Starting phenix.real_space_refine on Sat Sep 12 02:45:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vam_21143/09_2026/6vam_21143.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vam_21143/09_2026/6vam_21143.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vam_21143/09_2026/6vam_21143.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vam_21143/09_2026/6vam_21143.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vam_21143/09_2026/6vam_21143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vam_21143/09_2026/6vam_21143.map" } resolution = 3.63 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= 0.045 sd= 0.520 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 152 5.16 5 C 8704 2.51 5 N 2248 2.21 5 O 2256 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13360 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1670 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 203} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 13 Restraints were copied for chains: B, C, D, E, F, G, H Time building chain proxies: 1.88, per 1000 atoms: 0.14 Number of scatterers: 13360 At special positions: 0 Unit cell: (119.78, 119.78, 96.46, 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 152 16.00 O 2256 8.00 N 2248 7.00 C 8704 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 126 " distance=2.02 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 126 " distance=2.02 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 126 " distance=2.02 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 126 " distance=2.02 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 126 " distance=2.02 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 126 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 601.6 milliseconds 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3280 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 0 sheets defined 78.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 22 through 35 Processing helix chain 'A' and resid 48 through 70 removed outlier: 3.920A pdb=" N LEU A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY A 54 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Proline residue: A 59 - end of helix removed outlier: 3.772A pdb=" N PHE A 68 " --> pdb=" O PHE A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 83 removed outlier: 4.556A pdb=" N MET A 76 " --> pdb=" O ASN A 72 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG A 83 " --> pdb=" O GLU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 107 removed outlier: 3.841A pdb=" N GLN A 104 " --> pdb=" O CYS A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 121 removed outlier: 3.695A pdb=" N ALA A 111 " --> pdb=" O MET A 107 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A 112 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 128 Processing helix chain 'A' and resid 147 through 157 Processing helix chain 'A' and resid 171 through 201 removed outlier: 3.535A pdb=" N LEU A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 246 removed outlier: 3.715A pdb=" N ASP A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN A 246 " --> pdb=" O LYS A 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 35 Processing helix chain 'B' and resid 48 through 70 removed outlier: 3.920A pdb=" N LEU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) Proline residue: B 59 - end of helix removed outlier: 3.772A pdb=" N PHE B 68 " --> pdb=" O PHE B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 83 removed outlier: 4.556A pdb=" N MET B 76 " --> pdb=" O ASN B 72 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG B 83 " --> pdb=" O GLU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 107 removed outlier: 3.841A pdb=" N GLN B 104 " --> pdb=" O CYS B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 121 removed outlier: 3.696A pdb=" N ALA B 111 " --> pdb=" O MET B 107 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B 112 " --> pdb=" O ILE B 108 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY B 121 " --> pdb=" O THR B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 128 Processing helix chain 'B' and resid 147 through 157 Processing helix chain 'B' and resid 171 through 201 removed outlier: 3.535A pdb=" N LEU B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 246 removed outlier: 3.715A pdb=" N ASP B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN B 246 " --> pdb=" O LYS B 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 35 Processing helix chain 'C' and resid 48 through 70 removed outlier: 3.920A pdb=" N LEU C 53 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY C 54 " --> pdb=" O ALA C 50 " (cutoff:3.500A) Proline residue: C 59 - end of helix removed outlier: 3.772A pdb=" N PHE C 68 " --> pdb=" O PHE C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 83 removed outlier: 4.556A pdb=" N MET C 76 " --> pdb=" O ASN C 72 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG C 83 " --> pdb=" O GLU C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 107 removed outlier: 3.841A pdb=" N GLN C 104 " --> pdb=" O CYS C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 121 removed outlier: 3.695A pdb=" N ALA C 111 " --> pdb=" O MET C 107 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL C 112 " --> pdb=" O ILE C 108 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY C 121 " --> pdb=" O THR C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 128 Processing helix chain 'C' and resid 147 through 157 Processing helix chain 'C' and resid 171 through 201 removed outlier: 3.535A pdb=" N LEU C 178 " --> pdb=" O ALA C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 246 removed outlier: 3.715A pdb=" N ASP C 223 " --> pdb=" O SER C 219 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN C 246 " --> pdb=" O LYS C 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 35 Processing helix chain 'D' and resid 48 through 70 removed outlier: 3.920A pdb=" N LEU D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY D 54 " --> pdb=" O ALA D 50 " (cutoff:3.500A) Proline residue: D 59 - end of helix removed outlier: 3.771A pdb=" N PHE D 68 " --> pdb=" O PHE D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 83 removed outlier: 4.556A pdb=" N MET D 76 " --> pdb=" O ASN D 72 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG D 83 " --> pdb=" O GLU D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 107 removed outlier: 3.841A pdb=" N GLN D 104 " --> pdb=" O CYS D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 121 removed outlier: 3.695A pdb=" N ALA D 