Starting phenix.real_space_refine on Sat Aug 8 22:46:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ifm_35421/08_2026/8ifm_35421.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ifm_35421/08_2026/8ifm_35421.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8ifm_35421/08_2026/8ifm_35421.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ifm_35421/08_2026/8ifm_35421.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ifm_35421/08_2026/8ifm_35421.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ifm_35421/08_2026/8ifm_35421.map" model { file = "/net/cci-nas-00/data/ceres_data/8ifm_35421/08_2026/8ifm_35421.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ifm_35421/08_2026/8ifm_35421.cif" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.088 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: 6 Type Number sf(0) Gaussians P 160 5.49 5 Mg 4 5.21 5 S 84 5.16 5 C 19518 2.51 5 N 5198 2.21 5 O 6030 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30994 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3475 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 12, 'TRANS': 402} Chain breaks: 1 Chain: "B" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3449 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 24, 'TRANS': 403} Chain breaks: 4 Chain: "F" Number of atoms: 3450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3450 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 14, 'TRANS': 397} Chain breaks: 2 Chain: "G" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3449 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 24, 'TRANS': 403} Chain breaks: 4 Chain: "J" Number of atoms: 3475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3475 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 12, 'TRANS': 402} Chain breaks: 1 Chain: "K" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3449 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 24, 'TRANS': 403} Chain breaks: 4 Chain: "N" Number of atoms: 3450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3450 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 14, 'TRANS': 397} Chain breaks: 2 Chain: "O" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3449 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 24, 'TRANS': 403} Chain breaks: 4 Chain: "C" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 423 Classifications: {'RNAv2': 20} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 18} Chain: "D" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 413 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "H" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 423 Classifications: {'RNAv2': 20} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 18} Chain: "I" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 413 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "L" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 423 Classifications: {'RNAv2': 20} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 18} Chain: "M" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 413 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "P" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 423 Classifications: {'RNAv2': 20} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 18} Chain: "Q" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 413 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.42, per 1000 atoms: 0.24 Number of scatterers: 30994 At special positions: 0 Unit cell: (147.4, 202.4, 169.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 84 16.00 P 160 15.00 Mg 4 11.99 O 6030 8.00 N 5198 7.00 C 19518 6.00 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: 2.33 Conformation dependent library (CDL) restraints added in 1.2 seconds 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6384 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 42 sheets defined 37.4% alpha, 24.2% beta 68 base pairs and 110 stacking pairs defined. Time for finding SS restraints: 4.23 Creating SS restraints... Processing helix chain 'A' and resid 15 through 28 Processing helix chain 'A' and resid 34 through 39 Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 71 through 89 Processing helix chain 'A' and resid 123 through 138 Processing helix chain 'A' and resid 148 through 160 removed outlier: 4.201A pdb=" N LEU A 152 " --> pdb=" O SER A 148 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU A 153 " --> pdb=" O LYS A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 203 Processing helix chain 'A' and resid 227 through 231 Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 257 through 280 removed outlier: 3.579A pdb=" N LYS A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 302 No H-bonds generated for 'chain 'A' and resid 300 through 302' Processing helix chain 'A' and resid 353 through 368 removed outlier: 3.785A pdb=" N GLN A 357 " --> pdb=" O SER A 353 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASN A 367 " --> pdb=" O LYS A 363 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TRP A 368 " --> pdb=" O GLN A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 385 Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 22 through 31 Processing helix chain 'B' and resid 46 through 62 removed outlier: 3.648A pdb=" N GLN B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS B 62 " --> pdb=" O ASP B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 83 Processing helix chain 'B' and resid 113 through 131 removed outlier: 3.748A pdb=" N PHE B 121 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 215 Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 248 through 264 Processing helix chain 'B' and resid 331 through 351 Processing helix chain 'B' and resid 366 through 377 Processing helix chain 'B' and resid 451 through 463 Processing helix chain 'B' and resid 477 through 493 removed outlier: 3.964A pdb=" N SER B 493 " --> pdb=" O ILE B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'F' and resid 10 through 29 removed outlier: 5.660A pdb=" N ASP F 16 " --> pdb=" O PRO F 12 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N PHE F 17 " --> pdb=" O GLU F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 38 Processing helix chain 'F' and resid 45 through 56 removed outlier: 3.675A pdb=" N ASN F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 89 Processing helix chain 'F' and resid 109 through 114 removed outlier: 4.363A pdb=" N ARG F 114 " --> pdb=" O ILE F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 138 removed outlier: 4.052A pdb=" N LYS F 137 " --> pdb=" O ASP F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 157 removed outlier: 3.901A pdb=" N SER F 150 " --> pdb=" O ASP F 146 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE F 157 " --> pdb=" O LEU F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 203 removed outlier: 3.837A pdb=" N THR F 202 " --> pdb=" O ASP F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 231 removed outlier: 3.569A pdb=" N GLU F 231 " --> pdb=" O PRO F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 248 Processing helix chain 'F' and resid 257 through 279 Processing helix chain 'F' and resid 300 through 302 No H-bonds generated for 'chain 'F' and resid 300 through 302' Processing helix chain 'F' and resid 353 through 365 removed outlier: 3.651A pdb=" N GLN F 357 " --> pdb=" O SER F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 385 Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 22 through 30 Processing helix chain 'G' and resid 46 through 62 removed outlier: 3.596A pdb=" N GLN G 61 " --> pdb=" O LEU G 57 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS G 62 " --> pdb=" O ASP G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 83 Processing helix chain 'G' and resid 113 through 131 removed outlier: 3.798A pdb=" N PHE G 121 " --> pdb=" O LEU G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 214 Processing helix chain 'G' and resid 226 through 230 Processing helix chain 'G' and resid 248 through 264 Processing helix chain 'G' and resid 331 through 351 Processing helix chain 'G' and resid 366 through 377 Processing helix chain 'G' and resid 451 through 463 Processing helix chain 'G' and resid 477 through 493 removed outlier: 4.138A pdb=" N SER G 493 " --> pdb=" O ILE G 489 " (cutoff:3.500A) Processing helix chain 'G' and resid 502 through 506 Processing helix chain 'J' and resid 15 through 28 Processing helix chain 'J' and resid 44 through 56 Processing helix chain 'J' and resid 65 through 71 removed outlier: 4.047A pdb=" N LYS J 70 " --> pdb=" O THR J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 89 Processing helix chain 'J' and resid 123 through 138 Processing helix chain 'J' and resid 147 through 160 removed outlier: 3.910A pdb=" N ASN J 151 " --> pdb=" O HIS J 147 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LEU J 152 " --> pdb=" O SER J 148 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LEU J 153 " --> pdb=" O LYS J 149 " (cutoff:3.500A) Processing helix chain 'J' and resid 199 through 203 removed outlier: 3.810A pdb=" N LEU J 203 " --> pdb=" O VAL J 200 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 231 Processing helix chain 'J' and resid 243 through 248 Processing helix chain 'J' and resid 257 through 279 Processing helix chain 'J' and resid 300 through 302 No H-bonds generated for 'chain 'J' and resid 300 through 302' Processing helix chain 'J' and resid 354 through 366 Processing helix chain 'J' and resid 369 through 384 Processing helix chain 'K' and resid 15 through 17 No H-bonds generated for 'chain 'K' and resid 15 through 17' Processing helix chain 'K' and resid 22 through 30 Processing helix chain 'K' and resid 46 through 62 removed outlier: 3.695A pdb=" N LYS K 62 " --> pdb=" O ASP K 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 82 Processing helix chain 'K' and resid 113 through 131 removed outlier: 3.675A pdb=" N PHE K 121 " --> pdb=" O LEU K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 205 through 214 removed outlier: 3.542A pdb=" N LEU K 214 " --> pdb=" O LEU K 210 " (cutoff:3.500A) Processing helix chain 'K' and resid 226 through 230 Processing helix chain 'K' and resid 245 through 247 No H-bonds generated for 'chain 'K' and resid 245 through 247' Processing helix chain 'K' and resid 248 through 264 removed outlier: 3.547A pdb=" N ALA K 264 " --> pdb=" O ALA K 260 " (cutoff:3.500A) Processing helix chain 'K' and resid 331 through 351 Processing helix chain 'K' and resid 366 through 377 Processing helix chain 'K' and resid 427 through 430 Processing helix chain 'K' and resid 451 through 463 Processing helix chain 'K' and resid 477 through 493 removed outlier: 3.568A pdb=" N ARG K 481 " --> pdb=" O PRO K 477 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER K 493 " --> pdb=" O ILE K 489 " (cutoff:3.500A) Processing helix chain 'K' and resid 502 through 506 Processing helix chain 'N' and resid 14 through 28 removed outlier: 3.593A pdb=" N THR N 18 " --> pdb=" O ASP N 14 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 55 Processing helix chain 'N' and resid 71 through 89 Processing helix chain 'N' and resid 109 through 114 removed outlier: 3.949A pdb=" N ARG N 114 " --> pdb=" O ILE N 110 " (cutoff:3.500A) Processing helix chain 'N' and resid 123 through 138 Processing helix chain 'N' and resid 146 through 158 removed outlier: 4.429A pdb=" N SER N 150 " --> pdb=" O ASP N 146 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLN N 155 " --> pdb=" O ASN N 151 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLN N 156 " --> pdb=" O LEU N 152 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE N 157 " --> pdb=" O LEU N 153 " (cutoff:3.500A) Processing helix chain 'N' and resid 199 through 203 Processing helix chain 'N' and resid 227 through 231 removed outlier: 3.583A pdb=" N GLU N 231 " --> pdb=" O PRO N 228 " (cutoff:3.500A) Processing helix chain 'N' and resid 243 through 248 Processing helix chain 'N' and resid 257 through 280 removed outlier: 3.531A pdb=" N LYS N 278 " --> pdb=" O GLU N 274 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP N 279 " --> pdb=" O LEU N 275 " (cutoff:3.500A) Processing helix chain 'N' and resid 300 through 302 No H-bonds generated for 'chain 'N' and resid 300 through 302' Processing helix chain 'N' and resid 353 through 366 removed outlier: 3.517A pdb=" N GLN N 357 " --> pdb=" O SER N 353 " (cutoff:3.500A) Processing helix chain 'N' and resid 369 through 385 Processing helix chain 'O' and resid 15 through 17 No H-bonds generated for 'chain 'O' and resid 15 through 17' Processing helix chain 'O' and resid 22 through 30 Processing helix chain 'O' and resid 46 through 62 removed outlier: 3.639A pdb=" N LYS O 62 " --> pdb=" O ASP O 58 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 82 Processing helix chain 'O' and resid 87 through 91 removed outlier: 3.820A pdb=" N ASN O 90 " --> pdb=" O GLU O 87 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE O 91 " --> pdb=" O SER O 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 87 through 91' Processing helix chain 'O' and resid 113 through 131 removed outlier: 3.791A pdb=" N PHE O 121 " --> pdb=" O LEU O 117 " (cutoff:3.500A) Processing helix chain 'O' and resid 205 through 215 Processing helix chain 'O' and resid 226 through 230 Processing helix chain 'O' and resid 248 through 264 removed outlier: 3.732A pdb=" N SER O 257 " --> pdb=" O ALA O 253 " (cutoff:3.500A) Processing helix chain 'O' and resid 331 through 351 Processing helix chain 'O' and resid 366 through 377 Processing helix chain 'O' and resid 451 through 463 Processing helix chain 'O' and resid 477 through 493 removed outlier: 3.957A pdb=" N SER O 493 " --> pdb=" O ILE O 489 " (cutoff:3.500A) Processing helix chain 'O' and resid 502 through 506 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8 removed outlier: 6.568A pdb=" N PHE A 60 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LEU A 97 " --> pdb=" O PHE A 60 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE A 62 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ILE A 118 " --> pdb=" O ILE A 94 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 44 Processing sheet with id=AA3, first strand: chain 'A' and resid 169 through 172 removed outlier: 