Starting phenix.real_space_refine on Tue Sep 15 22:39:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z15_14441/09_2026/7z15_14441_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z15_14441/09_2026/7z15_14441.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z15_14441/09_2026/7z15_14441.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z15_14441/09_2026/7z15_14441.map" model { file = "/net/cci-nas-00/data/ceres_data/7z15_14441/09_2026/7z15_14441_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z15_14441/09_2026/7z15_14441_neut_trim.cif" } resolution = 1.93 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= 0.002 sd= 0.069 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 16 5.49 5 Mg 4 5.21 5 S 96 5.16 5 C 14134 2.51 5 N 4020 2.21 5 O 5481 1.98 5 H 22357 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 46112 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 2195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2195 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "B" Number of atoms: 2961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 2961 Classifications: {'peptide': 193} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 178} Chain: "C" Number of atoms: 5412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 5412 Classifications: {'peptide': 353} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 332} Chain: "D" Number of atoms: 4365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 4365 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 20, 'TRANS': 257} Chain: "E" Number of atoms: 2195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2195 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "F" Number of atoms: 2961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 2961 Classifications: {'peptide': 193} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 178} Chain: "G" Number of atoms: 5413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 5413 Classifications: {'peptide': 353} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 332} Chain: "H" Number of atoms: 4365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 4365 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 20, 'TRANS': 257} Chain: "I" Number of atoms: 3950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 3950 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} 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: 3950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 3950 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} 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: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {' ZN': 1, 'I9X': 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: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {' ZN': 1, 'I9X': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "B" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 210 Classifications: {'water': 210} Link IDs: {None: 209} Chain: "D" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 170 Classifications: {'water': 170} Link IDs: {None: 169} Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "F" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "G" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 220 Classifications: {'water': 220} Link IDs: {None: 219} Chain: "H" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 162 Classifications: {'water': 162} Link IDs: {None: 161} Chain: "I" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Classifications: {'water': 69} Link IDs: {None: 68} Chain: "J" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Classifications: {'water': 69} Link IDs: {None: 68} Chain: "K" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "L" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14374 SG CYS D 241 84.847 38.738 104.685 1.00 19.21 S ATOM 14413 SG CYS D 244 84.335 35.032 104.151 1.00 21.52 S ATOM 14733 SG CYS D 266 81.721 37.434 103.090 1.00 15.69 S ATOM 14813 SG CYS D 272 82.451 37.045 106.927 1.00 18.26 S ATOM 29308 SG CYS H 241 18.783 99.997 104.669 1.00 19.24 S ATOM 29347 SG CYS H 244 19.296 103.703 104.134 1.00 21.67 S ATOM 29667 SG CYS H 266 21.909 101.300 103.075 1.00 15.74 S ATOM 29747 SG CYS H 272 21.178 101.691 106.912 1.00 18.34 S Time building chain proxies: 7.82, per 1000 atoms: 0.17 Number of scatterers: 46112 At special positions: 0 Unit cell: (104.462, 139.562, 156.276, 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 16 15.00 Mg 4 11.99 O 5481 8.00 N 4020 7.00 C 14134 6.00 H 22357 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: 4.31 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C1000 " pdb="ZN ZN C1000 " - pdb=" NE2 HIS C 333 " pdb="ZN ZN C1000 " - pdb=" NE2 HIS C 328 " 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 333 " pdb="ZN ZN G1000 " - pdb=" NE2 HIS G 328 " pdb=" ZN H1000 " pdb="ZN ZN H1000 " - pdb=" SG CYS H 241 " pdb="ZN ZN H1000 " - pdb=" SG CYS H 244 " pdb="ZN ZN H1000 " - pdb=" SG CYS H 266 " pdb="ZN ZN H1000 " - pdb=" SG CYS H 272 " Number of angles added : 12 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5368 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 26 sheets defined 46.2% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 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 removed outlier: 3.621A pdb=" N GLN A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 115 removed outlier: 4.677A pdb=" N GLN A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ASN A 110 " --> pdb=" O ARG A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 136 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 82 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: 3.863A 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 84 removed outlier: 3.684A pdb=" N THR C 83 " --> pdb=" O ARG C 79 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR C 84 " --> pdb=" O ALA C 80 " (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 198 Processing helix chain 'C' and resid 200 through 213 Processing helix chain 'C' and resid 281 through 295 Processing helix chain 'C' and resid 295 through 300 Processing helix chain 'C' and resid 305 through 308 Processing helix chain 'C' and resid 309 through 316 removed outlier: 3.772A 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 13 through 30 Processing helix chain 'D' and resid 49 through 60 Processing