111 " --> pdb=" O MET D 107 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL D 112 " --> pdb=" O ILE D 108 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY D 121 " --> pdb=" O THR D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 128 Processing helix chain 'D' and resid 147 through 157 Processing helix chain 'D' and resid 171 through 201 removed outlier: 3.535A pdb=" N LEU D 178 " --> pdb=" O ALA D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 246 removed outlier: 3.715A pdb=" N ASP D 223 " --> pdb=" O SER D 219 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN D 246 " --> pdb=" O LYS D 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 35 Processing helix chain 'E' and resid 48 through 70 removed outlier: 3.920A pdb=" N LEU E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY E 54 " --> pdb=" O ALA E 50 " (cutoff:3.500A) Proline residue: E 59 - end of helix removed outlier: 3.772A pdb=" N PHE E 68 " --> pdb=" O PHE E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 83 removed outlier: 4.556A pdb=" N MET E 76 " --> pdb=" O ASN E 72 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG E 83 " --> pdb=" O GLU E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 107 removed outlier: 3.841A pdb=" N GLN E 104 " --> pdb=" O CYS E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 121 removed outlier: 3.695A pdb=" N ALA E 111 " --> pdb=" O MET E 107 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL E 112 " --> pdb=" O ILE E 108 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY E 121 " --> pdb=" O THR E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 128 Processing helix chain 'E' and resid 147 through 157 Processing helix chain 'E' and resid 171 through 201 removed outlier: 3.535A pdb=" N LEU E 178 " --> pdb=" O ALA E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 246 removed outlier: 3.715A pdb=" N ASP E 223 " --> pdb=" O SER E 219 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN E 246 " --> pdb=" O LYS E 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 35 Processing helix chain 'F' and resid 48 through 70 removed outlier: 3.920A pdb=" N LEU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLY F 54 " --> pdb=" O ALA F 50 " (cutoff:3.500A) Proline residue: F 59 - end of helix removed outlier: 3.772A pdb=" N PHE F 68 " --> pdb=" O PHE F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 83 removed outlier: 4.556A pdb=" N MET F 76 " --> pdb=" O ASN F 72 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG F 83 " --> pdb=" O GLU F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 107 removed outlier: 3.841A pdb=" N GLN F 104 " --> pdb=" O CYS F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 121 removed outlier: 3.696A pdb=" N ALA F 111 " --> pdb=" O MET F 107 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL F 112 " --> pdb=" O ILE F 108 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY F 121 " --> pdb=" O THR F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 128 Processing helix chain 'F' and resid 147 through 157 Processing helix chain 'F' and resid 171 through 201 removed outlier: 3.535A pdb=" N LEU F 178 " --> pdb=" O ALA F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 246 removed outlier: 3.715A pdb=" N ASP F 223 " --> pdb=" O SER F 219 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN F 246 " --> pdb=" O LYS F 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 35 Processing helix chain 'G' and resid 48 through 70 removed outlier: 3.920A pdb=" N LEU G 53 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY G 54 " --> pdb=" O ALA G 50 " (cutoff:3.500A) Proline residue: G 59 - end of helix removed outlier: 3.772A pdb=" N PHE G 68 " --> pdb=" O PHE G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 83 removed outlier: 4.556A pdb=" N MET G 76 " --> pdb=" O ASN G 72 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG G 83 " --> pdb=" O GLU G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 107 removed outlier: 3.842A pdb=" N GLN G 104 " --> pdb=" O CYS G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 121 removed outlier: 3.695A pdb=" N ALA G 111 " --> pdb=" O MET G 107 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL G 112 " --> pdb=" O ILE G 108 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY G 121 " --> pdb=" O THR G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 128 Processing helix chain 'G' and resid 147 through 157 Processing helix chain 'G' and resid 171 through 201 removed outlier: 3.536A pdb=" N LEU G 178 " --> pdb=" O ALA G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 246 removed outlier: 3.715A pdb=" N ASP G 223 " --> pdb=" O SER G 219 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN G 246 " --> pdb=" O LYS G 242 " (cutoff:3.500A) Processing helix chain 'H' and resid 23 through 35 Processing helix chain 'H' and resid 48 through 70 removed outlier: 3.920A pdb=" N LEU H 53 " --> pdb=" O LEU H 49 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY H 54 " --> pdb=" O ALA H 50 " (cutoff:3.500A) Proline residue: H 59 - end of helix removed outlier: 3.772A pdb=" N PHE H 68 " --> pdb=" O PHE H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 83 removed outlier: 4.556A pdb=" N MET H 76 " --> pdb=" O ASN H 72 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG H 83 " --> pdb=" O GLU H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 107 removed outlier: 3.841A pdb=" N GLN H 104 " --> pdb=" O CYS H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 121 removed outlier: 3.695A pdb=" N ALA H 111 " --> pdb=" O MET H 107 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL H 112 " --> pdb=" O ILE H 108 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY H 121 " --> pdb=" O THR H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 128 Processing helix chain 'H' and resid 147 through 157 Processing helix chain 'H' and resid 171 through 201 removed outlier: 3.536A pdb=" N LEU H 178 " --> pdb=" O ALA H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 246 removed outlier: 3.715A pdb=" N ASP H 223 " --> pdb=" O SER H 219 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN H 246 " --> pdb=" O LYS H 242 " (cutoff:3.500A) 929 hydrogen bonds defined for protein. 