7.275A pdb=" N LYS A 409 " --> pdb=" O LYS B 2 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N LEU B 4 " --> pdb=" O LYS A 409 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N PHE A 411 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N TYR B 6 " --> pdb=" O PHE A 411 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N GLU B 3 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ILE B 412 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN B 446 " --> pdb=" O GLY B 385 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N GLY B 385 " --> pdb=" O ASN B 446 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL B 357 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N VAL B 386 " --> pdb=" O VAL B 357 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE B 359 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ILE B 388 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ALA B 361 " --> pdb=" O ILE B 388 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL B 278 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LEU B 305 " --> pdb=" O VAL B 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 172 removed outlier: 7.275A pdb=" N LYS A 409 " --> pdb=" O LYS B 2 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N LEU B 4 " --> pdb=" O LYS A 409 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N PHE A 411 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N TYR B 6 " --> pdb=" O PHE A 411 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N GLU B 3 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ILE B 412 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN B 446 " --> pdb=" O GLY B 385 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N GLY B 385 " --> pdb=" O ASN B 446 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL B 357 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N VAL B 386 " --> pdb=" O VAL B 357 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE B 359 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ILE B 388 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ALA B 361 " --> pdb=" O ILE B 388 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL B 278 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LEU B 305 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ASN B 296 " --> pdb=" O TRP B 320 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TRP B 320 " --> pdb=" O ASN B 296 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N CYS B 298 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLY B 318 " --> pdb=" O CYS B 298 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 283 through 286 removed outlier: 6.849A pdb=" N PHE A 291 " --> pdb=" O ALA A 325 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ALA A 325 " --> pdb=" O PHE A 291 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 283 through 286 removed outlier: 6.849A pdb=" N PHE A 291 " --> pdb=" O ALA A 325 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ALA A 325 " --> pdb=" O PHE A 291 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU A 402 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 208 through 210 Processing sheet with id=AA8, first strand: chain 'A' and resid 304 through 305 Processing sheet with id=AA9, first strand: chain 'B' and resid 12 through 13 Processing sheet with id=AB1, first strand: chain 'B' and resid 92 through 95 removed outlier: 6.853A pdb=" N SER B 41 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N LYS B 94 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL B 43 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLY B 42 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE B 142 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL B 44 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N TRP B 139 " --> pdb=" O GLN B 222 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU B 224 " --> pdb=" O TRP B 139 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N VAL B 141 " --> pdb=" O LEU B 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 425 through 426 removed outlier: 3.605A pdb=" N SER B 431 " --> pdb=" O VAL B 426 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 32 through 33 removed outlier: 6.019A pdb=" N ILE F 5 " --> pdb=" O TRP F 33 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LYS F 4 " --> pdb=" O LYS F 59 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU F 61 " --> pdb=" O LYS F 4 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N PHE F 6 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL F 63 " --> pdb=" O PHE F 6 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER F 8 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N ILE F 95 " --> pdb=" O CYS F 58 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N PHE F 60 " --> pdb=" O ILE F 95 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N LEU F 97 " --> pdb=" O PHE F 60 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE F 62 " --> pdb=" O LEU F 97 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N ILE F 118 " --> pdb=" O ILE F 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'F' and resid 169 through 172 removed outlier: 6.659A pdb=" N GLU G 3 " --> pdb=" O ILE G 412 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ILE G 412 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY G 385 " --> pdb=" O ASN G 446 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL G 357 " --> pdb=" O VAL G 384 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL G 386 " --> pdb=" O VAL G 357 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE G 359 " --> pdb=" O VAL G 386 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ILE G 388 " --> pdb=" O ILE G 359 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ALA G 361 " --> pdb=" O ILE G 388 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 169 through 172 removed outlier: 6.659A pdb=" N GLU G 3 " --> pdb=" O ILE G 412 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ILE G 412 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY G 385 " --> pdb=" O ASN G 446 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL G 357 " --> pdb=" O VAL G 384 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL G 386 " --> pdb=" O VAL G 357 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE G 359 " --> pdb=" O VAL G 386 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ILE G 388 " --> pdb=" O ILE G 359 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ALA G 361 " --> pdb=" O ILE G 388 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 327 through 328 removed outlier: 6.663A pdb=" N LEU F 402 " --> pdb=" O ILE F 179 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 208 through 210 removed outlier: 3.611A pdb=" N HIS F 188 " --> pdb=" O LEU F 214 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 283 through 286 Processing sheet with id=AB9, first strand: chain 'F' and resid 283 through 286 Processing sheet with id=AC1, first strand: chain 'F' and resid 304 through 305 Processing sheet with id=AC2, first strand: chain 'G' and resid 12 through 13 Processing sheet with id=AC3, first strand: chain 'G' and resid 92 through 95 removed outlier: 6.686A pdb=" N GLY G 42 " --> pdb=" O PHE G 140 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE G 142 " --> pdb=" O GLY G 42 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL G 44 " --> pdb=" O ILE G 142 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N TRP G 139 " --> pdb=" O GLN G 222 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU G 224 " --> pdb=" O TRP G 139 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N VAL G 141 " --> pdb=" O LEU G 224 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 425 through 426 Processing sheet with id=AC5, first strand: chain 'J' and resid 32 through 33 removed outlier: 6.443A pdb=" N ILE J 5 " --> pdb=" O TRP J 33 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N PHE J 6 " --> pdb=" O LEU J 61 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N VAL J 63 " --> pdb=" O PHE J 6 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N SER J 8 " --> pdb=" O VAL J 63 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N PHE J 60 " --> pdb=" O ILE J 95 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N LEU J 97 " --> pdb=" O PHE J 60 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE J 62 " --> pdb=" O LEU J 97 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE J 118 " --> pdb=" O ILE J 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'J' and resid 169 through 171 removed outlier: 5.693A pdb=" N ILE K 443 " --> pdb=" O THR K 389 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N THR K 389 " --> pdb=" O ILE K 443 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ILE K 445 " --> pdb=" O THR K 387 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N THR K 387 " --> pdb=" O ILE K 445 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS K 447 " --> pdb=" O GLY K 385 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL K 357 " --> pdb=" O VAL K 384 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N VAL K 386 " --> pdb=" O VAL K 357 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE K 359 " --> pdb=" O VAL K 386 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N ILE K 388 " --> pdb=" O ILE K 359 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ALA K 361 " --> pdb=" O ILE K 388 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N CYS K 279 " --> pdb=" O PHE K 358 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N HIS K 360 " --> pdb=" O CYS K 279 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N LEU K 281 " --> pdb=" O HIS K 360 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 169 through 171 removed outlier: 5.693A pdb=" N ILE K 443 " --> pdb=" O THR K 389 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N THR K 389 " --> pdb=" O ILE K 443 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ILE K 445 " --> pdb=" O THR K 387 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N THR K 387 " --> pdb=" O ILE K 445 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS K 447 " --> pdb=" O GLY K 385 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL K 357 " --> pdb=" O VAL K 384 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N VAL K 386 " --> pdb=" O VAL K 357 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE K 359 " --> pdb=" O VAL K 386 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N ILE K 388 " --> pdb=" O ILE K 359 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ALA K 361 " --> pdb=" O ILE K 388 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N CYS K 279 " --> pdb=" O PHE K 358 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N HIS K 360 " --> pdb=" O CYS K 279 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N LEU K 281 " --> pdb=" O HIS K 360 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 311 through 314 removed outlier: 7.111A pdb=" N LEU J 402 " --> pdb=" O ILE J 179 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 208 through 210 removed outlier: 3.528A pdb=" N TYR J 210 " --> pdb=" O TYR J 213 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 283 through 286 Processing sheet with id=AD2, first strand: chain 'J' and resid 304 through 305 Processing sheet with id=AD3, first strand: chain 'K' and resid 12 through 13 Processing sheet with id=AD4, first strand: chain 'K' and resid 91 through 95 removed outlier: 6.537A pdb=" N GLY K 42 " --> pdb=" O PHE K 140 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE K 142 " --> pdb=" O GLY K 42 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL K 44 " --> pdb=" O ILE K 142 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N TRP K 139 " --> pdb=" O GLN K 222 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU K 224 " --> pdb=" O TRP K 139 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N VAL K 141 " --> pdb=" O LEU K 224 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 425 through 426 Processing sheet with id=AD6, first strand: chain 'N' and resid 31 through 33 removed outlier: 6.229A pdb=" N ILE N 5 " --> pdb=" O TRP N 33 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LYS N 4 " --> pdb=" O LYS N 59 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU N 61 " --> pdb=" O LYS N 4 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N PHE N 6 " --> pdb=" O LEU N 61 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N VAL N 63 " --> pdb=" O PHE N 6 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N SER N 8 " --> pdb=" O VAL N 63 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE N 60 " --> pdb=" O ILE N 95 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LEU N 97 " --> pdb=" O PHE N 60 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE N 62 " --> pdb=" O LEU N 97 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N ILE N 118 " --> pdb=" O ILE N 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'N' and resid 166 through 172 removed outlier: 6.119A pdb=" N LYS N 167 " --> pdb=" O MET N 414 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET N 414 " --> pdb=" O LYS N 167 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N LYS N 409 " --> pdb=" O LYS O 2 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N LEU O 4 " --> pdb=" O LYS N 409 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N PHE N 411 " --> pdb=" O LEU O 4 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N TYR O 6 " --> pdb=" O PHE N 411 " (cutoff:3.500A) removed outlier: 8.837A pdb=" N LYS N 413 " --> pdb=" O TYR O 6 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLU O 3 " --> pdb=" O ILE O 412 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ILE O 412 " --> pdb=" O GLU O 3 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN O 446 " --> pdb=" O GLY O 385 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N GLY O 385 " --> pdb=" O ASN O 446 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL O 357 " --> pdb=" O VAL O 384 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N VAL O 386 " --> pdb=" O VAL O 357 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE O 359 " --> pdb=" O VAL O 386 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N ILE O 388 " --> pdb=" O ILE O 359 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ALA