue 576 GLN Chi-restraints excluded: chain R residue 705 LEU Chi-restraints excluded: chain R residue 765 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 21 optimal weight: 0.9990 chunk 55 optimal weight: 0.0770 chunk 66 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 86 optimal weight: 0.0980 chunk 24 optimal weight: 0.1980 chunk 54 optimal weight: 1.9990 chunk 11 optimal weight: 0.3980 chunk 9 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 overall best weight: 0.3338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN B 110 ASN B 132 ASN R 539 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.157354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.129221 restraints weight = 13026.667| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.74 r_work: 0.3540 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8947 Z= 0.104 Angle : 0.495 7.916 12115 Z= 0.266 Chirality : 0.041 0.173 1376 Planarity : 0.003 0.046 1530 Dihedral : 4.143 28.157 1208 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.45 % Favored : 97.46 % Rotamer: Outliers : 1.99 % Allowed : 10.46 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.12 (0.26), residues: 1102 helix: 2.74 (0.29), residues: 351 sheet: 1.00 (0.32), residues: 260 loop : -0.96 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 96 TYR 0.018 0.001 TYR R 783 PHE 0.012 0.001 PHE B 199 TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 8945) covalent geometry : angle 0.49549 (12111) SS BOND : bond 0.00572 ( 2) SS BOND : angle 0.52018 ( 4) hydrogen bonds : bond 0.04255 ( 397) hydrogen bonds : angle 4.10100 ( 1098) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.6737 (mmm) cc_final: 0.6226 (tmm) REVERT: A 214 ASP cc_start: 0.7721 (m-30) cc_final: 0.7346 (m-30) REVERT: A 222 ASP cc_start: 0.7557 (t0) cc_final: 0.7269 (t0) REVERT: B 46 ARG cc_start: 0.7954 (ttm110) cc_final: 0.7579 (ttp80) REVERT: B 213 VAL cc_start: 0.7729 (t) cc_final: 0.7487 (m) REVERT: B 292 PHE cc_start: 0.7631 (m-80) cc_final: 0.7350 (m-80) REVERT: B 293 ASN cc_start: 0.7587 (p0) cc_final: 0.7238 (p0) REVERT: E 220 LEU cc_start: 0.8380 (mt) cc_final: 0.8112 (mt) REVERT: E 231 MET cc_start: 0.6798 (ttp) cc_final: 0.6123 (ttt) REVERT: G 21 MET cc_start: 0.7868 (mtm) cc_final: 0.7167 (mtm) REVERT: R 551 THR cc_start: 0.7376 (m) cc_final: 0.7026 (m) REVERT: R 796 GLU cc_start: 0.7283 (mm-30) cc_final: 0.6796 (mm-30) outliers start: 19 outliers final: 15 residues processed: 173 average time/residue: 0.1026 time to fit residues: 24.0342 Evaluate side-chains 174 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain R residue 537 MET Chi-restraints excluded: chain R residue 576 GLN Chi-restraints excluded: chain R residue 705 LEU Chi-restraints excluded: chain R residue 748 LEU Chi-restraints excluded: chain R residue 765 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 10 optimal weight: 3.9990 chunk 1 optimal weight: 0.0170 chunk 98 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 8 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 86 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN B 132 ASN R 539 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.154981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.126899 restraints weight = 13135.473| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.75 r_work: 0.3524 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8947 Z= 0.135 Angle : 0.542 11.011 12115 Z= 0.288 Chirality : 0.042 0.165 1376 Planarity : 0.003 0.046 1530 Dihedral : 4.274 28.234 1208 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.90 % Favored : 97.01 % Rotamer: Outliers : 2.09 % Allowed : 10.56 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.07 (0.26), residues: 1102 helix: 2.73 (0.29), residues: 345 sheet: 0.94 (0.31), residues: 267 loop : -0.97 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 18 TYR 0.017 0.002 TYR R 783 PHE 0.016 0.002 PHE B 253 TRP 0.016 0.002 TRP B 82 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 8945) covalent geometry : angle 0.54224 (12111) SS BOND : bond 0.00735 ( 2) SS BOND : angle 0.50017 ( 4) hydrogen bonds : bond 0.04981 ( 397) hydrogen bonds : angle 4.21259 ( 1098) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.6770 (mmm) cc_final: 0.6200 (tmm) REVERT: A 214 ASP cc_start: 0.7754 (m-30) cc_final: 0.7399 (m-30) REVERT: A 222 ASP cc_start: 0.7604 (t0) cc_final: 0.7314 (t0) REVERT: B 213 VAL cc_start: 0.7753 (t) cc_final: 0.7504 (m) REVERT: B 262 MET cc_start: 0.6232 (tpp) cc_final: 0.6027 (tpp) REVERT: B 292 PHE cc_start: 0.7706 (m-80) cc_final: 0.7402 (m-80) REVERT: B 293 ASN cc_start: 0.7621 (p0) cc_final: 0.7290 (p0) REVERT: E 220 LEU cc_start: 0.8380 (mt) cc_final: 0.8117 (mt) REVERT: E 231 MET cc_start: 0.6940 (ttp) cc_final: 0.6229 (ttt) REVERT: G 21 MET cc_start: 0.7851 (mtm) cc_final: 0.7187 (mtm) REVERT: R 551 THR cc_start: 0.7511 (m) cc_final: 0.7166 (m) REVERT: R 796 GLU cc_start: 0.7313 (mm-30) cc_final: 0.6825 (mm-30) outliers start: 20 outliers final: 15 residues processed: 180 average time/residue: 0.1014 time to fit residues: 24.7776 Evaluate side-chains 180 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 165 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain R residue 537 MET Chi-restraints excluded: chain R residue 576 GLN Chi-restraints excluded: chain R residue 705 LEU Chi-restraints excluded: chain R residue 765 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 88 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 91 optimal weight: 0.0770 chunk 72 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 65 optimal weight: 0.0570 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN B 132 ASN R 539 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.155110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.126949 restraints weight = 12949.668| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.73 r_work: 0.3530 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8947 Z= 0.121 Angle : 0.544 9.097 12115 Z= 0.286 Chirality : 0.041 0.144 1376 Planarity : 0.004 0.045 1530 Dihedral : 4.246 28.112 1208 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.72 % Favored : 97.19 % Rotamer: Outliers : 2.20 % Allowed : 11.51 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.08 (0.26), residues: 1102 helix: 2.72 (0.29), residues: 345 sheet: 0.91 (0.31), residues: 277 loop : -0.95 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 96 TYR 0.020 0.001 TYR R 783 PHE 0.014 0.001 PHE B 253 TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 8945) covalent geometry : angle 0.54378 (12111) SS BOND : bond 0.00670 ( 2) SS BOND : angle 0.44693 ( 4) hydrogen bonds : bond 0.04686 ( 397) hydrogen bonds : angle 4.13151 ( 1098) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.6741 (mmm) cc_final: 0.6161 (tmm) REVERT: A 214 ASP cc_start: 0.7744 (m-30) cc_final: 0.7389 (m-30) REVERT: A 222 ASP cc_start: 0.7597 (t0) cc_final: 0.7320 (t0) REVERT: B 292 PHE cc_start: 0.7672 (m-80) cc_final: 0.7391 (m-80) REVERT: B 293 ASN cc_start: 0.7597 (p0) cc_final: 0.7260 (p0) REVERT: E 18 ARG cc_start: 0.7818 (tpt-90) cc_final: 0.7536 (tpt-90) REVERT: E 220 LEU cc_start: 0.8363 (mt) cc_final: 0.8100 (mt) REVERT: E 231 MET cc_start: 0.6952 (ttp) cc_final: 0.6247 (ttt) REVERT: G 21 MET cc_start: 0.7848 (mtm) cc_final: 0.7187 (mtm) REVERT: R 551 THR cc_start: 0.7478 (m) cc_final: 0.7130 (m) REVERT: R 566 ILE cc_start: 0.7084 (mm) cc_final: 0.6867 (tp) REVERT: R 796 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6802 (mm-30) outliers start: 21 outliers final: 18 residues processed: 175 average time/residue: 0.1018 time to fit residues: 24.1263 Evaluate side-chains 184 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain R residue 537 MET Chi-restraints excluded: chain R residue 576 GLN Chi-restraints excluded: chain R residue 705 LEU Chi-restraints excluded: chain R residue 748 LEU Chi-restraints excluded: chain R residue 765 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 37 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 61 optimal weight: 0.0060 chunk 23 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 18 optimal weight: 0.1980 chunk 102 optimal weight: 0.0570 chunk 41 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 overall best weight: 0.4114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 110 ASN R 539 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.155632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.127487 restraints weight = 12960.200| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.74 r_work: 0.3535 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8947 Z= 0.113 Angle : 0.529 8.333 12115 Z= 0.279 Chirality : 0.041 0.142 1376 Planarity : 0.003 0.045 1530 Dihedral : 4.150 28.054 1208 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.90 % Favored : 97.01 % Rotamer: Outliers : 1.99 % Allowed : 11.30 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.14 (0.26), residues: 1102 helix: 2.72 (0.29), residues: 351 sheet: 0.97 (0.31), residues: 277 loop : -0.94 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 96 TYR 0.020 0.001 TYR R 783 PHE 0.015 0.001 PHE B 253 TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 8945) covalent geometry : angle 0.52933 (12111) SS BOND : bond 0.00611 ( 2) SS BOND : angle 0.44684 ( 4) hydrogen bonds : bond 0.04441 ( 397) hydrogen bonds : angle 4.06276 ( 1098) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 172 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.6741 (mmm) cc_final: 0.6167 (tmm) REVERT: A 214 ASP cc_start: 0.7746 (m-30) cc_final: 0.7388 (m-30) REVERT: A 222 ASP