2787 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: 1.65 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4184 1.34 - 1.46: 2675 1.46 - 1.57: 6597 1.57 - 1.69: 0 1.69 - 1.81: 200 Bond restraints: 13656 Sorted by residual: bond pdb=" N PRO C 146 " pdb=" CD PRO C 146 " ideal model delta sigma weight residual 1.473 1.521 -0.048 1.40e-02 5.10e+03 1.20e+01 bond pdb=" N PRO E 146 " pdb=" CD PRO E 146 " ideal model delta sigma weight residual 1.473 1.521 -0.048 1.40e-02 5.10e+03 1.20e+01 bond pdb=" N PRO A 146 " pdb=" CD PRO A 146 " ideal model delta sigma weight residual 1.473 1.521 -0.048 1.40e-02 5.10e+03 1.20e+01 bond pdb=" N PRO B 146 " pdb=" CD PRO B 146 " ideal model delta sigma weight residual 1.473 1.521 -0.048 1.40e-02 5.10e+03 1.19e+01 bond pdb=" N PRO F 146 " pdb=" CD PRO F 146 " ideal model delta sigma weight residual 1.473 1.521 -0.048 1.40e-02 5.10e+03 1.19e+01 ... (remaining 13651 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 18171 2.57 - 5.14: 309 5.14 - 7.71: 40 7.71 - 10.28: 0 10.28 - 12.85: 16 Bond angle restraints: 18536 Sorted by residual: angle pdb=" C LEU B 203 " pdb=" N ARG B 204 " pdb=" CA ARG B 204 " ideal model delta sigma weight residual 120.06 132.91 -12.85 1.19e+00 7.06e-01 1.17e+02 angle pdb=" C LEU F 203 " pdb=" N ARG F 204 " pdb=" CA ARG F 204 " ideal model delta sigma weight residual 120.06 132.90 -12.84 1.19e+00 7.06e-01 1.16e+02 angle pdb=" C LEU A 203 " pdb=" N ARG A 204 " pdb=" CA ARG A 204 " ideal model delta sigma weight residual 120.06 132.88 -12.82 1.19e+00 7.06e-01 1.16e+02 angle pdb=" C LEU C 203 " pdb=" N ARG C 204 " pdb=" CA ARG C 204 " ideal model delta sigma weight residual 120.06 132.88 -12.82 1.19e+00 7.06e-01 1.16e+02 angle pdb=" C LEU E 203 " pdb=" N ARG E 204 " pdb=" CA ARG E 204 " ideal model delta sigma weight residual 120.06 132.88 -12.82 1.19e+00 7.06e-01 1.16e+02 ... (remaining 18531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.29: 7232 16.29 - 32.59: 760 32.59 - 48.88: 120 48.88 - 65.17: 24 65.17 - 81.47: 48 Dihedral angle restraints: 8184 sinusoidal: 3152 harmonic: 5032 Sorted by residual: dihedral pdb=" CB CYS G 41 " pdb=" SG CYS G 41 " pdb=" SG CYS G 126 " pdb=" CB CYS G 126 " ideal model delta sinusoidal sigma weight residual -86.00 -155.76 69.76 1 1.00e+01 1.00e-02 6.28e+01 dihedral pdb=" CB CYS H 41 " pdb=" SG CYS H 41 " pdb=" SG CYS H 126 " pdb=" CB CYS H 126 " ideal model delta sinusoidal sigma weight residual -86.00 -155.75 69.75 1 1.00e+01 1.00e-02 6.28e+01 dihedral pdb=" CB CYS D 41 " pdb=" SG CYS D 41 " pdb=" SG CYS D 126 " pdb=" CB CYS D 126 " ideal model delta sinusoidal sigma weight residual -86.00 -155.75 69.75 1 1.00e+01 1.00e-02 6.28e+01 ... (remaining 8181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1375 0.034 - 0.068: 620 0.068 - 0.102: 109 0.102 - 0.136: 41 0.136 - 0.170: 15 Chirality restraints: 2160 Sorted by residual: chirality pdb=" CA ILE B 169 " pdb=" N ILE B 169 " pdb=" C ILE B 169 " pdb=" CB ILE B 169 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.20e-01 chirality pdb=" CA ILE F 169 " pdb=" N ILE F 169 " pdb=" C ILE F 169 " pdb=" CB ILE F 169 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.20e-01 chirality pdb=" CA ILE H 169 " pdb=" N ILE H 169 " pdb=" C ILE H 169 " pdb=" CB ILE H 169 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.20e-01 ... (remaining 2157 not shown) Planarity restraints: 2296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 59 " 0.035 5.00e-02 4.00e+02 5.26e-02 4.43e+00 pdb=" N PRO D 60 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO D 60 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 60 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 59 " 0.035 5.00e-02 4.00e+02 5.25e-02 4.42e+00 pdb=" N PRO C 60 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO C 60 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 60 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 59 " 0.035 5.00e-02 4.00e+02 5.25e-02 4.42e+00 pdb=" N PRO E 60 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO E 60 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 60 " 0.030 5.00e-02 4.00e+02 ... (remaining 2293 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3850 2.81 - 3.33: 13724 3.33 - 3.86: 20744 3.86 - 4.38: 21377 4.38 - 4.90: 37590 Nonbonded interactions: 97285 Sorted by model distance: nonbonded pdb=" OE1 GLU F 225 " pdb=" NH1 ARG F 226 " model vdw 2.290 3.120 nonbonded pdb=" OE1 GLU B 225 " pdb=" NH1 ARG B 226 " model vdw 2.290 3.120 nonbonded pdb=" OE1 GLU A 225 " pdb=" NH1 ARG A 226 " model vdw 2.290 3.120 nonbonded pdb=" OE1 GLU G 225 " pdb=" NH1 ARG G 226 " model vdw 2.290 3.120 nonbonded pdb=" OE1 GLU C 225 " pdb=" NH1 ARG C 226 " model vdw 2.290 3.120 ... (remaining 97280 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 11.140 Find NCS groups from input model: 0.140 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: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 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 : 0.005 0.048 13664 Z= 0.251 Angle : 0.844 12.848 18552 Z= 0.538 Chirality : 0.041 0.170 2160 Planarity : 0.005 0.053 2296 Dihedral : 14.629 81.467 4880 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.19), residues: 1664 helix: -0.64 (0.12), residues: 1304 sheet: None (None), residues: 0 loop : -3.16 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 226 TYR 0.014 0.002 TYR H 97 PHE 0.008 0.001 PHE H 229 TRP 0.020 0.001 TRP F 218 HIS 0.001 0.000 HIS B 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.25 (13656) covalent geometry : angle 0.84314 / 0.54 (18536) SS BOND : bond 0.00656 / 0.31 ( 8) SS BOND : angle 1.59915 / 0.92 ( 16) hydrogen bonds : bond 0.08586 / 5.90 ( 929) hydrogen bonds : angle 4.32021 / 3.12 ( 2787) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.458 Fit side-chains REVERT: A 102 MET cc_start: 0.8083 (ttp) cc_final: 0.7851 (ttm) REVERT: B 26 MET cc_start: 0.7340 (mmm) cc_final: 0.6989 (tpt) REVERT: B 235 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8523 (mm-30) REVERT: C 102 MET cc_start: 0.8084 (ttp) cc_final: 0.7851 (ttm) REVERT: D 26 MET cc_start: 0.7335 (mmm) cc_final: 0.6978 (tpt) REVERT: D 235 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8519 (mm-30) REVERT: E 102 MET cc_start: 0.8081 (ttp) cc_final: 0.7847 (ttm) REVERT: F 26 MET cc_start: 0.7331 (mmm) cc_final: 0.6980 (tpt) REVERT: F 235 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8515 (mm-30) REVERT: G 102 MET cc_start: 0.8081 (ttp) cc_final: 0.7846 (ttm) REVERT: H 26 MET cc_start: 0.7334 (mmm) cc_final: 0.6985 (tpt) REVERT: H 235 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8520 (mm-30) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.1084 time to fit residues: 43.7038 Evaluate side-chains 213 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.2980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 ASN A 73 ASN A 147 GLN B 40 ASN C 40 ASN C 73 ASN C 147 GLN D 40 ASN E 40 ASN E 73 ASN E 147 GLN F 40 ASN G 40 ASN G 73 ASN G 147 GLN H 40 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.116292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.098178 restraints weight = 28060.