O 361 " --> pdb=" O ILE O 388 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL O 278 " --> pdb=" O LEU O 305 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU O 305 " --> pdb=" O VAL O 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 166 through 172 removed outlier: 6.119A pdb=" N LYS N 167 " --> pdb=" O MET N 414 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET N 414 " --> pdb=" O LYS N 167 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N LYS N 409 " --> pdb=" O LYS O 2 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N LEU O 4 " --> pdb=" O LYS N 409 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N PHE N 411 " --> pdb=" O LEU O 4 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N TYR O 6 " --> pdb=" O PHE N 411 " (cutoff:3.500A) removed outlier: 8.837A pdb=" N LYS N 413 " --> pdb=" O TYR O 6 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLU O 3 " --> pdb=" O ILE O 412 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ILE O 412 " --> pdb=" O GLU O 3 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN O 446 " --> pdb=" O GLY O 385 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N GLY O 385 " --> pdb=" O ASN O 446 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL O 357 " --> pdb=" O VAL O 384 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N VAL O 386 " --> pdb=" O VAL O 357 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE O 359 " --> pdb=" O VAL O 386 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N ILE O 388 " --> pdb=" O ILE O 359 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ALA O 361 " --> pdb=" O ILE O 388 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL O 278 " --> pdb=" O LEU O 305 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU O 305 " --> pdb=" O VAL O 278 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ALA O 300 " --> pdb=" O GLY O 318 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N GLY O 318 " --> pdb=" O ALA O 300 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLN O 302 " --> pdb=" O GLU O 316 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N GLU O 316 " --> pdb=" O GLN O 302 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 311 through 314 removed outlier: 6.646A pdb=" N LEU N 402 " --> pdb=" O ILE N 179 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 208 through 210 Processing sheet with id=AE2, first strand: chain 'N' and resid 283 through 286 Processing sheet with id=AE3, first strand: chain 'N' and resid 304 through 305 Processing sheet with id=AE4, first strand: chain 'O' and resid 19 through 20 Processing sheet with id=AE5, first strand: chain 'O' and resid 92 through 95 removed outlier: 6.108A pdb=" N GLY O 42 " --> pdb=" O PHE O 140 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE O 142 " --> pdb=" O GLY O 42 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N VAL O 44 " --> pdb=" O ILE O 142 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TRP O 139 " --> pdb=" O GLN O 222 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LEU O 224 " --> pdb=" O TRP O 139 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N VAL O 141 " --> pdb=" O LEU O 224 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'O' and resid 425 through 426 removed outlier: 3.632A pdb=" N SER O 431 " --> pdb=" O VAL O 426 " (cutoff:3.500A) 1260 hydrogen bonds defined for protein. 3507 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 159 hydrogen bonds 318 hydrogen bond angles 0 basepair planarities 68 basepair parallelities 110 stacking parallelities Total time for adding SS restraints: 6.56 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6176 1.33 - 1.45: 8443 1.45 - 1.57: 17014 1.57 - 1.70: 315 1.70 - 1.82: 128 Bond restraints: 32076 Sorted by residual: bond pdb=" CG PRO B 23 " pdb=" CD PRO B 23 " ideal model delta sigma weight residual 1.503 1.368 0.135 3.40e-02 8.65e+02 1.58e+01 bond pdb=" C3' DA Q 16 " pdb=" C2' DA Q 16 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DA M 16 " pdb=" C2' DA M 16 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.85e+00 bond pdb=" CB PRO B 23 " pdb=" CG PRO B 23 " ideal model delta sigma weight residual 1.492 1.639 -0.147 5.00e-02 4.00e+02 8.64e+00 bond pdb=" C3' DA D 16 " pdb=" C2' DA D 16 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.11e+00 ... (remaining 32071 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.46: 43820 3.46 - 6.91: 202 6.91 - 10.37: 15 10.37 - 13.82: 3 13.82 - 17.28: 2 Bond angle restraints: 44042 Sorted by residual: angle pdb=" CA PRO B 23 " pdb=" N PRO B 23 " pdb=" CD PRO B 23 " ideal model delta sigma weight residual 112.00 94.72 17.28 1.40e+00 5.10e-01 1.52e+02 angle pdb=" N PRO B 23 " pdb=" CD PRO B 23 " pdb=" CG PRO B 23 " ideal model delta sigma weight residual 103.20 93.26 9.94 1.50e+00 4.44e-01 4.39e+01 angle pdb=" O4' DT Q 13 " pdb=" C4' DT Q 13 " pdb=" C3' DT Q 13 " ideal model delta sigma weight residual 106.00 103.29 2.71 6.00e-01 2.78e+00 2.04e+01 angle pdb=" CA LEU B 501 " pdb=" CB LEU B 501 " pdb=" CG LEU B 501 " ideal model delta sigma weight residual 116.30 131.72 -15.42 3.50e+00 8.16e-02 1.94e+01 angle pdb=" O4' DT M 13 " pdb=" C4' DT M 13 " pdb=" C3' DT M 13 " ideal model delta sigma weight residual 106.00 103.48 2.52 6.00e-01 2.78e+00 1.76e+01 ... (remaining 44037 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 15279 17.93 - 35.85: 2521 35.85 - 53.78: 828 53.78 - 71.71: 237 71.71 - 89.64: 67 Dihedral angle restraints: 18932 sinusoidal: 9064 harmonic: 9868 Sorted by residual: dihedral pdb=" C4' A C 1 " pdb=" C3' A C 1 " pdb=" C2' A C 1 " pdb=" C1' A C 1 " ideal model delta sinusoidal sigma weight residual 36.34 -37.09 73.43 1 3.10e+00 1.04e-01 7.14e+02 dihedral pdb=" C4' A P 1 " pdb=" C3' A P 1 " pdb=" C2' A P 1 " pdb=" C1' A P 1 " ideal model delta sinusoidal sigma weight residual 36.34 -37.08 73.43 1 3.10e+00 1.04e-01 7.14e+02 dihedral pdb=" C4' A H 1 " pdb=" C3' A H 1 " pdb=" C2' A H 1 " pdb=" C1' A H 1 " ideal model delta sinusoidal sigma weight residual 36.34 -36.22 72.56 1 3.10e+00 1.04e-01 7.00e+02 ... (remaining 18929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3876 0.057 - 0.114: 754 0.114 - 0.170: 101 0.170 - 0.227: 54 0.227 - 0.284: 45 Chirality restraints: 4830 Sorted by residual: chirality pdb=" C3' A C 1 " pdb=" C4' A C 1 " pdb=" O3' A C 1 " pdb=" C2' A C 1 " both_signs ideal model delta sigma weight residual False -2.50 -2.78 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C3' A H 1 " pdb=" C4' A H 1 " pdb=" O3' A H 1 " pdb=" C2' A H 1 " both_signs ideal model delta sigma weight residual False -2.50 -2.78 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C2' A P 1 " pdb=" C3' A P 1 " pdb=" O2' A P 1 " pdb=" C1' A P 1 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 4827 not shown) Planarity restraints: 4978 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 22 " -0.125 5.00e-02 4.00e+02 1.72e-01 4.71e+01 pdb=" N PRO B 23 " 0.296 5.00e-02 4.00e+02 pdb=" CA PRO B 23 " -0.086 5.00e-02 4.00e+02 pdb=" CD PRO B 23 " -0.085 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE O 219 " -0.071 5.00e-02 4.00e+02 1.05e-01 1.75e+01 pdb=" N PRO O 220 " 0.181 5.00e-02 4.00e+02 pdb=" CA PRO O 220 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO O 220 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS J 406 " -0.068 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO J 407 " 0.174 5.00e-02 4.00e+02 pdb=" CA PRO J 407 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO J 407 " -0.054 5.00e-02 4.00e+02 ... (remaining 4975 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 366 2.57 - 3.15: 25025 3.15 - 3.74: 53728 3.74 - 4.32: 75717 4.32 - 4.90: 118713 Nonbonded interactions: 273549 Sorted by model distance: nonbonded pdb=" OP1 A C 3 " pdb="MG MG C 101 " model vdw 1.990 2.170 nonbonded pdb=" OP2 A H 1 " pdb="MG MG H 101 " model vdw 1.995 2.170 nonbonded pdb=" OH TYR O 321 " pdb=" OE2 GLU O 495 " model vdw 1.997 3.040 nonbonded pdb=" OP1 A H 3 " pdb="MG MG H 101 " model vdw 1.999 2.170 nonbonded pdb=" OP2 A P 1 " pdb="MG MG P 601 " model vdw 2.002 2.170 ... (remaining 273544 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' and (resid 3 through 40 or resid 45 through 420)) selection = (chain 'F' and (resid 3 through 141 or resid 146 through 420)) selection = (chain 'J' and (resid 3 through 40 or resid 45 through 420)) selection = (chain 'N' and (resid 3 through 141 or resid 146 through 420)) } ncs_group { reference = chain 'B' selection = chain 'G' selection = (chain 'K' and resid 1 through 507) selection = chain 'O' } ncs_group { reference = (chain 'C' and resid 1 through 20) selection = (chain 'H' and resid 1 through 20) selection = chain 'L' selection = (chain 'P' and resid 1 through 20) } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'M' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.950 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: 0.030 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 32.020 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 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:6.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 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 : 0.004 0.147 32076 Z= 0.214 Angle : 0.704 17.275 44042 Z= 0.410 Chirality : 0.055 0.284 4830 Planarity : 0.006 0.172 4978 Dihedral : 20.040 89.635 12548 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.63 % Allowed : 29.40 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.14), residues: 3306 helix: 0.67 (0.15), residues: 1108 sheet: -0.78 (0.22), residues: 528 loop : -1.35 (0.14), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 71 TYR 0.018 0.001 TYR K 6 PHE 0.035 0.002 PHE J 343 TRP 0.041 0.002 TRP J 369 HIS 0.011 0.001 HIS N 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.21 (32076) covalent geometry : angle 0.70415 / 0.41 (44042) hydrogen bonds : bond 0.12633 / 8.26 ( 1293) hydrogen bonds : angle 6.26807 / 4.35 ( 3825) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 723 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 GLU cc_start: 0.6613 (pp20) cc_final: 0.6284 (pt0) REVERT: F 70 LYS cc_start: 0.7178 (mmtm) cc_final: 0.6536 (pttp) REVERT: F 190 TYR cc_start: 0.5616 (m-10) cc_final: 0.5360 (m-10) REVERT: F 294 TRP cc_start: 0.5723 (p-90) cc_final: 0.5511 (p-90) REVERT: F 414 MET cc_start: 0.8031 (mmt) cc_final: 0.7633 (mmt) REVERT: G 19 LYS cc_start: 0.7851 (ptpp) cc_final: 0.7624 (mttt) REVERT: G 113 ARG cc_start: 0.5260 (ptt-90) cc_final: 0.4435 (pmt170) REVERT: J 92 MET cc_start: 0.5105 (tpp) cc_final: 0.4849 (tpt) REVERT: K 206 PHE cc_start: 0.7038 (t80) cc_final: 0.6792 (t80) REVERT: N 78 LEU cc_start: 0.6744 (tp) cc_final: 0.5820 (tt) REVERT: O 356 GLU cc_start: 0.6209 (tm-30) cc_final: 0.5855 (pm20) REVERT: O 357 VAL cc_start: 0.7157 (t) cc_final: 0.6543 (t) REVERT: O 378 PRO cc_start: 0.3541 (Cg_endo) cc_final: 0.3217 (Cg_exo) REVERT: O 406 MET cc_start: 0.4863 (ppp) cc_final: 0.4490 (pp-130) outliers start: 19 outliers final: 5 residues processed: 735 average time/residue: 0.5927 time to fit residues: 526.8845 Evaluate side-chains 475 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 470 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain F residue 401 ILE Chi-restraints excluded: chain J residue 243 THR Chi-restraints excluded: chain K residue 359 ILE Chi-restraints excluded: chain O residue 364 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 ASN A 225 HIS ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 ASN B 382 ASN B 466 ASN F 156 GLN F 340 HIS ** F 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 ASN G 296 ASN ** G 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 409 ASN ** J 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 316 ASN ** J 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 207 HIS K 380 ASN K 382 ASN K 430 GLN ** K 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 87 HIS O 51 GLN O 67 HIS O 302 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.207214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.143146 restraints weight = 44864.926| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 2.63 r_work: 0.3780 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 32076 Z= 0.318 Angle : 0.895 20.211 44042 Z= 0.448 Chirality : 0.060 1.018 4830 Planarity : 0.007 0.146 4978 Dihedral : 16.276 143.681 5604 Min Nonbonded Distance : 1.702 Molprobity Statistics. All-atom Clashscore : 19.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 7.27 % Allowed : 29.10 % Favored : 63.