Starting phenix.real_space_refine on Wed Apr 8 20:53:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z16_14442/04_2026/7z16_14442_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z16_14442/04_2026/7z16_14442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7z16_14442/04_2026/7z16_14442_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z16_14442/04_2026/7z16_14442_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z16_14442/04_2026/7z16_14442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z16_14442/04_2026/7z16_14442.map" } resolution = 2.09 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= 0.003 sd= 0.127 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Zn 4 6.06 5 P 8 5.49 5 Mg 2 5.21 5 S 96 5.16 5 C 14074 2.51 5 N 4006 2.21 5 O 4260 1.98 5 H 22240 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 44690 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2187 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "B" Number of atoms: 2956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 2956 Classifications: {'peptide': 193} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 178} Chain: "C" Number of atoms: 5395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 5395 Classifications: {'peptide': 353} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 332} Chain: "D" Number of atoms: 4357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 4357 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 20, 'TRANS': 257} Chain: "E" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2187 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "F" Number of atoms: 2956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 2956 Classifications: {'peptide': 193} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 178} Chain: "G" Number of atoms: 5395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 5395 Classifications: {'peptide': 353} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 332} Chain: "H" Number of atoms: 4357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 4357 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 20, 'TRANS': 257} Chain: "I" Number of atoms: 3899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 3899 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 11, 'TRANS': 238} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 3899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 3899 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 11, 'TRANS': 238} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 3503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3503 Classifications: {'peptide': 224} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 212} Chain: "L" Number of atoms: 3503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3503 Classifications: {'peptide': 224} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 212} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' ZN': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' ZN': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 9 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 9 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14336 SG CYS D 241 40.982 105.150 105.378 1.00 23.38 S ATOM 14375 SG CYS D 244 42.954 108.356 104.773 1.00 24.42 S ATOM 14695 SG CYS D 266 44.401 105.071 103.784 1.00 20.80 S ATOM 14775 SG CYS D 272 43.856 105.870 107.579 1.00 23.09 S ATOM 29231 SG CYS H 241 73.634 20.939 105.376 1.00 23.36 S ATOM 29270 SG CYS H 244 71.664 17.731 104.771 1.00 24.37 S ATOM 29590 SG CYS H 266 70.215 21.016 103.782 1.00 20.77 S ATOM 29670 SG CYS H 272 70.760 20.216 107.577 1.00 23.05 S Time building chain proxies: 7.98, per 1000 atoms: 0.18 Number of scatterers: 44690 At special positions: 0 Unit cell: (114.611, 127.028, 157.591, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 S 96 16.00 P 8 15.00 Mg 2 11.99 O 4260 8.00 N 4006 7.00 C 14074 6.00 H 22240 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.00 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C1000 " pdb="ZN ZN C1000 " - pdb=" NE2 HIS C 328 " pdb="ZN ZN C1000 " - pdb=" NE2 HIS C 333 " pdb=" ZN D1000 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 241 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 244 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 266 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 272 " pdb=" ZN G1000 " pdb="ZN ZN G1000 " - pdb=" NE2 HIS G 328 " pdb="ZN ZN G1000 " - pdb=" NE2 HIS G 333 " pdb=" ZN H1000 " pdb="ZN ZN H1000 " - pdb=" SG CYS H 241 " pdb="ZN ZN H1000 " - pdb=" SG CYS H 266 " pdb="ZN ZN H1000 " - pdb=" SG CYS H 244 " pdb="ZN ZN H1000 " - pdb=" SG CYS H 272 " Number of angles added : 12 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5356 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 26 sheets defined 46.3% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 3 through 18 Processing helix chain 'A' and resid 19 through 31 Processing helix chain 'A' and resid 54 through 56 No H-bonds generated for 'chain 'A' and resid 54 through 56' Processing helix chain 'A' and resid 88 through 103 Processing helix chain 'A' and resid 104 through 115 removed outlier: 4.422A pdb=" N GLN A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ASN A 110 " --> pdb=" O ARG A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 135 Processing helix chain 'B' and resid 9 through 27 Processing helix chain 'B' and resid 45 through 56 Processing helix chain 'B' and resid 66 through 69 Processing helix chain 'B' and resid 70 through 81 Processing helix chain 'B' and resid 88 through 92 Processing helix chain 'B' and resid 102 through 109 Processing helix chain 'B' and resid 116 through 120 removed outlier: 4.039A pdb=" N GLY B 120 " --> pdb=" O PRO B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 164 Processing helix chain 'C' and resid 7 through 25 Processing helix chain 'C' and resid 33 through 41 Processing helix chain 'C' and resid 41 through 53 Processing helix chain 'C' and resid 56 through 67 Processing helix chain 'C' and resid 70 through 85 removed outlier: 3.556A pdb=" N THR C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU C 85 " --> pdb=" O TYR C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 99 Processing helix chain 'C' and resid 130 through 135 Processing helix chain 'C' and resid 154 through 162 Processing helix chain 'C' and resid 188 through 199 Processing helix chain 'C' and resid 200 through 213 Processing helix chain 'C' and resid 281 through 295 Processing helix chain 'C' and resid 296 through 300 Processing helix chain 'C' and resid 305 through 308 Processing helix chain 'C' and resid 309 through 316 removed outlier: 3.674A pdb=" N HIS C 316 " --> pdb=" O PHE C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 329 through 331 No H-bonds generated for 'chain 'C' and resid 329 through 331' Processing helix chain 'C' and resid 333 through 353 Processing helix chain 'D' and resid 8 through 12 removed outlier: 4.120A pdb=" N LEU D 12 " --> pdb=" O PHE D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 30 Processing helix chain 'D' and resid 49 through 60 Processing helix chain 'D' and resid 76 through 91 Processing helix chain 'D' and resid 137 through 147 removed outlier: 4.020A pdb=" N THR D 143 " --> pdb=" O THR D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 165 Processing helix chain 'D' and resid 189 through 197 Proline residue: D 194 - end of helix Processing helix chain 'D' and resid 268 through 279 Processing helix chain 'E' and resid 4 through 18 Processing helix chain 'E' and resid 19 through 31 Processing helix chain 'E' and resid 54 through 56 No H-bonds generated for 'chain 'E' and resid 54 through 56' Processing helix chain 'E' and resid 88 through 103 Processing helix chain 'E' and resid 104 through 115 removed outlier: 4.422A pdb=" N GLN E 109 " --> pdb=" O SER E 105 