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.100956 restraints weight = 13000.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.103027 restraints weight = 8052.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.104251 restraints weight = 5869.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.105273 restraints weight = 4813.720| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 13664 Z= 0.138 Angle : 0.599 5.778 18552 Z= 0.325 Chirality : 0.038 0.181 2160 Planarity : 0.005 0.054 2296 Dihedral : 5.180 22.720 1856 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 1.40 % Allowed : 14.04 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.21), residues: 1664 helix: 0.94 (0.14), residues: 1328 sheet: None (None), residues: 0 loop : -2.63 (0.39), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 179 TYR 0.008 0.001 TYR A 34 PHE 0.008 0.001 PHE D 128 TRP 0.009 0.001 TRP D 218 HIS 0.000 0.000 HIS B 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.14 (13656) covalent geometry : angle 0.59823 / 0.32 (18536) SS BOND : bond 0.00285 / 0.14 ( 8) SS BOND : angle 0.99722 / 0.57 ( 16) hydrogen bonds : bond 0.04001 / 2.64 ( 929) hydrogen bonds : angle 3.43698 / 2.49 ( 2787) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 252 time to evaluate : 0.486 Fit side-chains REVERT: A 76 MET cc_start: 0.8798 (ttp) cc_final: 0.8482 (tmm) REVERT: B 26 MET cc_start: 0.5948 (mmm) cc_final: 0.5576 (tpt) REVERT: B 107 MET cc_start: 0.8858 (tpp) cc_final: 0.8577 (ttt) REVERT: B 147 GLN cc_start: 0.8249 (tp40) cc_final: 0.7993 (tp-100) REVERT: B 235 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8546 (mm-30) REVERT: C 76 MET cc_start: 0.8793 (ttp) cc_final: 0.8475 (tmm) REVERT: D 26 MET cc_start: 0.5929 (mmm) cc_final: 0.5562 (tpt) REVERT: D 107 MET cc_start: 0.8855 (tpp) cc_final: 0.8577 (ttt) REVERT: D 147 GLN cc_start: 0.8255 (tp40) cc_final: 0.7997 (tp-100) REVERT: D 235 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8547 (mm-30) REVERT: E 76 MET cc_start: 0.8790 (ttp) cc_final: 0.8472 (tmm) REVERT: F 26 MET cc_start: 0.5906 (mmm) cc_final: 0.5533 (tpt) REVERT: F 107 MET cc_start: 0.8854 (tpp) cc_final: 0.8578 (ttt) REVERT: F 147 GLN cc_start: 0.8272 (tp40) cc_final: 0.8011 (tp-100) REVERT: F 235 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8546 (mm-30) REVERT: G 76 MET cc_start: 0.8798 (ttp) cc_final: 0.8480 (tmm) REVERT: H 26 MET cc_start: 0.5913 (mmm) cc_final: 0.5537 (tpt) REVERT: H 107 MET cc_start: 0.8852 (tpp) cc_final: 0.8575 (ttt) REVERT: H 147 GLN cc_start: 0.8264 (tp40) cc_final: 0.8004 (tp-100) REVERT: H 235 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8551 (mm-30) outliers start: 20 outliers final: 8 residues processed: 260 average time/residue: 0.0989 time to fit residues: 39.1205 Evaluate side-chains 225 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 217 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain H residue 243 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 154 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 86 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 59.6579 > 50:) chunk 6 optimal weight: 8.9990 chunk 126 optimal weight: 30.0000 chunk 122 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 ASN ** D 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 ASN F 40 ASN G 40 ASN ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.121924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.102460 restraints weight = 29945.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.105442 restraints weight = 14337.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.107601 restraints weight = 9191.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.108986 restraints weight = 6867.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.109875 restraints weight = 5681.378| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13664 Z= 0.171 Angle : 0.616 5.567 18552 Z= 0.334 Chirality : 0.039 0.174 2160 Planarity : 0.005 0.054 2296 Dihedral : 5.107 21.103 1856 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 1.69 % Allowed : 15.52 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.21), residues: 1664 helix: 1.22 (0.14), residues: 1344 sheet: None (None), residues: 0 loop : -2.39 (0.41), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 82 TYR 0.012 0.002 TYR H 97 PHE 0.008 0.001 PHE G 229 TRP 0.008 0.001 TRP H 218 HIS 0.000 0.000 HIS F 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.17 (13656) covalent geometry : angle 0.61527 / 0.33 (18536) SS BOND : bond 0.00416 / 0.20 ( 8) SS BOND : angle 1.22178 / 0.69 ( 16) hydrogen bonds : bond 0.04168 / 2.76 ( 929) hydrogen bonds : angle 3.49365 / 2.53 ( 2787) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 232 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8684 (ttp) cc_final: 0.8450 (ppp) REVERT: B 26 MET cc_start: 0.6041 (mmm) cc_final: 0.5643 (tpt) REVERT: B 147 GLN cc_start: 0.8138 (tp40) cc_final: 0.7890 (tp-100) REVERT: B 235 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8516 (mm-30) REVERT: C 76 MET cc_start: 0.8694 (ttp) cc_final: 0.8457 (ppp) REVERT: D 26 MET cc_start: 0.6091 (mmm) cc_final: 0.5696 (tpt) REVERT: D 147 GLN cc_start: 0.8139 (tp40) cc_final: 0.7890 (tp-100) REVERT: D 235 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8516 (mm-30) REVERT: E 76 MET cc_start: 0.8683 (ttp) cc_final: 0.8449 (ppp) REVERT: F 26 MET cc_start: 0.6095 (mmm) cc_final: 0.5699 (tpt) REVERT: F 147 GLN cc_start: 0.8141 (tp40) cc_final: 0.7894 (tp-100) REVERT: F 235 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8501 (mm-30) REVERT: G 76 MET cc_start: 0.8685 (ttp) cc_final: 0.8451 (ppp) REVERT: H 26 MET cc_start: 0.6069 (mmm) cc_final: 0.5677 (tpt) REVERT: H 147 GLN cc_start: 0.8148 (tp40) cc_final: 0.7900 (tp-100) REVERT: H 235 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8509 (mm-30) outliers start: 24 outliers final: 20 residues processed: 248 average time/residue: 0.0991 time to fit residues: 37.8570 Evaluate side-chains 250 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 230 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain H residue 243 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 116 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 105 optimal weight: 20.0000 chunk 121 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 chunk 90 optimal weight: 8.9990 chunk 136 optimal weight: 7.9990 chunk 110 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.118302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.098876 restraints weight = 28170.