helix chain 'D' and resid 76 through 90 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 137 through 147 removed outlier: 4.242A 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 removed outlier: 3.620A pdb=" N GLN E 103 " --> pdb=" O ASP E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 115 removed outlier: 4.678A pdb=" N GLN E 109 " --> pdb=" O SER E 105 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ASN E 110 " --> pdb=" O ARG E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 136 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 82 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: 3.863A 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 84 removed outlier: 3.684A pdb=" N THR G 83 " --> pdb=" O ARG G 79 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR G 84 " --> pdb=" O ALA G 80 " (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 198 Processing helix chain 'G' and resid 200 through 213 Processing helix chain 'G' and resid 281 through 295 Processing helix chain 'G' and resid 295 through 300 Processing helix chain 'G' and resid 305 through 308 Processing helix chain 'G' and resid 309 through 316 removed outlier: 3.772A 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 13 through 30 Processing helix chain 'H' and resid 49 through 60 Processing helix chain 'H' and resid 76 through 90 Processing helix chain 'H' and resid 97 through 101 Processing helix chain 'H' and resid 137 through 147 removed outlier: 4.242A 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: 4.395A pdb=" N ARG I 109 " --> pdb=" O ASN I 105 " (cutoff:3.500A) removed outlier: 3.680A 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 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: 4.396A pdb=" N ARG J 109 " --> pdb=" O ASN J 105 " (cutoff:3.500A) removed outlier: 3.680A 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 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 165 Processing helix chain 'K' and resid 181 through 198 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 165 Processing helix chain 'L' and resid 181 through 198 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: 4.926A pdb=" N ILE A 49 " --> pdb=" O ALA A 62 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ASP A 64 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL A 47 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N THR A 66 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLY A 45 " --> pdb=" O THR A 66 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N THR A 68 " --> pdb=" O GLU A 43 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLU A 43 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ALA A 70 " --> pdb=" O ALA A 41 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ALA A 41 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL A 72 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ILE A 39 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LEU A 74 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N GLU A 37 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N LYS C 87 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU A 46 " --> pdb=" O LYS C 87 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA C 89 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 139 removed outlier: 4.621A 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: 6.308A pdb=" N LEU B 123 " --> pdb=" O ILE B 175 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N THR B 177 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU B 125 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ALA B 95 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N GLN B 126 " --> pdb=" O ALA B 95 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR B 97 " --> pdb=" O GLN B 126 " (cutoff:3.500A) removed outlier: 6.480A 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: 6.519A pdb=" N SER C 227 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG C 104 " --> pdb=" O ILE C 225 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE C 225 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ALA C 222 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N VAL C 256 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY C 246 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE C 234 " --> pdb=" O ASN C 244 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ASN C 244 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE C 259 " --> pdb=" O HIS C 268 " (cutoff:3.500A) removed outlier: 6.230A 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: 6.447A pdb=" N ILE D 104 " --> pdb=" O ILE D 122 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N GLN D 124 " --> pdb=" O ILE D 104 " (cutoff:3.500A) removed outlier: 7.326A 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: 4.926A pdb=" N ILE E 49 " --> pdb=" O ALA E 62 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ASP E 64 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL E 47 " --> pdb=" O ASP E 64 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N THR E 66 " --> pdb=" O GLY E 45 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLY E 45 " --> pdb=" O THR E 66 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N THR E 68 " --> pdb=" O GLU E 43 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLU E 43 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ALA E 70 " --> pdb=" O ALA E 41 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ALA E 41 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL E 72 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ILE E 39 " --> pdb=" O VAL E 72 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LEU E 74 " --> pdb=" O GLU E 37 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N GLU E 37 " --> pdb=" O LEU E 74 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N LYS G 87 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LEU E 46 " --> pdb=" O LYS G 87 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA G 89 " --> pdb=" O LEU E 46 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 138 through 139 removed outlier: 4.616A 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: 6.308A pdb=" N LEU F 123 " --> pdb=" O ILE F 175 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N THR F 177 " --> pdb=" O LEU F 123 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU F 125 " --> pdb=" O THR F 177 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ALA F 95 " --> pdb=" O ILE F 124 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N GLN F 126 " --> pdb=" O ALA F 95 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR F 97 " --> pdb=" O GLN F 126 " (cutoff:3.500A) removed outlier: 6.481A 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: 6.519A pdb=" N SER G 227 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG G 104 " --> pdb=" O ILE G 225 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE G 225 " --> pdb=" O ARG G 104 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ALA G 222 " --> pdb=" O VAL G 256 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL G 256 " --> pdb=" O ALA G 222 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY G 246 " --> pdb=" O VAL G 232 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE G 234 " --> pdb=" O ASN G 244 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ASN G 244 " --> pdb=" O ILE G 234 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR G 270 " --> pdb=" O ASN G 257 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE G 259 " --> pdb=" O HIS G 268 " (cutoff:3.500A) removed outlier: 6.230A 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: 6.447A pdb=" N ILE H 104 " --> pdb=" O ILE H 122 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N GLN H 124 " --> pdb=" O ILE H 104 " (cutoff:3.500A) removed outlier: 7.326A 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: 7.684A pdb=" N GLY I 20 " --> pdb=" O TYR I 15 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N TYR I 15 " --> pdb=" O GLY I 20 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N SER I 22 " --> pdb=" O HIS I 13 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N HIS I 13 " --> pdb=" O SER I 22 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N PHE I 26 " --> pdb=" O ASN I 9 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ASN I 9 " --> pdb=" O PHE I 26 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LEU I 28 " --> pdb=" O SER I 7 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N SER I 7 " --> pdb=" O LEU I 28 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LEU I 11 " --> pdb=" O GLN I 59 " (cutoff:3.500A) removed outlier: 6.480A 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: 6.193A pdb=" N GLY I 86 " --> pdb=" O PHE I 168 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ASP I 170 " --> pdb=" O GLY I 86 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL I 88 " --> pdb=" O ASP I 170 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU I 216 " --> pdb=" O SER I 227 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N SER I 227 " --> pdb=" O LEU I 216 " (cutoff:3.500A) removed outlier: 6.869A 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: 6.734A pdb=" N GLY J 20 " --> pdb=" O LEU J 14 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU J 14 " --> pdb=" O GLY J 20 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N SER J 22 " --> pdb=" O THR J 12 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N THR J 12 " --> pdb=" O SER J 22 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N VAL J 24 " --> pdb=" O ASN J 10 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU J 11 " --> pdb=" O GLN J 59 " (cutoff:3.500A) removed outlier: 6.480A 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: 6.194A pdb=" N GLY J 86 " --> pdb=" O PHE J 168 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ASP J 170 " --> pdb=" O GLY J 86 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL J 88 " --> pdb=" O ASP J 170 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU J 226 " --> pdb=" O VAL J 218 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LYS J 220 " --> pdb=" O VAL J 224 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N VAL J 224 " --> pdb=" O LYS J 220 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 20 through 31 removed outlier: 7.047A pdb=" N LEU K 21 " --> pdb=" O ILE K 12 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ILE K 12 " --> pdb=" O LEU K 21 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL K 23 " --> pdb=" O THR K 10 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N THR K 10 " --> pdb=" O VAL K 23 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ASN K 25 " --> pdb=" O SER K 8 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N SER K 8 " --> pdb=" O ASN K 25 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ALA K 27 " --> pdb=" O ASN K 6 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL K 7 " --> pdb=" O GLU K 62 " (cutoff:3.500A) removed outlier: 6.694A 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 Processing sheet with id=AC7, first strand: chain 'L' and resid 20 through 31 removed outlier: 7.046A pdb=" N LEU L 21 " --> pdb=" O ILE L 12 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ILE L 12 " --> pdb=" O LEU L 21 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL L 23 " --> pdb=" O THR L 10 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N THR L 10 " --> pdb=" O VAL L 23 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ASN L 25 " --> pdb=" O SER L 8 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N SER L 8 " --> pdb=" O ASN L 25 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ALA L 27 " --> pdb=" O ASN L 6 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL L 7 " --> pdb=" O GLU L 62 " (cutoff:3.500A) removed outlier: 6.703A 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 1111 hydrogen bonds defined for protein. 3075 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: 12.74 Time building geometry restraints manager: 5.