Starting phenix.real_space_refine on Thu Dec 26 16:25:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z15_14441/12_2024/7z15_14441_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z15_14441/12_2024/7z15_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_14441/12_2024/7z15_14441.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z15_14441/12_2024/7z15_14441.map" model { file = "/net/cci-nas-00/data/ceres_data/7z15_14441/12_2024/7z15_14441_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z15_14441/12_2024/7z15_14441_neut_trim.cif" } resolution = 1.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 24.37, per 1000 atoms: 0.53 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: 12.71 Conformation dependent library (CDL) restraints added in 4.0 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: 4.24 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: 22.81 Time building geometry restraints manager: 14.85 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 353 or resid 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: 6.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.990 Extract box with map and model: 1.870 Check model and map are aligned: 0.340 Set scattering table: 0.400 Process input model: 121.530 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.210 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: 0.020 Load rotamer database and sin/cos tables:14.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 147.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 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 : 0.012 0.328 23016 Z= 0.822 Angle : 1.007 17.402 31322 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.032 0.002 TRP A 83 HIS 0.020 0.001 HIS G 219 PHE 0.099 0.003 PHE L 98 TYR 0.044 0.003 TYR H 158 ARG 0.029 0.001 ARG D 18 *********************** 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 : 3.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 7 residues processed: 334 average time/residue: 3.4530 time to fit residues: 1310.1930 Evaluate side-chains 291 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 284 time to evaluate : 4.453 ------------------------------------------------------------------------------- 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 239 optimal weight: 0.8980 chunk 215 optimal weight: 0.5980 chunk 119 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 222 optimal weight: 0.6980 chunk 86 optimal weight: 0.5980 chunk 135 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 chunk 257 optimal weight: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 162 GLN C 268 HIS D 274 GLN 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: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23016 Z= 0.181 Angle : 0.566 6.224 31322 Z= 0.289 Chirality : 0.042 0.156 3576 Planarity : 0.005 0.077 4098 Dihedral : 10.695 176.617 3312 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.75 % Allowed : 9.08 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.16), residues: 2864 helix: 1.93 (0.16), residues: 1146 sheet: 0.03 (0.24), residues: 482 loop : 0.59 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 11 HIS 0.006 0.001 HIS C 353 PHE 0.014 0.001 PHE F 18 TYR 0.016 0.001 TYR H 214 ARG 0.011 0.000 ARG H 18 *********************** 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 308 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 290 time to evaluate : 4.012 Fit side-chains outliers start: 18 outliers final: 7 residues processed: 300 average time/residue: 3.5368 time to fit residues: 1202.2455 Evaluate side-chains 278 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 271 time to evaluate : 3.716 ------------------------------------------------------------------------------- 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 143 optimal weight: 0.2980 chunk 80 optimal weight: 0.9980 chunk 214 optimal weight: 1.9990 chunk 175 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 258 optimal weight: 4.9990 chunk 279 optimal weight: 0.3980 chunk 230 optimal weight: 2.9990 chunk 256 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 HIS D 274 GLN F 190 HIS H 274 GLN I 137 ASN I 152 GLN I 223 GLN J 137 ASN J 152 GLN 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: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23016 Z= 0.180 Angle : 0.524 6.230 31322 Z= 0.269 Chirality : 0.042 0.152 3576 Planarity : 0.004 0.081 4098 Dihedral : 10.294 178.381 3300 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.88 % Allowed : 9.00 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.16), residues: 2864 helix: 2.09 (0.16), residues: 1144 sheet: 0.05 (0.24), residues: 484 loop : 0.69 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 11 HIS 0.007 0.001 HIS G 353 PHE 0.013 0.001 PHE F 18 TYR 0.015 0.001 TYR H 214 ARG 0.009 0.000 ARG L 26 *********************** 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 299 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 278 time to evaluate : 4.339 Fit side-chains outliers start: 21 outliers final: 11 residues processed: 290 average time/residue: 3.3647 time to fit residues: 1110.1226 Evaluate side-chains 276 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 265 time to evaluate : 3.855 ------------------------------------------------------------------------------- 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 223 GLU 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 J residue 23 ASP 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 255 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 173 optimal weight: 1.9990 chunk 259 optimal weight: 5.9990 chunk 274 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 245 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 274 GLN H 274 GLN I 137 ASN I 152 GLN I 223 GLN J 137 ASN J 152 GLN J 223 GLN K 6 ASN L 6 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 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 : 0.005 0.048 23016 Z= 0.314 Angle : 0.572 6.756 31322 Z= 0.298 Chirality : 0.043 0.185 3576 Planarity : 0.005 0.067 4098 Dihedral : 10.482 178.442 3300 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.17 % Allowed : 9.08 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.16), residues: 2864 helix: 1.94 (0.16), residues: 1144 sheet: 0.10 (0.25), residues: 486 loop : 0.63 (0.18), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 11 HIS 0.007 0.001 HIS C 353 PHE 0.017 0.002 PHE F 18 TYR 0.017 0.002 TYR I 241 ARG 0.012 0.001 ARG I 98 *********************** 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 301 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 273 time to evaluate : 3.734 Fit side-chains REVERT: C 104 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.7400 (tmt90) REVERT: G 104 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7396 (tmt90) outliers start: 28 outliers final: 16 residues processed: 292 average time/residue: 3.2766 time to fit residues: 1088.1533 Evaluate side-chains 283 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 265 time to evaluate : 3.