Starting phenix.real_space_refine on Fri Jul 3 14:48:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8es9_28572/07_2026/8es9_28572.cif Found real_map, /net/cci-nas-00/data/ceres_data/8es9_28572/07_2026/8es9_28572.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8es9_28572/07_2026/8es9_28572.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8es9_28572/07_2026/8es9_28572.map" model { file = "/net/cci-nas-00/data/ceres_data/8es9_28572/07_2026/8es9_28572.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8es9_28572/07_2026/8es9_28572.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8es9_28572/07_2026/8es9_28572.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8es9_28572/07_2026/8es9_28572.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3163 atoms to isotropic. 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 64 5.16 5 C 7526 2.51 5 N 1968 2.21 5 O 2286 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11844 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1972 Classifications: {'peptide': 251} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 238} Chain: "B" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2261 Classifications: {'peptide': 287} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 274} Chain: "Z" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 286 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 34} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Y" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 249 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "D" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 821 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain: "F" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain: "G" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 913 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "E" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 978 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "N" Number of atoms: 2246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2246 Classifications: {'peptide': 275} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 263} Chain: "M" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 837 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 94} Chain: "P" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 80 Classifications: {'peptide': 10} Modifications used: {'COO': 1} Link IDs: {'TRANS': 9} Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'NAG': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.11, per 1000 atoms: 0.26 Number of scatterers: 11844 At special positions: 0 Unit cell: (95.2, 100.3, 195.5, 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 64 16.00 O 2286 8.00 N 1968 7.00 C 7526 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 186 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 94 " distance=2.03 Simple disulfide: pdb=" SG CYS B 146 " - pdb=" SG CYS B 211 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 32 " - pdb=" SG CYS Y 32 " distance=2.03 Simple disulfide: pdb=" SG CYS D 37 " - pdb=" SG CYS D 73 " distance=2.04 Simple disulfide: pdb=" SG CYS D 93 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 49 " - pdb=" SG CYS F 98 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 122 " distance=2.03 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 87 " distance=2.03 Simple disulfide: pdb=" SG CYS G 104 " - pdb=" SG CYS G 107 " distance=2.04 Simple disulfide: pdb=" SG CYS E 49 " - pdb=" SG CYS E 98 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 122 " distance=2.03 Simple disulfide: pdb=" SG CYS N 101 " - pdb=" SG CYS N 164 " distance=2.03 Simple disulfide: pdb=" SG CYS N 203 " - pdb=" SG CYS N 259 " distance=2.04 Simple disulfide: pdb=" SG CYS M 25 " - pdb=" SG CYS M 80 " distance=2.05 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 Links applied BETA1-4 " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG L 1 " - " NAG L 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A1701 " - " ASN A 191 " " NAG A1702 " - " ASN A 180 " " NAG A1703 " - " ASN A 22 " " NAG B1701 " - " ASN B 185 " " NAG G1701 " - " ASN G 52 " " NAG G1702 " - " ASN G 92 " " NAG H 1 " - " ASN D 38 " " NAG L 1 " - " ASN D 74 " " NAG T 1 " - " ASN A 146 " Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 502.0 milliseconds 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2732 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 26 sheets defined 25.8% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 209 through 216 removed outlier: 3.830A pdb=" N SER A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 252 removed outlier: 3.644A pdb=" N ASN A 224 " --> pdb=" O ASP A 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 89 removed outlier: 3.617A pdb=" N SER B 89 " --> pdb=" O PRO B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 140 Processing helix chain 'B' and resid 199 through 203 Processing helix chain 'B' and resid 249 through 289 removed outlier: 3.548A pdb=" N LEU B 277 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG B 289 " --> pdb=" O ALA B 285 " (cutoff:3.500A) Processing helix chain 'Z' and resid 29 through 57 Processing helix chain 'Y' and resid 28 through 55 removed outlier: 4.395A pdb=" N CYS Y 32 " --> pdb=" O ASP Y 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 127 removed outlier: 3.752A pdb=" N GLY D 127 " --> pdb=" O PHE D 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 93 removed outlier: 3.675A pdb=" N SER F 93 " --> pdb=" O GLU F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 108 Processing helix chain 'F' and resid 126 through 156 Processing helix chain 'G' and resid 78 through 80 No H-bonds generated for 'chain 'G' and resid 78 through 80' Processing helix chain 'G' and resid 111 through 136 removed outlier: 