Starting phenix.real_space_refine on Sun Aug 9 04:21:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ffi_29043/08_2026/8ffi_29043_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ffi_29043/08_2026/8ffi_29043.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ffi_29043/08_2026/8ffi_29043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ffi_29043/08_2026/8ffi_29043.map" model { file = "/net/cci-nas-00/data/ceres_data/8ffi_29043/08_2026/8ffi_29043_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ffi_29043/08_2026/8ffi_29043_neut.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.106 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 164 5.49 5 Mg 4 5.21 5 S 88 5.16 5 C 20456 2.51 5 N 5416 2.21 5 O 6412 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32540 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3494 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 406} Chain: "B" Number of atoms: 3787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3787 Classifications: {'peptide': 469} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 444} Chain breaks: 1 Chain: "C" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 442 Classifications: {'RNA': 21} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 9, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 19} Chain: "D" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "E" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3494 Classifications: {'peptide': 419} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 406} Chain: "F" Number of atoms: 3787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3787 Classifications: {'peptide': 469} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 444} Chain breaks: 1 Chain: "G" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 442 Classifications: {'RNA': 21} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 11} Link IDs: {'rna3p': 20} Chain: "H" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "I" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3494 Classifications: {'peptide': 419} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 406} Chain: "J" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 442 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 2, 'rna3p': 18} Chain: "K" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "L" Number of atoms: 3787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3787 Classifications: {'peptide': 469} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 444} Chain breaks: 1 Chain: "M" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3494 Classifications: {'peptide': 419} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 406} Chain: "N" Number of atoms: 3787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3787 Classifications: {'peptide': 469} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 444} Chain breaks: 1 Chain: "O" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 442 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 2, 'rna3p': 18} Chain: "P" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.14, per 1000 atoms: 0.22 Number of scatterers: 32540 At special positions: 0 Unit cell: (222.3, 131.1, 168.15, 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 88 16.00 P 164 15.00 Mg 4 11.99 O 6412 8.00 N 5416 7.00 C 20456 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.82 Conformation dependent library (CDL) restraints added in 1.4 seconds 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6768 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 39 sheets defined 35.4% alpha, 20.5% beta 34 base pairs and 121 stacking pairs defined. Time for finding SS restraints: 3.96 Creating SS restraints... Processing helix chain 'A' and resid 14 through 29 Processing helix chain 'A' and resid 48 through 56 Processing helix chain 'A' and resid 71 through 88 Processing helix chain 'A' and resid 123 through 139 removed outlier: 3.918A pdb=" N GLY A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 158 Processing helix chain 'A' and resid 199 through 203 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 257 through 280 Processing helix chain 'A' and resid 300 through 304 removed outlier: 3.562A pdb=" N ASP A 303 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 365 Processing helix chain 'A' and resid 369 through 384 removed outlier: 3.597A pdb=" N LEU A 384 " --> pdb=" O PHE A 380 " (cutoff:3.500A) 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 30 Processing helix chain 'B' and resid 46 through 60 Processing helix chain 'B' and resid 77 through 83 Processing helix chain 'B' and resid 97 through 105 removed outlier: 3.623A pdb=" N ILE B 101 " --> pdb=" O THR B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 131 removed outlier: 3.683A pdb=" N LYS B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 151 removed outlier: 3.689A pdb=" N TYR B 150 " --> pdb=" O GLU B 146 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS B 151 " --> pdb=" O ILE B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 214 Processing helix chain 'B' and resid 226 through 230 removed outlier: 3.619A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) No H-bonds generated for '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 375 Processing helix chain 'B' and resid 451 through 463 removed outlier: 3.627A pdb=" N THR B 463 " --> pdb=" O ILE B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 490 removed outlier: 3.833A pdb=" N ALA B 483 " --> pdb=" O THR B 479 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP B 484 " --> pdb=" O LEU B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'E' and resid 14 through 29 Processing helix chain 'E' and resid 34 through 39 removed outlier: 3.694A pdb=" N LEU E 39 " --> pdb=" O ASP E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 56 Processing helix chain 'E' and resid 71 through 89 Processing helix chain 'E' and resid 109 through 114 removed outlier: 4.604A pdb=" N ARG E 114 " --> pdb=" O ILE E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 138 Processing helix chain 'E' and resid 149 through 157 removed outlier: 3.569A pdb=" N ILE E 157 " --> pdb=" O LEU E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 203 Processing helix chain 'E' and resid 234 through 238 removed outlier: 3.552A pdb=" N THR E 238 " --> pdb=" O LYS E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 249 Processing helix chain 'E' and resid 257 through 280 Processing helix chain 'E' and resid 300 through 302 No H-bonds generated for 'chain 'E' and resid 300 through 302' Processing helix chain 'E' and resid 353 through 365 Processing helix chain 'E' and resid 369 through 384 removed outlier: 3.712A pdb=" N LEU E 384 " --> pdb=" O PHE E 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 17 No H-bonds generated for 'chain 'F' and resid 15 through 17' Processing helix chain 'F' and resid 22 through 28 Processing helix chain 'F' and resid 46 through 60 Processing helix chain 'F' and resid 77 through 83 Processing helix chain 'F' and resid 97 through 105 removed outlier: 3.828A pdb=" N ILE F 101 " --> pdb=" O THR F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 131 removed outlier: 3.678A pdb=" N LYS F 124 " --> pdb=" O LEU F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 150 Processing helix chain 'F' and resid 205 through 214 removed outlier: 3.609A pdb=" N LEU F 214 " --> pdb=" O PHE F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 230 Processing helix chain 'F' and resid 248 through 264 Processing helix chain 'F' and resid 331 through 351 Processing helix chain 'F' and resid 366 through 376 removed outlier: 3.636A pdb=" N TRP F 370 " --> pdb=" O ASN F 366 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL F 376 " --> pdb=" O ALA F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 451 through 462 Processing helix chain 'F' and resid 477 through 480 Processing helix chain 'F' and resid 481 through 490 Processing helix chain 'F' and resid 502 through 506 removed outlier: 3.833A pdb=" N TYR F 505 " --> pdb=" O ALA F 502 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 29 Processing helix chain 'I' and resid 44 through 56 Processing helix chain 'I' and resid 71 through 89 Processing helix chain 'I' and resid 123 through 139 Processing helix chain 'I' and resid 149 through 157 removed outlier: 3.724A pdb=" N ILE I 157 " --> pdb=" O LEU I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 199 through 203 Processing helix chain 'I' and resid 243 through 247 Processing helix chain 'I' and resid 257 through 279 Processing helix chain 'I' and resid 300 through 304 Processing helix chain 'I' and resid 353 through 366 Processing helix chain 'I' and resid 369 through 385 Processing helix chain 'L' and resid 15 through 17 No H-bonds generated for 'chain 'L' and resid 15 through 17' Processing helix chain 'L' and resid 22 through 30 Processing helix chain 'L' and resid 46 through 60 Processing helix chain 'L' and resid 77 through 83 Processing helix chain 'L' and resid 97 through 105 removed outlier: 3.788A pdb=" N ILE L 101 " --> pdb=" O THR L 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 109 through 131 removed outlier: 4.154A pdb=" N LYS L 124 " --> pdb=" O LEU L 120 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE L 125 " --> pdb=" O PHE L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 144 through 149 removed outlier: 3.642A pdb=" N TYR L 148 " --> pdb=" O PRO L 144 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS L 149 " --> pdb=" O ASP L 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 144 through 149' Processing helix chain 'L' and resid 205 through 214 removed outlier: 3.632A pdb=" N LEU L 214 " --> pdb=" O PHE L 210 " (cutoff:3.500A) Processing helix chain 'L' and resid 226 through 230 Processing helix chain 'L' and resid 248 through 264 Processing helix chain 'L' and resid 331 through 