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ASN E 110 " --> pdb=" O ARG E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 135 Processing helix chain 'F' and resid 9 through 27 Processing helix chain 'F' and resid 45 through 56 Processing helix chain 'F' and resid 66 through 69 Processing helix chain 'F' and resid 70 through 81 Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 102 through 109 Processing helix chain 'F' and resid 116 through 120 removed outlier: 4.039A pdb=" N GLY F 120 " --> pdb=" O PRO F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 164 Processing helix chain 'G' and resid 7 through 25 Processing helix chain 'G' and resid 33 through 41 Processing helix chain 'G' and resid 41 through 53 Processing helix chain 'G' and resid 56 through 67 Processing helix chain 'G' and resid 70 through 85 removed outlier: 3.556A pdb=" N THR G 84 " --> pdb=" O ALA G 80 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU G 85 " --> pdb=" O TYR G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 99 Processing helix chain 'G' and resid 130 through 135 Processing helix chain 'G' and resid 154 through 162 Processing helix chain 'G' and resid 188 through 199 Processing helix chain 'G' and resid 200 through 213 Processing helix chain 'G' and resid 281 through 295 Processing helix chain 'G' and resid 296 through 300 Processing helix chain 'G' and resid 305 through 308 Processing helix chain 'G' and resid 309 through 316 removed outlier: 3.674A pdb=" N HIS G 316 " --> pdb=" O PHE G 312 " (cutoff:3.500A) Processing helix chain 'G' and resid 318 through 328 Processing helix chain 'G' and resid 329 through 331 No H-bonds generated for 'chain 'G' and resid 329 through 331' Processing helix chain 'G' and resid 333 through 353 Processing helix chain 'H' and resid 8 through 12 removed outlier: 4.120A pdb=" N LEU H 12 " --> pdb=" O PHE H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 30 Processing helix chain 'H' and resid 49 through 60 Processing helix chain 'H' and resid 76 through 91 Processing helix chain 'H' and resid 137 through 147 removed outlier: 4.019A pdb=" N THR H 143 " --> pdb=" O THR H 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 165 Processing helix chain 'H' and resid 189 through 197 Proline residue: H 194 - end of helix Processing helix chain 'H' and resid 268 through 279 Processing helix chain 'I' and resid 43 through 52 Processing helix chain 'I' and resid 73 through 84 Processing helix chain 'I' and resid 91 through 96 Processing helix chain 'I' and resid 101 through 113 removed outlier: 4.392A pdb=" N ARG I 109 " --> pdb=" O ASN I 105 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU I 110 " --> pdb=" O ILE I 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 132 Processing helix chain 'I' and resid 135 through 139 removed outlier: 3.628A pdb=" N ILE I 139 " --> pdb=" O ALA I 136 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 146 Processing helix chain 'I' and resid 147 through 161 Processing helix chain 'I' and resid 177 through 196 Processing helix chain 'I' and resid 205 through 213 Processing helix chain 'I' and resid 230 through 236 Processing helix chain 'I' and resid 239 through 248 Processing helix chain 'J' and resid 43 through 52 Processing helix chain 'J' and resid 73 through 84 Processing helix chain 'J' and resid 91 through 96 Processing helix chain 'J' and resid 101 through 113 removed outlier: 4.393A pdb=" N ARG J 109 " --> pdb=" O ASN J 105 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU J 110 " --> pdb=" O ILE J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 117 through 132 Processing helix chain 'J' and resid 135 through 139 removed outlier: 3.628A pdb=" N ILE J 139 " --> pdb=" O ALA J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 146 Processing helix chain 'J' and resid 147 through 161 Processing helix chain 'J' and resid 177 through 196 Processing helix chain 'J' and resid 205 through 213 Processing helix chain 'J' and resid 230 through 236 Processing helix chain 'J' and resid 239 through 248 Processing helix chain 'K' and resid 46 through 55 Processing helix chain 'K' and resid 80 through 91 Processing helix chain 'K' and resid 106 through 117 Proline residue: K 114 - end of helix Processing helix chain 'K' and resid 121 through 136 Processing helix chain 'K' and resid 139 through 143 Processing helix chain 'K' and resid 146 through 150 Processing helix chain 'K' and resid 151 through 164 Processing helix chain 'K' and resid 181 through 199 Processing helix chain 'K' and resid 208 through 216 Processing helix chain 'L' and resid 46 through 55 Processing helix chain 'L' and resid 80 through 91 Processing helix chain 'L' and resid 106 through 117 Proline residue: L 114 - end of helix Processing helix chain 'L' and resid 121 through 136 Processing helix chain 'L' and resid 139 through 143 Processing helix chain 'L' and resid 146 through 150 Processing helix chain 'L' and resid 151 through 164 Processing helix chain 'L' and resid 181 through 199 Processing helix chain 'L' and resid 208 through 216 Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 85 removed outlier: 5.338A pdb=" N PHE A 61 " --> pdb=" O ALA A 51 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA A 51 " --> pdb=" O PHE A 61 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLY A 63 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ALA A 71 " --> pdb=" O ALA A 41 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ALA A 41 " --> pdb=" O ALA A 71 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ARG A 73 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE A 39 " --> pdb=" O ARG A 73 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU C 88 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N LEU A 46 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N VAL C 90 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N GLN A 48 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 139 removed outlier: 4.441A pdb=" N GLN C 116 " --> pdb=" O VAL A 139 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 144 Processing sheet with id=AA4, first strand: chain 'B' and resid 32 through 33 removed outlier: 6.776A pdb=" N LEU B 123 " --> pdb=" O ILE B 175 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N THR B 177 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU B 125 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ALA B 95 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N GLN B 126 " --> pdb=" O ALA B 95 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR B 97 " --> pdb=" O GLN B 126 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N TRP B 63 " --> pdb=" O VAL B 96 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 147 through 149 Processing sheet with id=AA6, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AA7, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.631A pdb=" N SER C 227 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG C 104 " --> pdb=" O ILE C 225 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE C 225 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ALA C 222 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL C 256 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY C 246 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE C 234 " --> pdb=" O ASN C 244 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ASN C 244 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE C 259 " --> pdb=" O HIS C 268 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N HIS C 268 " --> pdb=" O PHE C 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 35 through 36 removed outlier: 6.370A pdb=" N ILE D 104 " --> pdb=" O ILE D 122 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N GLN D 124 " --> pdb=" O ILE D 104 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N THR D 106 " --> pdb=" O GLN D 124 