3.513A pdb=" N ILE G 115 " --> pdb=" O ASN G 111 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE G 136 " --> pdb=" O GLY G 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 93 Processing helix chain 'E' and resid 126 through 155 removed outlier: 3.625A pdb=" N VAL E 130 " --> pdb=" O ASP E 126 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASN E 154 " --> pdb=" O TYR E 150 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ARG E 155 " --> pdb=" O TRP E 151 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 53 removed outlier: 3.620A pdb=" N GLU N 53 " --> pdb=" O PRO N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 86 removed outlier: 3.559A pdb=" N GLY N 83 " --> pdb=" O GLY N 79 " (cutoff:3.500A) Processing helix chain 'N' and resid 138 through 149 removed outlier: 4.254A pdb=" N THR N 142 " --> pdb=" O MET N 138 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR N 143 " --> pdb=" O ALA N 139 " (cutoff:3.500A) Processing helix chain 'N' and resid 151 through 162 removed outlier: 3.844A pdb=" N GLN N 155 " --> pdb=" O HIS N 151 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR N 159 " --> pdb=" O GLN N 155 " (cutoff:3.500A) Processing helix chain 'N' and resid 162 through 175 Processing helix chain 'N' and resid 175 through 180 removed outlier: 3.657A pdb=" N GLN N 180 " --> pdb=" O LYS N 176 " (cutoff:3.500A) Processing helix chain 'N' and resid 253 through 255 No H-bonds generated for 'chain 'N' and resid 253 through 255' Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 14 removed outlier: 3.507A pdb=" N ALA A 110 " --> pdb=" O LEU A 11 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 45 through 49 removed outlier: 6.478A pdb=" N TRP A 35 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR A 49 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU A 33 " --> pdb=" O THR A 49 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY A 32 " --> pdb=" O GLN A 91 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 124 Processing sheet with id=AA5, first strand: chain 'A' and resid 121 through 124 Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 14 removed outlier: 3.572A pdb=" N CYS B 13 " --> pdb=" O THR B 113 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 19 through 22 Processing sheet with id=AA8, first strand: chain 'B' and resid 57 through 58 removed outlier: 5.195A pdb=" N LEU B 46 " --> pdb=" O ARG B 37 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ARG B 37 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 125 through 129 removed outlier: 5.628A pdb=" N TYR B 189 " --> pdb=" O GLY B 150 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 125 through 129 removed outlier: 5.628A pdb=" N TYR B 189 " --> pdb=" O GLY B 150 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 165 through 166 Processing sheet with id=AB3, first strand: chain 'D' and resid 26 through 28 removed outlier: 6.146A pdb=" N VAL D 33 " --> pdb=" O LEU D 60 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 42 through 46 removed outlier: 6.556A pdb=" N ILE D 70 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N GLY D 46 " --> pdb=" O ARG D 68 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ARG D 68 " --> pdb=" O GLY D 46 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N THR D 85 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N TYR E 113 " --> pdb=" O THR D 85 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLN D 87 " --> pdb=" O TYR E 113 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ARG E 115 " --> pdb=" O GLN D 87 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N HIS D 89 " --> pdb=" O ARG E 115 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE E 110 " --> pdb=" O CYS E 98 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N CYS E 98 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N TRP E 59 " --> pdb=" O ILE E 66 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 96 through 98 Processing sheet with id=AB6, first strand: chain 'F' and resid 37 through 41 Processing sheet with id=AB7, first strand: chain 'F' and resid 64 through 66 removed outlier: 4.085A pdb=" N TRP F 59 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG F 115 " --> pdb=" O TYR G 100 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLY G 63 " --> pdb=" O TRP G 55 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N LYS G 57 " --> pdb=" O MET G 61 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N MET G 61 " --> pdb=" O LYS G 57 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 122 through 123 Processing sheet with id=AB9, first strand: chain 'G' and resid 32 through 34 removed outlier: 5.633A pdb=" N VAL G 42 " --> pdb=" O LEU G 74 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 37 through 41 Processing sheet with id=AC2, first strand: chain 'N' and resid 46 through 47 removed outlier: 6.765A pdb=" N GLY N 26 " --> pdb=" O PHE N 33 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ARG N 35 " --> pdb=" O ALA N 24 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA N 24 " --> pdb=" O ARG N 35 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ASP N 37 " --> pdb=" O PHE N 22 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N PHE N 22 " --> pdb=" O ASP N 37 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG N 111 " --> pdb=" O ASP N 102 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N HIS N 114 " --> pdb=" O LEU N 126 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE N 124 " --> pdb=" O TYR N 116 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N TYR N 118 " --> pdb=" O ASP N 122 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ASP N 122 " --> pdb=" O TYR N 118 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 189 through 193 removed outlier: 5.816A pdb=" N PHE N 241 " --> pdb=" O SER N 207 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 189 through 193 removed outlier: 5.816A pdb=" N PHE N 241 " --> pdb=" O SER N 207 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 222 through 223 Processing sheet with id=AC6, first strand: chain 'M' and resid 6 through 11 removed outlier: 5.980A pdb=" N PHE M 62 " --> pdb=" O GLY M 29 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU M 50 " --> pdb=" O TYR M 67 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 6 through 11 removed outlier: 5.980A pdb=" N PHE M 62 " --> pdb=" O GLY M 29 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER M 55 " --> pdb=" O TYR M 63 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 44 through 45 601 hydrogen bonds defined for protein. 