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.14: 22388 1.14 - 1.44: 9617 1.44 - 1.74: 13196 1.74 - 2.04: 168 2.04 - 2.34: 4 Bond restraints: 45373 Sorted by residual: bond pdb=" C HIS G 219 " pdb=" O HIS G 219 " ideal model delta sigma weight residual 1.235 1.137 0.098 4.70e-03 4.53e+04 4.35e+02 bond pdb=" C HIS C 219 " pdb=" O HIS C 219 " ideal model delta sigma weight residual 1.235 1.140 0.095 4.70e-03 4.53e+04 4.04e+02 bond pdb=" C VAL G 245 " pdb=" O VAL G 245 " ideal model delta sigma weight residual 1.239 1.017 0.222 1.13e-02 7.83e+03 3.86e+02 bond pdb=" C VAL C 245 " pdb=" O VAL C 245 " ideal model delta sigma weight residual 1.239 1.017 0.222 1.13e-02 7.83e+03 3.86e+02 bond pdb=" C GLY D 151 " pdb=" O GLY D 151 " ideal model delta sigma weight residual 1.234 1.008 0.225 1.20e-02 6.94e+03 3.52e+02 ... (remaining 45368 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.48: 81367 3.48 - 6.96: 628 6.96 - 10.44: 64 10.44 - 13.92: 5 13.92 - 17.40: 10 Bond angle restraints: 82074 Sorted by residual: angle pdb=" C TYR H 171 " pdb=" CA TYR H 171 " pdb=" CB TYR H 171 " ideal model delta sigma weight residual 110.67 127.35 -16.68 2.23e+00 2.01e-01 5.60e+01 angle pdb=" C TYR D 171 " pdb=" CA TYR D 171 " pdb=" CB TYR D 171 " ideal model delta sigma weight residual 110.67 127.22 -16.55 2.23e+00 2.01e-01 5.51e+01 angle pdb=" N PRO G 220 " pdb=" CA PRO G 220 " pdb=" CB PRO G 220 " ideal model delta sigma weight residual 103.19 110.14 -6.95 9.50e-01 1.11e+00 5.35e+01 angle pdb=" CA GLU C 340 " pdb=" C GLU C 340 " pdb=" O GLU C 340 " ideal model delta sigma weight residual 120.90 113.11 7.79 1.07e+00 8.73e-01 5.29e+01 angle pdb=" N ALA G 339 " pdb=" CA ALA G 339 " pdb=" C ALA G 339 " ideal model delta sigma weight residual 111.14 103.46 7.68 1.08e+00 8.57e-01 5.05e+01 ... (remaining 82069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.12: 20656 35.12 - 70.25: 640 70.25 - 105.37: 51 105.37 - 140.49: 8 140.49 - 175.62: 2 Dihedral angle restraints: 21357 sinusoidal: 11932 harmonic: 9425 Sorted by residual: dihedral pdb=" C5' ADP J1000 " pdb=" O5' ADP J1000 " pdb=" PA ADP J1000 " pdb=" O2A ADP J1000 " ideal model delta sinusoidal sigma weight residual -60.00 -170.73 110.73 1 2.00e+01 2.50e-03 3.25e+01 dihedral pdb=" C5' ADP I1000 " pdb=" O5' ADP I1000 " pdb=" PA ADP I1000 " pdb=" O2A ADP I1000 " ideal model delta sinusoidal sigma weight residual -60.00 -170.68 110.68 1 2.00e+01 2.50e-03 3.25e+01 dihedral pdb=" C PHE G 221 " pdb=" N PHE G 221 " pdb=" CA PHE G 221 " pdb=" CB PHE G 221 " ideal model delta harmonic sigma weight residual -122.60 -109.18 -13.42 0 2.50e+00 1.60e-01 2.88e+01 ... (remaining 21354 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3167 0.079 - 0.158: 333 0.158 - 0.238: 37 0.238 - 0.317: 28 0.317 - 0.396: 11 Chirality restraints: 3576 Sorted by residual: chirality pdb=" C04 I9X D1001 " pdb=" C03 I9X D1001 " pdb=" O10 I9X D1001 " pdb=" P08 I9X D1001 " both_signs ideal model delta sigma weight residual True 1.45 -1.84 -0.40 2.00e-01 2.50e+01 3.92e+00 chirality pdb=" C04 I9X H1001 " pdb=" C03 I9X H1001 " pdb=" O10 I9X H1001 " pdb=" P08 I9X H1001 " both_signs ideal model delta sigma weight residual True 1.45 -1.84 -0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" CA THR F 162 " pdb=" N THR F 162 " pdb=" C THR F 162 " pdb=" CB THR F 162 " both_signs ideal model delta sigma weight residual False 2.53 2.16 0.37 2.00e-01 2.50e+01 3.42e+00 ... (remaining 3573 not shown) Planarity restraints: 6818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN K 6 " -0.015 2.00e-02 2.50e+03 4.42e-01 2.93e+03 pdb=" CG ASN K 6 " 0.006 2.00e-02 2.50e+03 pdb=" OD1 ASN K 6 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN K 6 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN K 6 " 0.763 2.00e-02 2.50e+03 pdb="HD22 ASN K 6 " -0.768 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN K 25 " -0.097 2.00e-02 2.50e+03 4.37e-01 2.87e+03 pdb=" CG ASN K 25 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN K 25 " 0.090 2.00e-02 2.50e+03 pdb=" ND2 ASN K 25 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN K 25 " 0.744 2.00e-02 2.50e+03 pdb="HD22 ASN K 25 " -0.759 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 244 " 0.119 2.00e-02 2.50e+03 4.33e-01 2.82e+03 pdb=" CG ASN C 244 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN C 244 " -0.106 2.00e-02 2.50e+03 pdb=" ND2 ASN C 244 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN C 244 " 0.749 2.00e-02 2.50e+03 pdb="HD22 ASN C 244 " -0.735 2.00e-02 2.50e+03 ... (remaining 6815 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 2269 2.16 - 2.77: 90403 2.77 - 3.38: 145217 3.38 - 3.99: 194915 3.99 - 4.60: 294903 Nonbonded interactions: 727707 Sorted by model distance: nonbonded pdb=" H GLY J 41 " pdb=" O2B ADP J1000 " model vdw 1.549 2.450 nonbonded pdb=" H GLY I 41 " pdb=" O2B ADP I1000 " model vdw 1.549 2.450 nonbonded pdb=" HG1 THR J 45 " pdb="MG MG J1002 " model vdw 1.565 1.700 nonbonded pdb=" HG1 THR I 45 " pdb="MG MG I1002 " model vdw 1.565 1.700 nonbonded pdb=" O PHE C 325 " pdb=" HD1 HIS C 328 " model vdw 1.592 2.450 ... (remaining 727702 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and (resid 1 through 15 or (resid 16 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE \ 1)) or resid 17 through 1000)) } 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: 7.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.390 Extract box with map and model: 0.750 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 55.260 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 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 : 0.013 0.328 23028 Z= 0.885 Angle : 1.010 17.402 31334 Z= 0.626 Chirality : 0.057 0.396 3576 Planarity : 0.009 0.258 4098 Dihedral : 15.882 175.618 8644 Min Nonbonded Distance : 1.723 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.83 % Allowed : 7.88 % Favored : 91.29 % Cbeta Deviations : 0.34 % 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: 1.32 (0.16), residues: 2864 helix: 1.76 (0.16), residues: 1134 sheet: 0.04 (0.24), residues: 492 loop : 0.55 (0.18), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG D 18 TYR 0.044 0.003 TYR H 158 PHE 0.099 0.003 PHE L 98 TRP 0.032 0.002 TRP A 83 HIS 0.020 0.001 HIS G 219 Details of bonding type rmsd/Z covalent geometry : bond 0.01215 / 0.88 (23016) covalent geometry : angle 1.00698 / 0.63 (31322) hydrogen bonds : bond 0.12462 / 8.57 ( 1111) hydrogen bonds : angle 6.16783 / 4.47 ( 3075) metal coordination : bond 0.13004 / 7.93 ( 12) metal coordination : angle 3.97031 / 2.33 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 338 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 318 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 7 residues processed: 334 average time/residue: 1.6103 time to fit residues: 615.7896 Evaluate side-chains 288 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 281 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain D residue 262 ARG Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 194 CYS Chi-restraints excluded: chain H residue 262 ARG Chi-restraints excluded: chain H residue 276 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 3.9990 chunk 183 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 62.9389 > 50:) chunk 111 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 162 GLN C 268 HIS D 274 GLN F 190 HIS G 162 GLN G 268 HIS H 274 GLN I 137 ASN I 223 GLN J 137 ASN J 223 GLN K 6 ASN K 40 HIS K 137 ASN L 6 ASN L 40 HIS L 137 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.104274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.079782 restraints weight = 77006.553| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.46 r_work: 0.2931 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23028 Z= 0.141 Angle : 0.573 6.364 31334 Z= 0.291 Chirality : 0.042 0.154 3576 Planarity : 0.005 0.074 4098 Dihedral : 10.774 177.513 3312 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.67 % Allowed : 9.08 % Favored : 90.25 % 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: 1.46 (0.16), residues: 2864 helix: 1.93 (0.16), residues: 1146 sheet: 0.05 (0.24), residues: 482 loop : 0.59 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 18 TYR 0.016 0.002 TYR D 214 PHE 0.015 0.001 PHE B 18 TRP 0.014 0.001 TRP E 11 HIS 0.006 0.001 HIS C 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (23016) covalent geometry : angle 0.56800 / 0.29 (31322) hydrogen bonds : bond 0.04519 / 3.10 ( 1111) hydrogen bonds : angle 5.36113 / 3.85 ( 3075) metal coordination : bond 0.00945 / 0.60 ( 12) metal coordination : angle 3.84310 / 2.25 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 293 time to evaluate : 1.205 Fit side-chains REVERT: A 12 MET cc_start: 0.8992 (mtp) cc_final: 0.8785 (mtp) REVERT: E 143 THR cc_start: 0.8914 (p) cc_final: 0.8695 (t) outliers start: 16 outliers final: 7 residues processed: 301 average time/residue: 1.4216 time to fit residues: 488.1272 Evaluate side-chains 277 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 270 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain J residue 23 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 69 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 260 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 262 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 182 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 42 GLN C 19 GLN F 42 GLN G 19 GLN I 137 ASN I 223 GLN J 137 ASN J 223 GLN K 6 ASN K 137 ASN K 213 ASN L 137 ASN L 213 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.100468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.075880 restraints weight = 78347.551| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.46 r_work: 0.2871 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 23028 Z= 0.208 Angle : 0.584 6.998 31334 Z= 0.302 Chirality : 0.043 0.185 3576 Planarity : 0.005 0.071 4098 Dihedral : 10.695 176.478 3300 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.83 % Allowed : 9.46 % Favored : 89.71 % 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: 2864 helix: 1.88 (0.15), residues: 1144 sheet: 0.11 (0.25), residues: 484 loop : 0.61 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 26 TYR 0.017 0.002 TYR I 241 PHE 0.017 0.002 PHE F 18 TRP 0.014 0.001 TRP A 11 HIS 0.005 0.001 HIS C 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.21 (23016) covalent geometry : angle 0.58033 / 0.30 (31322) hydrogen bonds : bond 0.04848 / 3.32 ( 1111) hydrogen bonds : angle 5.26080 / 3.78 ( 3075) metal coordination : bond 0.01000 / 0.64 ( 12) metal coordination : angle 3.39581 / 1.97 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 297 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 277 time to evaluate : 0.922 Fit side-chains REVERT: B 135 MET cc_start: 0.8474 (tpp) cc_final: 0.8250 (tpp) REVERT: C 104 ARG cc_start: 0.9118 (OUTLIER) cc_final: 0.7871 (tmt90) REVERT: E 143 THR cc_start: 0.8920 (p) cc_final: 0.8716 (t) REVERT: G 104 ARG cc_start: 0.9111 (OUTLIER) cc_final: 0.7865 (tmt90) REVERT: K 68 LYS cc_start: 0.8717 (mmmm) cc_final: 0.8146 (mmmm) REVERT: L 61 ASP cc_start: 0.8479 (m-30) cc_final: 0.8171 (m-30) REVERT: L 68 LYS cc_start: 0.8733 (mmmm) cc_final: 0.8247 (mmmm) outliers start: 20 outliers final: 11 residues processed: 289 average time/residue: 1.3001 time to fit residues: 429.3993 Evaluate side-chains 278 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 265 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 82 ASN Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 82 ASN Chi-restraints excluded: chain G residue 104 ARG Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain I residue 84 GLU Chi-restraints excluded: chain J residue 84 GLU Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain L residue 48 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 112 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 259 optimal weight: 4.9990 chunk 161 optimal weight: 0.5980 chunk 192 optimal weight: 0.5980 chunk 258 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 211 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 223 GLN J 223 GLN K 6 ASN K 64 GLN K 137 ASN L 6 ASN L 64 GLN L 137 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.101480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.077038 restraints weight = 78801.453| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.46 r_work: 0.2885 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23028 Z= 0.150 Angle : 0.550 6.522 31334 Z= 0.282 Chirality : 0.042 0.162 3576 Planarity : 0.004 0.066 4098 Dihedral : 10.471 179.106 3300 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.08 % Allowed : 9.46 % Favored : 89.46 % 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: 2864 helix: 1.94 (0.16), residues: 1144 sheet: 0.08 (0.25), residues: 486 loop : 0.60 (0.18), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 26 TYR 0.016 0.002 TYR H 214 PHE 0.015 0.001 PHE F 18 TRP 0.014 0.001 TRP E 11 HIS 0.005 0.001 HIS C 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (23016) covalent geometry : angle 0.54623 / 0.28 (31322) hydrogen bonds : bond 0.04325 / 2.96 ( 1111) hydrogen bonds : angle 5.12890 / 3.68 ( 3075) metal coordination : bond 0.00941 / 0.60 ( 12) metal coordination : angle 3.38814 / 1.99 