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 181 through 183 Processing sheet with id=AB1, first strand: chain 'D' and resid 251 through 255 Processing sheet with id=AB2, first strand: chain 'E' and resid 79 through 85 removed outlier: 5.338A pdb=" N PHE E 61 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA E 51 " --> pdb=" O PHE E 61 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY E 63 " --> pdb=" O ILE E 49 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ALA E 71 " --> pdb=" O ALA E 41 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ALA E 41 " --> pdb=" O ALA E 71 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ARG E 73 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE E 39 " --> pdb=" O ARG E 73 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU G 88 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LEU E 46 " --> pdb=" O LEU G 88 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N VAL G 90 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLN E 48 " --> pdb=" O VAL G 90 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 138 through 139 removed outlier: 4.452A pdb=" N GLN G 116 " --> pdb=" O VAL E 139 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 32 through 33 removed outlier: 6.775A pdb=" N LEU F 123 " --> pdb=" O ILE F 175 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N THR F 177 " --> pdb=" O LEU F 123 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU F 125 " --> pdb=" O THR F 177 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ALA F 95 " --> pdb=" O ILE F 124 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N GLN F 126 " --> pdb=" O ALA F 95 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR F 97 " --> pdb=" O GLN F 126 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N TRP F 63 " --> pdb=" O VAL F 96 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 147 through 149 Processing sheet with id=AB6, first strand: chain 'G' and resid 100 through 105 removed outlier: 6.632A pdb=" N SER G 227 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG G 104 " --> pdb=" O ILE G 225 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE G 225 " --> pdb=" O ARG G 104 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ALA G 222 " --> pdb=" O VAL G 256 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL G 256 " --> pdb=" O ALA G 222 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY G 246 " --> pdb=" O VAL G 232 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE G 234 " --> pdb=" O ASN G 244 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ASN G 244 " --> pdb=" O ILE G 234 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE G 259 " --> pdb=" O HIS G 268 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N HIS G 268 " --> pdb=" O PHE G 259 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 35 through 36 removed outlier: 6.370A pdb=" N ILE H 104 " --> pdb=" O ILE H 122 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N GLN H 124 " --> pdb=" O ILE H 104 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N THR H 106 " --> pdb=" O GLN H 124 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 181 through 183 Processing sheet with id=AB9, first strand: chain 'H' and resid 251 through 255 Processing sheet with id=AC1, first strand: chain 'I' and resid 19 through 28 removed outlier: 3.611A pdb=" N ALA I 16 " --> pdb=" O LYS I 19 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N PHE I 21 " --> pdb=" O LEU I 14 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU I 14 " --> pdb=" O PHE I 21 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASP I 23 " --> pdb=" O THR I 12 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N THR I 12 " --> pdb=" O ASP I 23 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N SER I 25 " --> pdb=" O ASN I 10 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ASN I 10 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ASP I 27 " --> pdb=" O VAL I 8 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VAL I 8 " --> pdb=" O ASP I 27 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU I 11 " --> pdb=" O GLN I 59 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLN I 59 " --> pdb=" O LEU I 11 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 85 through 88 removed outlier: 6.401A pdb=" N GLY I 86 " --> pdb=" O PHE I 168 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N ASP I 170 " --> pdb=" O GLY I 86 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL I 88 " --> pdb=" O ASP I 170 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL I 167 " --> pdb=" O VAL I 200 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N VAL I 202 " --> pdb=" O VAL I 167 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N MET I 169 " --> pdb=" O VAL I 202 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU I 216 " --> pdb=" O SER I 227 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N SER I 227 " --> pdb=" O LEU I 216 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL I 218 " --> pdb=" O VAL I 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 19 through 28 removed outlier: 3.611A pdb=" N ALA J 16 " --> pdb=" O LYS J 19 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N PHE J 21 " --> pdb=" O LEU J 14 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU J 14 " --> pdb=" O PHE J 21 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASP J 23 " --> pdb=" O THR J 12 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N THR J 12 " --> pdb=" O ASP J 23 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N SER J 25 " --> pdb=" O ASN J 10 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ASN J 10 " --> pdb=" O SER J 25 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASP J 27 " --> pdb=" O VAL J 8 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N VAL J 8 " --> pdb=" O ASP J 27 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU J 11 " --> pdb=" O GLN J 59 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLN J 59 " --> pdb=" O LEU J 11 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 85 through 88 removed outlier: 6.402A pdb=" N GLY J 86 " --> pdb=" O PHE J 168 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ASP J 170 " --> pdb=" O GLY J 86 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL J 88 " --> pdb=" O ASP J 170 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL J 167 " --> pdb=" O VAL J 200 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N VAL J 202 " --> pdb=" O VAL J 167 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N MET J 169 " --> pdb=" O VAL J 202 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU J 216 " --> pdb=" O SER J 227 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N SER J 227 " --> pdb=" O LEU J 216 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL J 218 " --> pdb=" O VAL J 225 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 20 through 31 removed outlier: 6.071A pdb=" N LYS K 9 " --> pdb=" O VAL K 23 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASN K 25 " --> pdb=" O VAL K 7 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL K 7 " --> pdb=" O ASN K 25 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ALA K 27 " --> pdb=" O GLN K 5 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLN K 5 " --> pdb=" O ALA K 27 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU K 29 " --> pdb=" O ASN K 3 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASN K 3 " --> pdb=" O LEU K 29 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL K 7 " --> pdb=" O GLU K 62 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLU K 62 " --> pdb=" O VAL K 7 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 92 through 95 removed outlier: 6.568A pdb=" N GLY K 93 " --> pdb=" O LEU K 172 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ASP K 174 " --> pdb=" O GLY K 93 