Starting phenix.real_space_refine on Wed May 28 17:03:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ifm_35421/05_2025/8ifm_35421.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ifm_35421/05_2025/8ifm_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ifm_35421/05_2025/8ifm_35421.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ifm_35421/05_2025/8ifm_35421.map" model { file = "/net/cci-nas-00/data/ceres_data/8ifm_35421/05_2025/8ifm_35421.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ifm_35421/05_2025/8ifm_35421.cif" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'RNA': 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: {'RNA': 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: {'RNA': 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: {'RNA': 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: 17.64, per 1000 atoms: 0.57 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: 7.30 Conformation dependent library (CDL) restraints added in 3.4 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: 11.35 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: 12.85 Time building geometry restraints manager: 8.52 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=" 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=" N PRO B 23 " pdb=" CD PRO B 23 " ideal model delta sigma weight residual 1.473 1.501 -0.028 1.40e-02 5.10e+03 4.04e+00 bond pdb=" N PRO B 23 " pdb=" CA PRO B 23 " ideal model delta sigma weight residual 1.472 1.446 0.026 1.32e-02 5.74e+03 3.80e+00 bond pdb=" CB PRO O 220 " pdb=" CG PRO O 220 " ideal model delta sigma weight residual 1.492 1.577 -0.085 5.00e-02 4.00e+02 2.89e+00 ... (remaining 32071 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.46: 43852 3.46 - 6.91: 170 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=" 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=" CA GLN O 430 " pdb=" CB GLN O 430 " pdb=" CG GLN O 430 " ideal model delta sigma weight residual 114.10 122.17 -8.07 2.00e+00 2.50e-01 1.63e+01 angle pdb=" CA GLU A 212 " pdb=" CB GLU A 212 " pdb=" CG GLU A 212 " ideal model delta sigma weight residual 114.10 122.11 -8.01 2.00e+00 2.50e-01 1.61e+01 ... (remaining 44037 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 15438 17.93 - 35.85: 2485 35.85 - 53.78: 808 53.78 - 71.71: 237 71.71 - 89.64: 60 Dihedral angle restraints: 19028 sinusoidal: 9160 harmonic: 9868 Sorted by residual: dihedral pdb=" CA PHE F 135 " pdb=" C PHE F 135 " pdb=" N GLU F 136 " pdb=" CA GLU F 136 " ideal model delta harmonic sigma weight residual 180.00 154.76 25.24 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA GLN A 286 " pdb=" C GLN A 286 " pdb=" N MET A 287 " pdb=" CA MET A 287 " ideal model delta harmonic sigma weight residual 180.00 155.36 24.64 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA GLU J 399 " pdb=" C GLU J 399 " pdb=" N LYS J 400 " pdb=" CA LYS J 400 " ideal model delta harmonic sigma weight residual -180.00 -157.85 -22.15 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 19025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 3280 0.036 - 0.073: 1053 0.073 - 0.109: 360 0.109 - 0.145: 126 0.145 - 0.181: 11 Chirality restraints: 4830 Sorted by residual: chirality pdb=" CB ILE F 112 " pdb=" CA ILE F 112 " pdb=" CG1 ILE F 112 " pdb=" CG2 ILE F 112 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.22e-01 chirality pdb=" CG LEU F 28 " pdb=" CB LEU F 28 " pdb=" CD1 LEU F 28 " pdb=" CD2 LEU F 28 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.22e-01 chirality pdb=" CA ILE O 443 " pdb=" N ILE O 443 " pdb=" C ILE O 443 " pdb=" CB ILE O 443 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.38e-01 ... (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: 3.070 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: 1.310 Check model and map are aligned: 0.230 Set scattering table: 0.290 Process input model: 73.720 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.140 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:10.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 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 : 0.003 0.147 32076 Z= 0.141 Angle : 0.653 17.275 44042 Z= 0.344 Chirality : 0.043 0.181 4830 Planarity : 0.006 0.172 4978 Dihedral : 19.792 89.635 12644 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 18.40 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.041 0.002 TRP J 369 HIS 0.011 0.001 HIS N 9 PHE 0.035 0.002 PHE J 343 TYR 0.018 0.001 TYR K 6 ARG 0.008 0.001 ARG A 71 Details of bonding type rmsd hydrogen bonds : bond 0.12633 ( 1293) hydrogen bonds : angle 6.26807 ( 3825) covalent geometry : bond 0.00337 (32076) covalent geometry : angle 0.65255 (44042) *********************** 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 : 3.178 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: A 212 GLU cc_start: 0.6613 (pp20) cc_final: 0.6283 (pt0) REVERT: F 70 LYS cc_start: 0.7178 (mmtm) cc_final: 0.6537 (pttp) REVERT: F 190 TYR cc_start: 0.5616 (m-10) cc_final: 0.5357 (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: 0.6791 (t80) REVERT: O 356 GLU cc_start: 0.6209 (tm-30) cc_final: 0.5860 (pm20) REVERT: O 357 VAL cc_start: 0.7157 (t) cc_final: 0.6394 (t) REVERT: O 378 PRO cc_start: 0.3541 (Cg_endo) cc_final: 0.3214 (Cg_exo) REVERT: O 406 MET cc_start: 0.4863 (ppp) cc_final: 0.4487 (pp-130) outliers start: 19 outliers final: 5 residues processed: 735 average time/residue: 1.2007 time to fit residues: 1062.8494 Evaluate side-chains 474 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 469 time to evaluate : 3.247 ------------------------------------------------------------------------------- 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 293 optimal weight: 0.2980 chunk 263 optimal weight: 6.9990 chunk 146 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 177 optimal weight: 4.9990 chunk 140 optimal weight: 0.0770 chunk 272 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 chunk 165 optimal weight: 0.9980 chunk 203 optimal weight: 6.9990 chunk 316 optimal weight: 0.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN A 225 HIS A 405 ASN 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 382 ASN B 466 ASN F 340 HIS G 296 ASN G 350 ASN ** J 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 262 GLN ** J 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 51 GLN ** K 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 207 HIS K 209 GLN 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 Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.214944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.156505 restraints weight = 44987.368| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 2.99 r_work: 0.3878 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 32076 Z= 0.148 Angle : 0.650 16.016 44042 Z= 0.339 Chirality : 0.044 0.210 4830 Planarity : 0.005 0.077 4978 Dihedral : 16.313 82.320 5700 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 5.23 % Allowed : 29.63 % Favored : 65.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.14), residues: 3306 helix: 0.98 (0.15), residues: 1114 sheet: -0.84 (0.22), residues: 508 loop : -1.33 (0.14), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 20 HIS 0.013 0.001 HIS O 217 PHE 0.034 0.002 PHE O 373 TYR 0.019 0.002 TYR G 285 ARG 0.008 0.001 ARG F 374 Details of bonding type rmsd hydrogen bonds : bond 0.03920 ( 1293) hydrogen bonds : angle 4.89557 ( 3825) covalent geometry : bond 0.00334 (32076) covalent geometry : angle 0.65022 (44042) *********************** 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 668 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 511 time to evaluate : 3.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 TRP cc_start: 0.7620 (OUTLIER) cc_final: 0.6661 (m-10) REVERT: A 260 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7447 (tm-30) REVERT: A 293 TYR cc_start: 0.7472 (m-80) cc_final: 0.7180 (m-80) REVERT: A 357 GLN cc_start: 0.7385 (tp40) cc_final: 0.6967 (mm-40) REVERT: B 3 GLU cc_start: 0.7893 (tt0) cc_final: 0.7338 (pm20) REVERT: B 203 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7920 (p0) REVERT: B 217 HIS cc_start: 0.6057 (OUTLIER) cc_final: 0.5513 (p90) REVERT: B 324 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6713 (mp0) REVERT: B 331 LYS cc_start: 0.8227 (mmmt) cc_final: 0.7942 (mmmm) REVERT: B 346 TYR cc_start: 0.7529 (t80) cc_final: 0.7241 (t80) REVERT: B 358 PHE cc_start: 0.8314 (t80) cc_final: 0.7885 (t80) REVERT: F 70 LYS cc_start: 0.7460 (mmtm) cc_final: 0.6024 (pttp) REVERT: F 100 ASP cc_start: 0.7942 (t0) cc_final: 0.7409 (t0) REVERT: F 122 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7950 (mmtt) REVERT: F 132 LEU cc_start: 0.8229 (mm) cc_final: 0.7953 (mt) REVERT: F 160 HIS cc_start: 0.7312 (OUTLIER) cc_final: 0.7056 (p90) REVERT: F 184 GLU cc_start: 0.6290 (pt0) cc_final: 0.6051 (pt0) REVERT: F 205 PHE cc_start: 0.6879 (m-80) cc_final: 0.6661 (m-80) REVERT: F 220 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.6108 (pm20) REVERT: F 267 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7199 (tt0) REVERT: F 274 GLU cc_start: 0.7471 (tp30) cc_final: 0.7040 (tp30) REVERT: F 294 TRP cc_start: 0.6054 (p-90) cc_final: 0.5220 (p-90) REVERT: F 307 LYS cc_start: 0.8193 (ptpp) cc_final: 0.7138 (pptt) REVERT: G 134 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7500 (pm20) REVERT: J 40 ASP cc_start: 0.6667 (t70) cc_final: 0.6411 (m-30) REVERT: J 54 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7682 (ptm160) REVERT: J 92 MET cc_start: 0.5455 (tpp) cc_final: 0.4911 (tpt) REVERT: J 149 LYS cc_start: 0.5689 (mptp) cc_final: 0.4762 (pptt) REVERT: J 184 GLU cc_start: 0.5558 (mm-30) cc_final: 0.5256 (mm-30) REVERT: J 260 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.7116 (mt-10) REVERT: J 285 TYR cc_start: 0.6041 (t80) cc_final: 0.5825 (t80) REVERT: J 297 LYS cc_start: 0.4680 (pttm) cc_final: 0.3780 (tptt) REVERT: K 1 MET cc_start: 0.3463 (tpp) cc_final: 0.3018 (tpp) REVERT: K 210 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7266 (mp) REVERT: K 279 CYS cc_start: 0.6830 (t) cc_final: 0.6615 (p) REVERT: K 286 LYS cc_start: 0.6837 (tptt) cc_final: 0.6517 (mmtm) REVERT: K 430 GLN cc_start: 0.7224 (mt0) cc_final: 0.6350 (pp30) REVERT: K 447 LYS cc_start: 0.5959 (mmtm) cc_final: 0.5337 (ptmt) REVERT: K 484 ASN cc_start: 0.6442 (t0) cc_final: 0.6184 (t0) REVERT: K 498 THR cc_start: 0.6076 (OUTLIER) cc_final: 0.5753 (t) REVERT: N 4 LYS cc_start: 0.6060 (mmtt) cc_final: 0.5250 (mtpm) REVERT: N 78 LEU cc_start: 0.6990 (tp) cc_final: 0.6349 (tt) REVERT: N 100 ASP cc_start: 0.6827 (t70) cc_final: 0.6442 (t0) REVERT: N 281 ASN cc_start: 0.6591 (OUTLIER) cc_final: 0.5443 (t0) REVERT: N 391 ILE cc_start: 0.5885 (OUTLIER) cc_final: 0.5576 (mt) REVERT: O 60 ILE cc_start: 0.5415 (OUTLIER) cc_final: 0.5195 (mp) REVERT: O 90 ASN cc_start: 0.6270 (t0) cc_final: 0.5641 (t0) REVERT: O 208 ASP cc_start: 0.5042 (OUTLIER) cc_final: 0.4795 (p0) REVERT: O 281 LEU cc_start: 0.6033 (tm) cc_final: 0.5627 (pt) REVERT: O 285 TYR cc_start: 0.6879 (m-80) cc_final: 0.6391 (m-80) REVERT: O 296 ASN cc_start: 0.6517 (t0) cc_final: 0.5442 (t0) REVERT: O 356 GLU cc_start: 0.6781 (tm-30) cc_final: 0.5257 (pm20) REVERT: O 357 VAL cc_start: 0.7327 (t) cc_final: 0.6928 (t) REVERT: O 359 ILE cc_start: 0.6283 (OUTLIER) cc_final: 0.5959 (tp) REVERT: O 373 PHE cc_start: 0.7891 (m-80) cc_final: 0.7615 (m-80) REVERT: O 406 MET cc_start: 0.3406 (ppp) cc_final: 0.2829 (pp-130) REVERT: O 506 TYR cc_start: 0.6829 (m-80) cc_final: 0.6472 (m-80) outliers start: 157 outliers final: 35 residues processed: 620 average time/residue: 1.1000 time to fit residues: 842.5529 Evaluate side-chains 494 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 440 time to evaluate : 3.138 ------------------------------------------------------------------------------- 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 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 B residue 7 ILE Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 138 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 324 GLU Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain F residue 122 LYS 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 221 TYR Chi-restraints excluded: chain F residue 267 GLN 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 60 ILE Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 303 MET Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain J residue 54 ARG 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 260 GLU Chi-restraints excluded: chain K residue 21 THR 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 333 LYS Chi-restraints excluded: chain K residue 405 ILE Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain K residue 470 CYS Chi-restraints excluded: chain K residue 498 THR Chi-restraints excluded: chain N residue 86 LYS Chi-restraints excluded: chain N residue 281 ASN Chi-restraints excluded: chain N residue 391 ILE Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain O residue 208 ASP Chi-restraints excluded: chain O residue 359 ILE Chi-restraints excluded: chain O residue 389 THR Chi-restraints excluded: chain O residue 411 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 109 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 233 optimal weight: 9.9990 chunk 197 optimal weight: 6.9990 chunk 6 optimal weight: 0.0060 chunk 153 optimal weight: 5.9990 chunk 248 optimal weight: 2.9990 chunk 310 optimal weight: 6.9990 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 HIS A 267 GLN A 340 HIS A 394 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 HIS ** F 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 ASN ** J 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 69 ASN ** K 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 286 GLN N 357 GLN O 207 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.210839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.147873 restraints weight = 45223.036| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 2.67 r_work: 0.3842 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 32076 Z= 0.184 Angle : 0.649 13.679 44042 Z= 0.337 Chirality : 0.045 0.238 4830 Planarity : 0.005 0.050 4978 Dihedral : 16.270 83.384 5691 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 5.73 % Allowed : 29.70 % Favored : 64.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.14), residues: 3306 helix: 0.84 (0.15), residues: 1120 sheet: -1.17 (0.20), residues: 646 loop : -1.39 (0.14), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 20 HIS 0.009 0.001 HIS O 217 PHE 0.025 0.002 PHE F 135 TYR 0.021 0.002 TYR A 330 ARG 0.006 0.001 ARG O 364 Details of bonding type rmsd hydrogen bonds : bond 0.04003 ( 1293) hydrogen bonds : angle 4.83883 ( 3825) covalent geometry : bond 0.00420 (32076) covalent geometry : angle 0.64946 (44042) *********************** 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 647 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 475 time to evaluate : 3.170 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: 0.7565 (OUTLIER) cc_final: 0.6507 (m-10) REVERT: A 212 GLU cc_start: 0.7746 (pt0) cc_final: 0.7079 (pp20) REVERT: A 277 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7707 (mpp) REVERT: A 293 TYR cc_start: 0.7367 (m-80) cc_final: 0.7106 (m-80) REVERT: A 339 SER cc_start: 0.8430 (m) cc_final: 0.8179 (p) REVERT: B 3 GLU cc_start: 0.8036 (tt0) cc_final: 0.7358 (pm20) REVERT: B 203 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7932 (p0) REVERT: B 217 HIS cc_start: 0.6299 (OUTLIER) cc_final: 0.5662 (p90) REVERT: B 324 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6920 (mp0) REVERT: B 346 TYR cc_start: 0.7613 (t80) cc_final: 0.7324 (t80) REVERT: F 100 ASP cc_start: 0.8074 (t0) cc_final: 0.7639 (t0) REVERT: F 133 ASP cc_start: 0.8261 (t0) cc_final: 0.7926 (t0) REVERT: F 179 ILE cc_start: 0.7370 (OUTLIER) cc_final: 0.7074 (mp) REVERT: F 220 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.6233 (pm20) REVERT: F 267 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7106 (tt0) REVERT: F 274 GLU cc_start: 0.7635 (tp30) cc_final: 0.7369 (tp30) REVERT: F 294 TRP cc_start: 0.6130 (p-90) cc_final: 0.5283 (p-90) REVERT: G 96 ILE cc_start: 0.7960 (OUTLIER) cc_final: 0.7635 (pt) REVERT: G 134 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7730 (pm20) REVERT: G 217 HIS cc_start: 0.6021 (OUTLIER) cc_final: 0.4715 (p90) REVERT: G 336 LYS cc_start: 0.7488 (OUTLIER) cc_final: 0.6950 (mppt) REVERT: G 383 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7746 (pt) REVERT: J 40 ASP cc_start: 0.6703 (t70) cc_final: 0.6478 (m-30) REVERT: J 92 MET cc_start: 0.5432 (tpp) cc_final: 0.4989 (tpt) REVERT: J 297 LYS cc_start: 0.4695 (pttm) cc_final: 0.3849 (tptt) REVERT: K 1 MET cc_start: 0.3723 (tpp) cc_final: 0.3334 (tpp) REVERT: K 12 ILE cc_start: 0.3765 (OUTLIER) cc_final: 0.3400 (pt) REVERT: K 79 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6956 (mt-10) REVERT: K 85 LYS cc_start: 0.7793 (OUTLIER) cc_final: 0.7284 (mtmm) REVERT: K 279 CYS cc_start: 0.7144 (OUTLIER) cc_final: 0.6588 (p) REVERT: K 447 LYS cc_start: 0.5869 (mmtm) cc_final: 0.5284 (ptmt) REVERT: K 498 THR cc_start: 0.6029 (OUTLIER) cc_final: 0.5712 (t) REVERT: N 4 LYS cc_start: 0.6447 (mmtt) cc_final: 0.6010 (mtpt) REVERT: N 20 TRP cc_start: 0.7261 (t60) cc_final: 0.7047 (t60) REVERT: N 78 LEU cc_start: 0.7190 (tp) cc_final: 0.6803 (tt) REVERT: N 100 ASP cc_start: 0.6770 (t70) cc_final: 0.6396 (t0) REVERT: N 281 ASN cc_start: 0.6807 (OUTLIER) cc_final: 0.6010 (t0) REVERT: N 313 LYS cc_start: 0.5071 (OUTLIER) cc_final: 0.4626 (mptt) REVERT: N 340 HIS cc_start: 0.5267 (OUTLIER) cc_final: 0.4903 (p90) REVERT: N 391 ILE cc_start: 0.5719 (OUTLIER) cc_final: 0.5415 (mt) REVERT: N 398 GLU cc_start: 0.4284 (OUTLIER) cc_final: 0.3713 (tt0) REVERT: O 60 ILE cc_start: 0.5541 (OUTLIER) cc_final: 0.5277 (mp) REVERT: O 90 ASN cc_start: 0.6429 (t0) cc_final: 0.5843 (t0) REVERT: O 281 LEU cc_start: 0.6099 (tm) cc_final: 0.5697 (pt) REVERT: O 285 TYR cc_start: 0.7149 (m-80) cc_final: 0.6580 (m-80) REVERT: O 296 ASN cc_start: 0.6536 (t0) cc_final: 0.5159 (t0) REVERT: O 365 PHE cc_start: 0.6789 (m-80) cc_final: 0.6541 (m-80) REVERT: O 368 GLU cc_start: 0.6077 (OUTLIER) cc_final: 0.5828 (pm20) REVERT: O 373 PHE cc_start: 0.7983 (m-80) cc_final: 0.7698 (m-80) REVERT: O 406 MET cc_start: 0.3513 (ppp) cc_final: 0.2834 (pp-130) REVERT: O 449 GLU cc_start: 0.6213 (tt0) cc_final: 0.5619 (pm20) outliers start: 172 outliers final: 54 residues processed: 592 average time/residue: 1.0134 time to fit residues: 746.5165 Evaluate side-chains 498 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 419 time to evaluate : 2.949 ------------------------------------------------------------------------------- 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 48 THR Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 277 MET 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 119 THR Chi-restraints excluded: chain B residue 138 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 229 LEU 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 405 ILE Chi-restraints excluded: chain F residue 48 THR 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 282 VAL Chi-restraints excluded: chain F residue 311 VAL 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 134 GLU Chi-restraints excluded: chain G residue 217 HIS Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 336 LYS 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 303 ASP Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain J residue 417 VAL Chi-restraints excluded: chain K residue 12 ILE 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 94 LYS Chi-restraints excluded: chain K residue 202 TYR Chi-restraints excluded: chain K residue 279 CYS 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 494 THR Chi-restraints excluded: chain K residue 498 THR 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 340 HIS Chi-restraints excluded: chain N residue 391 ILE Chi-restraints excluded: chain N residue 398 GLU Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain O residue 92 VAL Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 368 GLU Chi-restraints excluded: chain O residue 389 THR Chi-restraints excluded: chain O residue 405 ILE Chi-restraints excluded: chain O residue 413 VAL Chi-restraints excluded: chain O residue 470 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 38 optimal weight: 0.8980 chunk 255 optimal weight: 10.0000 chunk 334 optimal weight: 3.9990 chunk 331 optimal weight: 0.9990 chunk 271 optimal weight: 2.9990 chunk 319 optimal weight: 6.9990 chunk 180 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 288 optimal weight: 9.9990 chunk 265 optimal weight: 9.9990 chunk 325 optimal weight: 0.0670 overall best weight: 1.