351 removed outlier: 3.690A pdb=" N ALA L 337 " --> pdb=" O LYS L 333 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU L 338 " --> pdb=" O GLU L 334 " (cutoff:3.500A) Processing helix chain 'L' and resid 366 through 371 Processing helix chain 'L' and resid 451 through 462 Processing helix chain 'L' and resid 481 through 491 Processing helix chain 'L' and resid 502 through 506 removed outlier: 3.753A pdb=" N TYR L 505 " --> pdb=" O ALA L 502 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 28 Processing helix chain 'M' and resid 46 through 56 Processing helix chain 'M' and resid 71 through 89 Processing helix chain 'M' and resid 104 through 108 removed outlier: 3.866A pdb=" N ILE M 108 " --> pdb=" O TYR M 105 " (cutoff:3.500A) Processing helix chain 'M' and resid 123 through 138 Processing helix chain 'M' and resid 146 through 158 removed outlier: 4.204A pdb=" N SER M 150 " --> pdb=" O ASP M 146 " (cutoff:3.500A) Processing helix chain 'M' and resid 199 through 203 removed outlier: 3.549A pdb=" N LEU M 203 " --> pdb=" O VAL M 200 " (cutoff:3.500A) Processing helix chain 'M' and resid 234 through 236 No H-bonds generated for 'chain 'M' and resid 234 through 236' Processing helix chain 'M' and resid 243 through 249 Processing helix chain 'M' and resid 257 through 280 Processing helix chain 'M' and resid 300 through 302 No H-bonds generated for 'chain 'M' and resid 300 through 302' Processing helix chain 'M' and resid 353 through 365 Processing helix chain 'M' and resid 369 through 384 removed outlier: 3.800A pdb=" N LEU M 384 " --> pdb=" O PHE M 380 " (cutoff:3.500A) Processing helix chain 'N' and resid 15 through 17 No H-bonds generated for 'chain 'N' and resid 15 through 17' Processing helix chain 'N' and resid 22 through 30 Processing helix chain 'N' and resid 46 through 60 Processing helix chain 'N' and resid 77 through 83 Processing helix chain 'N' and resid 97 through 103 removed outlier: 3.819A pdb=" N LYS N 103 " --> pdb=" O GLU N 99 " (cutoff:3.500A) Processing helix chain 'N' and resid 109 through 131 removed outlier: 4.111A pdb=" N LYS N 124 " --> pdb=" O LEU N 120 " (cutoff:3.500A) Processing helix chain 'N' and resid 144 through 151 removed outlier: 3.619A pdb=" N TYR N 148 " --> pdb=" O PRO N 144 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR N 150 " --> pdb=" O GLU N 146 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N CYS N 151 " --> pdb=" O ILE N 147 " (cutoff:3.500A) Processing helix chain 'N' and resid 205 through 214 removed outlier: 3.605A pdb=" N LEU N 214 " --> pdb=" O PHE N 210 " (cutoff:3.500A) Processing helix chain 'N' and resid 226 through 230 removed outlier: 3.541A pdb=" N ALA N 230 " --> pdb=" O GLU N 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 226 through 230' Processing helix chain 'N' and resid 248 through 264 Processing helix chain 'N' and resid 331 through 351 Processing helix chain 'N' and resid 366 through 376 removed outlier: 3.756A pdb=" N VAL N 376 " --> pdb=" O ALA N 372 " (cutoff:3.500A) Processing helix chain 'N' and resid 451 through 462 Processing helix chain 'N' and resid 463 through 465 No H-bonds generated for 'chain 'N' and resid 463 through 465' Processing helix chain 'N' and resid 481 through 490 Processing helix chain 'N' and resid 502 through 506 removed outlier: 3.688A pdb=" N TYR N 505 " --> pdb=" O ALA N 502 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 33 removed outlier: 6.080A pdb=" N ILE A 5 " --> pdb=" O TRP A 33 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N LYS A 4 " --> pdb=" O CYS A 58 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N PHE A 60 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N PHE A 6 " --> pdb=" O PHE A 60 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LEU A 62 " --> pdb=" O PHE A 6 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N SER A 8 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N SER A 64 " --> pdb=" O SER A 8 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N ILE A 118 " --> pdb=" O ILE A 94 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 2 through 3 removed outlier: 4.391A pdb=" N LYS A 409 " --> pdb=" O TYR A 171 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N TYR A 171 " --> pdb=" O LYS A 409 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LYS A 411 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLU A 169 " --> pdb=" O LYS A 411 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASN A 413 " --> pdb=" O LYS A 167 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 177 removed outlier: 5.065A pdb=" N GLY A 325 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N THR A 291 " --> pdb=" O GLY A 325 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 175 through 177 Processing sheet with id=AA5, first strand: chain 'A' and resid 207 through 210 removed outlier: 3.529A pdb=" N TYR A 210 " --> pdb=" O TYR A 213 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 390 through 394 Processing sheet with id=AA7, first strand: chain 'B' and resid 5 through 6 removed outlier: 6.662A pdb=" N SER B 417 " --> pdb=" O VAL B 413 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLY B 385 " --> pdb=" O ASN B 446 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL B 357 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL B 386 " --> pdb=" O VAL B 357 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ILE B 359 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ILE B 388 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ALA B 361 " --> pdb=" O ILE B 388 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASN B 296 " --> pdb=" O TRP B 320 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N TRP B 320 " --> pdb=" O ASN B 296 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N CYS B 298 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N GLY B 318 " --> pdb=" O CYS B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 19 through 20 Processing sheet with id=AA9, first strand: chain 'B' and resid 91 through 95 removed outlier: 6.578A pdb=" N GLY B 42 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ILE B 142 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE B 44 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N TRP B 139 " --> pdb=" O GLN B 222 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N PHE B 224 " --> pdb=" O TRP B 139 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N VAL B 141 " --> pdb=" O PHE B 224 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 425 through 426 removed outlier: 3.546A pdb=" N THR B 431 " --> pdb=" O VAL B 426 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 32 through 33 removed outlier: 6.491A pdb=" N ILE E 5 " --> pdb=" O TRP E 33 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N PHE E 6 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N VAL E 63 " --> pdb=" O PHE E 6 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N SER E 8 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N PHE E 60 " --> pdb=" O ILE E 95 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU E 97 " --> pdb=" O PHE E 60 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N LEU E 62 " --> pdb=" O LEU E 97 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'F' and resid 311 through 315 removed outlier: 4.555A pdb=" N LEU F 305 " --> pdb=" O VAL F 278 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL F 278 " --> pdb=" O LEU F 305 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N CYS F 279 " --> pdb=" O PHE F 358 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N HIS F 360 " --> pdb=" O CYS F 279 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU F 281 " --> pdb=" O HIS F 360 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS F 447 " --> pdb=" O GLY F 385 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N THR F 387 " --> pdb=" O ILE F 445 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ILE F 445 " --> pdb=" O THR F 387 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N SER F 389 " --> pdb=" O ILE F 443 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ILE F 443 " --> pdb=" O SER F 389 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N VAL F 412 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLU F 3 " --> pdb=" O VAL F 412 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LYS E 411 " --> pdb=" O LEU F 4 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N TYR F 6 " --> pdb=" O LYS E 411 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 283 through 286 removed outlier: 7.336A pdb=" N THR E 291 " --> pdb=" O GLY E 325 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N GLY E 325 " --> pdb=" O THR E 291 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 283 through 286 removed outlier: 7.336A pdb=" N THR E 291 " --> pdb=" O GLY E 325 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N GLY E 325 " --> pdb=" O THR E 291 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU E 176 " --> pdb=" O LEU E 335 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N SER E 177 " --> pdb=" O SER E 404 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE E 402 " --> pdb=" O LEU E 179 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 208 through 210 Processing sheet with id=AB7, first strand: chain 'E' and resid 304 through 305 Processing sheet with id=AB8, first strand: chain 'F' and resid 12 through 13 Processing sheet with id=AB9, first strand: chain 'F' and resid 93 through 95 removed outlier: 8.414A pdb=" N LYS F 94 " --> pdb=" O SER F 41 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL F 43 " --> pdb=" O LYS F 94 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLY F 42 " --> pdb=" O PHE F 140 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ILE F 142 " --> pdb=" O GLY F 42 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE F 44 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N