1653 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: 1.84 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3371 1.33 - 1.46: 2787 1.46 - 1.58: 5870 1.58 - 1.70: 0 1.70 - 1.83: 89 Bond restraints: 12117 Sorted by residual: bond pdb=" CAI Y01 B1702 " pdb=" CAK Y01 B1702 " ideal model delta sigma weight residual 1.492 1.405 0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" C1 NAG G1702 " pdb=" O5 NAG G1702 " ideal model delta sigma weight residual 1.406 1.466 -0.060 2.00e-02 2.50e+03 9.02e+00 bond pdb=" CAI Y01 B1702 " pdb=" CAZ Y01 B1702 " ideal model delta sigma weight residual 1.332 1.382 -0.050 2.00e-02 2.50e+03 6.14e+00 bond pdb=" C1 NAG B1701 " pdb=" O5 NAG B1701 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.35e+00 bond pdb=" CAY Y01 B1702 " pdb=" OAG Y01 B1702 " ideal model delta sigma weight residual 1.207 1.252 -0.045 2.00e-02 2.50e+03 5.00e+00 ... (remaining 12112 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 16131 2.23 - 4.45: 268 4.45 - 6.68: 27 6.68 - 8.91: 6 8.91 - 11.14: 4 Bond angle restraints: 16436 Sorted by residual: angle pdb=" CA GLN E 60 " pdb=" CB GLN E 60 " pdb=" CG GLN E 60 " ideal model delta sigma weight residual 114.10 123.21 -9.11 2.00e+00 2.50e-01 2.08e+01 angle pdb=" C GLY B 107 " pdb=" N GLN B 108 " pdb=" CA GLN B 108 " ideal model delta sigma weight residual 121.54 129.05 -7.51 1.91e+00 2.74e-01 1.55e+01 angle pdb=" CAM Y01 B1702 " pdb=" CAY Y01 B1702 " pdb=" OAW Y01 B1702 " ideal model delta sigma weight residual 111.19 122.33 -11.14 3.00e+00 1.11e-01 1.38e+01 angle pdb=" OAG Y01 B1702 " pdb=" CAY Y01 B1702 " pdb=" OAW Y01 B1702 " ideal model delta sigma weight residual 123.38 112.86 10.52 3.00e+00 1.11e-01 1.23e+01 angle pdb=" CAV Y01 B1702 " pdb=" CAZ Y01 B1702 " pdb=" CBH Y01 B1702 " ideal model delta sigma weight residual 116.96 126.79 -9.83 3.00e+00 1.11e-01 1.07e+01 ... (remaining 16431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.14: 6324 16.14 - 32.27: 604 32.27 - 48.41: 151 48.41 - 64.54: 30 64.54 - 80.68: 15 Dihedral angle restraints: 7124 sinusoidal: 2878 harmonic: 4246 Sorted by residual: dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 122 " pdb=" CB CYS E 122 " ideal model delta sinusoidal sigma weight residual 93.00 42.75 50.25 1 1.00e+01 1.00e-02 3.46e+01 dihedral pdb=" CB CYS Z 32 " pdb=" SG CYS Z 32 " pdb=" SG CYS Y 32 " pdb=" CB CYS Y 32 " ideal model delta sinusoidal sigma weight residual 93.00 142.21 -49.21 1 1.00e+01 1.00e-02 3.33e+01 dihedral pdb=" CA GLY B 107 " pdb=" C GLY B 107 " pdb=" N GLN B 108 " pdb=" CA GLN B 108 " ideal model delta harmonic sigma weight residual 180.00 153.01 26.99 0 5.00e+00 4.00e-02 2.91e+01 ... (remaining 7121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 1788 0.114 - 0.227: 47 0.227 - 0.341: 7 0.341 - 0.454: 1 0.454 - 0.568: 1 Chirality restraints: 1844 Sorted by residual: chirality pdb=" C1 NAG A1703 " pdb=" ND2 ASN A 22 " pdb=" C2 NAG A1703 " pdb=" O5 NAG A1703 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.07e+00 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN A 146 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" C1 NAG G1701 " pdb=" ND2 ASN G 52 " pdb=" C2 NAG G1701 " pdb=" O5 NAG G1701 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.51e+00 ... (remaining 1841 not shown) Planarity restraints: 2090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU N 154 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.85e+00 pdb=" C GLU N 154 " 0.048 2.00e-02 2.50e+03 pdb=" O GLU N 154 " -0.018 2.00e-02 2.50e+03 pdb=" N GLN N 155 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 55 " 0.011 2.00e-02 2.50e+03 1.54e-02 5.93e+00 pdb=" CG TRP G 55 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP G 55 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP G 55 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP G 55 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP G 55 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP G 55 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 55 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 55 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP G 55 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA N 153 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.71e+00 pdb=" C ALA N 153 " 0.041 2.00e-02 2.50e+03 pdb=" O ALA N 153 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU N 154 " -0.014 2.00e-02 2.50e+03 ... (remaining 2087 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 513 2.72 - 3.27: 11108 3.27 - 3.81: 18179 3.81 - 4.36: 21618 4.36 - 4.90: 39023 Nonbonded interactions: 90441 Sorted by model distance: nonbonded pdb=" NZ LYS N 66 " pdb=" O TYR P 3 " model vdw 2.176 3.120 nonbonded pdb=" O LYS E 73 " pdb=" NZ LYS E 85 " model vdw 2.202 3.120 nonbonded pdb=" NH1 ARG A 234 " pdb=" OD2 ASP Y 36 " model vdw 2.204 3.120 nonbonded pdb=" OG1 THR G 66 " pdb=" OD1 ASP G 68 " model vdw 2.241 3.040 nonbonded pdb=" OG SER Z 23 " pdb=" OE1 GLN D 94 " model vdw 2.265 3.040 ... (remaining 90436 