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 HIS A 340 HIS ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 ASN F 160 HIS G 409 ASN ** J 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 357 GLN K 349 GLN K 380 ASN K 430 GLN ** K 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 314 GLN O 61 GLN O 295 GLN O 302 GLN O 484 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.208114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.148878 restraints weight = 44938.093| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 2.87 r_work: 0.3784 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 32076 Z= 0.203 Angle : 0.669 12.765 44042 Z= 0.347 Chirality : 0.046 0.244 4830 Planarity : 0.005 0.058 4978 Dihedral : 16.310 86.472 5691 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 6.87 % Allowed : 29.10 % Favored : 64.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.14), residues: 3306 helix: 0.68 (0.15), residues: 1114 sheet: -1.15 (0.20), residues: 616 loop : -1.43 (0.14), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP N 373 HIS 0.011 0.001 HIS F 160 PHE 0.028 0.002 PHE N 17 TYR 0.026 0.002 TYR F 330 ARG 0.004 0.001 ARG J 263 Details of bonding type rmsd hydrogen bonds : bond 0.04125 ( 1293) hydrogen bonds : angle 4.85917 ( 3825) covalent geometry : bond 0.00471 (32076) covalent geometry : angle 0.66937 (44042) *********************** 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 661 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 455 time to evaluate : 3.268 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: 0.8004 (ttpp) cc_final: 0.7502 (tppt) REVERT: A 212 GLU cc_start: 0.7850 (pt0) cc_final: 0.7220 (pp20) REVERT: A 273 PHE cc_start: 0.7822 (OUTLIER) cc_final: 0.7073 (m-80) REVERT: A 277 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7433 (mpt) REVERT: A 294 TRP cc_start: 0.7573 (p-90) cc_final: 0.7303 (p-90) REVERT: A 329 LEU cc_start: 0.9013 (mt) cc_final: 0.8677 (mt) REVERT: A 339 SER cc_start: 0.8510 (m) cc_final: 0.8279 (p) REVERT: B 3 GLU cc_start: 0.8044 (tt0) cc_final: 0.7374 (pm20) REVERT: B 217 HIS cc_start: 0.6435 (OUTLIER) cc_final: 0.6032 (p90) REVERT: B 324 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6973 (mp0) REVERT: B 346 TYR cc_start: 0.7650 (t80) cc_final: 0.7390 (t80) REVERT: B 362 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8031 (mtm180) REVERT: F 77 GLU cc_start: 0.7049 (pt0) cc_final: 0.6773 (mp0) REVERT: F 100 ASP cc_start: 0.8211 (t0) cc_final: 0.7887 (t0) REVERT: F 179 ILE cc_start: 0.7370 (OUTLIER) cc_final: 0.7079 (mp) REVERT: F 205 PHE cc_start: 0.7363 (m-80) cc_final: 0.7122 (m-80) REVERT: F 220 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6534 (pm20) REVERT: F 267 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7363 (tt0) REVERT: F 274 GLU cc_start: 0.7640 (tp30) cc_final: 0.7324 (tp30) REVERT: G 217 HIS cc_start: 0.6250 (OUTLIER) cc_final: 0.5035 (p90) REVERT: G 285 TYR cc_start: 0.8604 (OUTLIER) cc_final: 0.7854 (m-80) REVERT: G 336 LYS cc_start: 0.7435 (OUTLIER) cc_final: 0.6889 (mppt) REVERT: G 383 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7689 (pt) REVERT: J 37 LEU cc_start: 0.8684 (mp) cc_final: 0.8413 (mp) REVERT: J 40 ASP cc_start: 0.6750 (t70) cc_final: 0.6530 (m-30) REVERT: J 92 MET cc_start: 0.5359 (tpp) cc_final: 0.4869 (tpt) REVERT: J 297 LYS cc_start: 0.4667 (pttm) cc_final: 0.3976 (tptt) REVERT: K 1 MET cc_start: 0.3921 (tpp) cc_final: 0.3317 (tpp) REVERT: K 79 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6918 (mt-10) REVERT: K 85 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7533 (mtmm) REVERT: K 117 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7025 (tm) REVERT: K 210 LEU cc_start: 0.8187 (tp) cc_final: 0.7243 (mp) REVERT: K 447 LYS cc_start: 0.5927 (mmtm) cc_final: 0.5186 (ptpt) REVERT: K 498 THR cc_start: 0.5962 (OUTLIER) cc_final: 0.5613 (t) REVERT: N 20 TRP cc_start: 0.7166 (t60) cc_final: 0.6934 (t60) REVERT: N 78 LEU cc_start: 0.7165 (tp) cc_final: 0.6765 (tt) REVERT: N 281 ASN cc_start: 0.6916 (OUTLIER) cc_final: 0.5995 (t0) REVERT: N 313 LYS cc_start: 0.5108 (OUTLIER) cc_final: 0.4669 (mptt) REVERT: N 336 MET cc_start: 0.2640 (mmt) cc_final: 0.2355 (mmt) REVERT: N 345 MET cc_start: 0.2571 (ppp) cc_final: 0.2047 (ppp) REVERT: N 391 ILE cc_start: 0.5172 (OUTLIER) cc_final: 0.4875 (mt) REVERT: N 414 MET cc_start: 0.7379 (mmm) cc_final: 0.6877 (tpp) REVERT: O 64 ILE cc_start: 0.5968 (mm) cc_final: 0.5668 (mm) REVERT: O 123 ASP cc_start: 0.6913 (OUTLIER) cc_final: 0.6476 (t70) REVERT: O 208 ASP cc_start: 0.5075 (OUTLIER) cc_final: 0.4756 (p0) REVERT: O 245 PHE cc_start: 0.6119 (m-10) cc_final: 0.5789 (m-10) REVERT: O 281 LEU cc_start: 0.5884 (tm) cc_final: 0.5526 (pt) REVERT: O 284 VAL cc_start: 0.4836 (t) cc_final: 0.4504 (t) REVERT: O 285 TYR cc_start: 0.7138 (m-80) cc_final: 0.6651 (m-80) REVERT: O 296 ASN cc_start: 0.6525 (t0) cc_final: 0.5267 (t0) REVERT: O 356 GLU cc_start: 0.6518 (tp30) cc_final: 0.5293 (mm-30) REVERT: O 365 PHE cc_start: 0.6535 (m-80) cc_final: 0.6120 (m-80) REVERT: O 373 PHE cc_start: 0.8139 (m-80) cc_final: 0.7768 (m-80) REVERT: O 406 MET cc_start: 0.3835 (ppp) cc_final: 0.3231 (tmm) outliers start: 206 outliers final: 77 residues processed: 597 average time/residue: 0.9999 time to fit residues: 745.6223 Evaluate side-chains 515 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 417 time to evaluate : 3.367 ------------------------------------------------------------------------------- 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 48 THR 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 273 PHE Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 74 MET 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 229 LEU 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 339 LEU Chi-restraints excluded: chain B residue 362 ARG Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 109 ASN 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 267 GLN Chi-restraints excluded: chain F residue 273 PHE 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 74 MET 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 285 TYR Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 336 LYS 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 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 112 ILE Chi-restraints excluded: chain J residue 158 PHE Chi-restraints excluded: chain J residue 243 THR Chi-restraints excluded: chain J residue 303 ASP 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 333 LYS 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 494 THR Chi-restraints excluded: chain K residue 498 THR Chi-restraints excluded: chain N residue 25 LEU 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 281 ASN Chi-restraints excluded: chain N residue 313 LYS Chi-restraints excluded: chain N residue 391 ILE Chi-restraints excluded: chain O residue 51 GLN Chi-restraints excluded: chain O residue 91 ILE Chi-restraints excluded: chain O residue 123 ASP Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 208 ASP Chi-restraints excluded: chain O residue 283 LEU Chi-restraints excluded: chain O residue 304 PHE Chi-restraints excluded: chain O residue 389 THR Chi-restraints excluded: chain O residue 405 ILE Chi-restraints excluded: chain O residue 413 VAL Chi-restraints excluded: chain O residue 470 CYS Chi-restraints excluded: chain O residue 479 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 116 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 332 optimal weight: 4.9990 chunk 239 optimal weight: 1.9990 chunk 346 optimal weight: 20.0000 chunk 315 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 270 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 279 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 HIS B 207 HIS ** J 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 357 GLN K 430 GLN ** K 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 357 GLN O 47 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.206102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.143002 restraints weight = 45241.090| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 2.56 r_work: 0.3797 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3668 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 32076 Z= 0.201 Angle : 0.673 13.637 44042 Z= 0.349 Chirality : 0.046 0.242 4830 Planarity : 0.005 0.082 4978 Dihedral : 16.322 86.073 5691 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 6.40 % Allowed : 30.40 % Favored : 63.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.14), residues: 3306 helix: 0.58 (0.15), residues: 1118 sheet: -1.26 (0.20), residues: 626 loop : -1.47 (0.14), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 369 HIS 0.022 0.001 HIS F 160 PHE 0.028 0.002 PHE F 135 TYR 0.026 0.002 TYR A 330 ARG 0.005 0.001 ARG A 283 Details of bonding type rmsd hydrogen bonds : bond 0.04091 ( 1293) hydrogen bonds : angle 4.84009 ( 3825) covalent geometry : bond 0.00468 (32076) covalent geometry : angle 0.67293 (44042) *********************** 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 623 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 431 time to evaluate : 3.