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.101863 restraints weight = 13859.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.104016 restraints weight = 8860.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.105518 restraints weight = 6550.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.106479 restraints weight = 5331.196| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 13664 Z= 0.257 Angle : 0.716 7.502 18552 Z= 0.382 Chirality : 0.041 0.166 2160 Planarity : 0.005 0.055 2296 Dihedral : 5.286 20.303 1856 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 1.97 % Allowed : 16.92 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.21), residues: 1664 helix: 1.11 (0.14), residues: 1344 sheet: None (None), residues: 0 loop : -2.34 (0.42), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 82 TYR 0.015 0.002 TYR G 34 PHE 0.011 0.002 PHE C 229 TRP 0.008 0.001 TRP A 218 HIS 0.001 0.000 HIS E 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00610 / 0.26 (13656) covalent geometry : angle 0.71447 / 0.38 (18536) SS BOND : bond 0.00654 / 0.31 ( 8) SS BOND : angle 1.54300 / 0.88 ( 16) hydrogen bonds : bond 0.04869 / 3.22 ( 929) hydrogen bonds : angle 3.84435 / 2.79 ( 2787) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 254 time to evaluate : 0.511 Fit side-chains REVERT: A 32 GLN cc_start: 0.7857 (mt0) cc_final: 0.7590 (mt0) REVERT: A 76 MET cc_start: 0.8729 (ttp) cc_final: 0.8466 (ppp) REVERT: B 26 MET cc_start: 0.6061 (mmm) cc_final: 0.5550 (tpt) REVERT: B 147 GLN cc_start: 0.8169 (tp40) cc_final: 0.7908 (tp-100) REVERT: B 235 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8547 (mm-30) REVERT: C 32 GLN cc_start: 0.7857 (mt0) cc_final: 0.7576 (mt0) REVERT: C 76 MET cc_start: 0.8731 (ttp) cc_final: 0.8467 (ppp) REVERT: D 26 MET cc_start: 0.6049 (mmm) cc_final: 0.5532 (tpt) REVERT: D 147 GLN cc_start: 0.8180 (tp40) cc_final: 0.7917 (tp-100) REVERT: D 235 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8547 (mm-30) REVERT: E 32 GLN cc_start: 0.7862 (mt0) cc_final: 0.7579 (mt0) REVERT: E 76 MET cc_start: 0.8728 (ttp) cc_final: 0.8466 (ppp) REVERT: F 26 MET cc_start: 0.6036 (mmm) cc_final: 0.5525 (tpt) REVERT: F 147 GLN cc_start: 0.8180 (tp40) cc_final: 0.7919 (tp-100) REVERT: F 235 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8563 (mm-30) REVERT: G 32 GLN cc_start: 0.7864 (mt0) cc_final: 0.7582 (mt0) REVERT: G 76 MET cc_start: 0.8727 (ttp) cc_final: 0.8466 (ppp) REVERT: H 26 MET cc_start: 0.6055 (mmm) cc_final: 0.5539 (tpt) REVERT: H 147 GLN cc_start: 0.8175 (tp40) cc_final: 0.7914 (tp-100) REVERT: H 235 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8568 (mm-30) outliers start: 28 outliers final: 20 residues processed: 270 average time/residue: 0.0940 time to fit residues: 39.1648 Evaluate side-chains 264 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 244 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain H residue 243 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 13 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 135 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 HIS ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 HIS ** D 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 HIS ** F 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 236 HIS ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.124191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.104965 restraints weight = 29146.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.107925 restraints weight = 13887.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.110065 restraints weight = 8925.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.111450 restraints weight = 6674.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.112307 restraints weight = 5515.934| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13664 Z= 0.124 Angle : 0.585 7.185 18552 Z= 0.307 Chirality : 0.037 0.170 2160 Planarity : 0.005 0.056 2296 Dihedral : 4.862 21.905 1856 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.25 % Allowed : 17.84 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.21), residues: 1664 helix: 1.81 (0.14), residues: 1344 sheet: None (None), residues: 0 loop : -2.50 (0.37), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 216 TYR 0.025 0.001 TYR G 163 PHE 0.006 0.001 PHE E 229 TRP 0.007 0.001 TRP A 218 HIS 0.000 0.000 HIS E 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 (13656) covalent geometry : angle 0.58490 / 0.31 (18536) SS BOND : bond 0.00169 / 0.08 ( 8) SS BOND : angle 0.82815 / 0.46 ( 16) hydrogen bonds : bond 0.03694 / 2.43 ( 929) hydrogen bonds : angle 3.21750 / 2.32 ( 2787) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 248 time to evaluate : 0.624 Fit side-chains REVERT: B 26 MET cc_start: 0.6017 (mmm) cc_final: 0.5655 (tpt) REVERT: B 147 GLN cc_start: 0.8019 (tp40) cc_final: 0.7743 (tp-100) REVERT: B 235 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8475 (mm-30) REVERT: D 26 MET cc_start: 0.6042 (mmm) cc_final: 0.5673 (tpt) REVERT: D 147 GLN cc_start: 0.8029 (tp40) cc_final: 0.7747 (tp-100) REVERT: D 235 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8477 (mm-30) REVERT: F 26 MET cc_start: 0.6040 (mmm) cc_final: 0.5678 (tpt) REVERT: F 147 GLN cc_start: 0.8027 (tp40) cc_final: 0.7750 (tp-100) REVERT: F 235 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8471 (mm-30) REVERT: H 26 MET cc_start: 0.6020 (mmm) cc_final: 0.5655 (tpt) REVERT: H 147 GLN cc_start: 0.8022 (tp40) cc_final: 0.7745 (tp-100) REVERT: H 235 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8475 (mm-30) outliers start: 32 outliers final: 16 residues processed: 272 average time/residue: 0.0971 time to fit residues: 41.0429 Evaluate side-chains 252 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 236 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain H residue 243 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 93 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 167 optimal weight: 2.9990 chunk 108 optimal weight: 0.0980 chunk 28 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 chunk 118 optimal weight: 0.0060 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 48 ASN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN B 236 HIS ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 ASN ** D 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 ASN D 236 HIS ** E 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 ASN ** F 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 ASN F 236 HIS ** G 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 48 ASN ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 ASN H 236 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.125561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.106358 restraints weight = 28382.