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 299 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 273 time to evaluate : 0.867 Fit side-chains REVERT: B 135 MET cc_start: 0.8473 (tpp) cc_final: 0.8237 (tpp) REVERT: C 104 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.7623 (tmt90) REVERT: G 104 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.7611 (tmt90) REVERT: K 61 ASP cc_start: 0.8463 (m-30) cc_final: 0.8137 (m-30) REVERT: L 61 ASP cc_start: 0.8485 (m-30) cc_final: 0.8154 (m-30) outliers start: 26 outliers final: 14 residues processed: 291 average time/residue: 1.0646 time to fit residues: 354.0751 Evaluate side-chains 280 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 264 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 82 ASN Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 82 ASN Chi-restraints excluded: chain G residue 104 ARG Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 84 GLU Chi-restraints excluded: chain J residue 23 ASP Chi-restraints excluded: chain J residue 84 GLU Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain L residue 48 SER Chi-restraints excluded: chain L residue 140 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 124 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 146 optimal weight: 0.0870 chunk 227 optimal weight: 2.9990 chunk 166 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 171 optimal weight: 0.9980 chunk 194 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 273 optimal weight: 1.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 223 GLN J 223 GLN K 6 ASN K 137 ASN K 213 ASN L 6 ASN L 64 GLN L 137 ASN L 213 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.102426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.077884 restraints weight = 78298.038| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.47 r_work: 0.2904 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 23028 Z= 0.128 Angle : 0.531 6.244 31334 Z= 0.271 Chirality : 0.042 0.154 3576 Planarity : 0.004 0.070 4098 Dihedral : 10.282 179.734 3300 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.71 % Allowed : 9.71 % Favored : 89.58 % 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: 1.57 (0.16), residues: 2864 helix: 2.06 (0.16), residues: 1146 sheet: 0.04 (0.25), residues: 488 loop : 0.65 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 26 TYR 0.017 0.001 TYR H 214 PHE 0.013 0.001 PHE B 18 TRP 0.016 0.001 TRP E 11 HIS 0.005 0.001 HIS C 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (23016) covalent geometry : angle 0.52720 / 0.27 (31322) hydrogen bonds : bond 0.04017 / 2.75 ( 1111) hydrogen bonds : angle 4.97826 / 3.57 ( 3075) metal coordination : bond 0.00653 / 0.42 ( 12) metal coordination : angle 3.37450 / 1.98 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 276 time to evaluate : 0.768 Fit side-chains REVERT: B 135 MET cc_start: 0.8495 (tpp) cc_final: 0.8241 (tpp) REVERT: K 61 ASP cc_start: 0.8452 (m-30) cc_final: 0.8134 (m-30) REVERT: K 68 LYS cc_start: 0.8711 (mmmm) cc_final: 0.8314 (mmmm) REVERT: L 61 ASP cc_start: 0.8502 (m-30) cc_final: 0.8180 (m-30) REVERT: L 68 LYS cc_start: 0.8711 (mmmm) cc_final: 0.8320 (mmmm) outliers start: 17 outliers final: 11 residues processed: 287 average time/residue: 0.9987 time to fit residues: 327.3882 Evaluate side-chains 277 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 266 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 82 ASN Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 82 ASN Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain I residue 84 GLU Chi-restraints excluded: chain J residue 84 GLU Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain L residue 48 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 55 optimal weight: 2.9990 chunk 181 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 223 GLN J 223 GLN K 64 GLN K 137 ASN L 137 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.100044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.075369 restraints weight = 79127.467| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.47 r_work: 0.2858 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 23028 Z= 0.228 Angle : 0.583 6.896 31334 Z= 0.302 Chirality : 0.044 0.192 3576 Planarity : 0.005 0.070 4098 Dihedral : 10.520 178.215 3300 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.96 % Allowed : 9.79 % Favored : 89.25 % 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: 1.46 (0.16), residues: 2864 helix: 1.89 (0.15), residues: 1144 sheet: 0.12 (0.25), residues: 482 loop : 0.60 (0.18), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 26 TYR 0.018 0.002 TYR I 241 PHE 0.017 0.002 PHE B 18 TRP 0.015 0.001 TRP E 11 HIS 0.005 0.001 HIS C 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.23 (23016) covalent geometry : angle 0.57932 / 0.30 (31322) hydrogen bonds : bond 0.04710 / 3.22 ( 1111) hydrogen bonds : angle 5.15795 / 3.70 ( 3075) metal coordination : bond 0.01022 / 0.67 ( 12) metal coordination : angle 3.47035 / 1.99 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 294 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 271 time to evaluate : 0.822 Fit side-chains revert: symmetry clash REVERT: A 31 ASN cc_start: 0.8313 (t0) cc_final: 0.7826 (p0) REVERT: B 135 MET cc_start: 0.8496 (tpp) cc_final: 0.8276 (tpp) REVERT: C 104 ARG cc_start: 0.9136 (OUTLIER) cc_final: 0.7748 (tmt90) REVERT: E 31 ASN cc_start: 0.8344 (t0) cc_final: 0.7854 (p0) REVERT: G 104 ARG cc_start: 0.9132 (OUTLIER) cc_final: 0.7750 (tmt90) REVERT: K 61 ASP cc_start: 0.8482 (m-30) cc_final: 0.8115 (m-30) REVERT: L 61 ASP cc_start: 0.8504 (m-30) cc_final: 0.8177 (m-30) outliers start: 23 outliers final: 13 residues processed: 286 average time/residue: 0.9840 time to fit residues: 321.4811 Evaluate side-chains 281 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 266 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 82 ASN Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 82 ASN Chi-restraints excluded: chain G residue 104 ARG Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain I residue 84 GLU Chi-restraints excluded: chain J residue 84 GLU Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain L residue 48 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 8 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 190 