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'E' selection = (chain 'F' and resid 33 through 155) } ncs_group { reference = chain 'L' selection = chain 'T' } ncs_group { reference = chain 'Y' selection = (chain 'Z' and resid 25 through 55) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.680 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 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 0.087 12147 Z= 0.204 Angle : 0.773 21.962 16509 Z= 0.366 Chirality : 0.051 0.568 1844 Planarity : 0.004 0.036 2081 Dihedral : 13.893 80.678 4341 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.36 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: 0.26 (0.23), residues: 1437 helix: 2.28 (0.28), residues: 337 sheet: 0.72 (0.25), residues: 449 loop : -1.43 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 102 TYR 0.020 0.002 TYR M 67 PHE 0.016 0.002 PHE D 22 TRP 0.039 0.002 TRP G 55 HIS 0.003 0.001 HIS N 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 (12117) covalent geometry : angle 0.69825 / 0.35 (16436) SS BOND : bond 0.00537 / 0.31 ( 17) SS BOND : angle 1.35154 / 0.96 ( 34) hydrogen bonds : bond 0.12297 / 7.65 ( 548) hydrogen bonds : angle 5.74394 / 3.97 ( 1653) link_BETA1-4 : bond 0.00250 / 0.13 ( 4) link_BETA1-4 : angle 1.68511 / 1.21 ( 12) link_NAG-ASN : bond 0.01591 / 1.08 ( 9) link_NAG-ASN : angle 8.06606 / 5.96 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.8682 (tp) cc_final: 0.8482 (tp) REVERT: F 123 MET cc_start: 0.8081 (ppp) cc_final: 0.7685 (ppp) REVERT: G 55 TRP cc_start: 0.7607 (m100) cc_final: 0.7356 (m100) REVERT: E 65 ASN cc_start: 0.7551 (m-40) cc_final: 0.7250 (m-40) REVERT: E 66 ILE cc_start: 0.7723 (tp) cc_final: 0.7520 (tp) REVERT: E 92 GLN cc_start: 0.8343 (tp-100) cc_final: 0.7918 (tp-100) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.0895 time to fit residues: 27.5724 Evaluate side-chains 179 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 108 GLN F 65 ASN N 192 HIS M 31 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.163191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.108587 restraints weight = 17796.727| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.50 r_work: 0.3293 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12147 Z= 0.221 Angle : 0.739 20.229 16509 Z= 0.364 Chirality : 0.049 0.501 1844 Planarity : 0.004 0.053 2081 Dihedral : 5.566 57.260 1597 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.36 % Favored : 94.57 % Rotamer: Outliers : 0.94 % Allowed : 7.57 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: 0.33 (0.23), residues: 1437 helix: 2.35 (0.28), residues: 339 sheet: 0.73 (0.25), residues: 453 loop : -1.40 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 57 TYR 0.020 0.002 TYR G 34 PHE 0.020 0.002 PHE B 28 TRP 0.019 0.002 TRP G 55 HIS 0.005 0.001 HIS B 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.22 (12117) covalent geometry : angle 0.67895 / 0.35 (16436) SS BOND : bond 0.00553 / 0.31 ( 17) SS BOND : angle 1.39132 / 1.03 ( 34) hydrogen bonds : bond 0.04899 / 3.22 ( 548) hydrogen bonds : angle 4.85647 / 3.34 ( 1653) link_BETA1-4 : bond 0.00324 / 0.16 ( 4) link_BETA1-4 : angle 1.75772 / 1.44 ( 12) link_NAG-ASN : bond 0.01061 / 0.59 ( 9) link_NAG-ASN : angle 7.01633 / 5.22 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 192 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 GLN cc_start: 0.7418 (mp10) cc_final: 0.7185 (mp10) REVERT: B 27 ASP cc_start: 0.7366 (t0) cc_final: 0.7160 (t0) REVERT: B 274 TYR cc_start: 0.8435 (t80) cc_final: 0.8181 (t80) REVERT: F 123 MET cc_start: 0.8260 (ppp) cc_final: 0.7703 (ppp) REVERT: G 30 LEU cc_start: 0.7114 (mp) cc_final: 0.6829 (pp) REVERT: G 55 TRP cc_start: 0.7955 (m100) cc_final: 0.7701 (m100) REVERT: G 86 GLN cc_start: 0.7794 (mp10) cc_final: 0.7570 (mm-40) REVERT: E 66 ILE cc_start: 0.7870 (tp) cc_final: 0.7662 (tp) REVERT: E 85 LYS cc_start: 0.9098 (pttt) cc_final: 0.8780 (pttm) REVERT: E 92 GLN cc_start: 0.8573 (tp-100) cc_final: 0.8075 (tp-100) outliers start: 12 outliers final: 9 residues processed: 195 average time/residue: 0.0883 time to fit residues: 26.0764 Evaluate side-chains 188 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 179 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain M residue 50 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 56 optimal weight: 6.9990 chunk 129 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 108 optimal weight: 0.4980 chunk 17 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 chunk 134 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 3 GLN N 192 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.165860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.112910 restraints weight = 18072.864| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.76 r_work: 0.3276 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12147 Z= 0.143 Angle : 0.665 19.656 16509 Z= 0.328 Chirality : 0.046 0.438 1844 Planarity : 0.004 0.056 2081 Dihedral : 5.268 55.791 1597 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.38 % Favored : 95.55 % Rotamer: Outliers : 1.17 % Allowed : 10.62 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: 0.46 (0.23), residues: 1437 helix: 2.49 (0.28), residues: 339 sheet: 0.73 (0.25), residues: 462 loop : -1.30 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 72 TYR 0.018 0.001 TYR F 99 PHE 0.012 0.001 PHE M 30 TRP 0.015 0.001 TRP D 43 HIS 0.003 0.001 HIS N 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (12117) covalent geometry : angle 0.61007 / 0.32 (16436) SS BOND : bond 0.00512 / 0.32 ( 17) SS BOND : angle 1.12686 / 0.81 ( 34) hydrogen bonds : bond 0.04341 / 2.85 ( 548) hydrogen bonds : angle 4.59991 / 3.15 ( 1653) link_BETA1-4 : bond 0.00278 / 0.14 ( 4) link_BETA1-4 : angle 1.54034 / 1.15 ( 12) link_NAG-ASN : bond 0.01059 / 0.58 ( 9) link_NAG-ASN : angle 6.43618 / 4.82 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 185 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 ASP cc_start: 0.7425 (t0) cc_final: 0.7184 (t0) REVERT: B 274 TYR cc_start: 0.8488 (t80) cc_final: 0.8268 (t80) REVERT: E 66 ILE cc_start: 0.7917 (tp) cc_final: 0.7646 (tp) REVERT: E 85 LYS cc_start: 0.9064 (pttt) cc_final: 0.8759 (pttm) REVERT: E 92 GLN cc_start: 0.8569 (tp-100) cc_final: 0.8094 (tp-100) REVERT: N 223 ASP cc_start: 0.8346 (m-30) cc_final: 0.8132 (p0) outliers start: 15 outliers final: 11 residues processed: 191 average time/residue: 0.0939 time to fit residues: 26.9809 Evaluate side-chains 191 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 180 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain Y residue 26 LEU Chi-restraints excluded: chain D residue 73 CYS Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 216 THR Chi-restraints excluded: chain N residue 230 LEU Chi-restraints excluded: chain M residue 50 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 89 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 192 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.163943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.107089 restraints weight = 18162.310| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 3.02 r_work: 0.3218 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12147 Z= 0.222 Angle : 0.713 18.929 16509 Z= 0.351 Chirality : 0.048 0.480 1844 Planarity : 0.004 0.060 2081 Dihedral : 5.378 53.840 1597 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.22 % Favored : 94.71 % Rotamer: Outliers : 2.42 % Allowed : 11.48 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: 0.41 (0.23), residues: 1437 helix: 2.56 (0.27), residues: 333 sheet: 0.64 (0.25), residues: 459 loop : -1.30 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 72 TYR 0.018 0.002 TYR G 34 PHE 0.020 0.002 PHE M 30 TRP 0.036 0.002 TRP G 55 HIS 0.005 0.001 HIS N 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.22 (12117) covalent geometry : angle 0.66131 / 0.34 (16436) SS BOND : bond 0.00538 / 0.28 ( 17) SS BOND : angle 1.48192 / 1.09 ( 34) hydrogen bonds : bond 0.04712 / 3.11 ( 548) hydrogen bonds : angle 4.67370 / 3.19 ( 1653) link_BETA1-4 : bond 0.00335 / 0.17 ( 4) link_BETA1-4 : angle 1.62083 / 1.30 ( 12) link_NAG-ASN : bond 0.01002 / 0.55 ( 9) link_NAG-ASN : angle 6.35529 / 4.74 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 182 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 GLN cc_start: 0.7529 (mp10) cc_final: 0.7320 (mp10) REVERT: B 27 ASP cc_start: 0.7556 (t0) cc_final: 0.7322 (t0) REVERT: B 165 LYS cc_start: 0.8401 (mttt) cc_final: 0.8137 (mtpt) REVERT: G 30 LEU cc_start: 0.7204 (mp) cc_final: 0.6941 (pp) REVERT: G 86 GLN cc_start: 0.7746 (mm-40) cc_final: 0.6838 (mm-40) REVERT: E 85 LYS cc_start: 0.9043 (pttt) cc_final: 0.8742 (pttm) REVERT: E 92 GLN cc_start: 0.8595 (tp-100) cc_final: 0.8044 (tp-100) REVERT: N 223 ASP cc_start: 0.8436 (m-30) cc_final: 0.8139 (p0) outliers start: 31 outliers final: 22 residues processed: 201 average time/residue: 0.0998 time to fit residues: 30.0250 Evaluate side-chains 201 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain Y residue 26 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 73 CYS Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain F residue 98 CYS Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 194 VAL Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 216 THR Chi-restraints excluded: chain N residue 230 LEU Chi-restraints excluded: chain M residue 50 GLU Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 59 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 102 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 123 optimal weight: 9.9990 chunk 78 optimal weight: 0.0570 chunk 2 optimal weight: 0.8980 chunk 131 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 6 GLN N 192 HIS N 260 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.165415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.109999 restraints weight = 18082.786| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.88 r_work: 0.3274 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12147 Z= 0.139 Angle : 0.663 18.332 16509 Z= 0.325 Chirality : 0.046 0.464 1844 Planarity : 0.004 0.062 2081 Dihedral : 5.164 50.449 1597 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.11 % Favored : 95.82 % Rotamer: Outliers : 1.95 % Allowed : 13.58 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: 0.47 (0.22), residues: 1437 helix: 2.58 (0.27), residues: 340 sheet: 0.72 (0.25), residues: 453 loop : -1.31 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 72 TYR 0.036 0.001 TYR E 99 PHE 0.011 0.001 PHE M 30 TRP 0.030 0.001 TRP G 55 HIS 0.003 0.001 HIS N 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (12117) covalent geometry : angle 0.61530 / 0.31 (16436) SS BOND : bond 0.00461 / 0.28 ( 17) SS BOND : angle 1.42249 / 1.00 ( 34) hydrogen bonds : bond 0.04160 / 2.74 ( 548) hydrogen bonds : angle 4.47184 / 3.05 ( 1653) link_BETA1-4 : bond 0.00291 / 0.15 ( 4) link_BETA1-4 : angle 1.49284 / 1.12 ( 12) link_NAG-ASN : bond 0.01000 / 0.55 ( 9) link_NAG-ASN : angle 5.87568 / 4.41 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8120 (pm20) REVERT: A 244 ASN cc_start: 0.5915 (m-40) cc_final: 0.5532 (t0) REVERT: G 86 GLN cc_start: 0.7675 (mm-40) cc_final: 0.6892 (mm-40) REVERT: E 85 LYS cc_start: 0.9020 (pttt) cc_final: 0.8731 (pttm) REVERT: E 92 GLN cc_start: 0.8519 (tp-100) cc_final: 0.7980 (tp-100) REVERT: N 223 ASP cc_start: 0.8572 (m-30) cc_final: 0.8240 (p0) outliers start: 25 outliers final: 20 residues processed: 198 average time/residue: 0.0887 time to fit residues: 26.7758 Evaluate side-chains 197 