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.109331 restraints weight = 13750.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.111586 restraints weight = 8864.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.113057 restraints weight = 6597.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.114015 restraints weight = 5415.548| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13664 Z= 0.123 Angle : 0.595 9.310 18552 Z= 0.306 Chirality : 0.037 0.174 2160 Planarity : 0.004 0.055 2296 Dihedral : 4.586 19.534 1856 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 2.25 % Allowed : 18.82 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.21), residues: 1664 helix: 2.10 (0.14), residues: 1352 sheet: None (None), residues: 0 loop : -2.55 (0.37), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 82 TYR 0.019 0.001 TYR E 163 PHE 0.005 0.001 PHE E 229 TRP 0.023 0.001 TRP H 218 HIS 0.001 0.000 HIS D 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (13656) covalent geometry : angle 0.59256 / 0.30 (18536) SS BOND : bond 0.00174 / 0.08 ( 8) SS BOND : angle 1.88128 / 1.07 ( 16) hydrogen bonds : bond 0.03443 / 2.27 ( 929) hydrogen bonds : angle 3.09115 / 2.24 ( 2787) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 240 time to evaluate : 0.520 Fit side-chains REVERT: B 26 MET cc_start: 0.6066 (mmm) cc_final: 0.5752 (tpt) REVERT: B 117 THR cc_start: 0.9495 (t) cc_final: 0.9241 (t) REVERT: B 147 GLN cc_start: 0.8017 (tp40) cc_final: 0.7739 (tp-100) REVERT: B 235 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8421 (mm-30) REVERT: D 26 MET cc_start: 0.6065 (mmm) cc_final: 0.5746 (tpt) REVERT: D 117 THR cc_start: 0.9494 (t) cc_final: 0.9243 (t) REVERT: D 147 GLN cc_start: 0.8028 (tp40) cc_final: 0.7748 (tp-100) REVERT: D 235 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8426 (mm-30) REVERT: F 26 MET cc_start: 0.6073 (mmm) cc_final: 0.5761 (tpt) REVERT: F 117 THR cc_start: 0.9495 (t) cc_final: 0.9243 (t) REVERT: F 147 GLN cc_start: 0.8028 (tp40) cc_final: 0.7747 (tp-100) REVERT: F 235 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8421 (mm-30) REVERT: H 26 MET cc_start: 0.6052 (mmm) cc_final: 0.5724 (tpt) REVERT: H 117 THR cc_start: 0.9495 (t) cc_final: 0.9244 (t) REVERT: H 147 GLN cc_start: 0.8021 (tp40) cc_final: 0.7739 (tp-100) REVERT: H 235 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8423 (mm-30) outliers start: 32 outliers final: 24 residues processed: 264 average time/residue: 0.0965 time to fit residues: 39.4207 Evaluate side-chains 263 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 239 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain H residue 243 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 22 optimal weight: 5.9990 chunk 142 optimal weight: 0.7980 chunk 136 optimal weight: 3.9990 chunk 84 optimal weight: 30.0000 chunk 75 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 63 optimal weight: 20.0000 chunk 133 optimal weight: 2.9990 chunk 116 optimal weight: 8.9990 chunk 85 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN ** D 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 GLN ** F 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.121150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.101161 restraints weight = 28513.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.104194 restraints weight = 14536.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.106389 restraints weight = 9471.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.107685 restraints weight = 7130.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.108701 restraints weight = 5934.159| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13664 Z= 0.205 Angle : 0.679 6.987 18552 Z= 0.364 Chirality : 0.040 0.163 2160 Planarity : 0.005 0.054 2296 Dihedral : 4.872 18.225 1856 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 1.69 % Allowed : 20.01 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.21), residues: 1664 helix: 2.00 (0.14), residues: 1344 sheet: None (None), residues: 0 loop : -2.62 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 82 TYR 0.022 0.002 TYR A 163 PHE 0.008 0.001 PHE F 229 TRP 0.017 0.001 TRP B 218 HIS 0.001 0.000 HIS G 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.21 (13656) covalent geometry : angle 0.66114 / 0.36 (18536) SS BOND : bond 0.00770 / 0.37 ( 8) SS BOND : angle 5.35060 / 3.01 ( 16) hydrogen bonds : bond 0.04256 / 2.81 ( 929) hydrogen bonds : angle 3.49785 / 2.53 ( 2787) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 231 time to evaluate : 0.473 Fit side-chains REVERT: A 32 GLN cc_start: 0.7644 (mt0) cc_final: 0.7414 (mt0) REVERT: A 203 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7970 (mp) REVERT: B 26 MET cc_start: 0.6027 (mmm) cc_final: 0.5602 (tpt) REVERT: B 147 GLN cc_start: 0.8130 (tp40) cc_final: 0.7848 (tp-100) REVERT: B 231 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8521 (mm-30) REVERT: B 235 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8492 (mm-30) REVERT: C 32 GLN cc_start: 0.7674 (mt0) cc_final: 0.7439 (mt0) REVERT: C 203 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7969 (mp) REVERT: D 26 MET cc_start: 0.6020 (mmm) cc_final: 0.5593 (tpt) REVERT: D 147 GLN cc_start: 0.8095 (tp40) cc_final: 0.7818 (tp-100) REVERT: D 231 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8522 (mm-30) REVERT: D 235 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8490 (mm-30) REVERT: E 32 GLN cc_start: 0.7688 (mt0) cc_final: 0.7451 (mt0) REVERT: E 203 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7969 (mp) REVERT: F 26 MET cc_start: 0.6051 (mmm) cc_final: 0.5624 (tpt) REVERT: F 147 GLN cc_start: 0.8130 (tp40) cc_final: 0.7847 (tp-100) REVERT: F 231 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8527 (mm-30) REVERT: F 235 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8491 (mm-30) REVERT: G 32 GLN cc_start: 0.7649 (mt0) cc_final: 0.7404 (mt0) REVERT: G 203 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7966 (mp) REVERT: H 26 MET cc_start: 0.6012 (mmm) cc_final: 0.5590 (tpt) REVERT: H 147 GLN cc_start: 0.8087 (tp40) cc_final: 0.7811 (tp-100) REVERT: H 231 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8529 (mm-30) REVERT: H 235 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8494 (mm-30) outliers start: 24 outliers final: 20 residues processed: 255 average time/residue: 0.0982 time to fit residues: 38.4206 Evaluate side-chains 237 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 213 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain H residue 243 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 76 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 105 optimal weight: 20.0000 chunk 56 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.124049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.104485 restraints weight = 28261.