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 243 optimal weight: 0.7980 chunk 123 optimal weight: 0.5980 chunk 276 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 223 GLN J 223 GLN K 213 ASN L 64 GLN L 213 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.101875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.077362 restraints weight = 78395.980| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.47 r_work: 0.2896 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 23028 Z= 0.132 Angle : 0.540 6.369 31334 Z= 0.276 Chirality : 0.042 0.157 3576 Planarity : 0.004 0.073 4098 Dihedral : 10.301 179.685 3300 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.67 % Allowed : 10.00 % Favored : 89.33 % 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: 1.54 (0.16), residues: 2864 helix: 2.03 (0.16), residues: 1146 sheet: 0.04 (0.25), residues: 484 loop : 0.61 (0.18), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 26 TYR 0.017 0.002 TYR D 214 PHE 0.013 0.001 PHE F 18 TRP 0.015 0.001 TRP E 11 HIS 0.005 0.001 HIS C 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (23016) covalent geometry : angle 0.53618 / 0.28 (31322) hydrogen bonds : bond 0.04076 / 2.79 ( 1111) hydrogen bonds : angle 4.99039 / 3.57 ( 3075) metal coordination : bond 0.00725 / 0.47 ( 12) metal coordination : angle 3.35463 / 1.96 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 286 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 270 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 ASN cc_start: 0.8296 (t0) cc_final: 0.7828 (p0) REVERT: A 109 GLN cc_start: 0.8082 (tp-100) cc_final: 0.7834 (tp-100) REVERT: B 135 MET cc_start: 0.8533 (tpp) cc_final: 0.8209 (tpp) REVERT: C 104 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.7635 (tmt90) REVERT: E 31 ASN cc_start: 0.8299 (t0) cc_final: 0.7827 (p0) REVERT: E 109 GLN cc_start: 0.8083 (tp-100) cc_final: 0.7844 (tp-100) REVERT: G 104 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.7632 (tmt90) REVERT: K 61 ASP cc_start: 0.8477 (m-30) cc_final: 0.8110 (m-30) REVERT: K 68 LYS cc_start: 0.8717 (mmmm) cc_final: 0.8274 (mmmm) REVERT: L 61 ASP cc_start: 0.8508 (m-30) cc_final: 0.8175 (m-30) REVERT: L 68 LYS cc_start: 0.8722 (mmmm) cc_final: 0.8282 (mmmm) outliers start: 16 outliers final: 11 residues processed: 282 average time/residue: 0.9963 time to fit residues: 320.4271 Evaluate side-chains 280 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 267 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 82 ASN Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 82 ASN Chi-restraints excluded: chain G residue 104 ARG Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain I residue 84 GLU Chi-restraints excluded: chain J residue 84 GLU Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain L residue 48 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 17 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 167 optimal weight: 0.9980 chunk 281 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 223 GLN J 223 GLN K 64 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.100307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.075592 restraints weight = 79209.538| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 1.48 r_work: 0.2864 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 23028 Z= 0.207 Angle : 0.573 6.748 31334 Z= 0.296 Chirality : 0.043 0.188 3576 Planarity : 0.005 0.065 4098 Dihedral : 10.455 178.724 3300 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.92 % Allowed : 9.62 % Favored : 89.46 % 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: 2864 helix: 1.93 (0.16), residues: 1144 sheet: 0.13 (0.25), residues: 480 loop : 0.60 (0.18), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 134 TYR 0.018 0.002 TYR I 241 PHE 0.016 0.002 PHE B 18 TRP 0.015 0.001 TRP E 11 HIS 0.005 0.001 HIS C 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.21 (23016) covalent geometry : angle 0.56876 / 0.30 (31322) hydrogen bonds : bond 0.04536 / 3.10 ( 1111) hydrogen bonds : angle 5.10246 / 3.66 ( 3075) metal coordination : bond 0.01021 / 0.66 ( 12) metal coordination : angle 3.39880 / 1.96 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 297 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 275 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: A 31 ASN cc_start: 0.8314 (t0) cc_final: 0.7851 (p0) REVERT: C 104 ARG cc_start: 0.9126 (OUTLIER) cc_final: 0.7742 (tmt90) REVERT: E 31 ASN cc_start: 0.8308 (t0) cc_final: 0.7831 (p0) REVERT: G 104 ARG cc_start: 0.9120 (OUTLIER) cc_final: 0.7737 (tmt90) REVERT: K 61 ASP cc_start: 0.8485 (m-30) cc_final: 0.8115 (m-30) REVERT: K 68 LYS cc_start: 0.8756 (mmmm) cc_final: 0.8225 (mmmm) REVERT: L 61 ASP cc_start: 0.8511 (m-30) cc_final: 0.8191 (m-30) REVERT: L 68 LYS cc_start: 0.8760 (mmmm) cc_final: 0.8233 (mmmm) outliers start: 22 outliers final: 11 residues processed: 289 average time/residue: 0.9692 time to fit residues: 320.3799 Evaluate side-chains 278 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 265 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 82 ASN Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 82 ASN Chi-restraints excluded: chain G residue 104 ARG Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain I residue 84 GLU Chi-restraints excluded: chain J residue 84 GLU Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain L residue 48 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 233 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 277 optimal weight: 2.9990 chunk 269 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 137 optimal weight: 0.9980 chunk 196 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 223 GLN J 223 GLN K 32 ASN K 64 GLN L 32 ASN L 64 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.101235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.076465 restraints weight = 79251.550| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.47 r_work: 0.2881 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 23028 Z= 0.161 Angle : 0.556 6.544 31334 Z= 0.286 Chirality : 0.042 0.171 3576 Planarity : 0.005 0.080 4098 Dihedral : 10.366 179.196 3300 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.67 % Allowed : 10.04 % Favored : 89.29 % 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: 1.51 (0.16), residues: 2864 