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 ASN 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 C residue 353 HIS Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain F residue 70 ASN 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 353 HIS Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain J residue 23 ASP Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain L residue 48 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 228 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 204 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 234 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 246 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN D 274 GLN H 274 GLN I 223 GLN J 223 GLN K 137 ASN K 213 ASN L 137 ASN L 213 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23016 Z= 0.250 Angle : 0.553 6.688 31322 Z= 0.286 Chirality : 0.042 0.173 3576 Planarity : 0.005 0.068 4098 Dihedral : 10.411 178.630 3300 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.08 % Allowed : 9.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.16), residues: 2864 helix: 1.95 (0.16), residues: 1144 sheet: 0.08 (0.25), residues: 486 loop : 0.62 (0.18), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 11 HIS 0.006 0.001 HIS G 353 PHE 0.015 0.002 PHE B 18 TYR 0.017 0.002 TYR I 241 ARG 0.010 0.000 ARG K 26 *********************** 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 301 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 275 time to evaluate : 3.974 Fit side-chains REVERT: C 104 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.7364 (tmt90) REVERT: G 104 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.7361 (tmt90) outliers start: 26 outliers final: 16 residues processed: 294 average time/residue: 2.9825 time to fit residues: 999.3041 Evaluate side-chains 289 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 271 time to evaluate : 2.947 ------------------------------------------------------------------------------- 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 353 HIS Chi-restraints excluded: chain D residue 223 GLU 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 353 HIS 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 92 optimal weight: 2.9990 chunk 247 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 161 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 274 optimal weight: 0.7980 chunk 228 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 144 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN D 274 GLN H 274 GLN I 223 GLN J 223 GLN K 137 ASN L 137 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 23016 Z= 0.194 Angle : 0.534 6.326 31322 Z= 0.275 Chirality : 0.042 0.161 3576 Planarity : 0.004 0.069 4098 Dihedral : 10.284 179.999 3300 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.04 % Allowed : 9.54 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.16), residues: 2864 helix: 2.03 (0.16), residues: 1146 sheet: 0.07 (0.25), residues: 486 loop : 0.65 (0.18), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 11 HIS 0.006 0.001 HIS G 353 PHE 0.013 0.001 PHE F 18 TYR 0.016 0.001 TYR H 214 ARG 0.010 0.000 ARG L 26 *********************** 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 297 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 272 time to evaluate : 3.735 Fit side-chains REVERT: C 104 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7352 (tmt90) REVERT: G 104 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7348 (tmt90) outliers start: 25 outliers final: 16 residues processed: 288 average time/residue: 3.0465 time to fit residues: 995.2783 Evaluate side-chains 288 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 270 time to evaluate : 3.499 ------------------------------------------------------------------------------- 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 353 HIS Chi-restraints excluded: chain D residue 223 GLU 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 353 HIS 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 264 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 156 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 231 optimal weight: 0.6980 chunk 153 optimal weight: 0.9980 chunk 273 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN D 274 GLN H 274 GLN I 223 GLN J 152 GLN J 223 GLN K 64 GLN K 137 ASN K 213 ASN L 137 ASN L 213 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 23016 Z= 0.203 Angle : 0.534 6.306 31322 Z= 0.275 Chirality : 0.042 0.162 3576 Planarity : 0.004 0.076 4098 Dihedral : 10.239 179.965 3300 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.92 % Allowed : 9.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.16), residues: 2864 helix: 2.05 (0.16), residues: 1146 sheet: 0.05 (0.25), residues: 484 loop : 0.65 (0.18), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 11 HIS 0.006 0.001 HIS G 353 PHE 0.014 0.001 PHE B 18 TYR 0.016 0.002 TYR I 241 ARG 0.013 0.000 ARG L 26 *********************** 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 293 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 271 time to evaluate : 2.972 Fit side-chains REVERT: C 104 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7354 (tmt90) REVERT: G 104 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.7351 (tmt90) outliers start: 22 outliers final: 16 residues processed: 286 average time/residue: 2.7883 time to fit residues: 905.4085 Evaluate side-chains 288 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 270 time to evaluate : 2.881 ------------------------------------------------------------------------------- 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 353 HIS Chi-restraints excluded: chain D residue 223 GLU 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 353 HIS 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 169 optimal weight: 1.9990 chunk 109 optimal weight: 0.0870 chunk 163 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 174 optimal weight: 0.9980 chunk 186 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 215 optimal weight: 1.9990 chunk 249 optimal weight: 2.9990 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN D 274 GLN E 109 GLN H 274 GLN I 223 GLN J 152 GLN J 223 GLN K 137 ASN L 137 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23016 Z= 0.223 Angle : 0.541 6.419 31322 Z= 0.279 Chirality : 0.042 0.168 3576 Planarity : 0.004 0.078 4098 Dihedral : 10.250 179.731 3300 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.96 % Allowed : 9.