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ASN cc_start: 0.6755 (t0) cc_final: 0.6492 (t0) REVERT: A 126 LYS cc_start: 0.7997 (ttpp) cc_final: 0.7516 (tppt) REVERT: A 136 GLU cc_start: 0.7802 (tp30) cc_final: 0.7549 (tp30) REVERT: A 212 GLU cc_start: 0.7836 (pt0) cc_final: 0.7206 (pp20) REVERT: A 220 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7524 (pm20) REVERT: A 273 PHE cc_start: 0.7448 (OUTLIER) cc_final: 0.6854 (m-80) REVERT: A 277 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7340 (mpt) REVERT: A 293 TYR cc_start: 0.7486 (m-80) cc_final: 0.7255 (m-80) REVERT: A 294 TRP cc_start: 0.7617 (p-90) cc_final: 0.7383 (p-90) REVERT: A 329 LEU cc_start: 0.9007 (mt) cc_final: 0.8671 (mt) REVERT: A 345 MET cc_start: 0.6434 (ptp) cc_final: 0.6174 (ptp) REVERT: B 3 GLU cc_start: 0.8233 (tt0) cc_final: 0.7368 (pm20) REVERT: B 72 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7398 (ptp-170) REVERT: B 217 HIS cc_start: 0.6324 (OUTLIER) cc_final: 0.5860 (p90) REVERT: B 324 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6850 (mp0) REVERT: B 346 TYR cc_start: 0.7615 (t80) cc_final: 0.7361 (t80) REVERT: B 362 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8126 (mtm180) REVERT: F 52 GLU cc_start: 0.5697 (mm-30) cc_final: 0.5224 (mm-30) REVERT: F 100 ASP cc_start: 0.8462 (t0) cc_final: 0.8077 (t0) REVERT: F 132 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7836 (mt) REVERT: F 179 ILE cc_start: 0.7276 (OUTLIER) cc_final: 0.7008 (mp) REVERT: F 205 PHE cc_start: 0.7479 (m-80) cc_final: 0.7230 (m-80) REVERT: F 220 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6654 (pm20) REVERT: F 267 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.7392 (tt0) REVERT: F 271 LYS cc_start: 0.8416 (tppt) cc_final: 0.8068 (tppt) REVERT: F 274 GLU cc_start: 0.7750 (tp30) cc_final: 0.7426 (tp30) REVERT: G 116 ASP cc_start: 0.6762 (OUTLIER) cc_final: 0.6185 (m-30) REVERT: G 134 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7797 (pm20) REVERT: G 217 HIS cc_start: 0.6079 (OUTLIER) cc_final: 0.5776 (p90) REVERT: G 285 TYR cc_start: 0.8665 (OUTLIER) cc_final: 0.7906 (m-80) REVERT: G 336 LYS cc_start: 0.7436 (OUTLIER) cc_final: 0.6871 (mppt) REVERT: G 383 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7717 (pt) REVERT: J 37 LEU cc_start: 0.8700 (mp) cc_final: 0.8399 (mp) REVERT: J 40 ASP cc_start: 0.6704 (t70) cc_final: 0.6372 (m-30) REVERT: J 92 MET cc_start: 0.5368 (tpp) cc_final: 0.4991 (tpt) REVERT: J 297 LYS cc_start: 0.4556 (pttm) cc_final: 0.3952 (tptt) REVERT: J 320 HIS cc_start: 0.3288 (m170) cc_final: 0.3056 (m-70) REVERT: J 402 LEU cc_start: 0.6188 (OUTLIER) cc_final: 0.5962 (tm) REVERT: K 79 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6931 (mt-10) REVERT: K 85 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7549 (mtmm) REVERT: K 93 PHE cc_start: 0.7106 (t80) cc_final: 0.6759 (t80) REVERT: K 117 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7068 (tm) REVERT: K 208 ASP cc_start: 0.4611 (OUTLIER) cc_final: 0.4264 (m-30) REVERT: K 210 LEU cc_start: 0.8204 (tp) cc_final: 0.7261 (mp) REVERT: K 447 LYS cc_start: 0.5989 (mmtm) cc_final: 0.5279 (ptpt) REVERT: K 498 THR cc_start: 0.5758 (OUTLIER) cc_final: 0.5356 (t) REVERT: N 20 TRP cc_start: 0.7349 (t60) cc_final: 0.7130 (t60) REVERT: N 78 LEU cc_start: 0.7094 (tp) cc_final: 0.6706 (tt) REVERT: N 92 MET cc_start: 0.6087 (mtt) cc_final: 0.5135 (ppp) REVERT: N 233 TYR cc_start: 0.0594 (t80) cc_final: -0.0776 (t80) REVERT: N 240 ARG cc_start: 0.3796 (mmt90) cc_final: 0.2792 (pmt-80) REVERT: N 281 ASN cc_start: 0.6835 (OUTLIER) cc_final: 0.6094 (t0) REVERT: N 313 LYS cc_start: 0.5022 (OUTLIER) cc_final: 0.4602 (mptt) REVERT: N 336 MET cc_start: 0.2840 (mmt) cc_final: 0.2613 (mmt) REVERT: N 391 ILE cc_start: 0.5211 (OUTLIER) cc_final: 0.4912 (mt) REVERT: N 398 GLU cc_start: 0.4454 (OUTLIER) cc_final: 0.3862 (tt0) REVERT: N 414 MET cc_start: 0.7299 (mmm) cc_final: 0.6751 (OUTLIER) REVERT: O 52 ILE cc_start: 0.7472 (OUTLIER) cc_final: 0.7140 (mt) REVERT: O 64 ILE cc_start: 0.5869 (mm) cc_final: 0.5571 (mm) REVERT: O 74 MET cc_start: 0.4017 (pp-130) cc_final: 0.3268 (pp-130) REVERT: O 123 ASP cc_start: 0.6975 (OUTLIER) cc_final: 0.6568 (t70) REVERT: O 281 LEU cc_start: 0.5947 (tm) cc_final: 0.5500 (pt) REVERT: O 284 VAL cc_start: 0.5356 (t) cc_final: 0.5007 (t) REVERT: O 285 TYR cc_start: 0.7432 (m-80) cc_final: 0.6874 (m-80) REVERT: O 362 ARG cc_start: 0.7564 (ptp90) cc_final: 0.6932 (ptp90) REVERT: O 365 PHE cc_start: 0.6495 (m-80) cc_final: 0.5979 (m-80) REVERT: O 373 PHE cc_start: 0.8280 (m-10) cc_final: 0.7818 (m-80) REVERT: O 406 MET cc_start: 0.3957 (ppp) cc_final: 0.3298 (tmm) REVERT: O 480 LEU cc_start: 0.7011 (mt) cc_final: 0.6503 (mm) outliers start: 192 outliers final: 76 residues processed: 571 average time/residue: 1.0372 time to fit residues: 734.4545 Evaluate side-chains 508 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 404 time to evaluate : 2.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 48 THR 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 220 GLU Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 72 ARG Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 79 GLU 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 229 LEU 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 384 VAL Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 106 ASP Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain F residue 132 LEU 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 267 GLN Chi-restraints excluded: chain F residue 273 PHE 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 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 285 TYR Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 330 LEU Chi-restraints excluded: chain G residue 336 LYS 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 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 63 VAL Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 112 ILE Chi-restraints excluded: chain J residue 158 PHE Chi-restraints excluded: chain J residue 243 THR Chi-restraints excluded: chain J residue 303 ASP Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain J residue 336 MET 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 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 208 ASP 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 494 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 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 N residue 398 GLU Chi-restraints excluded: chain O residue 51 GLN Chi-restraints excluded: chain O residue 52 ILE Chi-restraints excluded: chain O residue 123 ASP Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 283 LEU Chi-restraints excluded: chain O residue 304 PHE Chi-restraints excluded: chain O residue 389 THR Chi-restraints excluded: chain O residue 405 ILE Chi-restraints excluded: chain O residue 447 LYS 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 142 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 344 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 295 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 239 optimal weight: 5.9990 chunk 213 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 HIS A 281 ASN A 320 HIS A 340 HIS ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 HIS G 430 GLN ** J 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 357 GLN K 430 GLN ** K 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.208534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.146136 restraints weight = 45218.617| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 2.55 r_work: 0.3839 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3710 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 32076 Z= 0.148 Angle : 0.644 13.925 44042 Z= 0.331 Chirality : 0.044 0.268 4830 Planarity : 0.004 0.048 4978 Dihedral : 16.270 86.729 5691 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 5.37 % Allowed : 32.03 % Favored : 62.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.14), residues: 3306 helix: 0.70 (0.15), residues: 1118 sheet: -1.20 (0.20), residues: 626 loop : -1.45 (0.14), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 369 HIS 0.013 0.001 HIS F 160 PHE 0.029 0.002 PHE N 17 TYR 0.026 0.001 TYR A 330 ARG 0.007 0.001 ARG J 71 Details of bonding type rmsd hydrogen bonds : bond 0.03733 ( 1293) hydrogen bonds : angle 4.69967 ( 3825) covalent geometry : bond 0.00341 (32076) covalent geometry : angle 0.64395 (44042) *********************** 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 599 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 438 time to evaluate : 3.350 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 109 ASN cc_start: 0.7004 (t0) cc_final: 0.6680 (t0) REVERT: A 126 LYS cc_start: 0.7947 (ttpp) cc_final: 0.7495 (tppt) REVERT: A 136 GLU cc_start: 0.7748 (tp30) cc_final: 0.7489 (tp30) REVERT: A 162 LYS cc_start: 0.7313 (OUTLIER) cc_final: 0.7062 (tptt) REVERT: A 212 GLU cc_start: 0.7831 (pt0) cc_final: 0.7214 (pp20) REVERT: A 273 PHE cc_start: 0.7408 (OUTLIER) cc_final: 0.6511 (m-80) REVERT: A 277 MET cc_start: 0.7920 (OUTLIER) cc_final: 0.7186 (mpt) REVERT: A 293 TYR cc_start: 0.7461 (m-80) cc_final: 0.7258 (m-80) REVERT: A 294 TRP cc_start: 0.7533 (p-90) cc_final: 0.7219 (p-90) REVERT: A 339 SER cc_start: 0.8366 (m) cc_final: 0.7863 (p) REVERT: A 345 MET cc_start: 0.6372 (ptp) cc_final: 0.5953 (ppp) REVERT: B 3 GLU cc_start: 0.8197 (tt0) cc_final: 0.7316 (pm20) REVERT: B 138 VAL cc_start: 0.8647 (OUTLIER) cc_final: 0.8355 (t) REVERT: B 217 HIS cc_start: 0.6144 (OUTLIER) cc_final: 0.5815 (p90) REVERT: B 324 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6850 (mp0) REVERT: B 333 LYS cc_start: 0.8438 (tppt) cc_final: 0.7906 (ttpt) REVERT: B 346 TYR cc_start: 0.7576 (t80) cc_final: 0.7312 (t80) REVERT: B 362 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.8039 (mtm180) REVERT: B 488 GLU cc_start: 0.7924 (tp30) cc_final: 0.7341 (tt0) REVERT: F 52 GLU cc_start: 0.5952 (mm-30) cc_final: 0.5532 (mm-30) REVERT: F 100 ASP cc_start: 0.8394 (t0) cc_final: 0.8001 (t0) REVERT: F 132 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7968 (mt) REVERT: F 205 PHE cc_start: 0.7515 (m-80) cc_final: 0.7236 (m-80) REVERT: F 219 TRP cc_start: 0.6082 (OUTLIER) cc_final: 0.5821 (t60) REVERT: F 220 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6745 (mp0) REVERT: F 267 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7415 (tt0) REVERT: F 274 GLU cc_start: 0.7743 (tp30) cc_final: 0.7398 (tp30) REVERT: G 134 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7833 (pm20) REVERT: G 145 GLU cc_start: 0.6645 (tp30) cc_final: 0.6402 (tp30) REVERT: G 217 HIS cc_start: 0.5973 (OUTLIER) cc_final: 0.5576 (p90) REVERT: G 285 TYR cc_start: 0.8595 (OUTLIER) cc_final: 0.7869 (m-80) REVERT: G 336 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.6942 (mppt) REVERT: G 383 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7716 (pt) REVERT: G 406 MET cc_start: 0.8764 (ttt) cc_final: 0.8421 (ttp) REVERT: G 449 GLU cc_start: 0.6678 (OUTLIER) cc_final: 0.6400 (pp20) REVERT: J 37 LEU cc_start: 0.8712 (mp) cc_final: 0.8425 (mp) REVERT: J 40 ASP cc_start: 0.6709 (t70) cc_final: 0.6354 (m-30) REVERT: J 46 TRP cc_start: 0.6505 (m-10) cc_final: 0.6109 (m100) REVERT: J 92 MET cc_start: 0.5400 (tpp) cc_final: 0.5100 (tpt) REVERT: J 149 LYS cc_start: 0.6401 (mptt) cc_final: 0.6150 (mptp) REVERT: J 297 LYS cc_start: 0.4632 (pttm) cc_final: 0.4024 (tptt) REVERT: J 402 LEU cc_start: 0.6528 (OUTLIER) cc_final: 0.6295 (tm) REVERT: K 79 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.7008 (mt-10) REVERT: K 85 