Starting phenix.real_space_refine on Tue Aug 26 02:16:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ffi_29043/08_2025/8ffi_29043_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ffi_29043/08_2025/8ffi_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_2025/8ffi_29043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ffi_29043/08_2025/8ffi_29043.map" model { file = "/net/cci-nas-00/data/ceres_data/8ffi_29043/08_2025/8ffi_29043_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ffi_29043/08_2025/8ffi_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 6.30, per 1000 atoms: 0.19 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: 2.16 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 3.40 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: 6.24 Time building geometry restraints manager: 2.98 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' DC P 4 " pdb=" O3' DC P 4 " ideal model delta sigma weight residual 1.422 1.467 -0.045 3.00e-02 1.11e+03 2.25e+00 bond pdb=" C3' DC K 22 " pdb=" O3' DC K 22 " ideal model delta sigma weight residual 1.422 1.464 -0.042 3.00e-02 1.11e+03 2.00e+00 bond pdb=" C3' DG H 15 " pdb=" O3' DG H 15 " ideal model delta sigma weight residual 1.422 1.462 -0.040 3.00e-02 1.11e+03 1.75e+00 bond pdb=" C3' DT D 12 " pdb=" O3' DT D 12 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.72e+00 bond pdb=" C3' DG D 15 " pdb=" O3' DG D 15 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.68e+00 ... (remaining 33671 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 45665 2.16 - 4.33: 551 4.33 - 6.49: 32 6.49 - 8.65: 3 8.65 - 10.82: 5 Bond angle restraints: 46256 Sorted by residual: 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=" C LYS E 211 " pdb=" CA LYS E 211 " pdb=" CB LYS E 211 " ideal model delta sigma weight residual 115.89 110.96 4.93 1.32e+00 5.74e-01 1.39e+01 angle pdb=" N GLY B 318 " pdb=" CA GLY B 318 " pdb=" C GLY B 318 " ideal model delta sigma weight residual 112.34 105.15 7.19 2.04e+00 2.40e-01 1.24e+01 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 1.50e+00 4.44e-01 1.12e+01 angle pdb=" C SER E 68 " pdb=" N ASN E 69 " pdb=" CA ASN E 69 " ideal model delta sigma weight residual 121.54 127.75 -6.21 1.91e+00 2.74e-01 1.06e+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: 4070 0.049 - 0.099: 775 0.099 - 0.148: 222 0.148 - 0.197: 8 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: 4.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 27.570 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.070 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:5.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 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 0.045 33676 Z= 0.125 Angle : 0.562 10.815 46256 Z= 0.310 Chirality : 0.042 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 aren 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 covalent geometry : bond 0.00258 (33676) covalent geometry : angle 0.56209 (46256) hydrogen bonds : bond 0.14455 ( 1235) hydrogen bonds : angle 6.23672 ( 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 : 1.032 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: 0.6456 (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: 0.6600 (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: 0.6782 (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: 0.6998 time to fit residues: 339.1437 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 : 0.817 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.134588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.113216 restraints weight = 53449.133| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.79 r_work: 0.3454 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33676 Z= 0.120 Angle : 0.547 9.784 46256 Z= 0.295 Chirality : 0.042 0.279 5076 Planarity : 0.004 0.050 5264 Dihedral : 18.427 179.524 6030 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.56 % Favored : 94.42 % Rotamer: Outliers : 1.45 % Allowed : 7.67 % Favored : 90.88 % 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 aren not related in a simple way. whole: -0.52 (0.14), residues: 3528 helix: 1.54 (0.16), residues: 1148 sheet: -0.29 (0.19), residues: 746 loop : -1.81 (0.14), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 243 TYR 0.018 0.001 TYR M 392 PHE 0.018 0.001 PHE F 14 TRP 0.018 0.001 TRP A 33 HIS 0.005 0.001 HIS M 9 Details of bonding type rmsd covalent geometry : bond 0.00265 (33676) covalent geometry : angle 0.54717 (46256) hydrogen bonds : bond 0.03996 ( 1235) hydrogen bonds : angle 4.75067 ( 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 