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.16), residues: 2864 helix: 2.03 (0.16), residues: 1146 sheet: 0.07 (0.25), residues: 484 loop : 0.63 (0.18), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 11 HIS 0.006 0.001 HIS G 353 PHE 0.015 0.001 PHE F 18 TYR 0.016 0.002 TYR I 241 ARG 0.011 0.000 ARG K 26 *********************** 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 296 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 273 time to evaluate : 2.864 Fit side-chains revert: symmetry clash REVERT: C 104 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7361 (tmt90) REVERT: G 104 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7358 (tmt90) outliers start: 23 outliers final: 15 residues processed: 287 average time/residue: 2.7044 time to fit residues: 880.3670 Evaluate side-chains 285 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 268 time to evaluate : 2.788 ------------------------------------------------------------------------------- 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 353 HIS Chi-restraints excluded: chain D residue 223 GLU 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 353 HIS 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 262 optimal weight: 5.9990 chunk 239 optimal weight: 0.6980 chunk 255 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 200 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 241 optimal weight: 0.9980 chunk 254 optimal weight: 0.8980 chunk 167 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN D 274 GLN E 109 GLN H 274 GLN I 223 GLN J 137 ASN J 223 GLN K 32 ASN ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN ** L 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23016 Z= 0.208 Angle : 0.537 6.334 31322 Z= 0.277 Chirality : 0.042 0.163 3576 Planarity : 0.005 0.072 4098 Dihedral : 10.204 179.947 3299 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.71 % Allowed : 10.12 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.16), residues: 2864 helix: 2.06 (0.16), residues: 1146 sheet: 0.09 (0.25), residues: 482 loop : 0.64 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 11 HIS 0.005 0.001 HIS G 353 PHE 0.014 0.001 PHE F 18 TYR 0.016 0.002 TYR I 241 ARG 0.013 0.000 ARG B 134 *********************** 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 286 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 269 time to evaluate : 2.813 Fit side-chains REVERT: C 104 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7356 (tmt90) REVERT: G 104 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7353 (tmt90) outliers start: 17 outliers final: 15 residues processed: 279 average time/residue: 2.7398 time to fit residues: 864.9568 Evaluate side-chains 282 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 265 time to evaluate : 2.892 ------------------------------------------------------------------------------- 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 353 HIS Chi-restraints excluded: chain D residue 223 GLU 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 353 HIS 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 269 optimal weight: 3.9990 chunk 164 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 282 optimal weight: 3.9990 chunk 260 optimal weight: 4.9990 chunk 225 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 178 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN D 274 GLN E 109 GLN H 274 GLN I 137 ASN J 223 GLN ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 23016 Z= 0.314 Angle : 0.574 6.832 31322 Z= 0.299 Chirality : 0.043 0.193 3576 Planarity : 0.004 0.047 4098 Dihedral : 10.388 178.243 3299 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.88 % Allowed : 9.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.16), residues: 2864 helix: 1.91 (0.16), residues: 1144 sheet: 0.22 (0.25), residues: 476 loop : 0.62 (0.18), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 11 HIS 0.005 0.001 HIS G 353 PHE 0.017 0.002 PHE B 18 TYR 0.018 0.002 TYR I 241 ARG 0.011 0.001 ARG F 134 ********************** 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 291 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 270 time to evaluate : 2.595 Fit side-chains REVERT: C 104 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.7428 (tmt90) REVERT: G 104 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7426 (tmt90) outliers start: 21 outliers final: 14 residues processed: 282 average time/residue: 2.6343 time to fit residues: 840.1132 Evaluate side-chains 283 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 267 time to evaluate : 2.765 ------------------------------------------------------------------------------- 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 353 HIS Chi-restraints excluded: chain D residue 223 GLU 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 353 HIS Chi-restraints excluded: chain H residue 276 SER 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 240 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 207 optimal weight: 0.0770 chunk 33 optimal weight: 1.9990 chunk 62 optimal weight: 0.3980 chunk 225 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 231 optimal weight: 0.0980 chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 overall best weight: 0.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN D 274 GLN E 109 GLN H 274 GLN I 223 GLN J 223 GLN K 64 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.102282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.077574 restraints weight = 79289.745| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.50 r_work: 0.2910 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23016 Z= 0.184 Angle : 0.536 6.298 31322 Z= 0.276 Chirality : 0.042 0.155 3576 Planarity : 0.004 0.088 4098 Dihedral : 10.194 179.782 3299 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.79 % Allowed : 10.04 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.16), residues: 2864 helix: 2.07 (0.16), residues: 1146 sheet: 0.17 (0.25), residues: 480 loop : 0.68 (0.18), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 11 HIS 0.005 0.001 HIS G 353 PHE 0.013 0.001 PHE B 18 TYR 0.017 0.001 TYR D 214 ARG 0.020 0.000 ARG L 26 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15760.71 seconds wall clock time: 273 minutes 25.73 seconds (16405.73 seconds total)