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7557 (mtmm) REVERT: K 117 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.6990 (tm) REVERT: K 132 ASP cc_start: 0.6042 (m-30) cc_final: 0.5573 (t0) REVERT: K 208 ASP cc_start: 0.4518 (OUTLIER) cc_final: 0.4219 (m-30) REVERT: K 210 LEU cc_start: 0.8153 (tp) cc_final: 0.7217 (mp) REVERT: K 432 THR cc_start: 0.7043 (p) cc_final: 0.6559 (t) REVERT: K 447 LYS cc_start: 0.5904 (mmtm) cc_final: 0.5309 (ptpt) REVERT: N 78 LEU cc_start: 0.7027 (tp) cc_final: 0.6604 (tt) REVERT: N 92 MET cc_start: 0.6149 (mtt) cc_final: 0.5163 (ppp) REVERT: N 224 ILE cc_start: 0.5523 (OUTLIER) cc_final: 0.4879 (mp) REVERT: N 240 ARG cc_start: 0.3342 (mmt90) cc_final: 0.2818 (pmt-80) REVERT: N 281 ASN cc_start: 0.6677 (OUTLIER) cc_final: 0.6215 (t0) REVERT: N 313 LYS cc_start: 0.5154 (OUTLIER) cc_final: 0.4613 (mppt) REVERT: N 336 MET cc_start: 0.2874 (mmp) cc_final: 0.2664 (mmt) REVERT: N 340 HIS cc_start: 0.5620 (OUTLIER) cc_final: 0.5337 (p90) REVERT: N 345 MET cc_start: 0.2952 (ppp) cc_final: 0.2745 (ppp) REVERT: N 391 ILE cc_start: 0.5215 (OUTLIER) cc_final: 0.4926 (mt) REVERT: N 398 GLU cc_start: 0.4448 (OUTLIER) cc_final: 0.3832 (tt0) REVERT: N 414 MET cc_start: 0.7378 (mmm) cc_final: 0.6813 (OUTLIER) REVERT: O 52 ILE cc_start: 0.7445 (OUTLIER) cc_final: 0.7069 (mt) REVERT: O 123 ASP cc_start: 0.6912 (OUTLIER) cc_final: 0.6537 (t70) REVERT: O 214 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.7106 (mt) REVERT: O 284 VAL cc_start: 0.5206 (t) cc_final: 0.4983 (t) REVERT: O 285 TYR cc_start: 0.7475 (m-80) cc_final: 0.7198 (m-80) REVERT: O 356 GLU cc_start: 0.6625 (tp30) cc_final: 0.5402 (mm-30) REVERT: O 362 ARG cc_start: 0.7451 (ptp90) cc_final: 0.7223 (pmm150) REVERT: O 365 PHE cc_start: 0.6292 (m-80) cc_final: 0.5733 (m-80) REVERT: O 373 PHE cc_start: 0.8263 (m-10) cc_final: 0.7766 (m-80) REVERT: O 406 MET cc_start: 0.4006 (ppp) cc_final: 0.3361 (tmm) outliers start: 161 outliers final: 75 residues processed: 552 average time/residue: 1.0315 time to fit residues: 708.5818 Evaluate side-chains 508 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 403 time to evaluate : 2.927 ------------------------------------------------------------------------------- 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 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 162 LYS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 74 MET 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 339 LEU Chi-restraints excluded: chain B residue 362 ARG Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 447 LYS Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 132 LEU 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 219 TRP Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 267 GLN Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 282 VAL 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 44 VAL 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 217 HIS 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 330 LEU Chi-restraints excluded: chain G residue 336 LYS 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 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 62 ILE Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 158 PHE Chi-restraints excluded: chain J residue 243 THR Chi-restraints excluded: chain J residue 303 ASP Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain J residue 336 MET 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 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 208 ASP 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 494 THR Chi-restraints excluded: chain N residue 16 ASP 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 224 ILE Chi-restraints excluded: chain N residue 281 ASN Chi-restraints excluded: chain N residue 313 LYS Chi-restraints excluded: chain N residue 340 HIS Chi-restraints excluded: chain N residue 391 ILE Chi-restraints excluded: chain N residue 398 GLU Chi-restraints excluded: chain O residue 52 ILE Chi-restraints excluded: chain O residue 91 ILE Chi-restraints excluded: chain O residue 123 ASP Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain O residue 283 LEU 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 507 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 26 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 331 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 chunk 196 optimal weight: 7.9990 chunk 93 optimal weight: 0.7980 chunk 182 optimal weight: 8.9990 chunk 255 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 HIS ** G 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 183 ASN ** J 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 357 GLN ** K 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 430 GLN ** K 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 18 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.206681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.144028 restraints weight = 44910.349| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 2.52 r_work: 0.3802 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3672 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 32076 Z= 0.185 Angle : 0.674 14.339 44042 Z= 0.347 Chirality : 0.045 0.323 4830 Planarity : 0.005 0.049 4978 Dihedral : 16.288 86.168 5691 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 5.73 % Allowed : 31.97 % Favored : 62.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.14), residues: 3306 helix: 0.67 (0.15), residues: 1110 sheet: -1.25 (0.20), residues: 626 loop : -1.48 (0.14), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP F 20 HIS 0.028 0.001 HIS F 160 PHE 0.031 0.002 PHE J 321 TYR 0.028 0.002 TYR A 190 ARG 0.005 0.001 ARG J 71 Details of bonding type rmsd hydrogen bonds : bond 0.03966 ( 1293) hydrogen bonds : angle 4.74529 ( 3825) covalent geometry : bond 0.00432 (32076) covalent geometry : angle 0.67424 (44042) *********************** 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 594 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 422 time to evaluate : 3.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ASN cc_start: 0.7064 (t0) cc_final: 0.6755 (t0) REVERT: A 126 LYS cc_start: 0.7971 (ttpp) cc_final: 0.7552 (tppt) REVERT: A 136 GLU cc_start: 0.7725 (tp30) cc_final: 0.7490 (tp30) REVERT: A 162 LYS cc_start: 0.7350 (OUTLIER) cc_final: 0.7112 (tptt) REVERT: A 212 GLU cc_start: 0.7869 (pt0) cc_final: 0.7218 (pp20) REVERT: A 273 PHE cc_start: 0.7518 (OUTLIER) cc_final: 0.6383 (m-80) REVERT: A 274 GLU cc_start: 0.7897 (tp30) cc_final: 0.7466 (tp30) REVERT: A 277 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7628 (mpp) REVERT: A 293 TYR cc_start: 0.7492 (m-80) cc_final: 0.7081 (m-80) REVERT: A 339 SER cc_start: 0.8478 (m) cc_final: 0.8030 (p) REVERT: A 345 MET cc_start: 0.6634 (ptp) cc_final: 0.6160 (ppp) REVERT: B 3 GLU cc_start: 0.8224 (tt0) cc_final: 0.7322 (pm20) REVERT: B 138 VAL cc_start: 0.8672 (OUTLIER) cc_final: 0.8394 (t) REVERT: B 217 HIS cc_start: 0.6276 (OUTLIER) cc_final: 0.5961 (p90) REVERT: B 324 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6852 (mp0) REVERT: B 333 LYS cc_start: 0.8510 (tppt) cc_final: 0.8130 (mmtm) REVERT: B 362 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8025 (mtm180) REVERT: B 447 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7778 (mmtp) REVERT: B 484 ASN cc_start: 0.7860 (OUTLIER) cc_final: 0.7475 (t0) REVERT: F 52 GLU cc_start: 0.6126 (mm-30) cc_final: 0.5757 (mm-30) REVERT: F 100 ASP cc_start: 0.8417 (t0) cc_final: 0.8049 (t0) REVERT: F 132 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7900 (mt) REVERT: F 205 PHE cc_start: 0.7478 (m-80) cc_final: 0.7232 (m-80) REVERT: F 219 TRP cc_start: 0.6322 (OUTLIER) cc_final: 0.5822 (t60) REVERT: F 220 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.5669 (mt-10) REVERT: F 233 TYR cc_start: 0.6089 (t80) cc_final: 0.5397 (t80) REVERT: F 267 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7309 (tt0) REVERT: F 274 GLU cc_start: 0.7733 (tp30) cc_final: 0.7327 (tp30) REVERT: G 116 ASP cc_start: 0.6886 (OUTLIER) cc_final: 0.6393 (m-30) REVERT: G 134 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7826 (pm20) REVERT: G 285 TYR cc_start: 0.8641 (OUTLIER) cc_final: 0.7938 (m-80) REVERT: G 336 LYS cc_start: 0.7493 (OUTLIER) cc_final: 0.6923 (mppt) REVERT: G 383 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7755 (pt) REVERT: G 449 GLU cc_start: 0.6738 (OUTLIER) cc_final: 0.6481 (pp20) REVERT: J 37 LEU cc_start: 0.8783 (mp) cc_final: 0.8474 (mp) REVERT: J 40 ASP cc_start: 0.6776 (t70) cc_final: 0.6419 (m-30) REVERT: J 92 MET cc_start: 0.5383 (tpp) cc_final: 0.5073 (tpt) REVERT: J 402 LEU cc_start: 0.6680 (OUTLIER) cc_final: 0.6421 (tm) REVERT: K 79 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6934 (mt-10) REVERT: K 85 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7553 (mtmm) REVERT: K 117 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.6905 (tm) REVERT: K 132 ASP cc_start: 0.6055 (m-30) cc_final: 0.5608 (t0) REVERT: K 210 LEU cc_start: 0.8194 (tp) cc_final: 0.7229 (mp) REVERT: K 226 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7072 (mp0) REVERT: K 432 THR cc_start: 0.7018 (p) cc_final: 0.6521 (t) REVERT: K 447 LYS cc_start: 0.5920 (mmtm) cc_final: 0.5332 (ptpt) REVERT: N 78 LEU cc_start: 0.7234 (tp) cc_final: 0.6848 (tt) REVERT: N 92 MET cc_start: 0.6229 (mtt) cc_final: 0.5194 (ppp) REVERT: N 224 ILE cc_start: 0.5683 (OUTLIER) cc_final: 0.5075 (mp) REVERT: N 240 ARG cc_start: 0.3434 (mmt90) cc_final: 0.2943 (pmt-80) REVERT: N 313 LYS cc_start: 0.5176 (OUTLIER) cc_final: 0.4613 (mppt) REVERT: N 336 MET cc_start: 0.2985 (mmp) cc_final: 0.2751 (mmt) REVERT: N 340 HIS cc_start: 0.5811 (OUTLIER) cc_final: 0.5538 (p90) REVERT: N 344 THR cc_start: 0.5273 (p) cc_final: 0.4710 (p) REVERT: N 345 MET cc_start: 0.2993 (ppp) cc_final: 0.2676 (ppp) REVERT: N 391 ILE cc_start: 0.5239 (OUTLIER) cc_final: 0.4964 (mt) REVERT: N 414 MET cc_start: 0.7384 (mmm) cc_final: 0.6880 (tpp) REVERT: O 52 ILE cc_start: 0.7502 (OUTLIER) cc_final: 0.7097 (mp) REVERT: O 64 ILE cc_start: 0.5830 (mm) cc_final: 0.5552 (mm) REVERT: O 123 ASP cc_start: 0.6939 (OUTLIER) cc_final: 0.6541 (t70) REVERT: O 134 GLU cc_start: 0.6583 (pt0) cc_final: 0.6138 (pm20) REVERT: O 214 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.7072 (mt) REVERT: O 284 VAL cc_start: 0.5512 (t) cc_final: 0.5227 (t) REVERT: O 285 TYR cc_start: 0.7374 (m-80) cc_final: 0.7042 (m-80) REVERT: O 296 ASN cc_start: 0.6355 (p0) cc_final: 0.6096 (p0) REVERT: O 302 GLN cc_start: 0.5197 (pt0) cc_final: 0.4991 (pm20) REVERT: O 356 GLU cc_start: 0.6544 (tp30) cc_final: 0.5298 (mm-30) REVERT: O 362 ARG cc_start: 0.7509 (ptp90) cc_final: 0.7169 (ptp90) REVERT: O 365 PHE cc_start: 0.6457 (m-80) cc_final: 0.5908 (m-80) REVERT: O 373 PHE cc_start: 0.8281 (m-10) cc_final: 0.7867 (m-80) REVERT: O 406 MET cc_start: 0.4001 (ppp) cc_final: 0.3385 (tmm) REVERT: O 429 LEU cc_start: 0.5454 (mt) cc_final: 0.5042 (tt) outliers start: 172 outliers final: 92 residues processed: 546 average time/residue: 0.9920 time to fit residues: 676.2884 Evaluate side-chains 516 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 394 time to evaluate : 3.