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL K 95 " --> pdb=" O ASP K 174 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 20 through 31 removed outlier: 6.072A pdb=" N LYS L 9 " --> pdb=" O VAL L 23 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASN L 25 " --> pdb=" O VAL L 7 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL L 7 " --> pdb=" O ASN L 25 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ALA L 27 " --> pdb=" O GLN L 5 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLN L 5 " --> pdb=" O ALA L 27 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU L 29 " --> pdb=" O ASN L 3 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASN L 3 " --> pdb=" O LEU L 29 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL L 7 " --> pdb=" O GLU L 62 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLU L 62 " --> pdb=" O VAL L 7 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 92 through 95 removed outlier: 6.568A pdb=" N GLY L 93 " --> pdb=" O LEU L 172 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ASP L 174 " --> pdb=" O GLY L 93 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL L 95 " --> pdb=" O ASP L 174 " (cutoff:3.500A) 1091 hydrogen bonds defined for protein. 3015 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: 11.09 Time building geometry restraints manager: 5.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 22224 1.02 - 1.22: 20 1.22 - 1.42: 9295 1.42 - 1.62: 13391 1.62 - 1.81: 182 Bond restraints: 45112 Sorted by residual: bond pdb=" C2' ANP I1002 " pdb=" C3' ANP I1002 " ideal model delta sigma weight residual 1.520 1.225 0.295 2.00e-02 2.50e+03 2.18e+02 bond pdb=" C2' ANP J1002 " pdb=" C3' ANP J1002 " ideal model delta sigma weight residual 1.520 1.225 0.295 2.00e-02 2.50e+03 2.17e+02 bond pdb=" C3' ANP I1002 " pdb=" O3' ANP I1002 " ideal model delta sigma weight residual 1.386 1.566 -0.180 2.00e-02 2.50e+03 8.11e+01 bond pdb=" C3' ANP J1002 " pdb=" O3' ANP J1002 " ideal model delta sigma weight residual 1.386 1.566 -0.180 2.00e-02 2.50e+03 8.10e+01 bond pdb=" C1' ANP I1002 " pdb=" C2' ANP I1002 " ideal model delta sigma weight residual 1.542 1.679 -0.137 2.00e-02 2.50e+03 4.71e+01 ... (remaining 45107 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.30: 81481 7.30 - 14.61: 27 14.61 - 21.91: 6 21.91 - 29.21: 13 29.21 - 36.52: 21 Bond angle restraints: 81548 Sorted by residual: angle pdb=" N THR F 2 " pdb=" CA THR F 2 " pdb=" HA THR F 2 " ideal model delta sigma weight residual 110.00 73.48 36.52 3.00e+00 1.11e-01 1.48e+02 angle pdb=" C ALA A 3 " pdb=" CA ALA A 3 " pdb=" HA ALA A 3 " ideal model delta sigma weight residual 109.00 72.50 36.50 3.00e+00 1.11e-01 1.48e+02 angle pdb=" N ALA A 3 " pdb=" CA ALA A 3 " pdb=" HA ALA A 3 " ideal model delta sigma weight residual 110.00 73.52 36.48 3.00e+00 1.11e-01 1.48e+02 angle pdb=" N ASP A 4 " pdb=" CA ASP A 4 " pdb=" HA ASP A 4 " ideal model delta sigma weight residual 110.00 73.57 36.43 3.00e+00 1.11e-01 1.47e+02 angle pdb=" CB ASP A 4 " pdb=" CA ASP A 4 " pdb=" HA ASP A 4 " ideal model delta sigma weight residual 109.00 72.84 36.16 3.00e+00 1.11e-01 1.45e+02 ... (remaining 81543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 19400 17.84 - 35.68: 1140 35.68 - 53.52: 473 53.52 - 71.36: 145 71.36 - 89.20: 66 Dihedral angle restraints: 21224 sinusoidal: 11818 harmonic: 9406 Sorted by residual: dihedral pdb=" CA ARG G 100 " pdb=" C ARG G 100 " pdb=" N LEU G 101 " pdb=" CA LEU G 101 " ideal model delta harmonic sigma weight residual -180.00 -159.61 -20.39 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA ARG C 100 " pdb=" C ARG C 100 " pdb=" N LEU C 101 " pdb=" CA LEU C 101 " ideal model delta harmonic sigma weight residual -180.00 -159.65 -20.35 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA LEU B 130 " pdb=" C LEU B 130 " pdb=" N SER B 131 " pdb=" CA SER B 131 " ideal model delta harmonic sigma weight residual -180.00 -162.26 -17.74 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 21221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 3393 0.104 - 0.208: 148 0.208 - 0.312: 11 0.312 - 0.416: 0 0.416 - 0.521: 4 Chirality restraints: 3556 Sorted by residual: chirality pdb=" CB THR F 5 " pdb=" CA THR F 5 " pdb=" OG1 THR F 5 " pdb=" CG2 THR F 5 " both_signs ideal model delta sigma weight residual False 2.55 2.03 0.52 2.00e-01 2.50e+01 6.78e+00 chirality pdb=" CB THR B 5 " pdb=" CA THR B 5 " pdb=" OG1 THR B 5 " pdb=" CG2 THR B 5 " both_signs ideal model delta sigma weight residual False 2.55 2.03 0.52 2.00e-01 2.50e+01 6.69e+00 chirality pdb=" CB THR F 2 " pdb=" CA THR F 2 " pdb=" OG1 THR F 2 " pdb=" CG2 THR F 2 " both_signs ideal model delta sigma weight residual False 2.55 2.08 0.48 2.00e-01 2.50e+01 5.65e+00 ... (remaining 3553 not shown) Planarity restraints: 6800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE L 98 " -0.043 2.00e-02 2.50e+03 4.07e-02 4.96e+01 pdb=" CG PHE L 98 " 0.080 2.00e-02 2.50e+03 pdb=" CD1 PHE L 98 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE L 98 " -0.071 2.00e-02 2.50e+03 pdb=" CE1 PHE L 98 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE L 98 " -0.029 2.00e-02 2.50e+03 pdb=" CZ PHE L 98 " -0.007 2.00e-02 2.50e+03 pdb=" HD1 PHE L 98 " 0.021 2.00e-02 2.50e+03 pdb=" HD2 PHE L 98 " 0.058 2.00e-02 2.50e+03 pdb=" HE1 PHE L 98 " -0.013 2.00e-02 2.50e+03 pdb=" HE2 PHE L 98 " -0.006 2.00e-02 2.50e+03 pdb=" HZ PHE L 98 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 98 " 0.030 2.00e-02 2.50e+03 3.63e-02 3.95e+01 pdb=" CG PHE K 98 " -0.100 2.00e-02 2.50e+03 pdb=" CD1 PHE K 98 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE K 98 " 0.047 2.00e-02 2.50e+03 pdb=" CE1 PHE K 98 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE K 98 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE K 98 " -0.025 2.00e-02 2.50e+03 pdb=" HD1 PHE K 98 " 0.024 2.00e-02 2.50e+03 pdb=" HD2 PHE K 98 " 0.015 2.00e-02 2.50e+03 pdb=" HE1 PHE K 98 " 0.022 2.00e-02 2.50e+03 pdb=" HE2 PHE K 98 " -0.009 2.00e-02 2.50e+03 pdb=" HZ PHE K 98 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN K 156 " -0.016 2.00e-02 2.50e+03 4.56e-02 3.12e+01 pdb=" CD GLN K 156 " 0.080 2.00e-02 2.50e+03 pdb=" OE1 GLN K 156 " -0.047 2.00e-02 2.50e+03 pdb=" NE2 GLN K 156 " 0.039 2.00e-02 2.50e+03 pdb="HE21 GLN K 156 " -0.045 2.00e-02 2.50e+03 pdb="HE22 GLN K 156 " -0.010 2.00e-02 2.50e+03 ... (remaining 6797 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 1014 2.09 - 2.72: 76812 2.72 - 3.34: 139666 3.34 - 3.97: 183420 3.97 - 4.60: 284085 Nonbonded interactions: 684997 Sorted by model distance: nonbonded pdb=" OE2 GLU A 58 " pdb=" H SER C 171 " model vdw 1.460 2.450 nonbonded pdb=" OE2 GLU E 58 " pdb=" H SER G 171 " model vdw 1.463 2.450 nonbonded pdb=" OE2 GLU A 37 " pdb="HH11 ARG A 73 " model vdw 1.509 2.450 nonbonded pdb=" OE2 GLU E 37 " pdb="HH11 ARG E 73 " model vdw 1.518 2.450 nonbonded pdb=" OD1 ASP G 95 " pdb=" HG1 THR G 97 " model vdw 1.570 2.450 ... (remaining 684992 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.200 Extract box with map and model: 0.600 Check model and map are aligned: 0.140 Set scattering table: 0.120 Process input model: 52.000 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.295 22884 Z= 0.271 Angle : 0.729 27.099 31108 Z= 0.353 Chirality : 0.048 0.521 3556 Planarity : 0.005 0.090 4086 Dihedral : 14.766 89.199 8542 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.04 % Allowed : 6.89 % Favored : 92.