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 176 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain Y residue 26 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 73 CYS Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 98 CYS Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 191 HIS Chi-restraints excluded: chain N residue 194 VAL Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 230 LEU Chi-restraints excluded: chain N residue 261 VAL Chi-restraints excluded: chain M residue 50 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 45 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 192 HIS N 260 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.162221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.109068 restraints weight = 18143.983| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.81 r_work: 0.3239 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 12147 Z= 0.258 Angle : 0.759 17.937 16509 Z= 0.371 Chirality : 0.049 0.507 1844 Planarity : 0.004 0.065 2081 Dihedral : 5.472 52.792 1597 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.36 % Favored : 94.57 % Rotamer: Outliers : 3.04 % Allowed : 13.97 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: 0.34 (0.23), residues: 1437 helix: 2.47 (0.27), residues: 340 sheet: 0.62 (0.25), residues: 445 loop : -1.34 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 72 TYR 0.023 0.002 TYR E 99 PHE 0.026 0.002 PHE B 28 TRP 0.035 0.002 TRP G 55 HIS 0.005 0.001 HIS B 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00623 / 0.26 (12117) covalent geometry : angle 0.70709 / 0.36 (16436) SS BOND : bond 0.00612 / 0.34 ( 17) SS BOND : angle 1.76681 / 1.23 ( 34) hydrogen bonds : bond 0.04953 / 3.27 ( 548) hydrogen bonds : angle 4.68582 / 3.20 ( 1653) link_BETA1-4 : bond 0.00326 / 0.16 ( 4) link_BETA1-4 : angle 1.72935 / 1.41 ( 12) link_NAG-ASN : bond 0.01115 / 0.69 ( 9) link_NAG-ASN : angle 6.49820 / 4.78 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 177 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.7722 (OUTLIER) cc_final: 0.7497 (tm130) REVERT: A 55 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8108 (pm20) REVERT: A 244 ASN cc_start: 0.6138 (m-40) cc_final: 0.5607 (t0) REVERT: A 247 MET cc_start: 0.7172 (OUTLIER) cc_final: 0.6925 (mmp) REVERT: F 82 LEU cc_start: 0.7735 (mt) cc_final: 0.7495 (mt) REVERT: F 128 MET cc_start: 0.7804 (tmm) cc_final: 0.7461 (tpp) REVERT: G 86 GLN cc_start: 0.7806 (mm-40) cc_final: 0.7259 (mm-40) REVERT: E 85 LYS cc_start: 0.9043 (pttt) cc_final: 0.8776 (pttm) REVERT: E 92 GLN cc_start: 0.8564 (tp-100) cc_final: 0.8164 (tp-100) REVERT: N 223 ASP cc_start: 0.8412 (m-30) cc_final: 0.8164 (p0) outliers start: 39 outliers final: 30 residues processed: 198 average time/residue: 0.0910 time to fit residues: 27.2615 Evaluate side-chains 207 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 174 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain Y residue 26 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 73 CYS Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 98 CYS Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 189 MET Chi-restraints excluded: chain N residue 194 VAL Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 216 THR Chi-restraints excluded: chain N residue 230 LEU Chi-restraints excluded: chain M residue 50 GLU Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 59 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 102 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 131 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 123 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 110 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 192 HIS N 260 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.164502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.112500 restraints weight = 18086.432| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.68 r_work: 0.3279 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12147 Z= 0.151 Angle : 0.681 17.390 16509 Z= 0.334 Chirality : 0.047 0.475 1844 Planarity : 0.004 0.066 2081 Dihedral : 5.226 53.097 1597 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.38 % Favored : 95.55 % Rotamer: Outliers : 2.58 % Allowed : 15.38 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: 0.46 (0.23), residues: 1437 helix: 2.62 (0.27), residues: 338 sheet: 0.74 (0.25), residues: 445 loop : -1.33 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 102 TYR 0.024 0.001 TYR E 99 PHE 0.012 0.001 PHE B 151 TRP 0.038 0.002 TRP G 55 HIS 0.003 0.001 HIS N 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (12117) covalent geometry : angle 0.63653 / 0.32 (16436) SS BOND : bond 0.00482 / 0.28 ( 17) SS BOND : angle 1.40456 / 0.97 ( 34) hydrogen bonds : bond 0.04272 / 2.82 ( 548) hydrogen bonds : angle 4.46103 / 3.05 ( 1653) link_BETA1-4 : bond 0.00268 / 0.13 ( 4) link_BETA1-4 : angle 1.56758 / 1.17 ( 12) link_NAG-ASN : bond 0.00965 / 0.53 ( 9) link_NAG-ASN : angle 5.75078 / 4.26 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 182 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8075 (pm20) REVERT: B 274 TYR cc_start: 0.8073 (t80) cc_final: 0.7755 (t80) REVERT: F 82 LEU cc_start: 0.7646 (mt) cc_final: 0.7351 (mt) REVERT: G 86 GLN cc_start: 0.7807 (mm-40) cc_final: 0.7072 (mm-40) REVERT: E 85 LYS cc_start: 0.9024 (pttt) cc_final: 0.8756 (pttm) REVERT: E 92 GLN cc_start: 0.8532 (tp-100) cc_final: 0.7989 (tp-100) REVERT: E 115 ARG cc_start: 0.8337 (ttm-80) cc_final: 0.8121 (ttm-80) REVERT: N 223 ASP cc_start: 0.8331 (m-30) cc_final: 0.8109 (p0) outliers start: 33 outliers final: 29 residues processed: 199 average time/residue: 0.0780 time to fit residues: 23.5589 Evaluate side-chains 209 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 179 