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.26 (0.14), residues: 3306 helix: 0.38 (0.15), residues: 1140 sheet: -1.28 (0.20), residues: 638 loop : -1.53 (0.14), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 189 TYR 0.022 0.002 TYR N 233 PHE 0.037 0.003 PHE F 135 TRP 0.034 0.003 TRP F 20 HIS 0.019 0.002 HIS O 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00729 / 0.32 (32076) covalent geometry : angle 0.89474 / 0.45 (44042) hydrogen bonds : bond 0.05068 / 3.34 ( 1293) hydrogen bonds : angle 5.29597 / 3.69 ( 3825) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 218 poor density : 478 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 TRP cc_start: 0.7702 (OUTLIER) cc_final: 0.6578 (m-10) REVERT: A 212 GLU cc_start: 0.7272 (pp20) cc_final: 0.6939 (pp20) REVERT: A 287 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7635 (mmm) REVERT: A 293 TYR cc_start: 0.7531 (m-80) cc_final: 0.7203 (m-80) REVERT: A 328 LYS cc_start: 0.8249 (ttmm) cc_final: 0.7986 (ttmm) REVERT: A 339 SER cc_start: 0.8730 (m) cc_final: 0.8475 (p) REVERT: A 357 GLN cc_start: 0.7310 (tp40) cc_final: 0.6920 (mm-40) REVERT: B 3 GLU cc_start: 0.7907 (tt0) cc_final: 0.7419 (pm20) REVERT: B 203 ASP cc_start: 0.8497 (OUTLIER) cc_final: 0.8166 (p0) REVERT: B 217 HIS cc_start: 0.6371 (OUTLIER) cc_final: 0.5693 (p90) REVERT: B 324 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7207 (mp0) REVERT: F 70 LYS cc_start: 0.7531 (mmtm) cc_final: 0.6106 (pttp) REVERT: F 100 ASP cc_start: 0.8096 (t70) cc_final: 0.7510 (t0) REVERT: F 122 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.8013 (mmtt) REVERT: F 132 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8171 (mt) REVERT: F 160 HIS cc_start: 0.7544 (OUTLIER) cc_final: 0.7314 (p90) REVERT: F 179 ILE cc_start: 0.7547 (OUTLIER) cc_final: 0.7281 (mp) REVERT: F 220 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6263 (pm20) REVERT: F 267 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7250 (tt0) REVERT: F 274 GLU cc_start: 0.7630 (tp30) cc_final: 0.7409 (tp30) REVERT: F 294 TRP cc_start: 0.6270 (p-90) cc_final: 0.5267 (p-90) REVERT: F 307 LYS cc_start: 0.8280 (ptpp) cc_final: 0.7149 (pptt) REVERT: G 217 HIS cc_start: 0.6407 (OUTLIER) cc_final: 0.5528 (p-80) REVERT: G 383 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7720 (pt) REVERT: J 40 ASP cc_start: 0.6671 (t70) cc_final: 0.6375 (m-30) REVERT: J 92 MET cc_start: 0.5363 (tpp) cc_final: 0.4997 (tpt) REVERT: J 149 LYS cc_start: 0.5881 (mptp) cc_final: 0.4835 (pmtt) REVERT: J 259 TYR cc_start: 0.7376 (t80) cc_final: 0.7173 (t80) REVERT: J 357 GLN cc_start: 0.6735 (mm-40) cc_final: 0.6494 (tm-30) REVERT: J 414 MET cc_start: 0.4611 (mmt) cc_final: 0.4288 (tpp) REVERT: K 1 MET cc_start: 0.3867 (tpp) cc_final: 0.3363 (tpp) REVERT: K 85 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7563 (mtmm) REVERT: K 206 PHE cc_start: 0.7454 (t80) cc_final: 0.7207 (t80) REVERT: K 210 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7418 (mp) REVERT: K 225 ARG cc_start: 0.6431 (OUTLIER) cc_final: 0.5253 (mtt90) REVERT: K 279 CYS cc_start: 0.7310 (OUTLIER) cc_final: 0.6773 (p) REVERT: K 407 ARG cc_start: 0.6666 (ptm160) cc_final: 0.6438 (ptm-80) REVERT: K 498 THR cc_start: 0.6074 (OUTLIER) cc_final: 0.5710 (t) REVERT: N 4 LYS cc_start: 0.6231 (mmtt) cc_final: 0.5346 (mtpm) REVERT: N 20 TRP cc_start: 0.7326 (t60) cc_final: 0.7062 (t60) REVERT: N 78 LEU cc_start: 0.7138 (tp) cc_final: 0.6766 (tt) REVERT: N 100 ASP cc_start: 0.6990 (t70) cc_final: 0.6679 (t0) REVERT: N 281 ASN cc_start: 0.6880 (OUTLIER) cc_final: 0.5743 (t0) REVERT: N 313 LYS cc_start: 0.5023 (OUTLIER) cc_final: 0.4604 (mptt) REVERT: N 391 ILE cc_start: 0.5863 (OUTLIER) cc_final: 0.5457 (mt) REVERT: O 90 ASN cc_start: 0.6597 (t0) cc_final: 0.5488 (t0) REVERT: O 285 TYR cc_start: 0.6904 (m-80) cc_final: 0.6631 (m-80) REVERT: O 296 ASN cc_start: 0.6625 (OUTLIER) cc_final: 0.5443 (t0) REVERT: O 321 TYR cc_start: 0.6896 (m-10) cc_final: 0.6678 (m-80) REVERT: O 356 GLU cc_start: 0.6773 (tm-30) cc_final: 0.5334 (pm20) REVERT: O 406 MET cc_start: 0.3689 (ppp) cc_final: 0.2991 (pp-130) REVERT: O 449 GLU cc_start: 0.6112 (tt0) cc_final: 0.5588 (pm20) REVERT: O 489 ILE cc_start: 0.7270 (mm) cc_final: 0.7066 (mm) outliers start: 218 outliers final: 74 residues processed: 627 average time/residue: 0.4938 time to fit residues: 386.8992 Evaluate side-chains 511 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 415 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 46 TRP Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 409 LYS Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 217 HIS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 106 ASP Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 162 LYS Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain F residue 267 GLN Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 418 THR Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 217 HIS Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 255 THR Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 383 LEU Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 470 CYS Chi-restraints excluded: chain G residue 471 ILE Chi-restraints excluded: chain G residue 479 THR Chi-restraints excluded: chain G residue 486 ILE Chi-restraints excluded: chain G residue 507 ILE Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 58 CYS Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 170 THR Chi-restraints excluded: chain J residue 243 THR Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain J residue 417 VAL Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 85 LYS Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 202 TYR Chi-restraints excluded: chain K residue 210 LEU Chi-restraints excluded: chain K residue 216 GLU Chi-restraints excluded: chain K residue 225 ARG Chi-restraints excluded: chain K residue 248 ILE Chi-restraints excluded: chain K residue 279 CYS Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain K residue 470 CYS Chi-restraints excluded: chain K residue 494 THR Chi-restraints excluded: chain K residue 497 LYS Chi-restraints excluded: chain K residue 498 THR Chi-restraints excluded: chain N residue 25 LEU Chi-restraints excluded: chain N residue 61 LEU Chi-restraints excluded: chain N residue 64 SER Chi-restraints excluded: chain N residue 86 LYS Chi-restraints excluded: chain N residue 281 ASN Chi-restraints excluded: chain N residue 313 LYS Chi-restraints excluded: chain N residue 337 VAL Chi-restraints excluded: chain N residue 391 ILE Chi-restraints excluded: chain O residue 91 ILE Chi-restraints excluded: chain O residue 92 VAL Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 258 THR Chi-restraints excluded: chain O residue 296 ASN Chi-restraints excluded: chain O residue 364 ARG Chi-restraints excluded: chain O residue 383 LEU Chi-restraints excluded: chain O residue 389 THR Chi-restraints excluded: chain O residue 405 ILE Chi-restraints excluded: chain O residue 411 TYR Chi-restraints excluded: chain O residue 470 CYS Chi-restraints excluded: chain O residue 479 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 306 optimal weight: 0.9990 chunk 127 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 188 optimal weight: 8.9990 chunk 346 optimal weight: 40.0000 chunk 308 optimal weight: 0.6980 chunk 30 optimal weight: 0.4980 chunk 21 optimal weight: 0.6980 chunk 223 optimal weight: 7.9990 chunk 252 optimal weight: 8.9990 chunk 52 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 225 HIS ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 ASN B 382 ASN F 156 GLN F 183 ASN ** F 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 350 ASN G 409 ASN ** J 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 262 GLN ** J 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 51 GLN K 69 ASN K 430 GLN ** K 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 340 HIS N 357 GLN O 51 GLN O 68 ASN O 207 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.211887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.153417 restraints weight = 44424.373| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 2.75 r_work: 0.3855 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 32076 Z= 0.160 Angle : 0.729 14.161 44042 Z= 0.366 Chirality : 0.052 0.534 4830 Planarity : 0.005 0.080 4978 Dihedral : 16.158 166.954 5599 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 5.07 % Allowed : 31.07 % Favored : 63.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.14), residues: 3306 helix: 0.67 (0.15), residues: 1118 sheet: -1.22 (0.20), residues: 622 loop : -1.48 (0.14), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 71 TYR 0.021 0.002 TYR F 330 PHE 0.025 0.002 PHE F 135 TRP 0.018 0.001 TRP F 20 HIS 0.013 0.001 HIS O 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (32076) covalent geometry : angle 0.72931 / 0.37 (44042) hydrogen bonds : bond 0.04192 / 2.78 ( 1293) hydrogen bonds : angle 4.99192 / 3.47 ( 3825) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 478 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 GLU cc_start: 0.7232 (pp20) cc_final: 0.6980 (pp20) REVERT: A 260 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7675 (tm-30) REVERT: A 294 TRP cc_start: 0.7340 (p-90) cc_final: 0.7132 (p-90) REVERT: A 328 LYS cc_start: 0.8294 (ttmm) cc_final: 0.8074 (ttmm) REVERT: A 357 GLN cc_start: 0.7275 (tp40) cc_final: 0.6903 (mm-40) REVERT: B 3 GLU cc_start: 0.7940 (tt0) cc_final: 0.7432 (pm20) REVERT: B 85 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8051 (mmmm) REVERT: B 217 HIS cc_start: 0.6391 (OUTLIER) cc_final: 0.5855 (p90) REVERT: B 324 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.7034 (mp0) REVERT: B 362 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.8040 (mtm180) REVERT: B 407 ARG cc_start: 0.8346 (ttt-90) cc_final: 0.8083 (ttt90) REVERT: F 100 ASP cc_start: 0.7960 (t70) cc_final: 0.7573 (t0) REVERT: F 132 LEU cc_start: 0.8392 (mm) cc_final: 0.8178 (mt) REVERT: F 179 ILE cc_start: 0.7341 (OUTLIER) cc_final: 0.7086 (mp) REVERT: F 220 GLU cc_start: 0.6875 (OUTLIER) cc_final: 0.6297 (pm20) REVERT: F 267 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7345 (tt0) REVERT: F 274 GLU cc_start: 0.7517 (tp30) cc_final: 0.7252 (tp30) REVERT: F 294 TRP cc_start: 0.6269 (p-90) cc_final: 0.5223 (p-90) REVERT: F 307 LYS cc_start: 0.8171 (ptpp) cc_final: 0.7060 (pptt) REVERT: G 134 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7680 (pm20) REVERT: G 383 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7833 (pt) REVERT: J 92 MET cc_start: 0.5307 (tpp) cc_final: 0.4904 (tpt) REVERT: J 287 MET cc_start: 0.7060 (mmm) cc_final: 0.6826 (mmm) REVERT: J 297 LYS cc_start: 0.4662 (pttm) cc_final: 0.3801 (tptt) REVERT: J 357 GLN cc_start: 0.6713 (mm-40) cc_final: 0.6449 (tm-30) REVERT: K 1 MET cc_start: 0.3921 (tpp) cc_final: 0.3351 (tpp) REVERT: K 79 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6946 (mt-10) REVERT: K 85 LYS cc_start: 0.7761 (OUTLIER) cc_final: 0.7337 (mtmm) REVERT: K 210 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7414 (mp) REVERT: K 286 LYS cc_start: 0.6660 (OUTLIER) cc_final: 0.6447 (mptt) REVERT: K 447 LYS cc_start: 0.5862 (mmtm) cc_final: 0.5307 (ptmt) REVERT: K 498 THR cc_start: 0.6058 (OUTLIER) cc_final: 0.5736 (t) REVERT: N 4 LYS cc_start: 0.6416 (mmtt) cc_final: 0.5485 (mtpm) REVERT: N 20 TRP cc_start: 0.7343 (t60) cc_final: 0.7101 (t60) REVERT: N 78 LEU cc_start: 0.7040 (tp) cc_final: 0.6638 (tt) REVERT: N 100 ASP cc_start: 0.6902 (t70) cc_final: 0.6463 (t0) REVERT: N 391 ILE cc_start: 0.5804 (OUTLIER) cc_final: 0.5526 (mt) REVERT: O 90 ASN cc_start: 0.6557 (t0) cc_final: 0.5803 (t0) REVERT: O 285 TYR cc_start: 0.6833 (m-80) cc_final: 0.6349 (m-80) REVERT: O 296 ASN cc_start: 0.6578 (t0) cc_final: 0.5503 (t0) REVERT: O 356 GLU cc_start: 0.6663 (tm-30) cc_final: 0.5228 (pm20) REVERT: O 373 PHE cc_start: 0.8092 (m-80) cc_final: 0.7683 (m-80) REVERT: O 406 MET cc_start: 0.3685 (ppp) cc_final: 0.2930 (pp-130) REVERT: O 447 LYS cc_start: 0.5269 (OUTLIER) cc_final: 0.4584 (mmtp) outliers start: 152 outliers final: 55 residues processed: 577 average time/residue: 0.5181 time to fit residues: 370.8471 Evaluate side-chains 476 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 404 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 CYS Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 409 LYS Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 217 HIS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 362 ARG Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain F residue 162 LYS Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 267 GLN Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 397 SER Chi-restraints excluded: chain F residue 418 THR Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 202 TYR Chi-restraints excluded: chain G residue 255 THR Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 383 LEU Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 58 CYS Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 243 THR Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain J residue 417 VAL Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 85 LYS Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 202 TYR Chi-restraints excluded: chain K residue 210 LEU Chi-restraints excluded: chain K residue 216 GLU Chi-restraints excluded: chain K residue 286 LYS Chi-restraints excluded: chain K residue 423 LEU Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain K residue 452 ILE Chi-restraints excluded: chain K residue 470 CYS Chi-restraints excluded: chain K residue 498 THR Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 86 LYS Chi-restraints excluded: chain N residue 391 ILE Chi-restraints excluded: chain O residue 213 ARG Chi-restraints excluded: chain O residue 389 THR Chi-restraints excluded: chain O residue 405 ILE Chi-restraints excluded: chain O residue 411 TYR Chi-restraints excluded: chain O residue 447 LYS Chi-restraints excluded: chain O residue 479 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 41 optimal weight: 0.0270 chunk 71 optimal weight: 4.9990 chunk 246 optimal weight: 10.0000 chunk 214 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 57 optimal weight: 0.0570 chunk 166 optimal weight: 5.9990 chunk 306 optimal weight: 0.1980 chunk 160 optimal weight: 0.0470 chunk 223 optimal weight: 20.0000 chunk 215 optimal weight: 0.9990 overall best weight: 0.2454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 225 HIS ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 HIS ** F 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 286 GLN N 340 HIS O 51 GLN O 61 GLN O 295 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.214332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.153086 restraints weight = 44334.377| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 2.57 r_work: 0.3906 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32076 Z= 0.140 Angle : 0.696 12.490 44042 Z= 0.350 Chirality : 0.050 0.414 4830 Planarity : 0.005 0.069 4978 Dihedral : 16.131 177.957 5595 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.97 % Allowed : 31.03 % Favored : 64.