TRP F 139 " --> pdb=" O GLN F 222 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N PHE F 224 " --> pdb=" O TRP F 139 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N VAL F 141 " --> pdb=" O PHE F 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'F' and resid 284 through 286 removed outlier: 3.539A pdb=" N TRP F 320 " --> pdb=" O CYS F 298 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 425 through 426 removed outlier: 3.660A pdb=" N THR F 431 " --> pdb=" O VAL F 426 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 32 through 33 removed outlier: 6.368A pdb=" N ILE I 5 " --> pdb=" O TRP I 33 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE I 6 " --> pdb=" O LEU I 61 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N VAL I 63 " --> pdb=" O PHE I 6 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N SER I 8 " --> pdb=" O VAL I 63 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 310 through 316 removed outlier: 3.634A pdb=" N GLY L 310 " --> pdb=" O ASP L 306 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ARG L 295 " --> pdb=" O VAL L 288 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU L 305 " --> pdb=" O VAL L 278 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL L 278 " --> pdb=" O LEU L 305 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL L 357 " --> pdb=" O VAL L 384 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N VAL L 386 " --> pdb=" O VAL L 357 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE L 359 " --> pdb=" O VAL L 386 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ILE L 388 " --> pdb=" O ILE L 359 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ALA L 361 " --> pdb=" O ILE L 388 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLY L 385 " --> pdb=" O ASN L 446 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N VAL L 412 " --> pdb=" O GLU L 3 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLU L 3 " --> pdb=" O VAL L 412 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASN I 413 " --> pdb=" O LEU L 4 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N TYR L 6 " --> pdb=" O ASN I 413 " (cutoff:3.500A) removed outlier: 10.165A pdb=" N SER I 415 " --> pdb=" O TYR L 6 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL I 414 " --> pdb=" O LYS I 167 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N LYS I 167 " --> pdb=" O VAL I 414 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 283 through 286 removed outlier: 7.014A pdb=" N THR I 291 " --> pdb=" O GLY I 325 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N GLY I 325 " --> pdb=" O THR I 291 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 283 through 286 removed outlier: 7.014A pdb=" N THR I 291 " --> pdb=" O GLY I 325 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N GLY I 325 " --> pdb=" O THR I 291 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N SER I 177 " --> pdb=" O SER I 404 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N PHE I 402 " --> pdb=" O LEU I 179 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 207 through 210 Processing sheet with id=AC8, first strand: chain 'L' and resid 19 through 20 Processing sheet with id=AC9, first strand: chain 'L' and resid 92 through 95 removed outlier: 6.915A pdb=" N SER L 41 " --> pdb=" O THR L 92 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N LYS L 94 " --> pdb=" O SER L 41 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL L 43 " --> pdb=" O LYS L 94 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLY L 42 " --> pdb=" O PHE L 140 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ILE L 142 " --> pdb=" O GLY L 42 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ILE L 44 " --> pdb=" O ILE L 142 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 425 through 426 Processing sheet with id=AD2, first strand: chain 'M' and resid 32 through 33 removed outlier: 6.447A pdb=" N ILE M 5 " --> pdb=" O TRP M 33 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N PHE M 60 " --> pdb=" O ILE M 95 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LEU M 97 " --> pdb=" O PHE M 60 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU M 62 " --> pdb=" O LEU M 97 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 2 through 3 removed outlier: 4.091A pdb=" N VAL M 414 " --> pdb=" O LYS M 167 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LYS M 167 " --> pdb=" O VAL M 414 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 283 through 286 removed outlier: 6.953A pdb=" N THR M 291 " --> pdb=" O GLY M 325 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLY M 325 " --> pdb=" O THR M 291 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 283 through 286 removed outlier: 6.953A pdb=" N THR M 291 " --> pdb=" O GLY M 325 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLY M 325 " --> pdb=" O THR M 291 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER M 324 " --> pdb=" O SER M 338 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N SER M 177 " --> pdb=" O SER M 404 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N PHE M 402 " --> pdb=" O LEU M 179 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 208 through 210 Processing sheet with id=AD7, first strand: chain 'M' and resid 304 through 305 Processing sheet with id=AD8, first strand: chain 'N' and resid 5 through 6 removed outlier: 6.666A pdb=" N GLY N 385 " --> pdb=" O ASN N 446 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL N 357 " --> pdb=" O VAL N 384 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL N 386 " --> pdb=" O VAL N 357 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE N 359 " --> pdb=" O VAL N 386 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ILE N 388 " --> pdb=" O ILE N 359 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ALA N 361 " --> pdb=" O ILE N 388 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N CYS N 279 " --> pdb=" O PHE N 358 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N HIS N 360 " --> pdb=" O CYS N 279 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU N 281 " --> pdb=" O HIS N 360 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 5 through 6 removed outlier: 6.666A pdb=" N GLY N 385 " --> pdb=" O ASN N 446 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL N 357 " --> pdb=" O VAL N 384 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL N 386 " --> pdb=" O VAL N 357 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE N 359 " --> pdb=" O VAL N 386 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ILE N 388 " --> pdb=" O ILE N 359 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ALA N 361 " --> pdb=" O ILE N 388 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N CYS N 279 " --> pdb=" O PHE N 358 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N HIS N 360 " --> pdb=" O CYS N 279 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU N 281 " --> pdb=" O HIS N 360 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 19 through 20 Processing sheet with id=AE2, first strand: chain 'N' and resid 92 through 95 removed outlier: 6.318A pdb=" N GLY N 42 " --> pdb=" O PHE N 140 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ILE N 142 " --> pdb=" O GLY N 42 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE N 44 " --> pdb=" O ILE N 142 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N TRP N 139 " --> pdb=" O GLN N 222 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N PHE N 224 " --> pdb=" O TRP N 139 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL N 141 " --> pdb=" O PHE N 224 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'N' and resid 425 through 426 1203 hydrogen bonds defined for protein. 3363 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 85 hydrogen bonds 170 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 121 stacking parallelities Total time for adding SS restraints: 7.71 Time building geometry restraints manager: 3.74 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: 6272 1.33 - 1.45: 9074 1.45 - 1.57: 17878 1.57 - 1.69: 320 1.69 - 1.81: 132 Bond restraints: 33676 Sorted by residual: bond pdb=" C3' DG H 15 " pdb=" C2' DG H 15 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 bond pdb=" C3' DA H 14 " pdb=" C2' DA H 14 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.60e+00 bond pdb=" C3' DC H 4 " pdb=" C2' DC H 4 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.43e+00 bond pdb=" C3' DA K 16 " pdb=" C2' DA K 16 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.97e+00 bond pdb=" C3' DC H 18 " pdb=" C2' DC H 18 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.92e+00 ... (remaining 33671 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 45408 2.16 - 4.33: 808 4.33 - 6.49: 32 6.49 - 8.65: 3 8.65 - 10.82: 5 Bond angle restraints: 46256 Sorted by residual: angle pdb=" O4' A J 11 " pdb=" C1' A J 11 " pdb=" N9 A J 11 " ideal model delta sigma weight residual 108.20 113.22 -5.02 8.00e-01 1.56e+00 3.95e+01 angle pdb=" O4' A O 11 " pdb=" C1' A O 11 " pdb=" N9 A O 11 " ideal model delta sigma weight residual 108.20 113.04 -4.84 8.00e-01 1.56e+00 3.66e+01 angle pdb=" C ASP B 306 " pdb=" N ASN B 307 " pdb=" CA ASN B 307 " ideal model delta sigma weight residual 126.45 136.45 -10.00 1.77e+00 3.19e-01 3.19e+01 angle pdb=" C1' U J 13 " pdb=" N1 U J 13 " pdb=" C2 U J 13 " ideal model delta sigma weight residual 117.70 123.62 -5.92 1.20e+00 6.94e-01 2.43e+01 angle pdb=" C1' U O 17 " pdb=" N1 U O 17 " pdb=" C2 U O 17 " ideal model delta sigma weight residual 117.70 123.58 -5.88 1.20e+00 6.94e-01 2.40e+01 ... (remaining 46251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 19333 35.84 - 71.68: 659 71.68 - 107.51: 34 107.51 - 143.35: 1 143.35 - 179.19: 21 Dihedral angle restraints: 20048 sinusoidal: 9572 harmonic: 10476 Sorted by residual: dihedral pdb=" O4' U G 13 " pdb=" C1' U G 13 " pdb=" N1 U G 13 " pdb=" C2 U G 13 " ideal model delta sinusoidal sigma weight residual 200.00 20.81 179.19 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U O 17 " pdb=" C1' U O 17 " pdb=" N1 U O 17 " pdb=" C2 U O 17 " ideal model delta sinusoidal sigma weight residual -160.00 19.03 -179.03 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U C 13 " pdb=" C1' U C 13 " pdb=" N1 U C 13 " pdb=" C2 U C 13 " ideal model delta sinusoidal sigma weight residual -160.00 17.31 -177.31 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 20045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 3913 0.049 - 0.099: 830 0.099 - 0.148: 321 0.148 - 0.197: 11 0.197 - 0.247: 1 Chirality restraints: 5076 Sorted by residual: chirality pdb=" CB ILE I 157 " pdb=" CA ILE I 157 " pdb=" CG1 ILE I 157 " pdb=" CG2 ILE I 157 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CB ILE M 418 " pdb=" CA ILE M 418 " pdb=" CG1 ILE M 418 " pdb=" CG2 ILE M 418 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.25e-01 chirality pdb=" CB ILE A 418 " pdb=" CA ILE A 418 " pdb=" CG1 ILE A 418 " pdb=" CG2 ILE A 418 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.99e-01 ... (remaining 5073 not shown) Planarity restraints: 5264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP M 33 " 0.022 2.00e-02 2.50e+03 2.29e-02 1.31e+01 pdb=" CG TRP M 33 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP M 33 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP M 33 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP M 33 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP M 33 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP M 33 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 33 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 33 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP M 33 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A O 11 " -0.034 2.00e-02 2.50e+03 1.69e-02 7.83e+00 pdb=" N9 A O 11 " 0.043 2.00e-02 2.50e+03 pdb=" C8 A O 11 " 0.000 2.00e-02 2.50e+03 pdb=" N7 A O 11 " -0.000 2.00e-02 2.50e+03 pdb=" C5 A O 11 " -0.003 2.00e-02 2.50e+03 pdb=" C6 A O 11 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A O 11 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A O 11 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A O 11 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A O 11 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A O 11 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A J 11 " -0.034 2.00e-02 2.50e+03 1.67e-02 7.69e+00 pdb=" N9 A J 11 " 0.042 2.00e-02 2.50e+03 pdb=" C8 A J 11 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A J 11 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A J 11 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A J 11 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A J 11 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A J 11 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A J 11 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A J 11 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A J 11 " 0.001 2.00e-02 2.50e+03 ... (remaining 5261 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 170 2.57 - 3.15: 24229 3.15 - 3.73: 48549 3.73 - 4.32: 71085 4.32 - 4.90: 116374 Nonbonded interactions: 260407 Sorted by model distance: nonbonded pdb=" OP2 U G 1 " pdb="MG MG F 601 " model vdw 1.987 2.170 nonbonded pdb=" OP2 U J 1 " pdb="MG MG L 601 " model vdw 2.067 2.170 nonbonded pdb=" OP1 A G 3 " pdb="MG MG F 601 " model vdw 2.116 2.170 nonbonded pdb=" OG SER B 67 " pdb=" OP1 DA D 23 " model vdw 2.198 3.040 nonbonded pdb=" O GLY F 487 " pdb=" OG1 THR F 491 " model vdw 2.205 3.040 ... (remaining 260402 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'J' selection = chain 'O' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'K' selection = chain 'P' } 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: 5.920 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: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 33.140 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 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 0.039 33676 Z= 0.216 Angle : 0.608 10.815 46256 Z= 0.422 Chirality : 0.047 0.247 5076 Planarity : 0.004 0.053 5264 Dihedral : 17.750 179.188 13280 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.14), residues: 3528 helix: 1.12 (0.16), residues: 1138 sheet: -0.44 (0.19), residues: 748 loop : -1.92 (0.14), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 407 TYR 0.015 0.001 TYR A 221 PHE 0.037 0.001 PHE M 6 TRP 0.057 0.002 TRP M 33 HIS 0.007 0.001 HIS M 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.22 (33676) covalent geometry : angle 0.60795 / 0.42 (46256) hydrogen bonds : bond 0.14455 / 9.43 ( 1235) hydrogen bonds : angle 6.23672 / 4.35 ( 3533) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 417 time to evaluate : 1.261 Fit side-chains REVERT: A 129 LYS cc_start: 0.7386 (mttp) cc_final: 0.7164 (mttp) REVERT: A 161 ASP cc_start: 0.7348 (p0) cc_final: 0.7005 (p0) REVERT: E 122 MET cc_start: 0.6457 (mmt) cc_final: 0.6203 (mmt) REVERT: E 189 GLU cc_start: 0.7295 (tt0) cc_final: 0.7074 (tt0) REVERT: F 216 LYS cc_start: 0.6851 (pttm) cc_final: 0.6601 (tptt) REVERT: F 314 LYS cc_start: 0.6738 (ptpp) cc_final: 0.6307 (mmtt) REVERT: I 283 GLN cc_start: 0.7812 (mm110) cc_final: 0.7481 (mp10) REVERT: N 131 ASN cc_start: 0.6781 (m-40) cc_final: 0.6053 (p0) REVERT: N 415 GLU cc_start: 0.6563 (tp30) cc_final: 0.6299 (tp30) outliers start: 0 outliers final: 1 residues processed: 417 average time/residue: 0.8008 time to fit residues: 388.7160 Evaluate side-chains 302 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 301 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 418 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.0770 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.0470 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 4.9990 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 ASN B 207 HIS B 296 ASN E 15 ASN ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 320 HIS E 364 GLN ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 ASN F 205 GLN L 302 GLN M 15 ASN M 370 ASN N 18 GLN N 368 GLN N 430 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.134373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.112996 restraints weight = 53403.558| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.78 r_work: 0.3454 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.0812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33676 Z= 0.127 Angle : 0.549 9.819 46256 Z= 0.311 Chirality : 0.044 0.353 5076 Planarity : 0.004 0.051 5264 Dihedral : 18.504 179.632 6030 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.70 % Favored : 94.27 % Rotamer: Outliers : 1.29 % Allowed : 7.86 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.14), residues: 3528 helix: 1.41 (0.16), residues: 1146 sheet: -0.31 (0.19), residues: 742 loop : -1.86 (0.14), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 243 TYR 0.017 0.001 TYR M 392 PHE 0.017 0.001 PHE F 14 TRP 0.025 0.001 TRP M 33 HIS 0.005 0.001 HIS M 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.13 (33676) covalent geometry : angle 0.54937 / 0.31 (46256) hydrogen bonds : bond 0.04609 / 3.00 ( 1235) hydrogen bonds : angle 4.94630 / 3.48 ( 3533) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 321 time to evaluate : 1.225 Fit side-chains REVERT: A 28 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7300 (mm) REVERT: A 161 ASP cc_start: 0.7634 (p0) cc_final: 0.7314 (p0) REVERT: A 190 TYR cc_start: 0.7528 (m-10) cc_final: 0.7212 (m-10) REVERT: A 229 LYS cc_start: 0.6805 (ttpt) cc_final: 0.5748 (tmmt) REVERT: B 8 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6842 (mm-30) REVERT: E 122 MET cc_start: 0.6811 (mmt) cc_final: 0.6448 (mmt) REVERT: E 299 LYS cc_start: 0.7379 (mtpt) cc_final: 0.7117 (ttpp) REVERT: F 314 LYS cc_start: 0.6760 (ptpp) cc_final: 0.6272 (mmtt) REVERT: F 356 GLU cc_start: 0.6148 (OUTLIER) cc_final: 0.5825 (mt-10) REVERT: I 234 HIS cc_start: 0.6066 (t-90) cc_final: 0.5677 (t70) REVERT: I 283 GLN cc_start: 0.7874 (mm110) cc_final: 0.7601 (mp10) REVERT: I 284 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7846 (pt0) REVERT: L 1 MET cc_start: 0.7779 (tpt) cc_final: 0.7393 (tpt) REVERT: L 327 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.8019 (tp-100) REVERT: L 350 ILE cc_start: 0.6878 (OUTLIER) cc_final: 0.6341 (mp) REVERT: M 307 LYS cc_start: 0.7447 (mptt) cc_final: 0.6954 (mppt) REVERT: N 235 LYS cc_start: 0.8601 (mttm) cc_final: 0.8258 (mttt) REVERT: N 348 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6895 (mt-10) REVERT: N 415 GLU cc_start: 0.6854 (tp30) cc_final: 0.6608 (tp30) outliers start: 41 outliers final: 16 residues processed: 337 average time/residue: 0.7747 time to fit residues: 306.0085 Evaluate side-chains 316 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 293 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain E residue 279 ASP Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 284 GLU Chi-restraints excluded: chain I residue 316 ASP Chi-restraints excluded: chain L residue 74 MET Chi-restraints excluded: chain L residue 327 GLN Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 496 ILE Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 144 VAL Chi-restraints excluded: chain N residue 203 ASP Chi-restraints excluded: chain N residue 348 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 317 optimal weight: 0.0980 chunk 252 optimal weight: 5.9990 chunk 255 optimal weight: 0.9990 chunk 160 optimal weight: 0.4980 chunk 149 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 292 optimal weight: 0.9990 chunk 247 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 318 ASN A 370 ASN ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 HIS E 320 HIS E 364 GLN E 370 ASN L 302 GLN M 3 ASN M 370 ASN N 18 GLN N 368 