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 357 GLN 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 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 339 LEU Chi-restraints excluded: chain B residue 362 ARG Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 447 LYS Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 484 ASN 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 132 LEU Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 162 LYS Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 219 TRP Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 267 GLN Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 339 SER 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 116 ASP Chi-restraints excluded: chain G residue 134 GLU 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 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 336 LYS 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 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 112 ILE Chi-restraints excluded: chain J residue 158 PHE 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 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 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 494 THR Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain N residue 61 LEU 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 224 ILE Chi-restraints excluded: chain N residue 313 LYS Chi-restraints excluded: chain N residue 337 VAL Chi-restraints excluded: chain N residue 340 HIS Chi-restraints excluded: chain N residue 391 ILE Chi-restraints excluded: chain O residue 51 GLN Chi-restraints excluded: chain O residue 52 ILE Chi-restraints excluded: chain O residue 118 VAL Chi-restraints excluded: chain O residue 123 ASP Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain O residue 283 LEU Chi-restraints excluded: chain O residue 304 PHE Chi-restraints excluded: chain O residue 389 THR Chi-restraints excluded: chain O residue 405 ILE Chi-restraints excluded: chain O residue 447 LYS Chi-restraints excluded: chain O residue 470 CYS Chi-restraints excluded: chain O residue 507 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 137 optimal weight: 0.8980 chunk 280 optimal weight: 3.9990 chunk 243 optimal weight: 0.8980 chunk 245 optimal weight: 0.0970 chunk 29 optimal weight: 0.1980 chunk 199 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 207 optimal weight: 0.2980 chunk 49 optimal weight: 0.9990 chunk 327 optimal weight: 6.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 HIS F 160 HIS ** J 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 69 ASN ** J 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 357 GLN ** K 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 129 ASN K 430 GLN ** K 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.210443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.148332 restraints weight = 45364.499| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 2.59 r_work: 0.3868 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3739 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 32076 Z= 0.133 Angle : 0.658 18.767 44042 Z= 0.335 Chirality : 0.044 0.299 4830 Planarity : 0.004 0.048 4978 Dihedral : 16.231 86.638 5691 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.27 % Allowed : 33.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.14), residues: 3306 helix: 0.73 (0.15), residues: 1112 sheet: -1.25 (0.19), residues: 684 loop : -1.43 (0.15), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP F 20 HIS 0.007 0.001 HIS A 225 PHE 0.033 0.002 PHE N 17 TYR 0.028 0.001 TYR A 233 ARG 0.006 0.000 ARG J 71 Details of bonding type rmsd hydrogen bonds : bond 0.03650 ( 1293) hydrogen bonds : angle 4.64464 ( 3825) covalent geometry : bond 0.00305 (32076) covalent geometry : angle 0.65802 (44042) *********************** 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 558 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 430 time to evaluate : 2.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ASN cc_start: 0.6998 (t0) cc_final: 0.6708 (t0) REVERT: A 126 LYS cc_start: 0.7898 (ttpp) cc_final: 0.7605 (tppt) REVERT: A 162 LYS cc_start: 0.7399 (OUTLIER) cc_final: 0.7127 (tptt) REVERT: A 212 GLU cc_start: 0.7788 (pt0) cc_final: 0.7047 (pp20) REVERT: A 273 PHE cc_start: 0.7258 (OUTLIER) cc_final: 0.6210 (m-80) REVERT: A 277 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.7612 (mpp) REVERT: A 336 MET cc_start: 0.7714 (mpt) cc_final: 0.7363 (mpt) REVERT: A 339 SER cc_start: 0.8343 (m) cc_final: 0.7802 (p) REVERT: A 345 MET cc_start: 0.6693 (ptp) cc_final: 0.6185 (ppp) REVERT: B 3 GLU cc_start: 0.8225 (tt0) cc_final: 0.7318 (pm20) REVERT: B 138 VAL cc_start: 0.8636 (OUTLIER) cc_final: 0.8374 (t) REVERT: B 217 HIS cc_start: 0.6096 (OUTLIER) cc_final: 0.5784 (p90) REVERT: B 324 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6852 (mp0) REVERT: B 333 LYS cc_start: 0.8461 (tppt) cc_final: 0.8054 (mmtm) REVERT: B 346 TYR cc_start: 0.7367 (t80) cc_final: 0.7007 (t80) REVERT: B 484 ASN cc_start: 0.7788 (OUTLIER) cc_final: 0.7577 (t0) REVERT: B 488 GLU cc_start: 0.7796 (tp30) cc_final: 0.7218 (tt0) REVERT: F 52 GLU cc_start: 0.6056 (mm-30) cc_final: 0.5744 (mm-30) REVERT: F 100 ASP cc_start: 0.8335 (t0) cc_final: 0.7994 (t0) REVERT: F 132 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7862 (mt) REVERT: F 189 ARG cc_start: 0.7672 (tpp80) cc_final: 0.7461 (tpp80) REVERT: F 205 PHE cc_start: 0.7518 (m-80) cc_final: 0.7305 (m-80) REVERT: F 219 TRP cc_start: 0.6266 (OUTLIER) cc_final: 0.6025 (t60) REVERT: F 220 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6721 (mp0) REVERT: F 267 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7354 (tt0) REVERT: F 274 GLU cc_start: 0.7683 (tp30) cc_final: 0.7300 (tp30) REVERT: F 315 LYS cc_start: 0.7842 (mmtp) cc_final: 0.7519 (mtpt) REVERT: G 19 LYS cc_start: 0.8026 (ptpp) cc_final: 0.7804 (mttt) REVERT: G 116 ASP cc_start: 0.6935 (OUTLIER) cc_final: 0.6520 (m-30) REVERT: G 134 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7879 (pm20) REVERT: G 145 GLU cc_start: 0.6093 (tp30) cc_final: 0.5710 (tp30) REVERT: G 217 HIS cc_start: 0.5748 (OUTLIER) cc_final: 0.4812 (p90) REVERT: G 285 TYR cc_start: 0.8562 (OUTLIER) cc_final: 0.7846 (m-80) REVERT: G 336 LYS cc_start: 0.7487 (OUTLIER) cc_final: 0.6956 (mppt) REVERT: G 383 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7788 (pt) REVERT: G 406 MET cc_start: 0.8696 (ttt) cc_final: 0.8413 (ttp) REVERT: G 449 GLU cc_start: 0.6655 (OUTLIER) cc_final: 0.6401 (pp20) REVERT: G 488 GLU cc_start: 0.6918 (mm-30) cc_final: 0.6436 (tp30) REVERT: J 33 TRP cc_start: 0.7808 (t60) cc_final: 0.7592 (t60) REVERT: J 37 LEU cc_start: 0.8745 (mp) cc_final: 0.8483 (mp) REVERT: J 40 ASP cc_start: 0.6558 (t70) cc_final: 0.6357 (m-30) REVERT: J 46 TRP cc_start: 0.6451 (m-10) cc_final: 0.6047 (m100) REVERT: J 92 MET cc_start: 0.5395 (tpp) cc_final: 0.5112 (tpt) REVERT: J 185 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7110 (pp) REVERT: J 277 MET cc_start: 0.6456 (mpt) cc_final: 0.6208 (ptp) REVERT: J 357 GLN cc_start: 0.4179 (OUTLIER) cc_final: 0.3334 (mt0) REVERT: J 392 TYR cc_start: 0.7026 (m-10) cc_final: 0.6794 (m-10) REVERT: J 402 LEU cc_start: 0.6790 (OUTLIER) cc_final: 0.6516 (tm) REVERT: K 79 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6422 (mp0) REVERT: K 117 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.6676 (tm) REVERT: K 210 LEU cc_start: 0.8120 (tp) cc_final: 0.7187 (mp) REVERT: K 222 GLN cc_start: 0.7617 (OUTLIER) cc_final: 0.7359 (tm-30) REVERT: K 226 GLU cc_start: 0.7613 (mt-10) cc_final: 0.6948 (mp0) REVERT: K 329 HIS cc_start: 0.4772 (m90) cc_final: 0.4160 (m-70) REVERT: K 432 THR cc_start: 0.6966 (p) cc_final: 0.6513 (t) REVERT: K 447 LYS cc_start: 0.5845 (mmtm) cc_final: 0.5207 (ptpt) REVERT: N 92 MET cc_start: 0.6163 (mtt) cc_final: 0.5283 (ppp) REVERT: N 240 ARG cc_start: 0.3756 (mmt90) cc_final: 0.3238 (pmt-80) REVERT: N 344 THR cc_start: 0.5020 (p) cc_final: 0.4490 (p) REVERT: N 345 MET cc_start: 0.2877 (ppp) cc_final: 0.2570 (ppp) REVERT: N 388 GLN cc_start: 0.5767 (tt0) cc_final: 0.5009 (tm130) REVERT: N 391 ILE cc_start: 0.5202 (OUTLIER) cc_final: 0.4908 (mt) REVERT: N 414 MET cc_start: 0.7401 (mmm) cc_final: 0.6917 (tpp) REVERT: O 52 ILE cc_start: 0.7457 (mm) cc_final: 0.7158 (mt) REVERT: O 64 ILE cc_start: 0.5752 (mm) cc_final: 0.5470 (mm) REVERT: O 74 MET cc_start: 0.4407 (pp-130) cc_final: 0.3576 (pp-130) REVERT: O 134 GLU cc_start: 0.6595 (pt0) cc_final: 0.6247 (pm20) REVERT: O 214 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6994 (mt) REVERT: O 245 PHE cc_start: 0.6400 (m-10) cc_final: 0.5979 (m-10) REVERT: O 284 VAL cc_start: 0.5336 (t) cc_final: 0.5118 (t) REVERT: O 285 TYR cc_start: 0.7360 (m-80) cc_final: 0.7083 (m-80) REVERT: O 296 ASN cc_start: 0.6528 (p0) cc_final: 0.6305 (p0) REVERT: O 302 GLN cc_start: 0.5136 (pt0) cc_final: 0.4887 (pm20) REVERT: O 356 GLU cc_start: 0.6541 (tp30) cc_final: 0.5344 (mm-30) REVERT: O 362 ARG cc_start: 0.7287 (ptp90) cc_final: 0.7057 (ptp90) REVERT: O 365 PHE cc_start: 0.6434 (m-80) cc_final: 0.5810 (m-80) REVERT: O 373 PHE cc_start: 0.8327 (m-10) cc_final: 0.7913 (m-80) REVERT: O 406 MET cc_start: 0.4071 (ppp) cc_final: 0.3459 (tmm) REVERT: O 429 LEU cc_start: 0.5419 (mt) cc_final: 0.4926 (tt) outliers start: 128 outliers final: 67 residues processed: 519 average time/residue: 1.0165 time to fit residues: 666.2502 Evaluate side-chains 496 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 403 time to evaluate : 3.