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.14), residues: 3306 helix: 0.78 (0.15), residues: 1114 sheet: -1.21 (0.20), residues: 622 loop : -1.45 (0.14), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 225 TYR 0.041 0.001 TYR F 330 PHE 0.037 0.002 PHE O 365 TRP 0.027 0.001 TRP O 370 HIS 0.014 0.001 HIS F 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (32076) covalent geometry : angle 0.69610 / 0.35 (44042) hydrogen bonds : bond 0.03919 / 2.60 ( 1293) hydrogen bonds : angle 4.81629 / 3.34 ( 3825) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 454 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 TRP cc_start: 0.7555 (OUTLIER) cc_final: 0.6516 (m-10) REVERT: B 3 GLU cc_start: 0.7946 (tt0) cc_final: 0.7349 (pm20) REVERT: B 68 ASN cc_start: 0.7764 (t0) cc_final: 0.7543 (t0) REVERT: B 85 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8070 (mmmm) REVERT: B 217 HIS cc_start: 0.6379 (OUTLIER) cc_final: 0.5848 (p90) REVERT: B 324 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.7020 (mp0) REVERT: B 362 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7968 (mtm180) REVERT: F 55 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6842 (tm-30) REVERT: F 87 HIS cc_start: 0.8402 (t-90) cc_final: 0.8155 (t-90) REVERT: F 100 ASP cc_start: 0.8016 (t70) cc_final: 0.7705 (t0) REVERT: F 150 SER cc_start: 0.8363 (t) cc_final: 0.7945 (p) REVERT: F 220 GLU cc_start: 0.6789 (OUTLIER) cc_final: 0.6239 (pm20) REVERT: F 267 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7496 (tt0) REVERT: F 294 TRP cc_start: 0.6251 (p-90) cc_final: 0.5272 (p-90) REVERT: F 307 LYS cc_start: 0.8175 (ptpp) cc_final: 0.7026 (pptt) REVERT: G 133 GLU cc_start: 0.7383 (tp30) cc_final: 0.7171 (tp30) REVERT: G 217 HIS cc_start: 0.6118 (OUTLIER) cc_final: 0.4869 (p90) REVERT: J 46 TRP cc_start: 0.6553 (m-10) cc_final: 0.6241 (m100) REVERT: J 92 MET cc_start: 0.5251 (tpp) cc_final: 0.4900 (tpt) REVERT: J 287 MET cc_start: 0.7188 (mmm) cc_final: 0.6986 (mmm) REVERT: J 297 LYS cc_start: 0.4655 (pttm) cc_final: 0.3867 (tptt) REVERT: J 357 GLN cc_start: 0.6712 (mm-40) cc_final: 0.6493 (tm-30) REVERT: K 1 MET cc_start: 0.4109 (tpp) cc_final: 0.3610 (tpp) REVERT: K 79 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6880 (mt-10) REVERT: K 210 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7422 (mp) REVERT: K 447 LYS cc_start: 0.5958 (mmtm) cc_final: 0.5450 (ptmt) REVERT: N 4 LYS cc_start: 0.6499 (mmtt) cc_final: 0.5776 (mtpm) REVERT: N 20 TRP cc_start: 0.7325 (t60) cc_final: 0.7092 (t60) REVERT: N 100 ASP cc_start: 0.6855 (t70) cc_final: 0.6416 (t0) REVERT: N 345 MET cc_start: 0.2607 (ppp) cc_final: 0.2205 (ppp) REVERT: N 391 ILE cc_start: 0.5699 (OUTLIER) cc_final: 0.5374 (mt) REVERT: O 29 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8476 (mm) REVERT: O 64 ILE cc_start: 0.5840 (mm) cc_final: 0.5592 (mm) REVERT: O 90 ASN cc_start: 0.6378 (t0) cc_final: 0.5812 (t0) REVERT: O 285 TYR cc_start: 0.6939 (m-80) cc_final: 0.6522 (m-80) REVERT: O 296 ASN cc_start: 0.6367 (t0) cc_final: 0.5062 (t0) REVERT: O 356 GLU cc_start: 0.6731 (tm-30) cc_final: 0.5293 (pm20) REVERT: O 362 ARG cc_start: 0.7558 (ptp90) cc_final: 0.7285 (ptp90) REVERT: O 406 MET cc_start: 0.3809 (ppp) cc_final: 0.2983 (pp-130) REVERT: O 449 GLU cc_start: 0.6312 (tt0) cc_final: 0.5759 (pm20) REVERT: O 480 LEU cc_start: 0.7065 (mt) cc_final: 0.6592 (mm) outliers start: 149 outliers final: 53 residues processed: 548 average time/residue: 0.4615 time to fit residues: 318.7691 Evaluate side-chains 455 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 389 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 TRP Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 217 HIS Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 362 ARG Chi-restraints excluded: chain F residue 55 GLU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 162 LYS Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 267 GLN Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 336 MET Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 397 SER Chi-restraints excluded: chain F residue 418 THR Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 96 ILE Chi-restraints excluded: chain G residue 202 TYR Chi-restraints excluded: chain G residue 217 HIS Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 437 VAL Chi-restraints excluded: chain G residue 498 THR Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 58 CYS Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 243 THR Chi-restraints excluded: chain J residue 417 VAL Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 202 TYR Chi-restraints excluded: chain K residue 210 LEU Chi-restraints excluded: chain K residue 221 THR Chi-restraints excluded: chain K residue 405 ILE Chi-restraints excluded: chain K residue 423 LEU Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain K residue 470 CYS Chi-restraints excluded: chain K residue 491 THR Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 64 SER Chi-restraints excluded: chain N residue 86 LYS Chi-restraints excluded: chain N residue 391 ILE Chi-restraints excluded: chain O residue 29 LEU Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 389 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 52 optimal weight: 0.9980 chunk 202 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 289 optimal weight: 9.9990 chunk 206 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 231 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 236 optimal weight: 2.9990 chunk 344 optimal weight: 9.9990 chunk 294 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 225 HIS A 286 GLN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN B 374 ASN ** B 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 HIS ** F 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 409 ASN ** J 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 340 HIS N 357 GLN O 484 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.204133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.140189 restraints weight = 44578.867| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 2.53 r_work: 0.3755 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3625 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.085 32076 Z= 0.350 Angle : 0.871 14.883 44042 Z= 0.435 Chirality : 0.057 0.547 4830 Planarity : 0.006 0.096 4978 Dihedral : 16.212 179.692 5595 Min Nonbonded Distance : 1.676 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 7.13 % Allowed : 30.03 % Favored : 62.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.14), residues: 3306 helix: 0.10 (0.14), residues: 1132 sheet: -1.41 (0.20), residues: 634 loop : -1.65 (0.14), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 407 TYR 0.031 0.003 TYR G 397 PHE 0.033 0.003 PHE F 135 TRP 0.034 0.003 TRP N 369 HIS 0.029 0.002 HIS F 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00807 / 0.35 (32076) covalent geometry : angle 0.87147 / 0.43 (44042) hydrogen bonds : bond 0.05200 / 3.46 ( 1293) hydrogen bonds : angle 5.20714 / 3.64 ( 3825) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 214 poor density : 418 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 TRP cc_start: 0.7890 (OUTLIER) cc_final: 0.6721 (m-10) REVERT: A 59 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8089 (ttmm) REVERT: A 126 LYS cc_start: 0.8111 (ttpp) cc_final: 0.7631 (tppt) REVERT: A 277 MET cc_start: 0.8568 (mmm) cc_final: 0.7931 (mpt) REVERT: A 286 GLN cc_start: 0.7150 (OUTLIER) cc_final: 0.6944 (mm-40) REVERT: B 3 GLU cc_start: 0.8269 (tt0) cc_final: 0.7494 (pm20) REVERT: B 72 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7616 (ptm160) REVERT: B 85 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.7866 (mmmm) REVERT: B 324 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7251 (mp0) REVERT: F 37 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7742 (mp) REVERT: F 52 GLU cc_start: 0.5816 (mm-30) cc_final: 0.5230 (mm-30) REVERT: F 100 ASP cc_start: 0.8485 (t70) cc_final: 0.8127 (t0) REVERT: F 122 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.8061 (mmtt) REVERT: F 136 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7620 (mt-10) REVERT: F 220 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6756 (pm20) REVERT: F 267 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7582 (tt0) REVERT: F 271 LYS cc_start: 0.8572 (tppt) cc_final: 0.8225 (tppt) REVERT: F 274 GLU cc_start: 0.7732 (tp30) cc_final: 0.7264 (tp30) REVERT: F 294 TRP cc_start: 0.6519 (p-90) cc_final: 0.5165 (p-90) REVERT: F 307 LYS cc_start: 0.8267 (ptpp) cc_final: 0.7108 (pptt) REVERT: G 7 ILE cc_start: 0.7783 (OUTLIER) cc_final: 0.7499 (mm) REVERT: G 79 GLU cc_start: 0.6713 (mp0) cc_final: 0.6485 (mp0) REVERT: G 113 ARG cc_start: 0.5414 (OUTLIER) cc_final: 0.4529 (pmt-80) REVERT: G 116 ASP cc_start: 0.6994 (OUTLIER) cc_final: 0.6327 (m-30) REVERT: G 133 GLU cc_start: 0.7892 (tp30) cc_final: 0.7661 (tp30) REVERT: G 285 TYR cc_start: 0.8746 (OUTLIER) cc_final: 0.8073 (m-80) REVERT: G 383 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7716 (pt) REVERT: G 435 MET cc_start: 0.8493 (mmt) cc_final: 0.7939 (mtt) REVERT: J 20 TRP cc_start: 0.7828 (t60) cc_final: 0.7587 (t60) REVERT: J 92 MET cc_start: 0.5442 (tpp) cc_final: 0.5085 (tpt) REVERT: J 263 ARG cc_start: 0.7079 (ptm160) cc_final: 0.6541 (mtp-110) REVERT: J 357 GLN cc_start: 0.6801 (mm-40) cc_final: 0.6448 (tm-30) REVERT: K 79 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6886 (mt-10) REVERT: K 117 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7038 (tm) REVERT: K 225 ARG cc_start: 0.6923 (OUTLIER) cc_final: 0.5796 (ptp-110) REVERT: K 279 CYS cc_start: 0.6594 (p) cc_final: 0.6122 (p) REVERT: K 407 ARG cc_start: 0.7071 (ptm160) cc_final: 0.6802 (ptm-80) REVERT: K 447 LYS cc_start: 0.6041 (mmtm) cc_final: 0.5066 (ptpt) REVERT: K 498 THR cc_start: 0.6168 (OUTLIER) cc_final: 0.5806 (t) REVERT: N 4 LYS cc_start: 0.6356 (mmtt) cc_final: 0.5863 (mmmt) REVERT: N 277 MET cc_start: 0.7646 (tpt) cc_final: 0.7183 (tpt) REVERT: N 281 ASN cc_start: 0.6800 (OUTLIER) cc_final: 0.5914 (t0) REVERT: N 313 LYS cc_start: 0.5069 (OUTLIER) cc_final: 0.4626 (mptt) REVERT: N 344 THR cc_start: 0.5227 (p) cc_final: 0.4653 (p) REVERT: N 345 MET cc_start: 0.2492 (ppp) cc_final: 0.1936 (ppp) REVERT: N 391 ILE cc_start: 0.5671 (OUTLIER) cc_final: 0.5395 (mt) REVERT: N 398 GLU cc_start: 0.4291 (OUTLIER) cc_final: 0.3761 (tt0) REVERT: O 64 ILE cc_start: 0.5870 (mm) cc_final: 0.5637 (mm) REVERT: O 134 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6810 (pt0) REVERT: O 245 PHE cc_start: 0.6120 (m-10) cc_final: 0.5769 (m-10) REVERT: O 285 TYR cc_start: 0.7333 (m-80) cc_final: 0.6751 (m-80) REVERT: O 296 ASN cc_start: 0.6350 (t0) cc_final: 0.5232 (t0) REVERT: O 302 GLN cc_start: 0.5229 (pt0) cc_final: 0.4985 (pt0) REVERT: O 356 GLU cc_start: 0.7134 (tm-30) cc_final: 0.5383 (mm-30) REVERT: O 362 ARG cc_start: 0.7552 (ptp90) cc_final: 0.7129 (ptp90) REVERT: O 406 MET cc_start: 0.4045 (ppp) cc_final: 0.3123 (pp-130) REVERT: O 449 GLU cc_start: 0.6293 (tt0) cc_final: 0.5765 (pm20) REVERT: O 480 LEU cc_start: 0.7014 (mt) cc_final: 0.6512 (mm) outliers start: 214 outliers final: 88 residues processed: 565 average time/residue: 0.4827 time to fit residues: 338.2239 Evaluate side-chains 498 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 385 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 34 CYS Chi-restraints excluded: chain A residue 46 TRP Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 409 LYS Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 72 ARG Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 106 ASP Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 162 LYS Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 267 GLN Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 339 SER Chi-restraints excluded: chain F residue 397 SER Chi-restraints excluded: chain F residue 418 THR Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 69 ASN Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 96 ILE Chi-restraints excluded: chain G residue 113 ARG Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 255 THR Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 383 LEU Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 470 CYS Chi-restraints excluded: chain G residue 479 THR Chi-restraints excluded: chain G residue 486 ILE Chi-restraints excluded: chain G residue 498 THR Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 170 THR Chi-restraints excluded: chain J residue 243 THR Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain J residue 417 VAL Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 85 LYS Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain K residue 202 TYR Chi-restraints excluded: chain K residue 225 ARG Chi-restraints excluded: chain K residue 405 ILE Chi-restraints excluded: chain K residue 423 LEU Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain K residue 470 CYS Chi-restraints excluded: chain K residue 478 VAL Chi-restraints excluded: chain K residue 491 THR Chi-restraints excluded: chain K residue 494 THR Chi-restraints excluded: chain K residue 497 LYS Chi-restraints excluded: chain K residue 498 THR Chi-restraints excluded: chain N residue 18 THR Chi-restraints excluded: chain N residue 25 LEU Chi-restraints excluded: chain N residue 61 LEU Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 86 LYS Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 281 ASN Chi-restraints excluded: chain N residue 313 LYS Chi-restraints excluded: chain N residue 391 ILE Chi-restraints excluded: chain N residue 398 GLU Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 91 ILE Chi-restraints excluded: chain O residue 134 GLU Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 258 THR Chi-restraints excluded: chain O residue 303 MET Chi-restraints excluded: chain O residue 389 THR Chi-restraints excluded: chain O residue 405 ILE Chi-restraints excluded: chain O residue 470 CYS Chi-restraints excluded: chain O residue 479 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 110 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 171 optimal weight: 0.8980 chunk 152 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 167 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 223 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 116 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 225 HIS A 286 GLN ** F 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 350 ASN G 409 ASN ** J 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 47 GLN ** K 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 349 GLN ** K 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 340 HIS N 357 GLN O 295 GLN O 484 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.209505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.146993 restraints weight = 44282.715| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 2.55 r_work: 0.3834 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3700 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 32076 Z= 0.160 Angle : 0.729 13.243 44042 Z= 0.363 Chirality : 0.051 0.419 4830 Planarity : 0.005 0.050 4978 Dihedral : 16.203 178.877 5595 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 5.07 % Allowed : 32.27 % Favored : 62.