cc_start: 0.7606 (t0) cc_final: 0.7340 (t0) REVERT: B 100 VAL cc_start: 0.8583 (p) cc_final: 0.8315 (m) REVERT: B 292 PHE cc_start: 0.7659 (m-80) cc_final: 0.7347 (m-80) REVERT: B 293 ASN cc_start: 0.7592 (p0) cc_final: 0.7276 (p0) REVERT: E 18 ARG cc_start: 0.7827 (tpt-90) cc_final: 0.7548 (tpt-90) REVERT: E 220 LEU cc_start: 0.8388 (mt) cc_final: 0.8145 (mt) REVERT: E 231 MET cc_start: 0.6928 (ttp) cc_final: 0.6217 (ttt) REVERT: G 21 MET cc_start: 0.7849 (mtm) cc_final: 0.7184 (mtm) REVERT: R 551 THR cc_start: 0.7505 (m) cc_final: 0.7163 (m) REVERT: R 566 ILE cc_start: 0.7120 (mm) cc_final: 0.6913 (tp) REVERT: R 796 GLU cc_start: 0.7301 (mm-30) cc_final: 0.6809 (mm-30) outliers start: 19 outliers final: 17 residues processed: 180 average time/residue: 0.1039 time to fit residues: 25.2096 Evaluate side-chains 187 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 170 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain R residue 537 MET Chi-restraints excluded: chain R residue 576 GLN Chi-restraints excluded: chain R residue 705 LEU Chi-restraints excluded: chain R residue 748 LEU Chi-restraints excluded: chain R residue 765 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 54 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 26 optimal weight: 0.0010 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN R 539 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.152724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.124775 restraints weight = 13026.425| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.71 r_work: 0.3495 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8947 Z= 0.163 Angle : 0.583 8.702 12115 Z= 0.310 Chirality : 0.043 0.146 1376 Planarity : 0.004 0.044 1530 Dihedral : 4.405 28.183 1208 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.45 % Favored : 96.46 % Rotamer: Outliers : 2.09 % Allowed : 11.40 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.97 (0.26), residues: 1102 helix: 2.58 (0.29), residues: 351 sheet: 0.78 (0.31), residues: 279 loop : -0.99 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 96 TYR 0.022 0.002 TYR R 783 PHE 0.020 0.002 PHE B 253 TRP 0.016 0.002 TRP B 82 HIS 0.005 0.001 HIS R 539 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 8945) covalent geometry : angle 0.58305 (12111) SS BOND : bond 0.00824 ( 2) SS BOND : angle 0.47260 ( 4) hydrogen bonds : bond 0.05555 ( 397) hydrogen bonds : angle 4.30227 ( 1098) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.6732 (mmm) cc_final: 0.6097 (tmm) REVERT: A 214 ASP cc_start: 0.7842 (m-30) cc_final: 0.7523 (m-30) REVERT: B 205 ASP cc_start: 0.7305 (m-30) cc_final: 0.7057 (m-30) REVERT: B 293 ASN cc_start: 0.7636 (p0) cc_final: 0.7301 (p0) REVERT: E 220 LEU cc_start: 0.8373 (mt) cc_final: 0.8117 (mt) REVERT: E 231 MET cc_start: 0.7089 (ttp) cc_final: 0.6431 (ttp) REVERT: G 21 MET cc_start: 0.7923 (mtm) cc_final: 0.7247 (mtm) REVERT: R 551 THR cc_start: 0.7612 (m) cc_final: 0.7257 (m) REVERT: R 566 ILE cc_start: 0.7369 (mm) cc_final: 0.7133 (tp) REVERT: R 796 GLU cc_start: 0.7302 (mm-30) cc_final: 0.6771 (mm-30) outliers start: 20 outliers final: 17 residues processed: 184 average time/residue: 0.1017 time to fit residues: 25.4169 Evaluate side-chains 191 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain R residue 537 MET Chi-restraints excluded: chain R residue 576 GLN Chi-restraints excluded: chain R residue 639 PHE Chi-restraints excluded: chain R residue 705 LEU Chi-restraints excluded: chain R residue 765 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 69 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 5 optimal weight: 0.0970 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.153293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.125462 restraints weight = 12852.646| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.70 r_work: 0.3509 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8947 Z= 0.141 Angle : 0.580 10.570 12115 Z= 0.304 Chirality : 0.042 0.145 1376 Planarity : 0.004 0.043 1530 Dihedral : 4.365 28.096 1208 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.27 % Favored : 96.64 % Rotamer: Outliers : 2.20 % Allowed : 11.82 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.97 (0.26), residues: 1102 helix: 2.59 (0.29), residues: 351 sheet: 0.82 (0.31), residues: 279 loop : -1.02 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 96 TYR 0.020 0.002 TYR R 783 PHE 0.016 0.002 PHE B 253 TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8945) covalent geometry : angle 0.57973 (12111) SS BOND : bond 0.00720 ( 2) SS BOND : angle 0.40466 ( 4) hydrogen bonds : bond 0.05113 ( 397) hydrogen bonds : angle 4.27918 ( 1098) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2167.29 seconds wall clock time: 37 minutes 43.73 seconds (2263.73 seconds total)