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR 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 159 LEU Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 74 MET 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 339 LEU Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 64 SER 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 208 ILE Chi-restraints excluded: chain F residue 219 TRP Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 267 GLN Chi-restraints excluded: chain F residue 273 PHE 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 116 ASP Chi-restraints excluded: chain G residue 134 GLU 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 336 LYS 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 112 ILE Chi-restraints excluded: chain J residue 185 LEU Chi-restraints excluded: chain J residue 243 THR Chi-restraints excluded: chain J residue 357 GLN 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 57 LEU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain K residue 202 TYR Chi-restraints excluded: chain K residue 222 GLN 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 N residue 16 ASP Chi-restraints excluded: chain N residue 25 LEU 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 277 MET Chi-restraints excluded: chain N residue 337 VAL Chi-restraints excluded: chain N residue 391 ILE Chi-restraints excluded: chain O residue 118 VAL Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain O residue 249 GLU Chi-restraints excluded: chain O residue 389 THR Chi-restraints excluded: chain O residue 447 LYS Chi-restraints excluded: chain O residue 470 CYS Chi-restraints excluded: chain O residue 507 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 301 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 266 optimal weight: 5.9990 chunk 314 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 320 optimal weight: 0.7980 chunk 220 optimal weight: 9.9990 chunk 323 optimal weight: 10.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 HIS F 160 HIS G 350 ASN ** G 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 357 GLN ** K 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 129 ASN K 430 GLN ** K 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.204932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.141195 restraints weight = 45047.119| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.54 r_work: 0.3769 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3638 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 32076 Z= 0.230 Angle : 0.734 20.266 44042 Z= 0.375 Chirality : 0.047 0.378 4830 Planarity : 0.005 0.061 4978 Dihedral : 16.287 85.123 5691 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 4.57 % Allowed : 33.90 % Favored : 61.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.14), residues: 3306 helix: 0.43 (0.15), residues: 1108 sheet: -1.27 (0.20), residues: 626 loop : -1.52 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP F 20 HIS 0.017 0.002 HIS F 160 PHE 0.032 0.002 PHE J 321 TYR 0.025 0.002 TYR A 233 ARG 0.009 0.001 ARG A 71 Details of bonding type rmsd hydrogen bonds : bond 0.04306 ( 1293) hydrogen bonds : angle 4.85327 ( 3825) covalent geometry : bond 0.00540 (32076) covalent geometry : angle 0.73364 (44042) *********************** 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 547 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 410 time to evaluate : 2.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ASN cc_start: 0.7151 (t0) cc_final: 0.6755 (t0) REVERT: A 126 LYS cc_start: 0.8004 (ttpp) cc_final: 0.7671 (tppt) REVERT: A 136 GLU cc_start: 0.7832 (tp30) cc_final: 0.7587 (tp30) REVERT: A 162 LYS cc_start: 0.7359 (OUTLIER) cc_final: 0.7112 (tptt) REVERT: A 212 GLU cc_start: 0.7874 (pt0) cc_final: 0.7213 (pp20) REVERT: A 345 MET cc_start: 0.6707 (ptp) cc_final: 0.6313 (pp-130) REVERT: B 3 GLU cc_start: 0.8254 (tt0) cc_final: 0.7299 (pm20) REVERT: B 85 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7589 (mmmm) REVERT: B 138 VAL cc_start: 0.8615 (OUTLIER) cc_final: 0.8358 (t) REVERT: B 217 HIS cc_start: 0.6272 (OUTLIER) cc_final: 0.5980 (p90) REVERT: B 324 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6924 (mp0) REVERT: B 484 ASN cc_start: 0.7846 (OUTLIER) cc_final: 0.7486 (t0) REVERT: F 52 GLU cc_start: 0.6311 (mm-30) cc_final: 0.5900 (mm-30) REVERT: F 77 GLU cc_start: 0.7361 (mp0) cc_final: 0.7139 (mp0) REVERT: F 100 ASP cc_start: 0.8452 (t0) cc_final: 0.8080 (t0) REVERT: F 132 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7954 (mt) REVERT: F 205 PHE cc_start: 0.7501 (m-80) cc_final: 0.7280 (m-80) REVERT: F 219 TRP cc_start: 0.6311 (OUTLIER) cc_final: 0.5592 (t-100) REVERT: F 220 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6859 (mp0) REVERT: F 267 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7413 (tt0) REVERT: F 271 LYS cc_start: 0.8459 (tppt) cc_final: 0.8065 (tppt) REVERT: F 293 TYR cc_start: 0.6110 (m-80) cc_final: 0.5576 (m-80) REVERT: F 315 LYS cc_start: 0.7919 (mmtp) cc_final: 0.7617 (mtpt) REVERT: G 116 ASP cc_start: 0.6962 (OUTLIER) cc_final: 0.6512 (m-30) REVERT: G 134 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7833 (pm20) REVERT: G 210 LEU cc_start: 0.8541 (tp) cc_final: 0.8338 (tt) REVERT: G 217 HIS cc_start: 0.5948 (OUTLIER) cc_final: 0.4789 (p90) REVERT: G 285 TYR cc_start: 0.8664 (OUTLIER) cc_final: 0.7978 (m-80) REVERT: G 343 LEU cc_start: 0.8221 (mt) cc_final: 0.8018 (mt) REVERT: G 351 LYS cc_start: 0.8947 (mmmt) cc_final: 0.8341 (mmtm) REVERT: G 383 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7716 (pt) REVERT: G 406 MET cc_start: 0.8747 (ttt) cc_final: 0.8440 (ttp) REVERT: G 449 GLU cc_start: 0.6782 (OUTLIER) cc_final: 0.6535 (pp20) REVERT: J 37 LEU cc_start: 0.8809 (mp) cc_final: 0.8481 (mp) REVERT: J 40 ASP cc_start: 0.6770 (t70) cc_final: 0.6371 (m-30) REVERT: J 92 MET cc_start: 0.5458 (tpp) cc_final: 0.5141 (tpt) REVERT: J 185 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7238 (pp) REVERT: J 263 ARG cc_start: 0.7177 (ptm160) cc_final: 0.6698 (mtp-110) REVERT: J 357 GLN cc_start: 0.4387 (OUTLIER) cc_final: 0.3643 (mt0) REVERT: J 392 TYR cc_start: 0.7085 (m-10) cc_final: 0.6818 (m-10) REVERT: J 402 LEU cc_start: 0.6972 (OUTLIER) cc_final: 0.6739 (tm) REVERT: K 79 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6874 (mt-10) REVERT: K 117 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.6861 (tm) REVERT: K 132 ASP cc_start: 0.6046 (m-30) cc_final: 0.5587 (t0) REVERT: K 206 PHE cc_start: 0.8158 (t80) cc_final: 0.7589 (t80) REVERT: K 210 LEU cc_start: 0.8209 (tp) cc_final: 0.7236 (mp) REVERT: K 222 GLN cc_start: 0.7660 (OUTLIER) cc_final: 0.7407 (tm-30) REVERT: K 226 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7014 (mp0) REVERT: K 247 LYS cc_start: 0.4920 (mmtp) cc_final: 0.4636 (mmtm) REVERT: K 312 VAL cc_start: 0.6627 (t) cc_final: 0.6417 (t) REVERT: K 432 THR cc_start: 0.7155 (p) cc_final: 0.6660 (t) REVERT: K 447 LYS cc_start: 0.5963 (mmtm) cc_final: 0.5145 (ptpt) REVERT: N 78 LEU cc_start: 0.7484 (tp) cc_final: 0.7149 (tt) REVERT: N 92 MET cc_start: 0.6233 (mtt) cc_final: 0.5173 (ppp) REVERT: N 240 ARG cc_start: 0.3755 (mmt90) cc_final: 0.3252 (pmt-80) REVERT: N 336 MET cc_start: 0.3317 (mmt) cc_final: 0.2995 (mpm) REVERT: N 344 THR cc_start: 0.5329 (p) cc_final: 0.4801 (p) REVERT: N 345 MET cc_start: 0.3098 (ppp) cc_final: 0.2785 (ppp) REVERT: N 388 GLN cc_start: 0.5775 (tt0) cc_final: 0.5104 (tm130) REVERT: N 391 ILE cc_start: 0.4950 (OUTLIER) cc_final: 0.4658 (mt) REVERT: N 414 MET cc_start: 0.7270 (mmm) cc_final: 0.6899 (tpp) REVERT: O 52 ILE cc_start: 0.7509 (OUTLIER) cc_final: 0.7112 (mp) REVERT: O 123 ASP cc_start: 0.6903 (OUTLIER) cc_final: 0.6480 (t70) REVERT: O 133 GLU cc_start: 0.5219 (pm20) cc_final: 0.4843 (pm20) REVERT: O 134 GLU cc_start: 0.6616 (pt0) cc_final: 0.6158 (pm20) REVERT: O 245 PHE cc_start: 0.6649 (m-10) cc_final: 0.6296 (m-10) REVERT: O 285 TYR cc_start: 0.7596 (m-80) cc_final: 0.7136 (m-80) REVERT: O 296 ASN cc_start: 0.6639 (p0) cc_final: 0.6375 (p0) REVERT: O 302 GLN cc_start: 0.5176 (pt0) cc_final: 0.4976 (pm20) REVERT: O 356 GLU cc_start: 0.6508 (tp30) cc_final: 0.5250 (mm-30) REVERT: O 362 ARG cc_start: 0.7290 (ptp90) cc_final: 0.6906 (ptp90) REVERT: O 365 PHE cc_start: 0.6646 (m-80) cc_final: 0.5972 (m-80) REVERT: O 373 PHE cc_start: 0.8289 (m-10) cc_final: 0.7430 (m-80) REVERT: O 406 MET cc_start: 0.4171 (ppp) cc_final: 0.3613 (tmm) REVERT: O 429 LEU cc_start: 0.5418 (mt) cc_final: 0.4886 (tt) outliers start: 137 outliers final: 85 residues processed: 506 average time/residue: 0.9639 time to fit residues: 610.9979 Evaluate side-chains 500 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 390 time to evaluate : 3.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 74 MET 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 339 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 219 TRP Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 267 GLN Chi-restraints excluded: chain F residue 273 PHE 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 116 ASP 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 248 ILE 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 449 GLU 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 112 ILE Chi-restraints excluded: chain J residue 185 LEU Chi-restraints excluded: chain J residue 243 THR Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain J residue 320 HIS Chi-restraints excluded: chain J residue 357 GLN 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 57 LEU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain K residue 202 TYR Chi-restraints excluded: chain K residue 216 GLU Chi-restraints excluded: chain K residue 222 GLN 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 478 VAL Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain N residue 18 THR Chi-restraints excluded: chain N residue 25 LEU 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 277 MET Chi-restraints excluded: chain N residue 337 VAL Chi-restraints excluded: chain N residue 341 ILE Chi-restraints excluded: chain N residue 391 ILE Chi-restraints excluded: chain O residue 12 ILE Chi-restraints excluded: chain O residue 52 ILE Chi-restraints excluded: chain O residue 118 VAL Chi-restraints excluded: chain O residue 123 ASP Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 249 GLU Chi-restraints excluded: chain O residue 283 LEU Chi-restraints excluded: chain O residue 304 PHE 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 152 optimal weight: 0.9990 chunk 319 optimal weight: 6.9990 chunk 269 optimal weight: 20.0000 chunk 313 optimal weight: 0.9980 chunk 182 optimal weight: 4.9990 chunk 276 optimal weight: 0.2980 chunk 261 optimal weight: 0.7980 chunk 337 optimal weight: 7.9990 chunk 263 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 chunk 345 optimal weight: 20.0000 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 HIS F 160 HIS ** J 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 357 GLN ** K 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 129 ASN K 329 HIS ** K 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.208565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.145641 restraints weight = 45304.179| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 2.58 r_work: 0.3831 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3705 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 32076 Z= 0.149 Angle : 0.693 18.897 44042 Z= 0.351 Chirality : 0.045 0.353 4830 Planarity : 0.004 0.049 4978 Dihedral : 16.249 85.575 5691 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.30 % Allowed : 35.27 % Favored : 61.