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.14), residues: 3306 helix: 0.45 (0.15), residues: 1114 sheet: -1.36 (0.20), residues: 626 loop : -1.55 (0.14), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 225 TYR 0.028 0.002 TYR F 330 PHE 0.033 0.002 PHE N 17 TRP 0.027 0.002 TRP N 369 HIS 0.010 0.001 HIS J 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (32076) covalent geometry : angle 0.72947 / 0.36 (44042) hydrogen bonds : bond 0.04098 / 2.73 ( 1293) hydrogen bonds : angle 4.88748 / 3.40 ( 3825) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 419 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8003 (ttmm) REVERT: A 92 MET cc_start: 0.3830 (mtm) cc_final: 0.3446 (ptm) REVERT: A 126 LYS cc_start: 0.8045 (ttpp) cc_final: 0.7513 (tppt) REVERT: A 136 GLU cc_start: 0.7845 (tp30) cc_final: 0.7615 (tp30) REVERT: A 189 ARG cc_start: 0.6490 (tpp80) cc_final: 0.6242 (tpp80) REVERT: A 212 GLU cc_start: 0.7686 (pt0) cc_final: 0.7120 (pp20) REVERT: A 286 GLN cc_start: 0.7390 (OUTLIER) cc_final: 0.7078 (tm-30) REVERT: A 329 LEU cc_start: 0.8931 (mt) cc_final: 0.8561 (mt) REVERT: B 3 GLU cc_start: 0.8204 (tt0) cc_final: 0.7465 (pm20) REVERT: B 85 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8075 (mmmm) REVERT: B 324 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7108 (mp0) REVERT: B 488 GLU cc_start: 0.8077 (tp30) cc_final: 0.7871 (tp30) REVERT: F 52 GLU cc_start: 0.5580 (mm-30) cc_final: 0.5104 (mm-30) REVERT: F 100 ASP cc_start: 0.8397 (t70) cc_final: 0.8120 (t0) REVERT: F 122 LYS cc_start: 0.8321 (mmtt) cc_final: 0.8032 (mmtt) REVERT: F 136 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7511 (mt-10) REVERT: F 150 SER cc_start: 0.8427 (t) cc_final: 0.7935 (p) REVERT: F 191 ASP cc_start: 0.6941 (m-30) cc_final: 0.6472 (p0) REVERT: F 220 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6716 (pm20) REVERT: F 267 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7520 (tt0) REVERT: F 307 LYS cc_start: 0.8175 (ptpp) cc_final: 0.7038 (pptt) REVERT: G 79 GLU cc_start: 0.6663 (mp0) cc_final: 0.6404 (mp0) REVERT: G 116 ASP cc_start: 0.6807 (OUTLIER) cc_final: 0.6208 (m-30) REVERT: G 217 HIS cc_start: 0.6370 (OUTLIER) cc_final: 0.5228 (p90) REVERT: G 243 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7539 (mtp180) REVERT: G 285 TYR cc_start: 0.8633 (OUTLIER) cc_final: 0.7889 (m-80) REVERT: G 383 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7767 (pt) REVERT: G 406 MET cc_start: 0.8746 (ttt) cc_final: 0.8533 (ttp) REVERT: G 435 MET cc_start: 0.8341 (mmt) cc_final: 0.7732 (mtt) REVERT: J 55 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7850 (mm-30) REVERT: J 357 GLN cc_start: 0.6782 (mm-40) cc_final: 0.6514 (tm-30) REVERT: J 402 LEU cc_start: 0.5526 (OUTLIER) cc_final: 0.5295 (tm) REVERT: K 79 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6845 (mt-10) REVERT: K 117 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7105 (tm) REVERT: K 210 LEU cc_start: 0.8189 (tp) cc_final: 0.7247 (mp) REVERT: K 225 ARG cc_start: 0.6654 (OUTLIER) cc_final: 0.5929 (ptp-110) REVERT: K 279 CYS cc_start: 0.6320 (p) cc_final: 0.5609 (p) REVERT: K 407 ARG cc_start: 0.6974 (ptm160) cc_final: 0.6753 (ptm160) REVERT: K 447 LYS cc_start: 0.5953 (mmtm) cc_final: 0.5211 (ptpt) REVERT: N 4 LYS cc_start: 0.6368 (mmtt) cc_final: 0.5860 (mmmt) REVERT: N 92 MET cc_start: 0.6218 (mtt) cc_final: 0.5215 (ppp) REVERT: N 231 GLU cc_start: 0.7075 (tt0) cc_final: 0.6831 (mp0) REVERT: N 277 MET cc_start: 0.7733 (tpt) cc_final: 0.7110 (tpt) REVERT: N 313 LYS cc_start: 0.5088 (OUTLIER) cc_final: 0.4635 (mptt) REVERT: N 336 MET cc_start: 0.2697 (mmt) cc_final: 0.2434 (mmt) REVERT: N 345 MET cc_start: 0.2591 (ppp) cc_final: 0.2152 (ppp) REVERT: N 391 ILE cc_start: 0.5562 (OUTLIER) cc_final: 0.5238 (mt) REVERT: N 398 GLU cc_start: 0.4310 (OUTLIER) cc_final: 0.3716 (tt0) REVERT: N 414 MET cc_start: 0.7420 (mmm) cc_final: 0.6507 (tpp) REVERT: O 29 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8519 (mm) REVERT: O 60 ILE cc_start: 0.5823 (OUTLIER) cc_final: 0.5576 (mp) REVERT: O 64 ILE cc_start: 0.5807 (mm) cc_final: 0.5551 (mm) REVERT: O 123 ASP cc_start: 0.7114 (t0) cc_final: 0.6702 (t70) REVERT: O 285 TYR cc_start: 0.7354 (m-80) cc_final: 0.6710 (m-80) REVERT: O 356 GLU cc_start: 0.6750 (tm-30) cc_final: 0.5446 (mm-30) REVERT: O 406 MET cc_start: 0.4098 (ppp) cc_final: 0.3455 (tmm) outliers start: 152 outliers final: 62 residues processed: 517 average time/residue: 0.4864 time to fit residues: 312.6715 Evaluate side-chains 464 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 382 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 162 LYS Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 267 GLN Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 397 SER Chi-restraints excluded: chain F residue 418 THR Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 96 ILE Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 217 HIS Chi-restraints excluded: chain G residue 243 ARG Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 383 LEU Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 61 LEU Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 243 THR Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain J residue 370 ASN Chi-restraints excluded: chain J residue 402 LEU Chi-restraints excluded: chain J residue 417 VAL Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 85 LYS Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain K residue 202 TYR Chi-restraints excluded: chain K residue 225 ARG Chi-restraints excluded: chain K residue 423 LEU Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain K residue 452 ILE Chi-restraints excluded: chain K residue 470 CYS Chi-restraints excluded: chain K residue 478 VAL Chi-restraints excluded: chain K residue 491 THR Chi-restraints excluded: chain N residue 18 THR Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 64 SER Chi-restraints excluded: chain N residue 86 LYS Chi-restraints excluded: chain N residue 129 GLN Chi-restraints excluded: chain N residue 313 LYS Chi-restraints excluded: chain N residue 391 ILE Chi-restraints excluded: chain N residue 398 GLU Chi-restraints excluded: chain O residue 29 LEU Chi-restraints excluded: chain O residue 51 GLN Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain O residue 91 ILE Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 389 THR Chi-restraints excluded: chain O residue 405 ILE Chi-restraints excluded: chain O residue 470 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 299 optimal weight: 0.5980 chunk 165 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 195 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 184 optimal weight: 20.0000 chunk 83 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 315 optimal weight: 10.0000 chunk 131 optimal weight: 0.5980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 225 HIS A 286 GLN ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 69 ASN ** K 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 295 GLN O 484 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.209006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.146754 restraints weight = 44776.210| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 2.54 r_work: 0.3837 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3707 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 32076 Z= 0.153 Angle : 0.715 14.565 44042 Z= 0.354 Chirality : 0.050 0.419 4830 Planarity : 0.004 0.050 4978 Dihedral : 16.181 179.518 5595 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 4.93 % Allowed : 32.80 % Favored : 62.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.14), residues: 3306 helix: 0.58 (0.15), residues: 1114 sheet: -1.36 (0.20), residues: 626 loop : -1.52 (0.14), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 225 TYR 0.027 0.002 TYR A 330 PHE 0.031 0.002 PHE J 321 TRP 0.039 0.002 TRP A 294 HIS 0.010 0.001 HIS N 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (32076) covalent geometry : angle 0.71530 / 0.35 (44042) hydrogen bonds : bond 0.03966 / 2.63 ( 1293) hydrogen bonds : angle 4.84340 / 3.36 ( 3825) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 424 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 TRP cc_start: 0.7770 (OUTLIER) cc_final: 0.6525 (m-10) REVERT: A 126 LYS cc_start: 0.8053 (ttpp) cc_final: 0.7493 (tppt) REVERT: A 136 GLU cc_start: 0.7768 (tp30) cc_final: 0.7550 (tp30) REVERT: A 189 ARG cc_start: 0.6419 (tpp80) cc_final: 0.5985 (tpp80) REVERT: A 212 GLU cc_start: 0.7664 (pt0) cc_final: 0.6984 (pp20) REVERT: B 3 GLU cc_start: 0.8213 (tt0) cc_final: 0.7364 (pm20) REVERT: B 85 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8096 (mmmm) REVERT: B 217 HIS cc_start: 0.6060 (OUTLIER) cc_final: 0.5573 (p90) REVERT: B 324 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6923 (mp0) REVERT: B 362 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7933 (mtm180) REVERT: B 488 GLU cc_start: 0.7919 (tp30) cc_final: 0.7687 (tp30) REVERT: F 52 GLU cc_start: 0.5889 (mm-30) cc_final: 0.5464 (mm-30) REVERT: F 100 ASP cc_start: 0.8346 (t70) cc_final: 0.7971 (t0) REVERT: F 130 ASP cc_start: 0.7348 (m-30) cc_final: 0.7120 (m-30) REVERT: F 136 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7582 (mt-10) REVERT: F 150 SER cc_start: 0.8410 (t) cc_final: 0.7910 (p) REVERT: F 191 ASP cc_start: 0.6892 (m-30) cc_final: 0.6594 (p0) REVERT: F 220 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6753 (pm20) REVERT: F 267 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7481 (tt0) REVERT: F 276 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7331 (tpt-90) REVERT: F 307 LYS cc_start: 0.8148 (ptpp) cc_final: 0.7031 (pptt) REVERT: G 19 LYS cc_start: 0.7994 (ptpp) cc_final: 0.7771 (mttt) REVERT: G 116 ASP cc_start: 0.6707 (OUTLIER) cc_final: 0.6087 (m-30) REVERT: G 217 HIS cc_start: 0.6200 (OUTLIER) cc_final: 0.5106 (p90) REVERT: G 285 TYR cc_start: 0.8673 (OUTLIER) cc_final: 0.7941 (m-80) REVERT: G 383 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7749 (pt) REVERT: G 449 GLU cc_start: 0.6584 (OUTLIER) cc_final: 0.6341 (pp20) REVERT: J 55 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7858 (mm-30) REVERT: J 92 MET cc_start: 0.5645 (mmt) cc_final: 0.5309 (tpt) REVERT: J 149 LYS cc_start: 0.6352 (mptt) cc_final: 0.6109 (mptp) REVERT: J 263 ARG cc_start: 0.7059 (ptm160) cc_final: 0.6414 (mtp-110) REVERT: J 357 GLN cc_start: 0.6902 (mm-40) cc_final: 0.6563 (tm-30) REVERT: J 402 LEU cc_start: 0.5565 (OUTLIER) cc_final: 0.5333 (tm) REVERT: K 75 PHE cc_start: 0.4443 (t80) cc_final: 0.4148 (t80) REVERT: K 79 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6883 (mt-10) REVERT: K 117 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7056 (tm) REVERT: K 132 ASP cc_start: 0.6114 (m-30) cc_final: 0.5587 (t0) REVERT: K 210 LEU cc_start: 0.8075 (tp) cc_final: 0.7109 (mp) REVERT: K 225 ARG cc_start: 0.6606 (OUTLIER) cc_final: 0.6201 (ptp-110) REVERT: K 226 GLU cc_start: 0.7397 (mt-10) cc_final: 0.7080 (mp0) REVERT: K 327 GLU cc_start: 0.5647 (tt0) cc_final: 0.4399 (tm-30) REVERT: K 447 LYS cc_start: 0.5713 (mmtm) cc_final: 0.5088 (ptpt) REVERT: N 4 LYS cc_start: 0.6356 (mmtt) cc_final: 0.5768 (mmmt) REVERT: N 78 LEU cc_start: 0.7386 (tp) cc_final: 0.7002 (tt) REVERT: N 92 MET cc_start: 0.6168 (mtt) cc_final: 0.5108 (ppp) REVERT: N 231 GLU cc_start: 0.7081 (tt0) cc_final: 0.6831 (mp0) REVERT: N 277 MET cc_start: 0.7620 (tpt) cc_final: 0.6983 (tpt) REVERT: N 345 MET cc_start: 0.2604 (ppp) cc_final: 0.2114 (ppp) REVERT: N 391 ILE cc_start: 0.5564 (OUTLIER) cc_final: 0.5232 (mt) REVERT: N 398 GLU cc_start: 0.4215 (OUTLIER) cc_final: 0.3693 (tt0) REVERT: N 414 MET cc_start: 0.7376 (mmm) cc_final: 0.6609 (tpp) REVERT: O 29 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8490 (mm) REVERT: O 60 ILE cc_start: 0.5785 (OUTLIER) cc_final: 0.5530 (mp) REVERT: O 64 ILE cc_start: 0.5791 (mm) cc_final: 0.5524 (mm) REVERT: O 123 ASP cc_start: 0.7157 (t0) cc_final: 0.6764 (t70) REVERT: O 245 PHE cc_start: 0.6340 (m-10) cc_final: 0.6011 (m-10) REVERT: O 285 TYR cc_start: 0.7354 (m-80) cc_final: 0.6762 (m-80) REVERT: O 302 GLN cc_start: 0.5282 (OUTLIER) cc_final: 0.5028 (pm20) REVERT: O 356 GLU cc_start: 0.6663 (tm-30) cc_final: 0.5409 (mm-30) REVERT: O 406 MET cc_start: 0.3907 (ppp) cc_final: 0.3273 (tmm) REVERT: O 449 GLU cc_start: 0.6322 (tt0) cc_final: 0.5699 (pm20) outliers start: 148 outliers final: 70 residues processed: 521 average time/residue: 0.5208 time to fit residues: 337.3542 Evaluate side-chains 485 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 393 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 TRP Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 217 HIS Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 362 ARG Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 162 LYS Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 267 GLN Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 276 ARG Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 397 SER Chi-restraints excluded: chain F residue 418 THR Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 96 ILE Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 217 HIS Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 330 LEU Chi-restraints excluded: chain G residue 383 LEU Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 437 VAL Chi-restraints excluded: chain G residue 449 GLU Chi-restraints excluded: chain G residue 470 CYS Chi-restraints excluded: chain G residue 498 THR Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 61 LEU Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 243 THR Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain J residue 335 LEU Chi-restraints excluded: chain J residue 370 ASN Chi-restraints excluded: chain J residue 402 LEU Chi-restraints excluded: chain J residue 417 VAL Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 85 LYS Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain K residue 202 TYR Chi-restraints excluded: chain K residue 225 ARG Chi-restraints excluded: chain K residue 317 VAL Chi-restraints excluded: chain K residue 405 ILE Chi-restraints excluded: chain K residue 423 LEU Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain K residue 470 CYS Chi-restraints excluded: chain K residue 478 VAL Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain N residue 18 THR Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 64 SER Chi-restraints excluded: chain N residue 86 LYS Chi-restraints excluded: chain N residue 391 ILE Chi-restraints excluded: chain N residue 398 GLU Chi-restraints excluded: chain O residue 29 LEU Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain O residue 91 ILE Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 296 ASN Chi-restraints excluded: chain O residue 302 GLN Chi-restraints excluded: chain O residue 389 THR Chi-restraints excluded: chain O residue 405 ILE Chi-restraints excluded: chain O residue 470 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 120 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 279 optimal weight: 6.9990 chunk 261 optimal weight: 0.9990 chunk 316 optimal weight: 10.0000 chunk 268 optimal weight: 0.9990 chunk 150 optimal weight: 0.9980 chunk 224 optimal weight: 0.9980 chunk 153 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 131 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 225 HIS B 35 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 47 GLN ** K 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 468 ASN ** N 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 357 GLN O 295 GLN O 484 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.209225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.147113 restraints weight = 44817.531| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 2.54 r_work: 0.3839 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3708 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 32076 Z= 0.157 Angle : 0.726 20.831 44042 Z= 0.357 Chirality : 0.050 0.420 4830 Planarity : 0.004 0.050 4978 Dihedral : 16.161 178.554 5595 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 4.60 % Allowed : 33.20 % Favored : 62.