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain Z residue 23 SER Chi-restraints excluded: chain Y residue 26 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 73 CYS Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 98 CYS Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 189 MET Chi-restraints excluded: chain N residue 191 HIS Chi-restraints excluded: chain N residue 194 VAL Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 216 THR Chi-restraints excluded: chain N residue 230 LEU Chi-restraints excluded: chain N residue 261 VAL Chi-restraints excluded: chain M residue 50 GLU Chi-restraints excluded: chain M residue 57 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 116 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 33 GLN G 105 GLN N 192 HIS N 260 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.162656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.109904 restraints weight = 18058.659| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.73 r_work: 0.3240 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12147 Z= 0.227 Angle : 0.735 16.988 16509 Z= 0.360 Chirality : 0.048 0.488 1844 Planarity : 0.004 0.068 2081 Dihedral : 5.387 54.324 1597 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.29 % Favored : 94.64 % Rotamer: Outliers : 2.81 % Allowed : 15.93 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: 0.34 (0.23), residues: 1437 helix: 2.56 (0.27), residues: 338 sheet: 0.62 (0.25), residues: 454 loop : -1.41 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 72 TYR 0.021 0.002 TYR E 99 PHE 0.020 0.002 PHE M 30 TRP 0.039 0.002 TRP G 55 HIS 0.005 0.001 HIS N 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.23 (12117) covalent geometry : angle 0.68834 / 0.35 (16436) SS BOND : bond 0.00561 / 0.31 ( 17) SS BOND : angle 1.64052 / 1.14 ( 34) hydrogen bonds : bond 0.04706 / 3.11 ( 548) hydrogen bonds : angle 4.57989 / 3.13 ( 1653) link_BETA1-4 : bond 0.00299 / 0.15 ( 4) link_BETA1-4 : angle 1.71412 / 1.35 ( 12) link_NAG-ASN : bond 0.01215 / 0.80 ( 9) link_NAG-ASN : angle 6.13269 / 4.53 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 182 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8127 (pm20) REVERT: A 244 ASN cc_start: 0.5873 (t0) cc_final: 0.5619 (t0) REVERT: B 274 TYR cc_start: 0.8289 (t80) cc_final: 0.8071 (t80) REVERT: F 128 MET cc_start: 0.7800 (tmm) cc_final: 0.7464 (tpp) REVERT: G 86 GLN cc_start: 0.7711 (mm-40) cc_final: 0.7100 (mm-40) REVERT: E 64 LYS cc_start: 0.7587 (tttt) cc_final: 0.7259 (tptp) REVERT: E 85 LYS cc_start: 0.9024 (pttt) cc_final: 0.8753 (pttm) REVERT: E 92 GLN cc_start: 0.8566 (tp-100) cc_final: 0.8151 (tp-100) REVERT: E 115 ARG cc_start: 0.8213 (ttm-80) cc_final: 0.7933 (ttm110) REVERT: N 223 ASP cc_start: 0.8352 (m-30) cc_final: 0.8147 (p0) outliers start: 36 outliers final: 29 residues processed: 202 average time/residue: 0.0882 time to fit residues: 26.7446 Evaluate side-chains 209 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 179 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain Z residue 23 SER Chi-restraints excluded: chain Y residue 26 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 73 CYS Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 98 CYS Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 189 MET Chi-restraints excluded: chain N residue 194 VAL Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 216 THR Chi-restraints excluded: chain N residue 230 LEU Chi-restraints excluded: chain M residue 50 GLU Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 89 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 125 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 134 optimal weight: 0.3980 chunk 99 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 33 GLN G 105 GLN E 65 ASN N 192 HIS N 260 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.163085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.106863 restraints weight = 17897.391| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.96 r_work: 0.3248 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12147 Z= 0.194 Angle : 0.708 16.683 16509 Z= 0.349 Chirality : 0.048 0.480 1844 Planarity : 0.004 0.070 2081 Dihedral : 5.337 54.441 1597 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.36 % Favored : 94.57 % Rotamer: Outliers : 2.50 % Allowed : 16.24 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: 0.39 (0.22), residues: 1437 helix: 2.60 (0.27), residues: 338 sheet: 0.63 (0.25), residues: 457 loop : -1.37 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 72 TYR 0.021 0.002 TYR E 99 PHE 0.016 0.002 PHE M 30 TRP 0.027 0.002 TRP G 55 HIS 0.004 0.001 HIS N 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.19 (12117) covalent geometry : angle 0.66996 / 0.34 (16436) SS BOND : bond 0.00533 / 0.30 ( 17) SS BOND : angle 1.50609 / 1.05 ( 34) hydrogen bonds : bond 0.04516 / 2.99 ( 548) hydrogen bonds : angle 4.52417 / 3.09 ( 1653) link_BETA1-4 : bond 0.00274 / 0.14 ( 4) link_BETA1-4 : angle 1.68742 / 1.28 ( 12) link_NAG-ASN : bond 0.00912 / 0.50 ( 9) link_NAG-ASN : angle 5.42924 / 4.05 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 180 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8103 (pm20) REVERT: A 244 ASN cc_start: 0.5888 (t0) cc_final: 0.5616 (t0) REVERT: B 117 ASP cc_start: 0.8537 (t70) cc_final: 0.8291 (t0) REVERT: B 119 ASN cc_start: 0.8815 (t0) cc_final: 0.8437 (t0) REVERT: B 274 TYR cc_start: 0.8319 (t80) cc_final: 0.8071 (t80) REVERT: F 106 GLU cc_start: 0.6784 (pm20) cc_final: 0.6222 (pt0) REVERT: F 107 ASP cc_start: 0.7016 (t70) cc_final: 0.6779 (t0) REVERT: F 128 MET cc_start: 0.7775 (tmm) cc_final: 0.7433 (tpp) REVERT: G 86 GLN cc_start: 0.7701 (mm-40) cc_final: 0.7263 (mm-40) REVERT: E 85 LYS cc_start: 0.9021 (pttt) cc_final: 0.8746 (pttm) REVERT: E 92 GLN cc_start: 0.8501 (tp-100) cc_final: 0.7965 (tp-100) REVERT: E 115 ARG cc_start: 0.8230 (ttm-80) cc_final: 0.7977 (ttm110) REVERT: N 223 ASP cc_start: 0.8424 (m-30) cc_final: 0.8184 (p0) REVERT: M 10 TYR cc_start: 0.8725 (p90) cc_final: 0.8347 (p90) outliers start: 32 outliers final: 27 residues processed: 198 average time/residue: 0.0830 time to fit residues: 24.7869 Evaluate side-chains 204 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain Z residue 23 SER Chi-restraints excluded: chain Y residue 26 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 73 CYS Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 98 CYS Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 189 MET Chi-restraints excluded: chain N residue 194 VAL Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 216 THR Chi-restraints excluded: chain N residue 230 LEU Chi-restraints excluded: chain M residue 50 GLU Chi-restraints excluded: chain M residue 57 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 48 optimal weight: 0.9990 chunk 66 optimal weight: 0.0970 chunk 26 optimal weight: 2.9990 chunk 31 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 7 optimal weight: 0.1980 chunk 72 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 33 GLN G 105 GLN N 192 HIS N 260 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.164359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.107842 restraints weight = 18049.657| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.62 r_work: 0.3272 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12147 Z= 0.145 Angle : 0.688 16.374 16509 Z= 0.338 Chirality : 0.047 0.471 1844 Planarity : 0.004 0.071 2081 Dihedral : 5.216 54.482 1597 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.01 % Favored : 94.92 % Rotamer: Outliers : 2.26 % Allowed : 16.55 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: 0.49 (0.22), residues: 1437 helix: 2.64 (0.27), residues: 338 sheet: 0.74 (0.25), residues: 450 loop : -1.30 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 102 TYR 0.022 0.001 TYR E 99 PHE 0.012 0.001 PHE M 30 TRP 0.048 0.002 TRP G 55 HIS 0.003 0.001 HIS N 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (12117) covalent geometry : angle 0.64594 / 0.33 (16436) SS BOND : bond 0.00462 / 0.26 ( 17) SS BOND : angle 1.32507 / 0.92 ( 34) hydrogen bonds : bond 0.04160 / 2.76 ( 548) hydrogen bonds : angle 4.41415 / 3.02 ( 1653) link_BETA1-4 : bond 0.00291 / 0.15 ( 4) link_BETA1-4 : angle 1.62164 / 1.19 ( 12) link_NAG-ASN : bond 0.01132 / 0.72 ( 9) link_NAG-ASN : angle 5.69401 / 4.25 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 183 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8110 (pm20) REVERT: A 244 ASN cc_start: 0.5883 (t0) cc_final: 0.5580 (t0) REVERT: B 117 ASP cc_start: 0.8476 (t70) cc_final: 0.8237 (t0) REVERT: B 119 ASN cc_start: 0.8776 (t0) cc_final: 0.8396 (t0) REVERT: F 82 LEU cc_start: 0.7410 (mt) cc_final: 0.7008 (mp) REVERT: F 106 GLU cc_start: 0.6724 (pm20) cc_final: 0.6241 (pt0) REVERT: F 107 ASP cc_start: 0.7074 (t70) cc_final: 0.6856 (t0) REVERT: F 128 MET cc_start: 0.7791 (tmm) cc_final: 0.7480 (tpp) REVERT: G 86 GLN cc_start: 0.7507 (mm-40) cc_final: 0.6900 (mm-40) REVERT: E 85 LYS cc_start: 0.9004 (pttt) cc_final: 0.8733 (pttm) REVERT: E 92 GLN cc_start: 0.8479 (tp-100) cc_final: 0.7941 (tp-100) REVERT: E 115 ARG cc_start: 0.8227 (ttm-80) cc_final: 0.7929 (ttm110) REVERT: N 223 ASP cc_start: 0.8467 (m-30) cc_final: 0.8214 (p0) outliers start: 29 outliers final: 27 residues processed: 198 average time/residue: 0.0839 time to fit residues: 25.4218 Evaluate side-chains 208 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 180 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain Z residue 23 SER Chi-restraints excluded: chain Y residue 26 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 73 CYS Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 98 CYS Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 189 MET Chi-restraints excluded: chain N residue 194 VAL Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 216 THR Chi-restraints excluded: chain N residue 230 LEU Chi-restraints excluded: chain N residue 261 VAL Chi-restraints excluded: chain M residue 50 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 86 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 137 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 192 HIS N 260 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.164158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.112581 restraints weight = 18007.406| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.91 r_work: 0.3273 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12147 Z= 0.166 Angle : 0.689 16.155 16509 Z= 0.340 Chirality : 0.048 0.467 1844 Planarity : 0.004 0.071 2081 Dihedral : 5.204 54.782 1597 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.08 % Favored : 94.85 % Rotamer: Outliers : 2.19 % Allowed : 16.78 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: 0.48 (0.22), residues: 1437 helix: 2.55 (0.27), residues: 341 sheet: 0.75 (0.25), residues: 450 loop : -1.30 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Y 52 TYR 0.021 0.001 TYR E 99 PHE 0.015 0.001 PHE M 30 TRP 0.027 0.002 TRP G 55 HIS 0.003 0.001 HIS N 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (12117) covalent geometry : angle 0.65389 / 0.33 (16436) SS BOND : bond 0.00485 / 0.27 ( 17) SS BOND : angle 1.40373 / 0.98 ( 34) hydrogen bonds : bond 0.04251 / 2.82 ( 548) hydrogen bonds : angle 4.41553 / 3.01 ( 1653) link_BETA1-4 : bond 0.00285 / 0.14 ( 4) link_BETA1-4 : angle 1.63144 / 1.22 ( 12) link_NAG-ASN : bond 0.00885 / 0.48 ( 9) link_NAG-ASN : angle 5.11654 / 3.86 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3726.92 seconds wall clock time: 64 minutes 21.89 seconds (3861.89 seconds total)