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.14), residues: 3306 helix: 0.52 (0.15), residues: 1110 sheet: -1.23 (0.20), residues: 626 loop : -1.48 (0.14), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP N 369 HIS 0.021 0.001 HIS F 160 PHE 0.035 0.002 PHE J 321 TYR 0.025 0.001 TYR A 259 ARG 0.007 0.000 ARG J 263 Details of bonding type rmsd hydrogen bonds : bond 0.03815 ( 1293) hydrogen bonds : angle 4.73526 ( 3825) covalent geometry : bond 0.00347 (32076) covalent geometry : angle 0.69290 (44042) ********************** 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 514 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 415 time to evaluate : 3.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.7960 (mp0) cc_final: 0.7574 (mp0) REVERT: A 109 ASN cc_start: 0.7071 (t0) cc_final: 0.6690 (t0) REVERT: A 126 LYS cc_start: 0.7892 (ttpp) cc_final: 0.7616 (tppt) REVERT: A 162 LYS cc_start: 0.7301 (OUTLIER) cc_final: 0.7033 (tptt) REVERT: A 212 GLU cc_start: 0.7864 (pt0) cc_final: 0.7214 (pp20) REVERT: A 339 SER cc_start: 0.8334 (m) cc_final: 0.7745 (p) REVERT: A 345 MET cc_start: 0.6849 (ptp) cc_final: 0.6399 (ppp) REVERT: B 3 GLU cc_start: 0.8275 (tt0) cc_final: 0.7321 (pm20) REVERT: B 85 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7553 (mmmm) REVERT: B 138 VAL cc_start: 0.8616 (OUTLIER) cc_final: 0.8362 (t) REVERT: B 217 HIS cc_start: 0.6086 (OUTLIER) cc_final: 0.5784 (p90) REVERT: B 324 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6952 (mp0) REVERT: B 346 TYR cc_start: 0.7322 (t80) cc_final: 0.6960 (t80) REVERT: B 484 ASN cc_start: 0.7789 (OUTLIER) cc_final: 0.7539 (t0) REVERT: B 488 GLU cc_start: 0.7888 (tp30) cc_final: 0.7290 (tt0) REVERT: F 52 GLU cc_start: 0.6149 (mm-30) cc_final: 0.5817 (mm-30) REVERT: F 100 ASP cc_start: 0.8362 (t0) cc_final: 0.8019 (t0) REVERT: F 132 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8042 (mt) REVERT: F 162 LYS cc_start: 0.6355 (OUTLIER) cc_final: 0.5907 (pmtt) REVERT: F 219 TRP cc_start: 0.6291 (OUTLIER) cc_final: 0.6038 (t-100) REVERT: F 220 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6883 (pm20) REVERT: F 267 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7410 (tt0) REVERT: F 307 LYS cc_start: 0.8144 (mtpp) cc_final: 0.7108 (pptt) REVERT: F 315 LYS cc_start: 0.7917 (mmtp) cc_final: 0.7642 (mtpt) REVERT: G 1 MET cc_start: 0.7312 (tpp) cc_final: 0.6863 (mpp) REVERT: G 79 GLU cc_start: 0.6637 (mp0) cc_final: 0.6367 (mp0) REVERT: G 116 ASP cc_start: 0.6895 (OUTLIER) cc_final: 0.6500 (m-30) REVERT: G 134 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7861 (pm20) REVERT: G 217 HIS cc_start: 0.5839 (OUTLIER) cc_final: 0.4747 (p90) REVERT: G 285 TYR cc_start: 0.8592 (OUTLIER) cc_final: 0.7999 (m-80) REVERT: G 351 LYS cc_start: 0.8882 (mmmt) cc_final: 0.8283 (mmtm) REVERT: G 383 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7742 (pt) REVERT: G 406 MET cc_start: 0.8757 (ttt) cc_final: 0.8424 (ttp) REVERT: G 449 GLU cc_start: 0.6708 (OUTLIER) cc_final: 0.6431 (pp20) REVERT: J 37 LEU cc_start: 0.8792 (mp) cc_final: 0.8483 (mp) REVERT: J 92 MET cc_start: 0.5391 (tpp) cc_final: 0.5094 (tpt) REVERT: J 171 TYR cc_start: 0.7363 (m-80) cc_final: 0.6964 (m-10) REVERT: J 185 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7208 (pp) REVERT: J 277 MET cc_start: 0.6489 (mpt) cc_final: 0.6178 (ptp) REVERT: J 357 GLN cc_start: 0.4513 (OUTLIER) cc_final: 0.3699 (mt0) REVERT: J 392 TYR cc_start: 0.7079 (m-10) cc_final: 0.6807 (m-10) REVERT: J 402 LEU cc_start: 0.7084 (OUTLIER) cc_final: 0.6837 (tm) REVERT: K 72 ARG cc_start: 0.4217 (ptm160) cc_final: 0.3892 (mtm110) REVERT: K 79 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6426 (mp0) REVERT: K 117 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.6847 (tm) REVERT: K 210 LEU cc_start: 0.8134 (tp) cc_final: 0.7181 (mp) REVERT: K 226 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7047 (mp0) REVERT: K 247 LYS cc_start: 0.4925 (mmtp) cc_final: 0.4647 (mmtm) REVERT: K 432 THR cc_start: 0.7086 (p) cc_final: 0.6608 (t) REVERT: K 447 LYS cc_start: 0.5879 (mmtm) cc_final: 0.5234 (ptpt) REVERT: N 78 LEU cc_start: 0.7448 (tp) cc_final: 0.6890 (tt) REVERT: N 92 MET cc_start: 0.6190 (mtt) cc_final: 0.5214 (ppp) REVERT: N 240 ARG cc_start: 0.3767 (mmt90) cc_final: 0.3288 (pmt-80) REVERT: N 336 MET cc_start: 0.3658 (mmt) cc_final: 0.3415 (mmt) REVERT: N 344 THR cc_start: 0.5173 (p) cc_final: 0.4680 (p) REVERT: N 345 MET cc_start: 0.3134 (ppp) cc_final: 0.2825 (ppp) REVERT: N 388 GLN cc_start: 0.5772 (tt0) cc_final: 0.5200 (tm130) REVERT: N 391 ILE cc_start: 0.5150 (OUTLIER) cc_final: 0.4878 (mt) REVERT: N 414 MET cc_start: 0.7278 (mmm) cc_final: 0.6774 (tpp) REVERT: O 52 ILE cc_start: 0.7495 (mm) cc_final: 0.7197 (mt) REVERT: O 60 ILE cc_start: 0.5658 (mp) cc_final: 0.5443 (mp) REVERT: O 133 GLU cc_start: 0.5378 (pm20) cc_final: 0.5017 (pm20) REVERT: O 134 GLU cc_start: 0.6670 (pt0) cc_final: 0.6232 (pm20) REVERT: O 245 PHE cc_start: 0.6547 (m-10) cc_final: 0.6338 (m-10) REVERT: O 285 TYR cc_start: 0.7493 (m-80) cc_final: 0.7039 (m-80) REVERT: O 296 ASN cc_start: 0.6712 (p0) cc_final: 0.6342 (p0) REVERT: O 356 GLU cc_start: 0.6569 (tp30) cc_final: 0.5355 (mm-30) REVERT: O 362 ARG cc_start: 0.7175 (ptp90) cc_final: 0.6911 (pmm-80) REVERT: O 365 PHE cc_start: 0.6561 (m-80) cc_final: 0.5931 (m-80) REVERT: O 373 PHE cc_start: 0.8262 (m-10) cc_final: 0.7359 (m-80) REVERT: O 406 MET cc_start: 0.4097 (ppp) cc_final: 0.3492 (tmm) REVERT: O 429 LEU cc_start: 0.5492 (mt) cc_final: 0.4969 (tt) outliers start: 99 outliers final: 68 residues processed: 485 average time/residue: 1.0161 time to fit residues: 621.8397 Evaluate side-chains 484 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 393 time to evaluate : 3.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 57 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 160 HIS Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 311 VAL 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 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 339 LEU Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 132 LEU 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 208 ILE Chi-restraints excluded: chain F residue 219 TRP Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 267 GLN Chi-restraints excluded: chain F residue 273 PHE 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 134 GLU Chi-restraints excluded: chain G residue 217 HIS Chi-restraints excluded: chain G residue 248 ILE 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 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 112 ILE Chi-restraints excluded: chain J residue 185 LEU Chi-restraints excluded: chain J residue 243 THR Chi-restraints excluded: chain J residue 357 GLN 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 79 GLU 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 478 VAL Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain N residue 36 ILE 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 277 MET Chi-restraints excluded: chain N residue 337 VAL Chi-restraints excluded: chain N residue 391 ILE Chi-restraints excluded: chain O residue 12 ILE Chi-restraints excluded: chain O residue 118 VAL Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 249 GLU Chi-restraints excluded: chain O residue 389 THR Chi-restraints excluded: chain O residue 470 CYS Chi-restraints excluded: chain O residue 507 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 133 optimal weight: 3.9990 chunk 203 optimal weight: 10.0000 chunk 335 optimal weight: 2.9990 chunk 274 optimal weight: 8.9990 chunk 150 optimal weight: 0.8980 chunk 341 optimal weight: 20.0000 chunk 68 optimal weight: 0.7980 chunk 305 optimal weight: 1.9990 chunk 173 optimal weight: 0.9980 chunk 182 optimal weight: 5.9990 chunk 239 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 HIS F 160 HIS F 183 ASN ** J 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 234 ASN ** J 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 329 HIS ** K 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 484 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.207793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.144853 restraints weight = 45017.656| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 2.56 r_work: 0.3820 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3690 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 32076 Z= 0.163 Angle : 0.708 18.682 44042 Z= 0.357 Chirality : 0.045 0.332 4830 Planarity : 0.004 0.048 4978 Dihedral : 16.230 86.108 5691 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.93 % Allowed : 35.23 % Favored : 60.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.14), residues: 3306 helix: 0.53 (0.15), residues: 1112 sheet: -1.21 (0.20), residues: 626 loop : -1.48 (0.14), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP N 369 HIS 0.020 0.001 HIS F 160 PHE 0.034 0.002 PHE J 321 TYR 0.024 0.002 TYR A 233 ARG 0.012 0.001 ARG J 263 Details of bonding type rmsd hydrogen bonds : bond 0.03862 ( 1293) hydrogen bonds : angle 4.74032 ( 3825) covalent geometry : bond 0.00383 (32076) covalent geometry : angle 0.70753 (44042) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29695.68 seconds wall clock time: 510 minutes 7.69 seconds (30607.69 seconds total)