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.133812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.112457 restraints weight = 53224.815| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.77 r_work: 0.3447 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 33676 Z= 0.129 Angle : 0.539 9.119 46256 Z= 0.304 Chirality : 0.044 0.309 5076 Planarity : 0.004 0.048 5264 Dihedral : 18.516 179.706 6028 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.50 % Favored : 94.47 % Rotamer: Outliers : 1.70 % Allowed : 9.94 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.14), residues: 3528 helix: 1.56 (0.16), residues: 1146 sheet: -0.24 (0.19), residues: 734 loop : -1.83 (0.14), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 19 TYR 0.020 0.001 TYR M 392 PHE 0.014 0.001 PHE F 14 TRP 0.013 0.001 TRP A 192 HIS 0.004 0.001 HIS M 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (33676) covalent geometry : angle 0.53909 / 0.30 (46256) hydrogen bonds : bond 0.04300 / 2.79 ( 1235) hydrogen bonds : angle 4.71164 / 3.32 ( 3533) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 302 time to evaluate : 1.282 Fit side-chains REVERT: A 28 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7251 (mm) REVERT: A 133 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7339 (mp0) REVERT: A 161 ASP cc_start: 0.7622 (p0) cc_final: 0.7301 (p0) REVERT: A 190 TYR cc_start: 0.7556 (m-10) cc_final: 0.7275 (m-10) REVERT: A 229 LYS cc_start: 0.6833 (ttpt) cc_final: 0.5760 (tmmt) REVERT: B 1 MET cc_start: 0.8503 (tpt) cc_final: 0.8069 (tpt) REVERT: B 8 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6835 (mm-30) REVERT: B 364 ARG cc_start: 0.8737 (mpt-90) cc_final: 0.8479 (mtt90) REVERT: E 122 MET cc_start: 0.6737 (mmt) cc_final: 0.6393 (mmt) REVERT: E 237 LYS cc_start: 0.6115 (mttt) cc_final: 0.5906 (mttm) REVERT: E 299 LYS cc_start: 0.7303 (mtpt) cc_final: 0.7037 (ttpp) REVERT: F 314 LYS cc_start: 0.6751 (ptpp) cc_final: 0.6259 (mmtt) REVERT: F 356 GLU cc_start: 0.6094 (OUTLIER) cc_final: 0.5778 (mt-10) REVERT: F 373 PHE cc_start: 0.7961 (m-10) cc_final: 0.7594 (m-10) REVERT: F 453 LYS cc_start: 0.8221 (ttmm) cc_final: 0.7977 (mtmt) REVERT: I 122 MET cc_start: 0.7329 (OUTLIER) cc_final: 0.7053 (ptm) REVERT: I 234 HIS cc_start: 0.6022 (t-90) cc_final: 0.5645 (t70) REVERT: I 237 LYS cc_start: 0.7258 (ttmm) cc_final: 0.6281 (ttmt) REVERT: I 284 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7727 (pt0) REVERT: L 48 GLN cc_start: 0.7235 (OUTLIER) cc_final: 0.7029 (mm-40) REVERT: L 327 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.8128 (tp-100) REVERT: L 350 ILE cc_start: 0.6891 (OUTLIER) cc_final: 0.6248 (mp) REVERT: M 307 LYS cc_start: 0.7542 (mptt) cc_final: 0.6993 (mppt) REVERT: N 1 MET cc_start: 0.8264 (tpp) cc_final: 0.7954 (mmm) REVERT: N 235 LYS cc_start: 0.8603 (mttm) cc_final: 0.8271 (mttt) REVERT: N 348 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6917 (mt-10) REVERT: N 415 GLU cc_start: 0.6839 (tp30) cc_final: 0.6585 (tp30) outliers start: 54 outliers final: 18 residues processed: 328 average time/residue: 0.7696 time to fit residues: 294.8103 Evaluate side-chains 311 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 283 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain F residue 400 GLU Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 122 MET Chi-restraints excluded: chain I residue 161 ASP Chi-restraints excluded: chain I residue 284 GLU Chi-restraints excluded: chain L residue 48 GLN Chi-restraints excluded: chain L residue 74 MET Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 327 GLN Chi-restraints excluded: chain L residue 344 GLN Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 496 ILE Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 144 VAL Chi-restraints excluded: chain M residue 261 CYS Chi-restraints excluded: chain N residue 203 ASP Chi-restraints excluded: chain N residue 348 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 295 optimal weight: 5.9990 chunk 224 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 289 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 220 optimal weight: 0.9990 chunk 337 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 ASN B 414 ASN E 138 GLN E 320 HIS E 364 GLN ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 ASN M 370 ASN N 18 GLN N 276 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.130147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.108432 restraints weight = 52639.537| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.72 r_work: 0.3371 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 33676 Z= 0.251 Angle : 0.689 9.967 46256 Z= 0.375 Chirality : 0.050 0.368 5076 Planarity : 0.005 0.059 5264 Dihedral : 18.622 179.486 6028 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.03 % Favored : 92.94 % Rotamer: Outliers : 2.23 % Allowed : 11.79 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.14), residues: 3528 helix: 1.10 (0.15), residues: 1146 sheet: -0.42 (0.19), residues: 744 loop : -1.99 (0.14), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 374 TYR 0.024 0.002 TYR M 285 PHE 0.023 0.003 PHE L 304 TRP 0.016 0.002 TRP I 319 HIS 0.006 0.001 HIS F 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.25 (33676) covalent geometry : angle 0.68888 / 0.38 (46256) hydrogen bonds : bond 0.05828 / 3.78 ( 1235) hydrogen bonds : angle 4.95369 / 3.48 ( 3533) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 295 time to evaluate : 1.201 Fit side-chains REVERT: A 28 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7307 (mm) REVERT: A 189 GLU cc_start: 0.8336 (tt0) cc_final: 0.8124 (tt0) REVERT: A 190 TYR cc_start: 0.7628 (m-10) cc_final: 0.7291 (m-10) REVERT: A 229 LYS cc_start: 0.6924 (ttpt) cc_final: 0.5847 (tmmt) REVERT: A 391 PHE cc_start: 0.6798 (OUTLIER) cc_final: 0.4934 (t80) REVERT: B 8 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6949 (mm-30) REVERT: B 85 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8457 (mtpt) REVERT: E 122 MET cc_start: 0.7022 (mmt) cc_final: 0.6775 (mpp) REVERT: E 237 LYS cc_start: 0.6185 (mttt) cc_final: 0.5982 (mttm) REVERT: E 257 ARG cc_start: 0.7280 (mmm-85) cc_final: 0.7045 (mmm160) REVERT: E 299 LYS cc_start: 0.7417 (mtpt) cc_final: 0.7125 (ttpp) REVERT: F 356 GLU cc_start: 0.6201 (OUTLIER) cc_final: 0.5879 (mt-10) REVERT: I 284 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7718 (pt0) REVERT: L 48 GLN cc_start: 0.7387 (OUTLIER) cc_final: 0.7130 (mm-40) REVERT: L 350 ILE cc_start: 0.7042 (OUTLIER) cc_final: 0.6528 (mp) REVERT: N 235 LYS cc_start: 0.8654 (mttm) cc_final: 0.8313 (mttt) REVERT: N 348 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7027 (mt-10) REVERT: N 415 GLU cc_start: 0.7142 (tp30) cc_final: 0.6902 (tp30) outliers start: 71 outliers final: 38 residues processed: 332 average time/residue: 0.6966 time to fit residues: 272.6094 Evaluate side-chains 330 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 283 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain F residue 400 GLU Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain F residue 496 ILE Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 122 MET Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 161 ASP Chi-restraints excluded: chain I residue 284 GLU Chi-restraints excluded: chain I residue 316 ASP Chi-restraints excluded: chain L residue 48 GLN Chi-restraints excluded: chain L residue 74 MET Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 317 VAL Chi-restraints excluded: chain L residue 327 GLN Chi-restraints excluded: chain L residue 344 GLN Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 391 THR Chi-restraints excluded: chain L residue 496 ILE Chi-restraints excluded: chain L residue 498 THR Chi-restraints excluded: chain M residue 51 LYS Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 144 VAL Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain M residue 261 CYS Chi-restraints excluded: chain N residue 203 ASP Chi-restraints excluded: chain N residue 348 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 294 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 321 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 chunk 149 optimal weight: 0.9980 chunk 342 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 ASN B 414 ASN E 320 HIS E 364 GLN ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 ASN M 370 ASN N 18 GLN N 276 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.131422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.110068 restraints weight = 52930.584| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.76 r_work: 0.3402 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 33676 Z= 0.171 Angle : 0.600 10.158 46256 Z= 0.334 Chirality : 0.046 0.316 5076 Planarity : 0.005 0.058 5264 Dihedral : 18.585 179.251 6028 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.39 % Allowed : 13.18 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.14), residues: 3528 helix: 1.23 (0.16), residues: 1154 sheet: -0.39 (0.19), residues: 736 loop : -1.97 (0.14), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 257 TYR 0.017 0.002 TYR A 221 PHE 0.016 0.002 PHE L 304 TRP 0.015 0.002 TRP M 319 HIS 0.004 0.001 HIS E 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (33676) covalent geometry : angle 0.60022 / 0.33 (46256) hydrogen bonds : bond 0.04896 / 3.18 ( 1235) hydrogen bonds : angle 4.80183 / 3.38 ( 3533) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 291 time to evaluate : 1.132 Fit side-chains REVERT: A 28 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7286 (mm) REVERT: A 189 GLU cc_start: 0.8258 (tt0) cc_final: 0.8053 (tt0) REVERT: A 190 TYR cc_start: 0.7608 (m-10) cc_final: 0.7347 (m-10) REVERT: A 221 TYR cc_start: 0.5777 (p90) cc_final: 0.4989 (p90) REVERT: A 229 LYS cc_start: 0.6900 (ttpt) cc_final: 0.5808 (pptt) REVERT: A 391 PHE cc_start: 0.6745 (OUTLIER) cc_final: 