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.16), residues: 2858 helix: 1.82 (0.16), residues: 1134 sheet: 0.26 (0.23), residues: 490 loop : 0.61 (0.18), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG L 52 TYR 0.034 0.002 TYR L 58 PHE 0.094 0.002 PHE K 98 TRP 0.013 0.001 TRP A 11 HIS 0.015 0.001 HIS L 144 Details of bonding type rmsd covalent geometry : bond 0.00552 (22872) covalent geometry : angle 0.72602 (31096) hydrogen bonds : bond 0.11646 ( 1091) hydrogen bonds : angle 6.15726 ( 3015) metal coordination : bond 0.00433 ( 12) metal coordination : angle 3.23092 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 444 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 419 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 287 MET cc_start: 0.8659 (ttt) cc_final: 0.8279 (ttt) REVERT: H 153 MET cc_start: 0.8396 (tpp) cc_final: 0.8190 (tpp) REVERT: K 74 VAL cc_start: 0.8610 (OUTLIER) cc_final: 0.8388 (t) REVERT: K 89 LYS cc_start: 0.8154 (ttmt) cc_final: 0.7953 (ttmt) REVERT: L 74 VAL cc_start: 0.8580 (OUTLIER) cc_final: 0.8357 (t) REVERT: L 144 HIS cc_start: 0.7724 (m-70) cc_final: 0.7522 (m-70) outliers start: 25 outliers final: 8 residues processed: 433 average time/residue: 1.4097 time to fit residues: 697.4576 Evaluate side-chains 327 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 317 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain G residue 141 THR Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 242 THR Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain J residue 242 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 28 ASN A 90 GLN B 107 ASN D 34 GLN E 19 GLN E 28 ASN E 90 GLN F 107 ASN H 34 GLN I 89 HIS J 89 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.110804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.081869 restraints weight = 81098.016| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.58 r_work: 0.2966 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 22884 Z= 0.153 Angle : 0.564 11.060 31108 Z= 0.292 Chirality : 0.054 1.328 3556 Planarity : 0.005 0.056 4086 Dihedral : 7.481 67.124 3222 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.13 % Allowed : 9.27 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.16), residues: 2858 helix: 1.89 (0.16), residues: 1138 sheet: 0.12 (0.23), residues: 488 loop : 0.66 (0.18), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 134 TYR 0.022 0.002 TYR I 241 PHE 0.013 0.001 PHE B 18 TRP 0.013 0.001 TRP E 11 HIS 0.006 0.001 HIS G 316 Details of bonding type rmsd covalent geometry : bond 0.00344 (22872) covalent geometry : angle 0.56039 (31096) hydrogen bonds : bond 0.04354 ( 1091) hydrogen bonds : angle 5.27599 ( 3015) metal coordination : bond 0.00721 ( 12) metal coordination : angle 3.25921 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 351 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 324 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 ASN cc_start: 0.8444 (m-40) cc_final: 0.8197 (m-40) REVERT: H 153 MET cc_start: 0.9038 (tpp) cc_final: 0.8743 (tpp) REVERT: K 74 VAL cc_start: 0.8318 (t) cc_final: 0.8117 (t) REVERT: K 89 LYS cc_start: 0.8258 (ttmt) cc_final: 0.7614 (tppt) REVERT: L 10 THR cc_start: 0.6280 (p) cc_final: 0.5662 (t) REVERT: L 74 VAL cc_start: 0.8216 (t) cc_final: 0.7903 (t) outliers start: 27 outliers final: 12 residues processed: 340 average time/residue: 1.4698 time to fit residues: 567.9977 Evaluate side-chains 318 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 306 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain G residue 141 THR Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain I residue 127 LYS Chi-restraints excluded: chain J residue 127 LYS Chi-restraints excluded: chain K residue 159 ASN Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain L residue 159 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 272 optimal weight: 0.7980 chunk 242 optimal weight: 6.9990 chunk 136 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 251 optimal weight: 4.9990 chunk 124 optimal weight: 0.3980 chunk 71 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 221 optimal weight: 3.9990 chunk 244 optimal weight: 10.0000 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 28 ASN A 90 GLN B 74 ASN ** C 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 GLN E 28 ASN E 90 GLN F 74 ASN ** G 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 32 ASN L 156 GLN L 159 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.109543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.080483 restraints weight = 81549.898| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.60 r_work: 0.2943 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22884 Z= 0.153 Angle : 0.542 10.932 31108 Z= 0.281 Chirality : 0.054 1.331 3556 Planarity : 0.004 0.046 4086 Dihedral : 7.382 64.160 3216 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.79 % Allowed : 10.40 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.16), residues: 2858 helix: 1.91 (0.16), residues: 1144 sheet: 0.03 (0.24), residues: 490 loop : 0.64 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 134 TYR 0.019 0.001 TYR I 241 PHE 0.013 0.001 PHE B 18 TRP 0.014 0.001 TRP E 11 HIS 0.004 0.001 HIS G 316 Details of bonding type rmsd covalent geometry : bond 0.00347 (22872) covalent geometry : angle 0.53948 (31096) hydrogen bonds : bond 0.04143 ( 1091) hydrogen bonds : angle 5.10444 ( 3015) metal coordination : bond 0.00553 ( 12) metal coordination : angle 2.77779 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 334 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 315 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 ASN cc_start: 0.8419 (m-40) cc_final: 0.8170 (m-40) REVERT: B 180 GLU cc_start: 0.8177 (pm20) cc_final: 0.7919 (pm20) REVERT: C 150 GLN cc_start: 0.7349 (mm-40) cc_final: 0.6898 (mt0) REVERT: C 287 MET cc_start: 0.9305 (ttt) cc_final: 0.8975 (ttt) REVERT: F 145 GLU cc_start: 0.7783 (mp0) cc_final: 0.7506 (mm-30) REVERT: F 180 GLU cc_start: 0.8163 (pm20) cc_final: 0.7915 (pm20) REVERT: G 150 GLN cc_start: 0.7354 (mm-40) cc_final: 0.6903 (mt0) REVERT: G 287 MET cc_start: 0.9305 (ttt) cc_final: 0.8977 (ttt) REVERT: H 153 MET cc_start: 0.9050 (tpp) cc_final: 0.8667 (tpp) REVERT: I 111 MET cc_start: 0.9066 (mtm) cc_final: 0.8688 (mtm) REVERT: J 111 MET cc_start: 0.9042 (mtm) cc_final: 0.8804 (mtm) REVERT: K 65 ILE cc_start: 0.7353 (mt) cc_final: 0.7068 (mp) REVERT: K 74 VAL cc_start: 0.8369 (t) cc_final: 0.8037 (t) REVERT: K 89 LYS cc_start: 0.8190 (ttmt) cc_final: 0.7563 (tppt) REVERT: K 109 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7536 (mp0) REVERT: K 156 GLN cc_start: 0.7003 (tp40) cc_final: 0.6732 (tp-100) REVERT: L 10 THR cc_start: 0.6222 (p) cc_final: 0.5575 (t) REVERT: L 65 ILE cc_start: 0.7321 (mt) cc_final: 0.7105 (mp) REVERT: L 74 VAL cc_start: 0.8336 (t) cc_final: 0.8094 (t) REVERT: L 109 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7528 (mp0) outliers start: 19 outliers final: 8 residues processed: 324 average time/residue: 1.5235 time to fit residues: 558.4696 Evaluate side-chains 319 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 309 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain G residue 141 THR Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain I residue 127 LYS Chi-restraints excluded: chain J residue 127 LYS Chi-restraints excluded: chain K residue 109 GLU Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain L residue 109 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 169 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 120 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 274 optimal weight: 0.0670 chunk 221 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 156 optimal weight: 0.6980 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 28 ASN A 90 GLN A 131 GLN C 149 GLN C 353 HIS E 19 GLN E 28 ASN E 90 GLN G 149 GLN K 159 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.109461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.081347 restraints weight = 83145.880| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.55 r_work: 0.2976 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22884 Z= 0.119 Angle : 0.520 11.105 31108 Z= 0.268 Chirality : 0.054 1.371 3556 Planarity : 0.004 0.044 4086 