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.107530 restraints weight = 14292.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.109736 restraints weight = 9279.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.111080 restraints weight = 6935.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.112088 restraints weight = 5749.586| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13664 Z= 0.139 Angle : 0.609 6.377 18552 Z= 0.323 Chirality : 0.038 0.162 2160 Planarity : 0.005 0.056 2296 Dihedral : 4.725 21.058 1856 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.83 % Allowed : 19.52 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.21), residues: 1664 helix: 2.31 (0.14), residues: 1344 sheet: None (None), residues: 0 loop : -2.68 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 179 TYR 0.018 0.002 TYR G 163 PHE 0.005 0.001 PHE H 229 TRP 0.014 0.001 TRP H 218 HIS 0.001 0.000 HIS C 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 (13656) covalent geometry : angle 0.60021 / 0.32 (18536) SS BOND : bond 0.00276 / 0.13 ( 8) SS BOND : angle 3.61220 / 2.03 ( 16) hydrogen bonds : bond 0.03713 / 2.44 ( 929) hydrogen bonds : angle 3.26340 / 2.36 ( 2787) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 225 time to evaluate : 0.399 Fit side-chains REVERT: B 26 MET cc_start: 0.5808 (mmm) cc_final: 0.5450 (tpt) REVERT: B 147 GLN cc_start: 0.8091 (tp40) cc_final: 0.7682 (tp-100) REVERT: B 231 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8478 (mm-30) REVERT: B 235 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8395 (mm-30) REVERT: D 26 MET cc_start: 0.5808 (mmm) cc_final: 0.5454 (tpt) REVERT: D 147 GLN cc_start: 0.8090 (tp40) cc_final: 0.7839 (tp40) REVERT: D 231 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8473 (mm-30) REVERT: D 235 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8393 (mm-30) REVERT: F 26 MET cc_start: 0.5803 (mmm) cc_final: 0.5444 (tpt) REVERT: F 147 GLN cc_start: 0.8090 (tp40) cc_final: 0.7680 (tp-100) REVERT: F 231 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8485 (mm-30) REVERT: F 235 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8395 (mm-30) REVERT: H 26 MET cc_start: 0.5797 (mmm) cc_final: 0.5438 (tpt) REVERT: H 147 GLN cc_start: 0.8090 (tp40) cc_final: 0.7839 (tp40) REVERT: H 231 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8482 (mm-30) REVERT: H 235 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8405 (mm-30) outliers start: 26 outliers final: 26 residues processed: 251 average time/residue: 0.0995 time to fit residues: 38.1387 Evaluate side-chains 244 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 218 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 180 CYS Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain H residue 243 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 49 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 162 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 21 optimal weight: 20.0000 chunk 152 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN ** D 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 GLN ** F 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 GLN ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.124467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.104835 restraints weight = 28382.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.107941 restraints weight = 14411.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.110158 restraints weight = 9360.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.111534 restraints weight = 6997.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.112565 restraints weight = 5781.081| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13664 Z= 0.138 Angle : 0.622 9.306 18552 Z= 0.325 Chirality : 0.038 0.170 2160 Planarity : 0.004 0.055 2296 Dihedral : 4.609 18.849 1856 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.90 % Allowed : 21.28 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.21), residues: 1664 helix: 2.37 (0.14), residues: 1352 sheet: None (None), residues: 0 loop : -2.79 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 179 TYR 0.021 0.002 TYR G 163 PHE 0.005 0.001 PHE F 229 TRP 0.012 0.001 TRP H 218 HIS 0.001 0.000 HIS A 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (13656) covalent geometry : angle 0.61617 / 0.32 (18536) SS BOND : bond 0.00320 / 0.15 ( 8) SS BOND : angle 2.95556 / 1.66 ( 16) hydrogen bonds : bond 0.03682 / 2.43 ( 929) hydrogen bonds : angle 3.24198 / 2.35 ( 2787) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 220 time to evaluate : 0.510 Fit side-chains REVERT: A 76 MET cc_start: 0.8369 (ppp) cc_final: 0.8114 (ppp) REVERT: A 122 LYS cc_start: 0.8743 (mttp) cc_final: 0.8542 (mttm) REVERT: B 26 MET cc_start: 0.5879 (mmm) cc_final: 0.5547 (tpt) REVERT: B 117 THR cc_start: 0.9488 (t) cc_final: 0.9241 (t) REVERT: B 147 GLN cc_start: 0.8041 (tp40) cc_final: 0.7650 (tp-100) REVERT: B 231 GLU cc_start: 0.8837 (mm-30) cc_final: 0.8437 (mm-30) REVERT: B 235 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8373 (mm-30) REVERT: C 76 MET cc_start: 0.8376 (ppp) cc_final: 0.8119 (ppp) REVERT: C 122 LYS cc_start: 0.8742 (mttp) cc_final: 0.8536 (mttm) REVERT: D 26 MET cc_start: 0.5881 (mmm) cc_final: 0.5554 (tpt) REVERT: D 117 THR cc_start: 0.9487 (t) cc_final: 0.9242 (t) REVERT: D 147 GLN cc_start: 0.8044 (tp40) cc_final: 0.7799 (tp40) REVERT: D 231 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8432 (mm-30) REVERT: D 235 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8379 (mm-30) REVERT: E 76 MET cc_start: 0.8375 (ppp) cc_final: 0.8118 (ppp) REVERT: E 122 LYS cc_start: 0.8742 (mttp) cc_final: 0.8537 (mttm) REVERT: F 26 MET cc_start: 