0.4821 (t80) REVERT: B 8 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6862 (mm-30) REVERT: B 85 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8421 (mtpt) REVERT: E 122 MET cc_start: 0.6904 (mmt) cc_final: 0.6658 (mpp) REVERT: E 237 LYS cc_start: 0.6131 (mttt) cc_final: 0.5920 (mttm) REVERT: F 356 GLU cc_start: 0.6121 (OUTLIER) cc_final: 0.5791 (mt-10) REVERT: I 122 MET cc_start: 0.7471 (OUTLIER) cc_final: 0.7210 (ptm) REVERT: I 284 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7676 (pt0) REVERT: L 48 GLN cc_start: 0.7347 (OUTLIER) cc_final: 0.7066 (mm-40) REVERT: L 350 ILE cc_start: 0.6919 (OUTLIER) cc_final: 0.6327 (mp) REVERT: L 435 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.7309 (mtt) REVERT: M 307 LYS cc_start: 0.7624 (mptt) cc_final: 0.7142 (mtpt) REVERT: N 1 MET cc_start: 0.8200 (tpp) cc_final: 0.7969 (mmm) REVERT: N 235 LYS cc_start: 0.8625 (mttm) cc_final: 0.8282 (mttt) REVERT: N 243 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.8003 (mtp85) REVERT: N 348 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6996 (mt-10) REVERT: N 415 GLU cc_start: 0.7026 (tp30) cc_final: 0.6788 (tp30) outliers start: 76 outliers final: 35 residues processed: 329 average time/residue: 0.6865 time to fit residues: 265.6997 Evaluate side-chains 323 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 276 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain F residue 400 GLU Chi-restraints excluded: chain F residue 496 ILE Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 122 MET Chi-restraints excluded: chain I residue 143 GLU Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 161 ASP Chi-restraints excluded: chain I residue 284 GLU Chi-restraints excluded: chain I residue 316 ASP Chi-restraints excluded: chain L residue 48 GLN Chi-restraints excluded: chain L residue 74 MET Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 317 VAL Chi-restraints excluded: chain L residue 327 GLN Chi-restraints excluded: chain L residue 344 GLN Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 391 THR Chi-restraints excluded: chain L residue 435 MET Chi-restraints excluded: chain L residue 496 ILE Chi-restraints excluded: chain L residue 498 THR Chi-restraints excluded: chain M residue 51 LYS Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 144 VAL Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain M residue 261 CYS Chi-restraints excluded: chain N residue 79 GLU Chi-restraints excluded: chain N residue 203 ASP Chi-restraints excluded: chain N residue 243 ARG Chi-restraints excluded: chain N residue 348 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 32 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 244 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 289 optimal weight: 2.9990 chunk 176 optimal weight: 0.7980 chunk 322 optimal weight: 0.8980 chunk 271 optimal weight: 0.5980 chunk 196 optimal weight: 0.0870 chunk 1 optimal weight: 0.8980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 318 ASN A 370 ASN B 414 ASN E 320 HIS E 364 GLN ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 409 ASN M 370 ASN N 18 GLN N 276 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.133309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.111612 restraints weight = 52815.545| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.75 r_work: 0.3427 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 33676 Z= 0.125 Angle : 0.542 10.900 46256 Z= 0.305 Chirality : 0.044 0.291 5076 Planarity : 0.004 0.051 5264 Dihedral : 18.552 179.709 6028 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.01 % Allowed : 14.37 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.14), residues: 3528 helix: 1.57 (0.16), residues: 1152 sheet: -0.29 (0.19), residues: 726 loop : -1.91 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 257 TYR 0.025 0.001 TYR M 392 PHE 0.015 0.001 PHE M 45 TRP 0.015 0.001 TRP M 319 HIS 0.003 0.001 HIS E 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (33676) covalent geometry : angle 0.54232 / 0.31 (46256) hydrogen bonds : bond 0.04064 / 2.65 ( 1235) hydrogen bonds : angle 4.58814 / 3.23 ( 3533) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 284 time to evaluate : 0.960 Fit side-chains REVERT: A 28 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7279 (mm) REVERT: A 190 TYR cc_start: 0.7599 (m-10) cc_final: 0.7347 (m-10) REVERT: A 229 LYS cc_start: 0.6947 (ttpt) cc_final: 0.5804 (tmmt) REVERT: A 391 PHE cc_start: 0.6631 (OUTLIER) cc_final: 0.4771 (t80) REVERT: B 8 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6803 (mm-30) REVERT: E 122 MET cc_start: 0.6857 (mmt) cc_final: 0.6643 (mpp) REVERT: E 237 LYS cc_start: 0.6153 (mttt) cc_final: 0.5793 (ttmm) REVERT: E 244 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7565 (pp20) REVERT: I 122 MET cc_start: 0.7450 (OUTLIER) cc_final: 0.7192 (ptm) REVERT: I 143 GLU cc_start: 0.7554 (tm-30) cc_final: 0.7305 (tp30) REVERT: I 234 HIS cc_start: 0.5881 (t-90) cc_final: 0.5531 (t70) REVERT: I 284 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7705 (pt0) REVERT: I 394 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7371 (mt-10) REVERT: L 327 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.8079 (tp-100) REVERT: L 347 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7995 (tttp) REVERT: L 350 ILE cc_start: 0.6933 (OUTLIER) cc_final: 0.6288 (mp) REVERT: M 307 LYS cc_start: 0.7595 (mptt) cc_final: 0.7137 (mppt) REVERT: M 370 ASN cc_start: 0.7279 (t0) cc_final: 0.7077 (t0) REVERT: N 1 MET cc_start: 0.8252 (tpp) cc_final: 0.7932 (mmm) REVERT: N 235 LYS cc_start: 0.8624 (mttm) cc_final: 0.8296 (mttt) REVERT: N 348 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6927 (mt-10) REVERT: N 415 GLU cc_start: 0.6925 (tp30) cc_final: 0.6685 (tp30) REVERT: N 430 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7719 (mp-120) outliers start: 64 outliers final: 33 residues processed: 321 average time/residue: 0.6773 time to fit residues: 257.0938 Evaluate side-chains 320 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 275 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 400 GLU Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 122 MET Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 161 ASP Chi-restraints excluded: chain I residue 284 GLU Chi-restraints excluded: chain I residue 316 ASP Chi-restraints excluded: chain I residue 394 GLU Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 305 LEU Chi-restraints excluded: chain L residue 317 VAL Chi-restraints excluded: chain L residue 327 GLN Chi-restraints excluded: chain L residue 339 LEU Chi-restraints excluded: chain L residue 344 GLN Chi-restraints excluded: chain L residue 347 LYS Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 496 ILE Chi-restraints excluded: chain M residue 51 LYS Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 144 VAL Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain M residue 261 CYS Chi-restraints excluded: chain N residue 79 GLU Chi-restraints excluded: chain N residue 203 ASP Chi-restraints excluded: chain N residue 276 ASN Chi-restraints excluded: chain N residue 348 GLU Chi-restraints excluded: chain N residue 430 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 10 optimal weight: 4.9990 chunk 196 optimal weight: 6.9990 chunk 115 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 135 optimal weight: 0.3980 chunk 304 optimal weight: 0.9990 chunk 14 optimal weight: 0.3980 chunk 117 optimal weight: 1.9990 chunk 319 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 ASN B 414 ASN E 320 HIS E 364 GLN E 370 ASN N 18 GLN N 276 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.132418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.110613 restraints weight = 53178.478| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.76 r_work: 0.3409 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 33676 Z= 0.153 Angle : 0.573 11.847 46256 Z= 0.318 Chirality : 0.045 0.313 5076 Planarity : 0.004 0.057 5264 Dihedral : 18.539 179.263 6028 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.39 % Allowed : 14.25 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.14), residues: 3528 helix: 1.53 (0.16), residues: 1152 sheet: -0.28 (0.19), residues: 726 loop : -1.91 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 19 TYR 0.024 0.001 TYR M 392 PHE 0.014 0.002 PHE L 304 TRP 0.014 0.001 TRP I 319 HIS 0.003 0.001 HIS E 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (33676) covalent geometry : angle 0.57288 / 0.32 (46256) hydrogen bonds : bond 0.04401 / 2.86 ( 1235) hydrogen bonds : angle 4.60987 / 3.25 ( 3533) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 289 time to evaluate : 1.536 Fit side-chains REVERT: A 28 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7300 (mm) REVERT: A 190 TYR cc_start: 0.7608 (m-10) cc_final: 0.7260 (m-10) REVERT: A 221 TYR cc_start: 0.5779 (p90) cc_final: 0.5022 (p90) REVERT: A 229 LYS cc_start: 0.6953 (ttpt) cc_final: 0.5764 (pptt) REVERT: A 391 PHE cc_start: 0.6705 (OUTLIER) cc_final: 0.4809 (t80) REVERT: B 8 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6863 (mm-30) REVERT: E 237 LYS cc_start: 0.6186 (mttt) cc_final: 0.5829 (ttmm) REVERT: E 244 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7599 (pp20) REVERT: E 393 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7519 (mt) REVERT: F 356 GLU cc_start: 0.6074 (OUTLIER) cc_final: 0.5743 (mt-10) REVERT: F 453 LYS cc_start: 0.8262 (ttmm) cc_final: 0.7993 (mtmt) REVERT: I 122 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.7178 (ptm) REVERT: I 143 GLU cc_start: 0.7553 (tm-30) cc_final: 0.7202 (tp30) REVERT: I 229 LYS cc_start: 0.8023 (mtmt) cc_final: 0.7372 (pttp) REVERT: I 234 HIS cc_start: 0.5918 (t-90) cc_final: 0.5563 (t70) REVERT: I 284 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7688 (pt0) REVERT: I 394 