Dihedral : 6.974 61.988 3216 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.88 % Allowed : 10.23 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.16), residues: 2858 helix: 2.01 (0.16), residues: 1146 sheet: -0.06 (0.23), residues: 502 loop : 0.62 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 135 TYR 0.018 0.001 TYR J 241 PHE 0.013 0.001 PHE B 18 TRP 0.014 0.001 TRP E 11 HIS 0.005 0.001 HIS G 353 Details of bonding type rmsd covalent geometry : bond 0.00267 (22872) covalent geometry : angle 0.51742 (31096) hydrogen bonds : bond 0.03784 ( 1091) hydrogen bonds : angle 4.94024 ( 3015) metal coordination : bond 0.00509 ( 12) metal coordination : angle 2.84365 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 333 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 312 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7962 (pt0) cc_final: 0.7730 (pt0) REVERT: B 107 ASN cc_start: 0.8423 (m-40) cc_final: 0.8137 (m-40) REVERT: B 180 GLU cc_start: 0.8135 (pm20) cc_final: 0.7890 (pm20) REVERT: C 150 GLN cc_start: 0.7401 (mm-40) cc_final: 0.6943 (mt0) REVERT: C 287 MET cc_start: 0.9311 (ttt) cc_final: 0.8982 (ttt) REVERT: D 153 MET cc_start: 0.8968 (tpp) cc_final: 0.8616 (tpp) REVERT: F 180 GLU cc_start: 0.8122 (pm20) cc_final: 0.7873 (pm20) REVERT: G 150 GLN cc_start: 0.7400 (mm-40) cc_final: 0.6936 (mt0) REVERT: G 287 MET cc_start: 0.9315 (ttt) cc_final: 0.8982 (ttt) REVERT: H 153 MET cc_start: 0.9047 (tpp) cc_final: 0.8681 (tpp) REVERT: I 32 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8406 (pt0) REVERT: I 111 MET cc_start: 0.9056 (mtm) cc_final: 0.8658 (mtm) REVERT: J 32 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8389 (pt0) REVERT: J 111 MET cc_start: 0.9011 (mtm) cc_final: 0.8644 (mtm) REVERT: K 65 ILE cc_start: 0.7323 (mt) cc_final: 0.7104 (mp) REVERT: K 74 VAL cc_start: 0.8340 (OUTLIER) cc_final: 0.8076 (t) REVERT: K 89 LYS cc_start: 0.8201 (ttmt) cc_final: 0.7601 (tppt) REVERT: K 109 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7527 (mp0) REVERT: K 140 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7564 (tm-30) REVERT: K 156 GLN cc_start: 0.7033 (tp40) cc_final: 0.6743 (tp-100) REVERT: L 10 THR cc_start: 0.6467 (p) cc_final: 0.5820 (t) REVERT: L 65 ILE cc_start: 0.7345 (mt) cc_final: 0.7139 (mp) REVERT: L 74 VAL cc_start: 0.8371 (OUTLIER) cc_final: 0.8112 (t) REVERT: L 109 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7538 (mp0) outliers start: 21 outliers final: 6 residues processed: 321 average time/residue: 1.4803 time to fit residues: 538.9506 Evaluate side-chains 315 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 303 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain I residue 32 GLU Chi-restraints excluded: chain I residue 127 LYS Chi-restraints excluded: chain J residue 32 GLU Chi-restraints excluded: chain J residue 127 LYS Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 109 GLU Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 109 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 124 optimal weight: 0.8980 chunk 156 optimal weight: 2.9990 chunk 210 optimal weight: 2.9990 chunk 72 optimal weight: 0.0070 chunk 95 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 222 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 28 ASN A 90 GLN C 149 GLN E 19 GLN E 28 ASN E 90 GLN G 149 GLN K 32 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.109002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.079921 restraints weight = 81499.119| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.60 r_work: 0.2934 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22884 Z= 0.146 Angle : 0.528 11.080 31108 Z= 0.273 Chirality : 0.054 1.378 3556 Planarity : 0.004 0.058 4086 Dihedral : 6.630 61.316 3214 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.63 % Allowed : 10.61 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.16), residues: 2858 helix: 2.02 (0.16), residues: 1144 sheet: -0.02 (0.24), residues: 498 loop : 0.65 (0.18), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 67 TYR 0.017 0.001 TYR J 241 PHE 0.014 0.001 PHE B 18 TRP 0.016 0.001 TRP E 11 HIS 0.004 0.001 HIS G 316 Details of bonding type rmsd covalent geometry : bond 0.00331 (22872) covalent geometry : angle 0.52489 (31096) hydrogen bonds : bond 0.03888 ( 1091) hydrogen bonds : angle 4.90239 ( 3015) metal coordination : bond 0.00578 ( 12) metal coordination : angle 2.80692 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 316 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 301 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 ASN cc_start: 0.8496 (m-40) cc_final: 0.8228 (m-40) REVERT: B 180 GLU cc_start: 0.8149 (pm20) cc_final: 0.7895 (pm20) REVERT: C 150 GLN cc_start: 0.7451 (mm-40) cc_final: 0.6939 (mt0) REVERT: C 287 MET cc_start: 0.9296 (ttt) cc_final: 0.8991 (ttt) REVERT: D 153 MET cc_start: 0.8985 (tpp) cc_final: 0.8617 (tpp) REVERT: F 180 GLU cc_start: 0.8147 (pm20) cc_final: 0.7892 (pm20) REVERT: G 150 GLN cc_start: 0.7423 (mm-40) cc_final: 0.6919 (mt0) REVERT: G 287 MET cc_start: 0.9306 (ttt) cc_final: 0.9003 (ttt) REVERT: H 153 MET cc_start: 0.9055 (tpp) cc_final: 0.8686 (tpp) REVERT: I 32 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8482 (pt0) REVERT: I 61 GLU cc_start: 0.7740 (tp30) cc_final: 0.7320 (mp0) REVERT: I 189 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.8112 (mmp-170) REVERT: J 32 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8460 (pt0) REVERT: J 61 GLU cc_start: 0.7786 (tp30) cc_final: 0.7358 (mp0) REVERT: J 111 MET cc_start: 0.9045 (mtm) cc_final: 0.8682 (mtm) REVERT: J 189 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8084 (mmp-170) REVERT: K 74 VAL cc_start: 0.8347 (OUTLIER) cc_final: 0.8105 (t) REVERT: K 89 LYS cc_start: 0.8168 (ttmt) cc_final: 0.7556 (tppt) REVERT: K 109 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7528 (mp0) REVERT: K 140 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7555 (tm-30) REVERT: L 10 THR cc_start: 0.6463 (p) cc_final: 0.5781 (t) REVERT: L 65 ILE cc_start: 0.7301 (mt) cc_final: 0.7095 (mp) REVERT: L 74 VAL cc_start: 0.8336 (OUTLIER) cc_final: 0.8071 (t) REVERT: L 140 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7551 (tm-30) outliers start: 15 outliers final: 6 residues processed: 309 average time/residue: 1.4588 time to fit residues: 512.4029 Evaluate side-chains 306 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 293 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain I residue 32 GLU Chi-restraints excluded: chain I residue 127 LYS Chi-restraints excluded: chain I residue 189 ARG Chi-restraints excluded: chain J residue 32 GLU Chi-restraints excluded: chain J residue 127 LYS Chi-restraints excluded: chain J residue 189 ARG Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 109 GLU Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 107 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 225 optimal weight: 3.9990 chunk 283 optimal weight: 8.9990 chunk 178 optimal weight: 1.9990 chunk 211 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 191 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 90 GLN C 149 GLN E 19 GLN E 28 ASN E 90 GLN I 223 GLN J 223 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.106807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.077503 restraints weight = 82209.558| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.59 r_work: 0.2896 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 22884 Z= 0.235 Angle : 0.579 11.017 31108 Z= 0.303 Chirality : 0.056 1.384 3556 Planarity : 0.005 0.046 4086 Dihedral : 6.433 61.472 3214 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.84 % Allowed : 10.74 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.16), residues: 2858 helix: 1.80 (0.15), residues: 1144 sheet: -0.08 (0.24), residues: 484 loop : 0.51 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 