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.14), residues: 3306 helix: 0.62 (0.15), residues: 1118 sheet: -1.37 (0.20), residues: 626 loop : -1.51 (0.14), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 186 TYR 0.031 0.002 TYR A 293 PHE 0.043 0.002 PHE N 17 TRP 0.030 0.002 TRP A 294 HIS 0.007 0.001 HIS J 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (32076) covalent geometry : angle 0.72610 / 0.36 (44042) hydrogen bonds : bond 0.03943 / 2.63 ( 1293) hydrogen bonds : angle 4.78463 / 3.32 ( 3825) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 396 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 LYS cc_start: 0.8039 (ttpp) cc_final: 0.7497 (tppt) REVERT: A 136 GLU cc_start: 0.7787 (tp30) cc_final: 0.7549 (tp30) REVERT: A 189 ARG cc_start: 0.6432 (tpp80) cc_final: 0.6061 (tpp80) REVERT: A 212 GLU cc_start: 0.7659 (pt0) cc_final: 0.6982 (pp20) REVERT: A 339 SER cc_start: 0.8306 (m) cc_final: 0.7827 (p) REVERT: B 3 GLU cc_start: 0.8223 (tt0) cc_final: 0.7344 (pm20) REVERT: B 85 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8107 (mmmm) REVERT: B 217 HIS cc_start: 0.6094 (OUTLIER) cc_final: 0.5666 (p90) REVERT: B 324 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6907 (mp0) REVERT: B 362 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7932 (mtm180) REVERT: B 488 GLU cc_start: 0.7936 (tp30) cc_final: 0.7705 (tp30) REVERT: F 52 GLU cc_start: 0.5878 (mm-30) cc_final: 0.5497 (mm-30) REVERT: F 100 ASP cc_start: 0.8331 (t70) cc_final: 0.7948 (t0) REVERT: F 136 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7640 (mt-10) REVERT: F 150 SER cc_start: 0.8410 (t) cc_final: 0.7910 (p) REVERT: F 191 ASP cc_start: 0.6985 (m-30) cc_final: 0.6624 (p0) REVERT: F 220 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6717 (pm20) REVERT: F 267 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7518 (tt0) REVERT: F 276 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7318 (tpt-90) REVERT: F 307 LYS cc_start: 0.8163 (ptpp) cc_final: 0.7054 (pptt) REVERT: G 19 LYS cc_start: 0.8004 (ptpp) cc_final: 0.7770 (mttt) REVERT: G 79 GLU cc_start: 0.6444 (mp0) cc_final: 0.6211 (mp0) REVERT: G 116 ASP cc_start: 0.6701 (OUTLIER) cc_final: 0.6097 (m-30) REVERT: G 217 HIS cc_start: 0.6251 (OUTLIER) cc_final: 0.5170 (p90) REVERT: G 285 TYR cc_start: 0.8671 (OUTLIER) cc_final: 0.7876 (m-80) REVERT: G 383 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7781 (pt) REVERT: G 406 MET cc_start: 0.8736 (ttt) cc_final: 0.8498 (ttp) REVERT: G 449 GLU cc_start: 0.6620 (OUTLIER) cc_final: 0.6379 (pp20) REVERT: J 55 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7814 (mm-30) REVERT: J 92 MET cc_start: 0.5560 (mmt) cc_final: 0.5193 (mmt) REVERT: J 149 LYS cc_start: 0.6419 (mptt) cc_final: 0.6176 (mptp) REVERT: J 357 GLN cc_start: 0.6919 (mm-40) cc_final: 0.6544 (tm-30) REVERT: J 402 LEU cc_start: 0.5838 (OUTLIER) cc_final: 0.5609 (tm) REVERT: K 75 PHE cc_start: 0.4300 (t80) cc_final: 0.3984 (t80) REVERT: K 79 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6881 (mt-10) REVERT: K 117 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7051 (tm) REVERT: K 210 LEU cc_start: 0.8055 (tp) cc_final: 0.7100 (mp) REVERT: K 225 ARG cc_start: 0.6520 (OUTLIER) cc_final: 0.5826 (ptp-110) REVERT: K 226 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7246 (mp0) REVERT: K 447 LYS cc_start: 0.5646 (mmtm) cc_final: 0.5054 (ptpt) REVERT: N 78 LEU cc_start: 0.7310 (tp) cc_final: 0.6854 (tt) REVERT: N 92 MET cc_start: 0.6170 (mtt) cc_final: 0.5093 (ppp) REVERT: N 240 ARG cc_start: 0.3691 (mmt180) cc_final: 0.2851 (pmt-80) REVERT: N 277 MET cc_start: 0.7631 (tpt) cc_final: 0.6984 (tpt) REVERT: N 313 LYS cc_start: 0.5102 (OUTLIER) cc_final: 0.4532 (mptt) REVERT: N 336 MET cc_start: 0.2875 (mmt) cc_final: 0.2597 (mmt) REVERT: N 391 ILE cc_start: 0.5238 (OUTLIER) cc_final: 0.4930 (mt) REVERT: N 398 GLU cc_start: 0.4275 (OUTLIER) cc_final: 0.3675 (tt0) REVERT: N 414 MET cc_start: 0.7356 (mmm) cc_final: 0.6832 (tpp) REVERT: O 60 ILE cc_start: 0.5568 (OUTLIER) cc_final: 0.5280 (mp) REVERT: O 64 ILE cc_start: 0.5803 (mm) cc_final: 0.5534 (mm) REVERT: O 123 ASP cc_start: 0.7187 (t0) cc_final: 0.6785 (t70) REVERT: O 245 PHE cc_start: 0.6438 (m-10) cc_final: 0.6110 (m-10) REVERT: O 281 LEU cc_start: 0.5813 (pp) cc_final: 0.5567 (pt) REVERT: O 285 TYR cc_start: 0.7447 (m-80) cc_final: 0.6747 (m-80) REVERT: O 302 GLN cc_start: 0.5076 (OUTLIER) cc_final: 0.4862 (pm20) REVERT: O 356 GLU cc_start: 0.6671 (tm-30) cc_final: 0.5409 (mm-30) REVERT: O 390 LYS cc_start: 0.6303 (tppt) cc_final: 0.6061 (tptt) REVERT: O 406 MET cc_start: 0.3962 (ppp) cc_final: 0.3297 (tmm) REVERT: O 429 LEU cc_start: 0.5577 (mt) cc_final: 0.5193 (tt) outliers start: 138 outliers final: 74 residues processed: 487 average time/residue: 0.5055 time to fit residues: 307.2677 Evaluate side-chains 487 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 392 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 217 HIS Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 362 ARG Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 407 ARG Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 162 LYS Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 267 GLN Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 276 ARG Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 397 SER Chi-restraints excluded: chain F residue 418 THR Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 96 ILE Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 217 HIS Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 383 LEU Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 449 GLU Chi-restraints excluded: chain G residue 479 THR Chi-restraints excluded: chain G residue 498 THR Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 243 THR Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain J residue 370 ASN Chi-restraints excluded: chain J residue 402 LEU Chi-restraints excluded: chain J residue 417 VAL Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 85 LYS Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain K residue 202 TYR Chi-restraints excluded: chain K residue 225 ARG Chi-restraints excluded: chain K residue 317 VAL Chi-restraints excluded: chain K residue 405 ILE Chi-restraints excluded: chain K residue 423 LEU Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain K residue 470 CYS Chi-restraints excluded: chain K residue 478 VAL Chi-restraints excluded: chain K residue 491 THR Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain N residue 18 THR Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 64 SER Chi-restraints excluded: chain N residue 86 LYS Chi-restraints excluded: chain N residue 283 ARG Chi-restraints excluded: chain N residue 313 LYS Chi-restraints excluded: chain N residue 391 ILE Chi-restraints excluded: chain N residue 398 GLU Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain O residue 96 ILE Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 302 GLN Chi-restraints excluded: chain O residue 317 VAL Chi-restraints excluded: chain O residue 389 THR Chi-restraints excluded: chain O residue 405 ILE Chi-restraints excluded: chain O residue 470 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 118 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 236 optimal weight: 7.9990 chunk 192 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 141 optimal weight: 0.0270 chunk 156 optimal weight: 0.8980 chunk 297 optimal weight: 5.9990 chunk 219 optimal weight: 6.9990 chunk 263 optimal weight: 3.9990 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN A 225 HIS ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 409 ASN ** J 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 47 GLN O 295 GLN O 484 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.209093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.150017 restraints weight = 44632.799| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 2.73 r_work: 0.3814 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 32076 Z= 0.165 Angle : 0.729 18.443 44042 Z= 0.359 Chirality : 0.050 0.420 4830 Planarity : 0.004 0.050 4978 Dihedral : 16.154 178.580 5595 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 4.27 % Allowed : 33.57 % Favored : 62.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.19 (0.14), residues: 3306 helix: 0.55 (0.15), residues: 1118 sheet: -1.36 (0.20), residues: 626 loop : -1.51 (0.14), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 240 TYR 0.028 0.002 TYR A 293 PHE 0.036 0.002 PHE N 17 TRP 0.032 0.002 TRP N 369 HIS 0.010 0.001 HIS J 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (32076) covalent geometry : angle 0.72949 / 0.36 (44042) hydrogen bonds : bond 0.03976 / 2.65 ( 1293) hydrogen bonds : angle 4.81140 / 3.33 ( 3825) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 395 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.7699 (mp0) cc_final: 0.7301 (mp0) REVERT: A 109 ASN cc_start: 0.6900 (t0) cc_final: 0.6539 (t0) REVERT: A 126 LYS cc_start: 0.7974 (ttpp) cc_final: 0.7496 (tppt) REVERT: A 136 GLU cc_start: 0.7752 (tp30) cc_final: 0.7526 (tp30) REVERT: A 189 ARG cc_start: 0.6386 (tpp80) cc_final: 0.6027 (tpp80) REVERT: A 212 GLU cc_start: 0.7629 (pt0) cc_final: 0.6984 (pp20) REVERT: A 339 SER cc_start: 0.8218 (m) cc_final: 0.7753 (p) REVERT: B 3 GLU cc_start: 0.8070 (tt0) cc_final: 0.7323 (pm20) REVERT: B 85 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8099 (mmmm) REVERT: B 217 HIS cc_start: 0.6305 (OUTLIER) cc_final: 0.5871 (p90) REVERT: B 324 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6956 (mp0) REVERT: B 362 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7843 (mtm180) REVERT: B 488 GLU cc_start: 0.7783 (tp30) cc_final: 0.7566 (tp30) REVERT: F 52 GLU cc_start: 0.5797 (mm-30) cc_final: 0.5415 (mm-30) REVERT: F 100 ASP cc_start: 0.8156 (t70) cc_final: 0.7837 (t0) REVERT: F 136 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7405 (mt-10) REVERT: F 191 ASP cc_start: 0.6940 (m-30) cc_final: 0.6515 (p0) REVERT: F 220 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6680 (pm20) REVERT: F 267 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7529 (tt0) REVERT: F 276 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.7440 (mmt180) REVERT: F 307 LYS cc_start: 0.8191 (ptpp) cc_final: 0.7087 (pptt) REVERT: G 19 LYS cc_start: 0.7962 (ptpp) cc_final: 0.7723 (mttt) REVERT: G 113 ARG cc_start: 0.5223 (OUTLIER) cc_final: 0.4422 (pmt-80) REVERT: G 116 ASP cc_start: 0.6678 (OUTLIER) cc_final: 0.6171 (m-30) REVERT: G 145 GLU cc_start: 0.5736 (tp30) cc_final: 0.5530 (tp30) REVERT: G 217 HIS cc_start: 0.6246 (OUTLIER) cc_final: 0.5107 (p90) REVERT: G 285 TYR cc_start: 0.8664 (OUTLIER) cc_final: 0.7831 (m-80) REVERT: G 383 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7703 (pt) REVERT: G 406 MET cc_start: 0.8730 (ttt) cc_final: 0.8412 (ttp) REVERT: J 55 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7769 (mm-30) REVERT: J 92 MET cc_start: 0.5649 (mmt) cc_final: 0.5241 (mmt) REVERT: J 149 LYS cc_start: 0.6495 (mptt) cc_final: 0.6292 (mptp) REVERT: J 339 SER cc_start: 0.8264 (OUTLIER) cc_final: 0.7557 (t) REVERT: J 357 GLN cc_start: 0.6960 (mm-40) cc_final: 0.6597 (tm-30) REVERT: J 402 LEU cc_start: 0.5918 (OUTLIER) cc_final: 0.5686 (tm) REVERT: K 72 ARG cc_start: 0.4517 (ptm160) cc_final: 0.3946 (mtt90) REVERT: K 75 PHE cc_start: 0.4248 (t80) cc_final: 0.3944 (t80) REVERT: K 79 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6827 (mt-10) REVERT: K 117 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.6978 (tm) REVERT: K 210 LEU cc_start: 0.8072 (tp) cc_final: 0.7126 (mp) REVERT: K 225 ARG cc_start: 0.6436 (OUTLIER) cc_final: 0.5941 (ptp-110) REVERT: K 226 GLU cc_start: 0.7388 (mt-10) cc_final: 0.7153 (mp0) REVERT: K 447 LYS cc_start: 0.5891 (mmtm) cc_final: 0.5396 (ptpt) REVERT: K 498 THR cc_start: 0.5954 (OUTLIER) cc_final: 0.5611 (t) REVERT: N 78 LEU cc_start: 0.7295 (tp) cc_final: 0.6825 (tt) REVERT: N 92 MET cc_start: 0.6114 (mtt) cc_final: 0.5124 (ppp) REVERT: N 240 ARG cc_start: 0.3647 (mmt180) cc_final: 0.2871 (pmt-80) REVERT: N 277 MET cc_start: 0.7668 (tpt) cc_final: 