0.5877 (mmm) cc_final: 0.5548 (tpt) REVERT: F 117 THR cc_start: 0.9482 (t) cc_final: 0.9236 (t) REVERT: F 147 GLN cc_start: 0.8051 (tp40) cc_final: 0.7654 (tp-100) REVERT: F 231 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8440 (mm-30) REVERT: F 235 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8371 (mm-30) REVERT: G 76 MET cc_start: 0.8369 (ppp) cc_final: 0.8108 (ppp) REVERT: G 122 LYS cc_start: 0.8747 (mttp) cc_final: 0.8543 (mttm) REVERT: H 26 MET cc_start: 0.5874 (mmm) cc_final: 0.5548 (tpt) REVERT: H 117 THR cc_start: 0.9483 (t) cc_final: 0.9234 (t) REVERT: H 147 GLN cc_start: 0.8047 (tp40) cc_final: 0.7804 (tp40) REVERT: H 231 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8422 (mm-30) REVERT: H 235 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8385 (mm-30) outliers start: 27 outliers final: 27 residues processed: 247 average time/residue: 0.1020 time to fit residues: 37.9832 Evaluate side-chains 240 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 213 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain H residue 180 CYS Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain H residue 243 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 1 optimal weight: 0.6980 chunk 27 optimal weight: 0.0980 chunk 109 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 51 optimal weight: 0.3980 chunk 80 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 93 optimal weight: 0.4980 chunk 32 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.122973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.104810 restraints weight = 27547.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.107906 restraints weight = 13107.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.110064 restraints weight = 8141.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.111491 restraints weight = 5933.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.112342 restraints weight = 4778.063| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13664 Z= 0.122 Angle : 0.599 9.388 18552 Z= 0.309 Chirality : 0.036 0.159 2160 Planarity : 0.004 0.055 2296 Dihedral : 4.430 20.211 1856 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.77 % Allowed : 22.75 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.52 (0.22), residues: 1664 helix: 2.43 (0.14), residues: 1384 sheet: None (None), residues: 0 loop : -2.48 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 179 TYR 0.020 0.001 TYR A 163 PHE 0.004 0.001 PHE H 229 TRP 0.010 0.001 TRP B 218 HIS 0.000 0.000 HIS E 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (13656) covalent geometry : angle 0.59451 / 0.31 (18536) SS BOND : bond 0.00251 / 0.12 ( 8) SS BOND : angle 2.46129 / 1.38 ( 16) hydrogen bonds : bond 0.03263 / 2.15 ( 929) hydrogen bonds : angle 3.08462 / 2.23 ( 2787) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 219 time to evaluate : 0.513 Fit side-chains REVERT: A 76 MET cc_start: 0.8383 (ppp) cc_final: 0.8146 (ppp) REVERT: B 26 MET cc_start: 0.5874 (mmm) cc_final: 0.5670 (tpt) REVERT: B 107 MET cc_start: 0.8548 (ttt) cc_final: 0.8185 (ttp) REVERT: B 193 MET cc_start: 0.7302 (tpt) cc_final: 0.6886 (tpp) REVERT: B 231 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8426 (mm-30) REVERT: B 235 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8359 (mm-30) REVERT: C 76 MET cc_start: 0.8405 (ppp) cc_final: 0.8162 (ppp) REVERT: D 26 MET cc_start: 0.5839 (mmm) cc_final: 0.5635 (tpt) REVERT: D 107 MET cc_start: 0.8537 (ttt) cc_final: 0.8168 (ttp) REVERT: D 193 MET cc_start: 0.7316 (tpt) cc_final: 0.6900 (tpp) REVERT: D 231 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8402 (mm-30) REVERT: D 235 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8338 (mm-30) REVERT: E 76 MET cc_start: 0.8383 (ppp) cc_final: 0.8142 (ppp) REVERT: F 26 MET cc_start: 0.5904 (mmm) cc_final: 0.5700 (tpt) REVERT: F 107 MET cc_start: 0.8542 (ttt) cc_final: 0.8178 (ttp) REVERT: F 193 MET cc_start: 0.7295 (tpt) cc_final: 0.6881 (tpp) REVERT: F 231 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8421 (mm-30) REVERT: F 235 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8357 (mm-30) REVERT: G 76 MET cc_start: 0.8407 (ppp) cc_final: 0.8162 (ppp) REVERT: H 26 MET cc_start: 0.5844 (mmm) cc_final: 0.5639 (tpt) REVERT: H 107 MET cc_start: 0.8554 (ttt) cc_final: 0.8186 (ttp) REVERT: H 193 MET cc_start: 0.7313 (tpt) cc_final: 0.6883 (tpp) REVERT: H 235 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8336 (mm-30) outliers start: 11 outliers final: 3 residues processed: 230 average time/residue: 0.1059 time to fit residues: 36.5160 Evaluate side-chains 211 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 208 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 180 CYS Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain H residue 180 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 31 optimal weight: 2.9990 chunk 54 optimal weight: 0.0770 chunk 52 optimal weight: 0.9990 chunk 62 optimal weight: 9.9990 chunk 122 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 overall best weight: 0.9544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.127420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.107891 restraints weight = 28269.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.110948 restraints weight = 14344.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.113179 restraints weight = 9255.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.114531 restraints weight = 6883.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.115604 restraints weight = 5705.925| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13664 Z= 0.128 Angle : 0.608 9.373 18552 Z= 0.315 Chirality : 0.037 0.160 2160 Planarity : 0.004 0.055 2296 Dihedral : 4.333 18.116 1856 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.28 % Allowed : 23.88 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.51 (0.21), residues: 1664 helix: 2.42 (0.14), residues: 1384 sheet: None (None), residues: 0 loop : -2.54 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 179 TYR 0.025 0.001 TYR G 163 PHE 0.004 0.001 PHE F 229 TRP 0.010 0.001 TRP H 218 HIS 0.000 0.000 HIS E 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (13656) covalent geometry : angle 0.60401 / 0.31 (18536) SS BOND : bond 0.00283 / 0.13 ( 8) SS BOND : angle 2.56537 / 1.44 ( 16) hydrogen bonds : bond 0.03390 / 2.24 ( 929) hydrogen bonds : angle 3.11445 / 2.25 ( 2787) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1905.12 seconds wall clock time: 33 minutes 49.77 seconds (2029.77 seconds total)