67 TYR 0.016 0.002 TYR J 241 PHE 0.017 0.002 PHE B 18 TRP 0.014 0.001 TRP A 11 HIS 0.005 0.001 HIS C 316 Details of bonding type rmsd covalent geometry : bond 0.00540 (22872) covalent geometry : angle 0.57621 (31096) hydrogen bonds : bond 0.04453 ( 1091) hydrogen bonds : angle 5.07941 ( 3015) metal coordination : bond 0.00741 ( 12) metal coordination : angle 2.77244 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 309 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 289 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 ASN cc_start: 0.8656 (m-40) cc_final: 0.8284 (m-40) REVERT: B 180 GLU cc_start: 0.8203 (pm20) cc_final: 0.7938 (pm20) REVERT: C 150 GLN cc_start: 0.7520 (mm-40) cc_final: 0.7012 (mt0) REVERT: C 287 MET cc_start: 0.9308 (ttt) cc_final: 0.9035 (ttt) REVERT: D 153 MET cc_start: 0.9008 (tpp) cc_final: 0.8603 (tpp) REVERT: F 180 GLU cc_start: 0.8208 (pm20) cc_final: 0.7940 (pm20) REVERT: G 148 GLU cc_start: 0.7449 (tm-30) cc_final: 0.7246 (tm-30) REVERT: G 150 GLN cc_start: 0.7499 (mm-40) cc_final: 0.7000 (mt0) REVERT: G 287 MET cc_start: 0.9297 (ttt) cc_final: 0.9029 (ttt) REVERT: H 153 MET cc_start: 0.9069 (tpp) cc_final: 0.8691 (tpp) REVERT: I 61 GLU cc_start: 0.7832 (tp30) cc_final: 0.7334 (mp0) REVERT: I 189 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.8314 (mmp-170) REVERT: I 251 GLN cc_start: 0.7249 (mm-40) cc_final: 0.6995 (mm-40) REVERT: J 32 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8468 (pt0) REVERT: J 61 GLU cc_start: 0.7833 (tp30) cc_final: 0.7336 (mp0) REVERT: J 111 MET cc_start: 0.9115 (mtm) cc_final: 0.8784 (mtm) REVERT: J 189 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.8266 (mmp-170) REVERT: K 74 VAL cc_start: 0.8367 (OUTLIER) cc_final: 0.8132 (t) REVERT: K 89 LYS cc_start: 0.8222 (ttmt) cc_final: 0.7668 (tppt) REVERT: L 10 THR cc_start: 0.6536 (p) cc_final: 0.5853 (t) REVERT: L 74 VAL cc_start: 0.8358 (OUTLIER) cc_final: 0.8096 (t) outliers start: 20 outliers final: 10 residues processed: 299 average time/residue: 1.3627 time to fit residues: 463.4811 Evaluate side-chains 296 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 281 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain I residue 127 LYS Chi-restraints excluded: chain I residue 189 ARG Chi-restraints excluded: chain J residue 32 GLU Chi-restraints excluded: chain J residue 127 LYS Chi-restraints excluded: chain J residue 189 ARG Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 109 GLU Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 44 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 264 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 chunk 239 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 209 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 28 ASN A 90 GLN C 149 GLN E 19 GLN E 90 GLN G 149 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.107386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.078060 restraints weight = 81824.030| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.59 r_work: 0.2906 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22884 Z= 0.186 Angle : 0.554 11.173 31108 Z= 0.289 Chirality : 0.055 1.396 3556 Planarity : 0.004 0.046 4086 Dihedral : 6.033 60.213 3214 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.96 % Allowed : 11.03 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.16), residues: 2858 helix: 1.82 (0.15), residues: 1144 sheet: -0.17 (0.24), residues: 486 loop : 0.51 (0.18), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 67 TYR 0.017 0.002 TYR J 241 PHE 0.014 0.002 PHE H 191 TRP 0.023 0.001 TRP E 11 HIS 0.005 0.001 HIS C 316 Details of bonding type rmsd covalent geometry : bond 0.00422 (22872) covalent geometry : angle 0.55146 (31096) hydrogen bonds : bond 0.04176 ( 1091) hydrogen bonds : angle 5.00186 ( 3015) metal coordination : bond 0.00703 ( 12) metal coordination : angle 2.96573 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 306 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 283 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 180 GLU cc_start: 0.8202 (pm20) cc_final: 0.7940 (pm20) REVERT: C 150 GLN cc_start: 0.7518 (mm-40) cc_final: 0.7032 (mt0) REVERT: F 180 GLU cc_start: 0.8208 (pm20) cc_final: 0.7946 (pm20) REVERT: G 150 GLN cc_start: 0.7494 (mm-40) cc_final: 0.7027 (mt0) REVERT: I 189 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.8232 (mmp-170) REVERT: I 251 GLN cc_start: 0.7236 (mm-40) cc_final: 0.6993 (mm-40) REVERT: J 111 MET cc_start: 0.9112 (mtm) cc_final: 0.8891 (mtm) REVERT: J 189 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8207 (mmp-170) REVERT: J 251 GLN cc_start: 0.7198 (mm-40) cc_final: 0.6941 (mm-40) REVERT: K 74 VAL cc_start: 0.8443 (OUTLIER) cc_final: 0.8209 (t) REVERT: K 89 LYS cc_start: 0.8233 (ttmt) cc_final: 0.7673 (tppt) REVERT: L 10 THR cc_start: 0.6651 (p) cc_final: 0.5954 (t) REVERT: L 74 VAL cc_start: 0.8385 (OUTLIER) cc_final: 0.8133 (t) outliers start: 23 outliers final: 9 residues processed: 292 average time/residue: 1.3393 time to fit residues: 444.7757 Evaluate side-chains 289 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 276 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain I residue 127 LYS Chi-restraints excluded: chain I residue 189 ARG Chi-restraints excluded: chain J residue 127 LYS Chi-restraints excluded: chain J residue 189 ARG Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 109 GLU Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 86 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 158 optimal weight: 0.0870 chunk 91 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 214 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 119 optimal weight: 0.0980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 90 GLN C 149 GLN E 19 GLN E 90 GLN G 149 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.109328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.080345 restraints weight = 82394.588| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.60 r_work: 0.2945 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22884 Z= 0.098 Angle : 0.510 11.326 31108 Z= 0.263 Chirality : 0.054 1.397 3556 Planarity : 0.004 0.044 4086 Dihedral : 5.601 59.741 3214 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.67 % Allowed : 11.40 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.16), residues: 2858 helix: 2.04 (0.16), residues: 1148 sheet: -0.13 (0.24), residues: 484 loop : 0.59 (0.18), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 67 TYR 0.016 0.001 TYR J 241 PHE 0.010 0.001 PHE B 18 TRP 0.019 0.001 TRP A 11 HIS 0.003 0.001 HIS C 316 Details of bonding type rmsd covalent geometry : bond 0.00218 (22872) covalent geometry : angle 0.50636 (31096) hydrogen bonds : bond 0.03546 ( 1091) hydrogen bonds : angle 4.76112 ( 3015) metal coordination : bond 0.00507 ( 12) metal coordination : angle 3.18450 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 304 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 288 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 ASN cc_start: 0.8147 (t0) cc_final: 0.7905 (t0) REVERT: B 180 GLU cc_start: 0.8138 (pm20) cc_final: 0.7855 (pm20) REVERT: C 150 GLN cc_start: 0.7472 (mm-40) cc_final: 0.6993 (mt0) REVERT: F 180 GLU cc_start: 0.8149 (pm20) cc_final: 0.7861 (pm20) REVERT: G 150 GLN cc_start: 0.7466 (mm-40) cc_final: 0.6987 (mt0) REVERT: I 189 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.8162 (mmp-170) REVERT: J 189 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.8180 (mmp-170) REVERT: J 251 GLN cc_start: 0.7205 (mm-40) cc_final: 0.6969 (mm-40) REVERT: K 74 VAL cc_start: 0.8455 (OUTLIER) cc_final: 0.8242 (t) REVERT: K 89 LYS cc_start: 0.8173 (ttmt) cc_final: 0.7589 (tppt) REVERT: L 10 THR cc_start: 0.6606 (p) cc_final: 0.5910 (t) REVERT: L 74 VAL cc_start: 0.8445 (OUTLIER) cc_final: 0.8218 (t) outliers