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7349 (mt-10) REVERT: L 347 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.8136 (tttp) REVERT: L 350 ILE cc_start: 0.6955 (OUTLIER) cc_final: 0.6304 (mp) REVERT: M 23 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7434 (mt) REVERT: M 307 LYS cc_start: 0.7606 (mptt) cc_final: 0.7139 (mppt) REVERT: M 370 ASN cc_start: 0.7276 (t0) cc_final: 0.7043 (t0) REVERT: N 1 MET cc_start: 0.8204 (tpp) cc_final: 0.7926 (mmm) REVERT: N 235 LYS cc_start: 0.8631 (mttm) cc_final: 0.8300 (mttt) REVERT: N 275 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7474 (ptt90) REVERT: N 348 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.7019 (mt-10) REVERT: N 415 GLU cc_start: 0.6962 (tp30) cc_final: 0.6721 (tp30) REVERT: N 430 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7723 (mp-120) outliers start: 76 outliers final: 35 residues processed: 338 average time/residue: 0.7383 time to fit residues: 295.1227 Evaluate side-chains 328 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 278 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain F residue 400 GLU Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 122 MET Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 161 ASP Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 284 GLU Chi-restraints excluded: chain I residue 316 ASP Chi-restraints excluded: chain I residue 394 GLU Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 305 LEU Chi-restraints excluded: chain L residue 317 VAL Chi-restraints excluded: chain L residue 339 LEU Chi-restraints excluded: chain L residue 344 GLN Chi-restraints excluded: chain L residue 347 LYS Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 391 THR Chi-restraints excluded: chain L residue 496 ILE Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 51 LYS Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 144 VAL Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain M residue 261 CYS Chi-restraints excluded: chain N residue 79 GLU Chi-restraints excluded: chain N residue 203 ASP Chi-restraints excluded: chain N residue 275 ARG Chi-restraints excluded: chain N residue 348 GLU Chi-restraints excluded: chain N residue 430 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 19 optimal weight: 0.0270 chunk 68 optimal weight: 0.7980 chunk 307 optimal weight: 1.9990 chunk 341 optimal weight: 2.9990 chunk 286 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 294 optimal weight: 2.9990 chunk 360 optimal weight: 6.9990 chunk 189 optimal weight: 0.5980 chunk 356 optimal weight: 1.9990 chunk 140 optimal weight: 0.4980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 ASN B 414 ASN E 320 HIS E 364 GLN ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 ASN N 18 GLN N 276 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.133687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.112198 restraints weight = 52940.224| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.86 r_work: 0.3432 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 33676 Z= 0.121 Angle : 0.541 12.802 46256 Z= 0.303 Chirality : 0.043 0.287 5076 Planarity : 0.004 0.072 5264 Dihedral : 18.495 179.701 6028 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.26 % Allowed : 14.50 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.14), residues: 3528 helix: 1.68 (0.16), residues: 1148 sheet: -0.24 (0.19), residues: 726 loop : -1.84 (0.14), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG M 19 TYR 0.025 0.001 TYR M 392 PHE 0.013 0.001 PHE I 158 TRP 0.015 0.001 TRP A 319 HIS 0.003 0.001 HIS E 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (33676) covalent geometry : angle 0.54080 / 0.30 (46256) hydrogen bonds : bond 0.03928 / 2.56 ( 1235) hydrogen bonds : angle 4.51062 / 3.18 ( 3533) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 294 time to evaluate : 1.232 Fit side-chains REVERT: A 19 ARG cc_start: 0.7332 (OUTLIER) cc_final: 0.6778 (ttt180) REVERT: A 28 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7273 (mm) REVERT: A 190 TYR cc_start: 0.7559 (m-10) cc_final: 0.7181 (m-10) REVERT: A 221 TYR cc_start: 0.5662 (p90) cc_final: 0.4965 (p90) REVERT: A 229 LYS cc_start: 0.6912 (ttpt) cc_final: 0.5735 (pptt) REVERT: A 297 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7246 (ttpp) REVERT: A 391 PHE cc_start: 0.6499 (OUTLIER) cc_final: 0.4720 (t80) REVERT: B 8 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6786 (mm-30) REVERT: B 146 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.5588 (pp20) REVERT: B 364 ARG cc_start: 0.8784 (mpt-90) cc_final: 0.8525 (mtt-85) REVERT: E 86 LYS cc_start: 0.8207 (ttmm) cc_final: 0.7879 (tmmt) REVERT: E 237 LYS cc_start: 0.6146 (mttt) cc_final: 0.5784 (ttmm) REVERT: E 244 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7532 (pp20) REVERT: E 393 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7483 (mt) REVERT: F 348 GLU cc_start: 0.6046 (pp20) cc_final: 0.5702 (pp20) REVERT: F 356 GLU cc_start: 0.6045 (OUTLIER) cc_final: 0.5685 (mt-10) REVERT: F 453 LYS cc_start: 0.8259 (ttmm) cc_final: 0.7989 (mtmt) REVERT: I 122 MET cc_start: 0.7385 (OUTLIER) cc_final: 0.7139 (ptm) REVERT: I 143 GLU cc_start: 0.7522 (tm-30) cc_final: 0.7165 (tp30) REVERT: I 161 ASP cc_start: 0.7027 (OUTLIER) cc_final: 0.6812 (t0) REVERT: I 229 LYS cc_start: 0.7966 (mtmt) cc_final: 0.7590 (pttp) REVERT: I 234 HIS cc_start: 0.5816 (t-90) cc_final: 0.5468 (t70) REVERT: I 394 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7360 (mt-10) REVERT: L 350 ILE cc_start: 0.6900 (OUTLIER) cc_final: 0.6249 (mp) REVERT: M 23 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7409 (mt) REVERT: M 45 PHE cc_start: 0.6108 (t80) cc_final: 0.5874 (t80) REVERT: M 112 ILE cc_start: 0.8508 (OUTLIER) cc_final: 0.8209 (pp) REVERT: M 307 LYS cc_start: 0.7584 (mptt) cc_final: 0.7092 (mppt) REVERT: M 316 ASP cc_start: 0.7427 (p0) cc_final: 0.7028 (p0) REVERT: N 1 MET cc_start: 0.8196 (tpp) cc_final: 0.7834 (mmm) REVERT: N 235 LYS cc_start: 0.8618 (mttm) cc_final: 0.8285 (mttt) REVERT: N 348 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6931 (mt-10) REVERT: N 415 GLU cc_start: 0.6899 (tp30) cc_final: 0.6650 (tp30) REVERT: N 430 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7680 (mp-120) REVERT: N 443 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8711 (mp) outliers start: 72 outliers final: 35 residues processed: 336 average time/residue: 0.6952 time to fit residues: 274.8679 Evaluate side-chains 338 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 285 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ARG Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain F residue 400 GLU Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 122 MET Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 161 ASP Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 316 ASP Chi-restraints excluded: chain I residue 394 GLU Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 305 LEU Chi-restraints excluded: chain L residue 317 VAL Chi-restraints excluded: chain L residue 339 LEU Chi-restraints excluded: chain L residue 344 GLN Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 496 ILE Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 51 LYS Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 112 ILE Chi-restraints excluded: chain M residue 144 VAL Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain M residue 261 CYS Chi-restraints excluded: chain N residue 203 ASP Chi-restraints excluded: chain N residue 276 ASN Chi-restraints excluded: chain N residue 348 GLU Chi-restraints excluded: chain N residue 430 GLN Chi-restraints excluded: chain N residue 443 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 255 optimal weight: 2.9990 chunk 362 optimal weight: 10.0000 chunk 22 optimal weight: 0.7980 chunk 294 optimal weight: 5.9990 chunk 205 optimal weight: 1.9990 chunk 250 optimal weight: 0.8980 chunk 247 optimal weight: 2.9990 chunk 327 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 265 optimal weight: 0.8980 chunk 223 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 ASN B 414 ASN E 320 HIS E 364 GLN ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 ASN M 258 ASN N 18 GLN N 276 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.131932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.110061 restraints weight = 52638.185| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.76 r_work: 0.3401 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 33676 Z= 0.170 Angle : 0.606 12.871 46256 Z= 0.333 Chirality : 0.046 0.323 5076 Planarity : 0.005 0.067 5264 Dihedral : 18.504 179.758 6028 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 2.39 % Allowed : 14.78 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.14), residues: 3528 helix: 1.51 (0.16), residues: 1148 sheet: -0.28 (0.19), residues: 726 loop : -1.89 (0.14), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG M 19 TYR 0.025 0.002 TYR M 392 PHE 0.016 0.002 PHE L 304 TRP 0.014 0.002 TRP A 192 HIS 0.004 0.001 HIS B 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (33676) covalent geometry : angle 0.60558 / 0.33 (46256) hydrogen bonds : bond 0.04641 / 3.02 ( 1235) hydrogen bonds : angle 4.62793 / 3.26 ( 3533) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 291 time to evaluate : 1.247 Fit side-chains REVERT: A 19 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.7039 (ttt180) REVERT: A 28 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7315 (mm) REVERT: A 190 TYR cc_start: 0.7586 (m-10) cc_final: 0.7178 (m-10) REVERT: A 221 TYR cc_start: 0.5622 (p90) cc_final: 0.4927 (p90) REVERT: A 229 LYS cc_start: 0.6934 (ttpt) cc_final: 0.5769 (pptt) REVERT: A 297 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7163 (ttpp) REVERT: A 391 PHE cc_start: 0.6690 (OUTLIER) cc_final: 0.4900 (t80) REVERT: B 8 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6890 (mm-30) REVERT: B 85 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8415 (mtpt) REVERT: B 146 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.5551 (pp20) REVERT: E 237 LYS cc_start: 0.6217 (mttt) cc_final: 0.5848 (ttmm) REVERT: E 244 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7554 (pp20) REVERT: E 257 ARG cc_start: 0.7366 (mmm-85) cc_final: 0.6944 (mmp80) REVERT: E 283 GLN cc_start: 0.7022 (mm-40) cc_final: 0.6543 (mm-40) REVERT: E 393 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7631 (mt) REVERT: F 453 LYS cc_start: 0.8271 (ttmm) cc_final: 0.8010 (mtmt) REVERT: I 229 LYS cc_start: 0.7837 (mtmt) cc_final: 0.7528 (pttp) REVERT: I 234 HIS cc_start: 0.5909 (t-90) cc_final: 0.5566 (t70) REVERT: I 394 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7371 (mt-10) REVERT: L 350 ILE cc_start: 0.7007 (OUTLIER) cc_final: 0.6339 (mp) REVERT: M 23 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7471 (mt) REVERT: M 45 PHE cc_start: 0.6193 (t80) cc_final: 0.5925 (t80) REVERT: M 112 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.8265 (pp) REVERT: M 307 LYS cc_start: 0.7696 (mptt) cc_final: 0.7177 (mppt) REVERT: N 1 MET cc_start: 0.8193 (tpp) cc_final: 0.7913 (mmm) REVERT: N 235 LYS cc_start: 0.8636 (mttm) cc_final: 0.8308 (mttt) REVERT: N 243 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7601 (mtt180) REVERT: N 275 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7417 (ptt90) REVERT: N 348 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6968 (mt-10) REVERT: N 415 GLU cc_start: 0.6994 (tp30) cc_final: 0.6752 (tp30) REVERT: N 430 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7734 (mp-120) REVERT: N 443 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8742 (mp) outliers start: 76 outliers final: 38 residues processed: 339 average time/residue: 0.7137 time to fit residues: 285.0137 Evaluate side-chains 339 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 283 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ARG Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 400 GLU Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 161 ASP Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 316 ASP Chi-restraints excluded: chain I residue 394 GLU Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 305 LEU Chi-restraints excluded: chain L residue 317 VAL Chi-restraints excluded: chain L residue 339 LEU Chi-restraints excluded: chain L residue 344 GLN Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 369 GLU Chi-restraints excluded: chain L residue 391 THR Chi-restraints excluded: chain L residue 496 ILE Chi-restraints excluded: chain L residue 498 THR Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 51 LYS Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 112 ILE Chi-restraints excluded: chain M residue 144 VAL Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain M residue 261 CYS Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 203 ASP Chi-restraints excluded: chain N residue 243 ARG Chi-restraints excluded: chain N residue 275 ARG Chi-restraints excluded: chain N residue 348 GLU Chi-restraints excluded: chain N residue 430 GLN Chi-restraints excluded: chain N residue 443 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 138 optimal weight: 0.9980 chunk 203 optimal weight: 2.9990 chunk 265 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 119 optimal weight: 0.0970 chunk 8 optimal weight: 2.9990 chunk 336 optimal weight: 0.9980 chunk 359 optimal weight: 0.0030 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 318 ASN A 370 ASN B 414 ASN E 320 HIS E 364 GLN ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 ASN N 18 GLN N 276 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.133345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.111796 restraints weight = 52984.519| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.85 r_work: 0.3424 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33676 Z= 0.129 Angle : 0.560 14.383 46256 Z= 0.312 Chirality : 0.044 0.287 5076 Planarity : 0.004 0.049 5264 Dihedral : 18.474 179.643 6028 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.79 % Allowed : 15.57 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.14), residues: 3528 helix: 1.66 (0.16), residues: 1148 sheet: -0.22 (0.19), residues: 726 loop : -1.85 (0.14), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 257 TYR 0.026 0.001 TYR M 392 PHE 0.027 0.001 PHE F 14 TRP 0.014 0.001 TRP M 319 HIS 0.003 0.001 HIS E 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (33676) covalent geometry : angle 0.56035 / 0.31 (46256) hydrogen bonds : bond 0.04043 / 2.63 ( 1235) hydrogen bonds : angle 4.53773 / 3.20 ( 3533) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 290 time to evaluate : 1.241 Fit side-chains REVERT: A 19 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.6773 (ttt180) REVERT: A 28 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7280 (mm) REVERT: A 133 GLU cc_start: 0.7374 (mp0) cc_final: 0.6950 (mm-30) REVERT: A 190 TYR cc_start: 0.7567 (m-10) cc_final: 0.7173 (m-10) REVERT: A 221 TYR cc_start: 0.5563 (p90) cc_final: 0.4955 (p90) REVERT: A 229 LYS cc_start: 0.6890 (ttpt) cc_final: 0.5719 (pptt) REVERT: A 297 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7386 (ttpp) REVERT: A 391 PHE cc_start: 0.6581 (OUTLIER) cc_final: 0.4887 (t80) REVERT: B 8 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6814 (mm-30) REVERT: E 86 LYS cc_start: 0.8207 (ttmm) cc_final: 0.7873 (tmmt) REVERT: E 237 LYS cc_start: 0.6164 (mttt) cc_final: 0.5819 (ttmm) REVERT: E 244 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7541 (pp20) REVERT: E 283 GLN cc_start: 0.7036 (mm-40) cc_final: 0.6546 (mm-40) REVERT: E 393 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7577 (mt) REVERT: F 348 GLU cc_start: 0.6240 (pp20) cc_final: 0.5911 (pp20) REVERT: I 143 GLU cc_start: 0.7552 (tm-30) cc_final: 0.7206 (tp30) REVERT: I 229 LYS cc_start: 0.7821 (mtmt) cc_final: 0.7532 (pttp) REVERT: I 234 HIS cc_start: 0.5908 (t-90) cc_final: 0.5557 (t70) REVERT: I 394 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7347 (mt-10) REVERT: L 350 ILE cc_start: 0.6918 (OUTLIER) cc_final: 0.6222 (mp) REVERT: M 23 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7440 (mt) REVERT: M 45 PHE cc_start: 0.6151 (t80) cc_final: 0.5886 (t80) REVERT: M 112 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.8224 (pp) REVERT: M 307 LYS cc_start: 0.7683 (mptt) cc_final: 0.7170 (mtpt) REVERT: M 316 ASP cc_start: 0.7392 (p0) cc_final: 0.6985 (p0) REVERT: N 1 MET cc_start: 0.8191 (tpp) cc_final: 0.7844 (mmm) REVERT: N 235 LYS cc_start: 0.8620 (mttm) cc_final: 0.8285 (mttt) REVERT: N 243 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7594 (mtt180) REVERT: N 348 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6959 (mt-10) REVERT: N 415 GLU cc_start: 0.6913 (tp30) cc_final: 0.6674 (tp30) REVERT: N 430 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.7695 (mp-120) REVERT: N 443 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8711 (mp) outliers start: 57 outliers final: 33 residues processed: 329 average time/residue: 0.7911 time to fit residues: 304.9875 Evaluate side-chains 334 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 286 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ARG Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 400 GLU Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 316 ASP Chi-restraints excluded: chain I residue 394 GLU Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 305 LEU Chi-restraints excluded: chain L residue 317 VAL Chi-restraints excluded: chain L residue 339 LEU Chi-restraints excluded: chain L residue 344 GLN Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 391 THR Chi-restraints excluded: chain L residue 496 ILE Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 51 LYS Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 112 ILE Chi-restraints excluded: chain M residue 144 VAL Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain M residue 261 CYS Chi-restraints excluded: chain N residue 203 ASP Chi-restraints excluded: chain N residue 243 ARG Chi-restraints excluded: chain N residue 348 GLU Chi-restraints excluded: chain N residue 430 GLN Chi-restraints excluded: chain N residue 443 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 209 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 234 optimal weight: 0.5980 chunk 243 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 173 optimal weight: 3.9990 chunk 213 optimal weight: 0.9980 chunk 334 optimal weight: 0.8980 chunk 278 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 ASN E 320 HIS E 364 GLN ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 ASN N 18 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.131286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.109393 restraints weight = 53032.806| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.75 r_work: 0.3390 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 33676 Z= 0.194 Angle : 0.637 13.617 46256 Z= 0.348 Chirality : 0.047 0.340 5076 Planarity : 0.005 0.054 5264 Dihedral : 18.507 178.944 6028 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 2.08 % Allowed : 15.38 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.14), residues: 3528 helix: 1.43 (0.16), residues: 1140 sheet: -0.30 (0.19), residues: 726 loop : -1.91 (0.14), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 257 TYR 0.026 0.002 TYR M 392 PHE 0.028 0.002 PHE F 14 TRP 0.014 0.002 TRP A 192 HIS 0.005 0.001 HIS I 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.19 (33676) covalent geometry : angle 0.63707 / 0.35 (46256) hydrogen bonds : bond 0.04944 / 3.22 ( 1235) hydrogen bonds : angle 4.69613 / 3.31 ( 3533) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12452.89 seconds wall clock time: 212 minutes 34.78 seconds (12754.78 seconds total)