0.7057 (tpt) REVERT: N 313 LYS cc_start: 0.5292 (OUTLIER) cc_final: 0.4741 (mppt) REVERT: N 336 MET cc_start: 0.2865 (mmt) cc_final: 0.2556 (mmt) REVERT: N 345 MET cc_start: 0.2615 (ppp) cc_final: 0.2383 (ppp) REVERT: N 391 ILE cc_start: 0.5232 (OUTLIER) cc_final: 0.4933 (mt) REVERT: N 398 GLU cc_start: 0.4307 (OUTLIER) cc_final: 0.3676 (tt0) REVERT: N 414 MET cc_start: 0.7373 (mmm) cc_final: 0.6846 (tpp) REVERT: O 60 ILE cc_start: 0.5569 (OUTLIER) cc_final: 0.5291 (mp) REVERT: O 64 ILE cc_start: 0.5736 (mm) cc_final: 0.5453 (mm) REVERT: O 123 ASP cc_start: 0.7233 (OUTLIER) cc_final: 0.6807 (t70) REVERT: O 245 PHE cc_start: 0.6515 (m-10) cc_final: 0.6222 (m-10) REVERT: O 285 TYR cc_start: 0.7226 (m-80) cc_final: 0.6585 (m-80) REVERT: O 302 GLN cc_start: 0.4959 (OUTLIER) cc_final: 0.4742 (pm20) REVERT: O 356 GLU cc_start: 0.6678 (tm-30) cc_final: 0.5422 (mm-30) REVERT: O 390 LYS cc_start: 0.6338 (tppt) cc_final: 0.6010 (tptt) REVERT: O 406 MET cc_start: 0.3861 (ppp) cc_final: 0.3210 (tmm) REVERT: O 429 LEU cc_start: 0.5483 (mt) cc_final: 0.5063 (tt) REVERT: O 449 GLU cc_start: 0.6442 (tt0) cc_final: 0.5655 (pm20) outliers start: 128 outliers final: 76 residues processed: 483 average time/residue: 0.5116 time to fit residues: 307.6096 Evaluate side-chains 484 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 384 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 217 HIS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 362 ARG Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 407 ARG Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 162 LYS Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 267 GLN Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 276 ARG Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 397 SER Chi-restraints excluded: chain F residue 418 THR Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 96 ILE Chi-restraints excluded: chain G residue 113 ARG Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 217 HIS Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 330 LEU Chi-restraints excluded: chain G residue 348 GLU Chi-restraints excluded: chain G residue 383 LEU Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 470 CYS Chi-restraints excluded: chain G residue 479 THR Chi-restraints excluded: chain G residue 498 THR Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 61 LEU Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 243 THR Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain J residue 339 SER Chi-restraints excluded: chain J residue 370 ASN Chi-restraints excluded: chain J residue 402 LEU Chi-restraints excluded: chain J residue 417 VAL Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 85 LYS Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain K residue 202 TYR Chi-restraints excluded: chain K residue 225 ARG Chi-restraints excluded: chain K residue 317 VAL Chi-restraints excluded: chain K residue 405 ILE Chi-restraints excluded: chain K residue 423 LEU Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain K residue 470 CYS Chi-restraints excluded: chain K residue 478 VAL Chi-restraints excluded: chain K residue 491 THR Chi-restraints excluded: chain K residue 498 THR Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 64 SER Chi-restraints excluded: chain N residue 86 LYS Chi-restraints excluded: chain N residue 313 LYS Chi-restraints excluded: chain N residue 391 ILE Chi-restraints excluded: chain N residue 398 GLU Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain O residue 123 ASP Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 302 GLN Chi-restraints excluded: chain O residue 317 VAL Chi-restraints excluded: chain O residue 389 THR Chi-restraints excluded: chain O residue 405 ILE Chi-restraints excluded: chain O residue 470 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 264 optimal weight: 0.2980 chunk 327 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 272 optimal weight: 6.9990 chunk 226 optimal weight: 5.9990 chunk 181 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 105 optimal weight: 0.3980 chunk 10 optimal weight: 0.4980 chunk 221 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 225 HIS ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 HIS ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 409 ASN J 69 ASN ** J 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 340 HIS O 295 GLN O 484 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.211117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.151897 restraints weight = 44631.362| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 2.89 r_work: 0.3845 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 32076 Z= 0.142 Angle : 0.728 17.735 44042 Z= 0.358 Chirality : 0.050 0.415 4830 Planarity : 0.004 0.049 4978 Dihedral : 16.149 178.447 5595 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.57 % Allowed : 34.50 % Favored : 61.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.11 (0.14), residues: 3306 helix: 0.61 (0.15), residues: 1118 sheet: -1.34 (0.20), residues: 606 loop : -1.45 (0.14), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 243 TYR 0.032 0.002 TYR N 233 PHE 0.057 0.002 PHE N 17 TRP 0.046 0.002 TRP N 369 HIS 0.012 0.001 HIS F 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (32076) covalent geometry : angle 0.72786 / 0.36 (44042) hydrogen bonds : bond 0.03841 / 2.55 ( 1293) hydrogen bonds : angle 4.77945 / 3.31 ( 3825) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 411 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.7680 (mp0) cc_final: 0.7301 (mp0) REVERT: A 109 ASN cc_start: 0.6941 (t0) cc_final: 0.6367 (t0) REVERT: A 126 LYS cc_start: 0.7908 (ttpp) cc_final: 0.7478 (tppt) REVERT: A 189 ARG cc_start: 0.6570 (tpp80) cc_final: 0.6186 (tpp80) REVERT: A 212 GLU cc_start: 0.7661 (pt0) cc_final: 0.7067 (pp20) REVERT: A 339 SER cc_start: 0.8219 (m) cc_final: 0.7679 (p) REVERT: B 1 MET cc_start: 0.7701 (tpp) cc_final: 0.7445 (mpp) REVERT: B 3 GLU cc_start: 0.8052 (tt0) cc_final: 0.7290 (pm20) REVERT: B 85 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8062 (mmmm) REVERT: B 138 VAL cc_start: 0.8587 (OUTLIER) cc_final: 0.8329 (t) REVERT: B 217 HIS cc_start: 0.6259 (OUTLIER) cc_final: 0.5845 (p90) REVERT: B 247 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.7178 (mmtp) REVERT: B 324 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6836 (mp0) REVERT: B 333 LYS cc_start: 0.8497 (tppp) cc_final: 0.7791 (ttpt) REVERT: B 346 TYR cc_start: 0.7291 (t80) cc_final: 0.7016 (t80) REVERT: B 362 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7858 (mtm180) REVERT: F 52 GLU cc_start: 0.5753 (mm-30) cc_final: 0.5368 (mm-30) REVERT: F 100 ASP cc_start: 0.8115 (t70) cc_final: 0.7804 (t0) REVERT: F 136 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7533 (mt-10) REVERT: F 189 ARG cc_start: 0.7723 (tpp80) cc_final: 0.7394 (tpp80) REVERT: F 220 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6737 (pm20) REVERT: F 267 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7602 (tt0) REVERT: F 276 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7415 (mmt180) REVERT: F 307 LYS cc_start: 0.8171 (ptpp) cc_final: 0.7069 (pptt) REVERT: G 19 LYS cc_start: 0.7929 (ptpp) cc_final: 0.7726 (mttt) REVERT: G 116 ASP cc_start: 0.6759 (OUTLIER) cc_final: 0.6241 (m-30) REVERT: G 217 HIS cc_start: 0.6185 (OUTLIER) cc_final: 0.5032 (p90) REVERT: G 285 TYR cc_start: 0.8631 (OUTLIER) cc_final: 0.7809 (m-80) REVERT: G 351 LYS cc_start: 0.8843 (mmmt) cc_final: 0.8296 (mmtm) REVERT: G 383 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7698 (pt) REVERT: G 406 MET cc_start: 0.8733 (ttt) cc_final: 0.8408 (ttp) REVERT: J 55 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7704 (mm-30) REVERT: J 339 SER cc_start: 0.8252 (OUTLIER) cc_final: 0.7540 (t) REVERT: J 357 GLN cc_start: 0.6950 (mm-40) cc_final: 0.6602 (tm-30) REVERT: J 392 TYR cc_start: 0.7013 (m-10) cc_final: 0.6747 (m-10) REVERT: J 402 LEU cc_start: 0.6173 (OUTLIER) cc_final: 0.5945 (tm) REVERT: K 68 ASN cc_start: 0.7454 (m110) cc_final: 0.6999 (t0) REVERT: K 72 ARG cc_start: 0.4482 (ptm160) cc_final: 0.3971 (mtm110) REVERT: K 75 PHE cc_start: 0.4128 (t80) cc_final: 0.3844 (t80) REVERT: K 79 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6255 (mp0) REVERT: K 117 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.6952 (tm) REVERT: K 210 LEU cc_start: 0.8016 (tp) cc_final: 0.7029 (mp) REVERT: K 417 LYS cc_start: 0.6845 (mmtp) cc_final: 0.6539 (mmtt) REVERT: K 447 LYS cc_start: 0.5825 (mmtm) cc_final: 0.5337 (ptpt) REVERT: N 78 LEU cc_start: 0.7235 (tp) cc_final: 0.6714 (tt) REVERT: N 92 MET cc_start: 0.6102 (mtt) cc_final: 0.5033 (ppp) REVERT: N 240 ARG cc_start: 0.3843 (mmt180) cc_final: 0.3115 (pmt-80) REVERT: N 277 MET cc_start: 0.7543 (tpt) cc_final: 0.6941 (tpt) REVERT: N 313 LYS cc_start: 0.5211 (OUTLIER) cc_final: 0.4667 (mppt) REVERT: N 336 MET cc_start: 0.3067 (mmt) cc_final: 0.2774 (mmt) REVERT: N 344 THR cc_start: 0.5009 (p) cc_final: 0.4661 (p) REVERT: N 345 MET cc_start: 0.2730 (ppp) cc_final: 0.2417 (ppp) REVERT: N 391 ILE cc_start: 0.5245 (OUTLIER) cc_final: 0.4942 (mt) REVERT: N 398 GLU cc_start: 0.4283 (OUTLIER) cc_final: 0.3675 (tt0) REVERT: N 414 MET cc_start: 0.7467 (mmm) cc_final: 0.6928 (tpp) REVERT: O 60 ILE cc_start: 0.5524 (OUTLIER) cc_final: 0.5259 (mp) REVERT: O 64 ILE cc_start: 0.5716 (mm) cc_final: 0.5430 (mm) REVERT: O 85 LYS cc_start: 0.6805 (mppt) cc_final: 0.6572 (mppt) REVERT: O 123 ASP cc_start: 0.7222 (t0) cc_final: 0.6803 (t70) REVERT: O 245 PHE cc_start: 0.6507 (m-10) cc_final: 0.6213 (m-10) REVERT: O 285 TYR cc_start: 0.7271 (m-80) cc_final: 0.6674 (m-80) REVERT: O 302 GLN cc_start: 0.4985 (OUTLIER) cc_final: 0.4777 (pm20) REVERT: O 356 GLU cc_start: 0.6657 (tm-30) cc_final: 0.5405 (mm-30) REVERT: O 362 ARG cc_start: 0.7501 (ptp90) cc_final: 0.6847 (ptp90) REVERT: O 390 LYS cc_start: 0.6330 (tppt) cc_final: 0.6056 (tptt) REVERT: O 406 MET cc_start: 0.3903 (ppp) cc_final: 0.3256 (tmm) REVERT: O 429 LEU cc_start: 0.5443 (mt) cc_final: 0.5026 (tt) REVERT: O 449 GLU cc_start: 0.6438 (tt0) cc_final: 0.5648 (pm20) REVERT: O 480 LEU cc_start: 0.6899 (mt) cc_final: 0.6484 (mt) outliers start: 107 outliers final: 68 residues processed: 482 average time/residue: 0.5255 time to fit residues: 314.6785 Evaluate side-chains 477 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 387 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 217 HIS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 247 LYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 362 ARG Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 162 LYS Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 267 GLN Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 276 ARG Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 397 SER Chi-restraints excluded: chain F residue 418 THR Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 217 HIS Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 330 LEU Chi-restraints excluded: chain G residue 383 LEU Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 479 THR Chi-restraints excluded: chain G residue 498 THR Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 46 TRP Chi-restraints excluded: chain J residue 61 LEU Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 243 THR Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain J residue 339 SER Chi-restraints excluded: chain J residue 370 ASN Chi-restraints excluded: chain J residue 402 LEU Chi-restraints excluded: chain J residue 417 VAL Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 85 LYS Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain K residue 202 TYR Chi-restraints excluded: chain K residue 317 VAL Chi-restraints excluded: chain K residue 405 ILE Chi-restraints excluded: chain K residue 423 LEU Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain K residue 470 CYS Chi-restraints excluded: chain K residue 478 VAL Chi-restraints excluded: chain K residue 491 THR Chi-restraints excluded: chain N residue 18 THR Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 64 SER Chi-restraints excluded: chain N residue 86 LYS Chi-restraints excluded: chain N residue 313 LYS Chi-restraints excluded: chain N residue 391 ILE Chi-restraints excluded: chain N residue 398 GLU Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 302 GLN Chi-restraints excluded: chain O residue 317 VAL Chi-restraints excluded: chain O residue 389 THR Chi-restraints excluded: chain O residue 405 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 75 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 79 optimal weight: 0.0870 chunk 106 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 182 optimal weight: 10.0000 chunk 311 optimal weight: 2.9990 chunk 176 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 340 optimal weight: 9.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 225 HIS ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 HIS ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 430 GLN ** J 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 183 ASN O 295 GLN O 484 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.210874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.151790 restraints weight = 44745.301| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 2.97 r_work: 0.3836 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 32076 Z= 0.149 Angle : 0.732 18.099 44042 Z= 0.360 Chirality : 0.050 0.412 4830 Planarity : 0.004 0.048 4978 Dihedral : 16.135 179.919 5595 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.67 % Allowed : 34.67 % Favored : 61.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.09 (0.14), residues: 3306 helix: 0.60 (0.15), residues: 1118 sheet: -1.29 (0.21), residues: 606 loop : -1.44 (0.14), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 225 TYR 0.025 0.001 TYR A 293 PHE 0.033 0.002 PHE J 321 TRP 0.053 0.002 TRP N 369 HIS 0.029 0.001 HIS F 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (32076) covalent geometry : angle 0.73233 / 0.36 (44042) hydrogen bonds : bond 0.03837 / 2.56 ( 1293) hydrogen bonds : angle 4.77079 / 3.30 ( 3825) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13824.68 seconds wall clock time: 235 minutes 54.43 seconds (14154.43 seconds total)