helix: 1.96 (0.16), residues: 1146 sheet: 0.12 (0.25), residues: 480 loop : 0.61 (0.18), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG K 26 TYR 0.016 0.002 TYR I 241 PHE 0.015 0.002 PHE F 18 TRP 0.015 0.001 TRP A 11 HIS 0.005 0.001 HIS C 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (23016) covalent geometry : angle 0.55221 / 0.29 (31322) hydrogen bonds : bond 0.04268 / 2.92 ( 1111) hydrogen bonds : angle 5.03131 / 3.60 ( 3075) metal coordination : bond 0.00801 / 0.51 ( 12) metal coordination : angle 3.33237 / 1.95 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 288 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 272 time to evaluate : 0.767 Fit side-chains revert: symmetry clash REVERT: A 31 ASN cc_start: 0.8284 (t0) cc_final: 0.7832 (p0) REVERT: A 109 GLN cc_start: 0.8103 (tp-100) cc_final: 0.7877 (tp-100) REVERT: C 104 ARG cc_start: 0.9122 (OUTLIER) cc_final: 0.7748 (tmt90) REVERT: E 31 ASN cc_start: 0.8253 (t0) cc_final: 0.7813 (p0) REVERT: E 109 GLN cc_start: 0.8098 (tp-100) cc_final: 0.7870 (tp-100) REVERT: G 104 ARG cc_start: 0.9113 (OUTLIER) cc_final: 0.7737 (tmt90) REVERT: K 61 ASP cc_start: 0.8475 (m-30) cc_final: 0.8110 (m-30) REVERT: K 68 LYS cc_start: 0.8759 (mmmm) cc_final: 0.8230 (mmmm) REVERT: L 61 ASP cc_start: 0.8501 (m-30) cc_final: 0.8173 (m-30) REVERT: L 68 LYS cc_start: 0.8759 (mmmm) cc_final: 0.8240 (mmmm) outliers start: 16 outliers final: 10 residues processed: 284 average time/residue: 0.9058 time to fit residues: 293.6679 Evaluate side-chains 283 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 271 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 82 ASN Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 82 ASN Chi-restraints excluded: chain G residue 104 ARG Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain I residue 84 GLU Chi-restraints excluded: chain J residue 84 GLU Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain L residue 48 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 65 optimal weight: 1.9990 chunk 232 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 262 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 278 optimal weight: 0.6980 chunk 283 optimal weight: 4.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 223 GLN J 223 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.099735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.075045 restraints weight = 79671.162| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 1.48 r_work: 0.2854 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 23028 Z= 0.226 Angle : 0.591 6.935 31334 Z= 0.307 Chirality : 0.044 0.196 3576 Planarity : 0.005 0.083 4098 Dihedral : 10.524 178.016 3299 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.67 % Allowed : 10.08 % Favored : 89.25 % 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: 1.44 (0.16), residues: 2864 helix: 1.84 (0.15), residues: 1142 sheet: 0.20 (0.25), residues: 476 loop : 0.57 (0.18), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 26 TYR 0.018 0.002 TYR I 241 PHE 0.017 0.002 PHE F 18 TRP 0.015 0.001 TRP A 11 HIS 0.004 0.001 HIS J 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.23 (23016) covalent geometry : angle 0.58740 / 0.31 (31322) hydrogen bonds : bond 0.04710 / 3.22 ( 1111) hydrogen bonds : angle 5.15698 / 3.69 ( 3075) metal coordination : bond 0.01024 / 0.66 ( 12) metal coordination : angle 3.41425 / 1.96 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 288 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 272 time to evaluate : 0.739 Fit side-chains revert: symmetry clash REVERT: A 31 ASN cc_start: 0.8276 (t0) cc_final: 0.7829 (p0) REVERT: A 109 GLN cc_start: 0.8087 (tp-100) cc_final: 0.7816 (tp-100) REVERT: C 104 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.7786 (tmt90) REVERT: E 31 ASN cc_start: 0.8280 (t0) cc_final: 0.7831 (p0) REVERT: E 109 GLN cc_start: 0.8083 (tp-100) cc_final: 0.7815 (tp-100) REVERT: G 104 ARG cc_start: 0.9132 (OUTLIER) cc_final: 0.7757 (tmt90) REVERT: K 61 ASP cc_start: 0.8502 (m-30) cc_final: 0.8159 (m-30) REVERT: L 61 ASP cc_start: 0.8504 (m-30) cc_final: 0.8172 (m-30) outliers start: 16 outliers final: 10 residues processed: 281 average time/residue: 0.9211 time to fit residues: 295.3200 Evaluate side-chains 280 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 268 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 82 ASN Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 82 ASN Chi-restraints excluded: chain G residue 104 ARG Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain I residue 84 GLU Chi-restraints excluded: chain J residue 84 GLU Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain L residue 48 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 84 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 202 optimal weight: 1.9990 chunk 167 optimal weight: 0.9990 chunk 166 optimal weight: 0.8980 chunk 250 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 227 optimal weight: 1.9990 chunk 270 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 223 GLN J 223 GLN K 64 GLN L 64 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.101165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.076613 restraints weight = 79220.017| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.47 r_work: 0.2884 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23028 Z= 0.146 Angle : 0.555 6.477 31334 Z= 0.285 Chirality : 0.042 0.164 3576 Planarity : 0.005 0.083 4098 Dihedral : 10.359 179.467 3299 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.58 % Allowed : 10.04 % Favored : 89.38 % 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: 1.51 (0.16), residues: 2864 helix: 1.96 (0.16), residues: 1146 sheet: 0.09 (0.25), residues: 482 loop : 0.62 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 26 TYR 0.017 0.002 TYR D 214 PHE 0.014 0.001 PHE F 18 TRP 0.015 0.001 TRP A 11 HIS 0.005 0.001 HIS G 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (23016) covalent geometry : angle 0.55123 / 0.29 (31322) hydrogen bonds : bond 0.04203 / 2.88 ( 1111) hydrogen bonds : angle 5.02534 / 3.60 ( 3075) metal coordination : bond 0.00748 / 0.48 ( 12) metal coordination : angle 3.33317 / 1.95 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14081.77 seconds wall clock time: 237 minutes 51.43 seconds (14271.43 seconds total)