start: 16 outliers final: 8 residues processed: 295 average time/residue: 1.1726 time to fit residues: 395.3466 Evaluate side-chains 285 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 273 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain I residue 127 LYS Chi-restraints excluded: chain I residue 189 ARG Chi-restraints excluded: chain J residue 127 LYS Chi-restraints excluded: chain J residue 189 ARG Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 109 GLU Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 52 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 46 optimal weight: 0.1980 chunk 73 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 93 optimal weight: 0.2980 chunk 166 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 109 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN C 149 GLN E 19 GLN E 90 GLN ** K 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.109154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.080210 restraints weight = 81920.296| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.59 r_work: 0.2944 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22884 Z= 0.112 Angle : 0.518 11.217 31108 Z= 0.266 Chirality : 0.054 1.392 3556 Planarity : 0.004 0.044 4086 Dihedral : 5.461 59.948 3214 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.58 % Allowed : 11.74 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.16), residues: 2858 helix: 2.07 (0.16), residues: 1148 sheet: -0.08 (0.24), residues: 494 loop : 0.62 (0.18), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 67 TYR 0.015 0.001 TYR J 241 PHE 0.011 0.001 PHE F 18 TRP 0.023 0.001 TRP E 11 HIS 0.003 0.001 HIS C 316 Details of bonding type rmsd covalent geometry : bond 0.00254 (22872) covalent geometry : angle 0.51505 (31096) hydrogen bonds : bond 0.03582 ( 1091) hydrogen bonds : angle 4.72239 ( 3015) metal coordination : bond 0.00508 ( 12) metal coordination : angle 2.94500 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 293 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 279 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 ASN cc_start: 0.8147 (t0) cc_final: 0.7909 (t0) REVERT: B 180 GLU cc_start: 0.8144 (pm20) cc_final: 0.7885 (pm20) REVERT: F 180 GLU cc_start: 0.8143 (pm20) cc_final: 0.7889 (pm20) REVERT: G 150 GLN cc_start: 0.7492 (mm-40) cc_final: 0.7024 (mt0) REVERT: I 189 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.8050 (mmp-170) REVERT: I 251 GLN cc_start: 0.7248 (mm-40) cc_final: 0.7030 (mm-40) REVERT: J 189 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.8038 (mmp-170) REVERT: J 251 GLN cc_start: 0.7225 (mm-40) cc_final: 0.6986 (mm-40) REVERT: K 74 VAL cc_start: 0.8471 (OUTLIER) cc_final: 0.8264 (t) REVERT: K 89 LYS cc_start: 0.8162 (ttmt) cc_final: 0.7593 (tppt) REVERT: L 10 THR cc_start: 0.6631 (p) cc_final: 0.5934 (t) REVERT: L 74 VAL cc_start: 0.8465 (OUTLIER) cc_final: 0.8244 (t) outliers start: 14 outliers final: 6 residues processed: 285 average time/residue: 0.9043 time to fit residues: 295.7963 Evaluate side-chains 284 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 274 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain I residue 189 ARG Chi-restraints excluded: chain J residue 189 ARG Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 109 GLU Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 278 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 266 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 chunk 279 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 253 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 90 GLN C 149 GLN C 150 GLN E 19 GLN E 90 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.107700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.078474 restraints weight = 82069.530| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.59 r_work: 0.2914 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22884 Z= 0.185 Angle : 0.553 11.112 31108 Z= 0.287 Chirality : 0.055 1.390 3556 Planarity : 0.004 0.045 4086 Dihedral : 5.551 60.203 3214 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.54 % Allowed : 11.95 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.16), residues: 2858 helix: 1.96 (0.15), residues: 1144 sheet: -0.18 (0.24), residues: 486 loop : 0.56 (0.18), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 67 TYR 0.015 0.002 TYR J 241 PHE 0.016 0.002 PHE F 18 TRP 0.028 0.001 TRP A 11 HIS 0.005 0.001 HIS J 13 Details of bonding type rmsd covalent geometry : bond 0.00425 (22872) covalent geometry : angle 0.54996 (31096) hydrogen bonds : bond 0.04051 ( 1091) hydrogen bonds : angle 4.86808 ( 3015) metal coordination : bond 0.00696 ( 12) metal coordination : angle 2.80853 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 287 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 274 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 180 GLU cc_start: 0.8203 (pm20) cc_final: 0.7942 (pm20) REVERT: C 298 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8160 (mp0) REVERT: F 180 GLU cc_start: 0.8209 (pm20) cc_final: 0.7946 (pm20) REVERT: I 189 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8125 (mmp-170) REVERT: I 251 GLN cc_start: 0.7280 (mm-40) cc_final: 0.7062 (mm-40) REVERT: J 189 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8103 (mmp-170) REVERT: J 251 GLN cc_start: 0.7203 (mm-40) cc_final: 0.6958 (mm-40) REVERT: K 74 VAL cc_start: 0.8465 (OUTLIER) cc_final: 0.8264 (t) REVERT: K 89 LYS cc_start: 0.8171 (ttmt) cc_final: 0.7586 (tppt) REVERT: L 10 THR cc_start: 0.6621 (p) cc_final: 0.5922 (t) REVERT: L 74 VAL cc_start: 0.8462 (OUTLIER) cc_final: 0.8244 (t) REVERT: L 89 LYS cc_start: 0.8138 (ttmt) cc_final: 0.7703 (tppt) REVERT: L 140 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7550 (tm-30) outliers start: 13 outliers final: 6 residues processed: 280 average time/residue: 0.8918 time to fit residues: 286.0705 Evaluate side-chains 283 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 272 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain I residue 189 ARG Chi-restraints excluded: chain J residue 189 ARG Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 109 GLU Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 255 optimal weight: 4.9990 chunk 131 optimal weight: 0.0980 chunk 120 optimal weight: 0.0570 chunk 140 optimal weight: 1.9990 chunk 231 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 142 optimal weight: 0.0040 chunk 91 optimal weight: 0.2980 chunk 34 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 overall best weight: 0.2310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 90 GLN C 149 GLN E 19 GLN E 90 GLN G 150 GLN K 57 ASN L 57 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.109789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.080923 restraints weight = 82150.216| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.60 r_work: 0.2957 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22884 Z= 0.097 Angle : 0.511 11.279 31108 Z= 0.262 Chirality : 0.053 1.391 3556 Planarity : 0.004 0.043 4086 Dihedral : 5.394 59.781 3214 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.54 % Allowed : 11.78 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.16), residues: 2858 helix: 2.13 (0.16), residues: 1148 sheet: -0.14 (0.24), residues: 496 loop : 0.64 (0.18), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 67 TYR 0.015 0.001 TYR J 241 PHE 0.010 0.001 PHE F 18 TRP 0.026 0.001 TRP A 11 HIS 0.003 0.001 HIS C 316 Details of bonding type rmsd covalent geometry : bond 0.00214 (22872) covalent geometry : angle 0.50759 (31096) hydrogen bonds : bond 0.03447 ( 1091) hydrogen bonds : angle 4.66108 ( 3015) metal coordination : bond 0.00470 ( 12) metal coordination : angle 3.13222 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15535.63 seconds wall clock time: 262 minutes 17.70 seconds (15737.70 seconds total)