374 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 328 time to evaluate : 1.089 Fit side-chains REVERT: A 28 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7281 (mm) REVERT: A 161 ASP cc_start: 0.7645 (p0) cc_final: 0.7315 (p0) REVERT: A 229 LYS cc_start: 0.6815 (ttpt) cc_final: 0.5743 (tmmt) REVERT: A 244 GLU cc_start: 0.6429 (mm-30) cc_final: 0.6200 (mm-30) REVERT: B 8 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6843 (mm-30) REVERT: E 122 MET cc_start: 0.6801 (mmt) cc_final: 0.6465 (mmt) REVERT: E 155 GLN cc_start: 0.6830 (tm-30) cc_final: 0.6588 (tm-30) REVERT: E 189 GLU cc_start: 0.7234 (tt0) cc_final: 0.7021 (tt0) REVERT: E 299 LYS cc_start: 0.7299 (mtpt) cc_final: 0.7050 (ttpp) REVERT: F 314 LYS cc_start: 0.6694 (ptpp) cc_final: 0.6237 (mmtt) REVERT: F 356 GLU cc_start: 0.6069 (OUTLIER) cc_final: 0.5791 (mt-10) REVERT: F 453 LYS cc_start: 0.8229 (ttmm) cc_final: 0.7974 (mtmt) REVERT: I 122 MET cc_start: 0.7347 (ptm) cc_final: 0.7098 (ptm) REVERT: I 189 GLU cc_start: 0.7593 (tt0) cc_final: 0.7390 (tt0) REVERT: I 234 HIS cc_start: 0.6034 (t-90) cc_final: 0.5688 (t70) REVERT: I 237 LYS cc_start: 0.7306 (ttmm) cc_final: 0.6184 (ttmm) REVERT: I 284 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7746 (pt0) REVERT: L 1 MET cc_start: 0.7947 (tpt) cc_final: 0.7563 (tpt) REVERT: L 327 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.8017 (tp-100) REVERT: L 350 ILE cc_start: 0.6885 (OUTLIER) cc_final: 0.6278 (mp) REVERT: M 307 LYS cc_start: 0.7431 (mptt) cc_final: 0.6952 (mppt) REVERT: N 79 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7295 (pt0) REVERT: N 235 LYS cc_start: 0.8605 (mttm) cc_final: 0.8259 (mttt) REVERT: N 348 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6897 (mt-10) REVERT: N 415 GLU cc_start: 0.6794 (tp30) cc_final: 0.6554 (tp30) outliers start: 46 outliers final: 12 residues processed: 347 average time/residue: 0.6919 time to fit residues: 280.5803 Evaluate side-chains 316 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 296 time to evaluate : 0.988 ------------------------------------------------------------------------------- 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 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 F residue 356 GLU Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 183 GLU Chi-restraints excluded: chain I residue 284 GLU Chi-restraints excluded: chain L residue 89 THR 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 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 348 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 317 optimal weight: 0.9980 chunk 252 optimal weight: 5.9990 chunk 255 optimal weight: 0.9990 chunk 160 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 292 optimal weight: 3.9990 chunk 247 optimal weight: 0.0070 chunk 130 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 ASN A 370 ASN E 188 HIS E 320 HIS E 364 GLN E 370 ASN F 129 ASN F 302 GLN M 370 ASN N 18 GLN N 276 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.132089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.110202 restraints weight = 53045.592| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.73 r_work: 0.3402 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 33676 Z= 0.169 Angle : 0.599 9.629 46256 Z= 0.320 Chirality : 0.044 0.193 5076 Planarity : 0.004 0.051 5264 Dihedral : 18.452 179.991 6028 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.92 % Favored : 94.05 % Rotamer: Outliers : 1.98 % Allowed : 10.44 % Favored : 87.58 % 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 aren not related in a simple way. whole: -0.59 (0.14), residues: 3528 helix: 1.45 (0.16), residues: 1152 sheet: -0.28 (0.19), residues: 746 loop : -1.87 (0.14), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 257 TYR 0.015 0.001 TYR A 221 PHE 0.018 0.002 PHE F 14 TRP 0.014 0.002 TRP A 192 HIS 0.004 0.001 HIS F 251 Details of bonding type rmsd covalent geometry : bond 0.00394 (33676) covalent geometry : angle 0.59881 (46256) hydrogen bonds : bond 0.04683 ( 1235) hydrogen bonds : angle 4.74156 ( 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 367 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 304 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7256 (mm) REVERT: A 161 ASP cc_start: 0.7678 (p0) cc_final: 0.7358 (p0) REVERT: A 189 GLU cc_start: 0.8307 (tt0) cc_final: 0.8104 (tt0) REVERT: A 190 TYR cc_start: 0.7546 (m-10) cc_final: 0.7282 (m-10) REVERT: A 229 LYS cc_start: 0.6887 (ttpt) cc_final: 0.5805 (tmmt) REVERT: A 391 PHE cc_start: 0.6546 (OUTLIER) cc_final: 0.4727 (t80) REVERT: B 8 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6907 (mm-30) REVERT: B 85 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8424 (mtpt) REVERT: B 364 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8511 (mtt-85) REVERT: E 122 MET cc_start: 0.6925 (mmt) cc_final: 0.6568 (mmt) REVERT: E 189 GLU cc_start: 0.7349 (tt0) cc_final: 0.7128 (tt0) REVERT: E 244 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7565 (pp20) REVERT: E 283 GLN cc_start: 0.7071 (mm110) cc_final: 0.6662 (mm-40) REVERT: F 356 GLU cc_start: 0.6123 (OUTLIER) cc_final: 0.5787 (mt-10) REVERT: F 400 GLU cc_start: 0.6782 (pm20) cc_final: 0.6540 (mp0) REVERT: I 122 MET cc_start: 0.7485 (OUTLIER) cc_final: 0.7240 (ptm) REVERT: I 234 HIS cc_start: 0.6078 (t-90) cc_final: 0.5690 (t70) REVERT: I 284 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7729 (pt0) REVERT: L 48 GLN cc_start: 0.7354 (OUTLIER) cc_final: 0.7118 (mm-40) REVERT: L 243 ARG cc_start: 0.8010 (mpp80) cc_final: 0.7731 (mpp80) REVERT: L 350 ILE cc_start: 0.6981 (OUTLIER) cc_final: 0.6355 (mp) REVERT: L 415 GLU cc_start: 0.8106 (tp30) cc_final: 0.7898 (tp30) REVERT: L 435 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.7249 (mtt) REVERT: M 307 LYS cc_start: 0.7682 (mptt) cc_final: 0.7151 (mtpt) REVERT: M 370 ASN cc_start: 0.7375 (t0) cc_final: 0.7167 (t0) REVERT: N 1 MET cc_start: 0.8233 (tpp) cc_final: 0.7890 (mmm) REVERT: N 235 LYS cc_start: 0.8634 (mttm) cc_final: 0.8308 (mttt) REVERT: N 348 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.6942 (mt-10) REVERT: N 415 GLU cc_start: 0.6965 (tp30) cc_final: 0.6724 (tp30) REVERT: N 430 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7728 (mp-120) outliers start: 63 outliers final: 29 residues processed: 334 average time/residue: 0.6840 time to fit residues: 266.7331 Evaluate side-chains 321 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 278 time to evaluate : 0.739 ------------------------------------------------------------------------------- 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 364 ARG 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 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 183 GLU 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 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 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 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 Chi-restraints excluded: chain N residue 430 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 295 optimal weight: 4.9990 chunk 224 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 289 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 chunk 337 optimal weight: 0.9980 chunk 230 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3847 r_free = 0.3847 target = 0.130088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.108295 restraints weight = 52731.701| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.73 r_work: 0.3369 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 33676 Z= 0.236 Angle : 0.677 10.077 46256 Z= 0.359 Chirality : 0.047 0.207 5076 Planarity : 0.005 0.062 5264 Dihedral : 18.553 178.774 6028 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.61 % Allowed : 12.26 % Favored : 85.13 % 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 aren not related in a simple way. whole: -0.87 (0.14), residues: 3528 helix: 1.16 (0.16), residues: 1144 sheet: -0.41 (0.19), residues: 738 loop : -1.97 (0.14), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 257 TYR 0.021 0.002 TYR M 392 PHE 0.021 0.002 PHE I 45 TRP 0.015 0.002 TRP I 319 HIS 0.005 0.001 HIS F 251 Details of bonding type rmsd covalent geometry : bond 0.00563 (33676) covalent geometry : angle 0.67701 (46256) hydrogen bonds : bond 0.05495 ( 1235) hydrogen bonds : angle 4.91941 ( 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 375 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 292 time to evaluate : 1.033 Fit side-chains REVERT: A 28 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7254 (mm) REVERT: A 189 GLU cc_start: 0.8276 (tt0) cc_final: 0.8071 (tt0) REVERT: A 221 TYR cc_start: 0.5654 (p90) cc_final: 0.4827 (p90) REVERT: A 229 LYS cc_start: 0.6953 (ttpt) cc_final: 0.5823 (pptt) REVERT: A 391 PHE cc_start: 0.6944 (OUTLIER) cc_final: 0.5249 (t80) REVERT: A 399 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7766 (mm-30) REVERT: B 8 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.6923 (mm-30) REVERT: B 85 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8473 (mtpt) REVERT: B 364 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8519 (mtt-85) REVERT: E 122 MET cc_start: 0.6999 (mmt) cc_final: 0.6740 (mpp) REVERT: E 189 GLU cc_start: 0.7405 (tt0) cc_final: 0.7141 (tt0) REVERT: E 244 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7576 (pp20) REVERT: E 393 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7481 (mt) REVERT: I 122 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.7222 (ptm) REVERT: L 48 GLN cc_start: 0.7356 (OUTLIER) cc_final: 0.7081 (mm-40) REVERT: L 350 ILE cc_start: 0.6983 (OUTLIER) cc_final: 0.6410 (mp) REVERT: L 435 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.7286 (mtt) REVERT: M 45 PHE cc_start: 0.6291 (t80) cc_final: 0.5897 (t80) REVERT: M 307 LYS cc_start: 0.7788 (mptt) cc_final: 0.7265 (mppt) REVERT: M 316 ASP cc_start: 0.7483 (p0) cc_final: 0.7124 (p0) REVERT: N 235 LYS cc_start: 0.8648 (mttm) cc_final: 0.8313 (mttt) REVERT: N 243 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.8040 (mtp85) REVERT: N 275 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7478 (ptt90) REVERT: N 348 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7115 (mt-10) REVERT: N 415 GLU cc_start: 0.7152 (tp30) cc_final: 0.6911 (tp30) REVERT: N 430 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7837 (mp-120) outliers start: 83 outliers final: 39 residues processed: 339 average time/residue: 0.6859 time to fit residues: 271.6192 Evaluate side-chains 337 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 282 time to evaluate : 1.088 ------------------------------------------------------------------------------- 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 246 ILE Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 399 GLU 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 364 ARG 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 253 SER 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 334 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 133 GLU 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 183 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 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 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: 0.0870 chunk 321 optimal weight: 0.9980 chunk 106 optimal weight: 0.1980 chunk 99 optimal weight: 0.7980 chunk 142 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 189 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 chunk 342 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 ASN A 370 ASN B 414 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 409 ASN M 318 ASN M 370 ASN N 18 GLN N 276 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.133633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.111815 restraints weight = 53280.780| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.77 r_work: 0.3429 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1318 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= 0.123 Angle : 0.546 11.292 46256 Z= 0.295 Chirality : 0.042 0.289 5076 Planarity : 0.004 0.048 5264 Dihedral : 18.373 179.597 6028 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.95 % Allowed : 13.87 % Favored : 84.18 % 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 aren not related in a simple way. whole: -0.55 (0.14), residues: 3528 helix: 1.56 (0.16), residues: 1148 sheet: -0.26 (0.19), residues: 732 loop : -1.89 (0.14), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 257 TYR 0.012 0.001 TYR A 221 PHE 0.013 0.001 PHE I 158 TRP 0.015 0.001 TRP M 319 HIS 0.003 0.001 HIS E 160 Details of bonding type rmsd covalent geometry : bond 0.00274 (33676) covalent geometry : angle 0.54644 (46256) hydrogen bonds : bond 0.03787 ( 1235) hydrogen bonds : angle 4.52642 ( 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 349 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 287 time to evaluate : 1.174 Fit side-chains REVERT: A 28 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7270 (mm) REVERT: A 190 TYR cc_start: 0.7581 (m-10) cc_final: 0.7213 (m-10) REVERT: A 221 TYR cc_start: 0.5516 (p90) cc_final: 0.4810 (p90) REVERT: A 229 LYS cc_start: 0.6955 (ttpt) cc_final: 0.5759 (pptt) REVERT: A 391 PHE cc_start: 0.6732 (OUTLIER) cc_final: 0.5144 (t80) REVERT: B 1 MET cc_start: 0.8517 (tpt) cc_final: 0.8066 (tpp) REVERT: B 364 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8448 (mtt-85) REVERT: E 86 LYS cc_start: 0.8229 (ttmm) cc_final: 0.7892 (tmmt) REVERT: E 189 GLU cc_start: 0.7366 (tt0) cc_final: 0.7105 (tt0) REVERT: E 244 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7540 (pp20) REVERT: E 393 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7517 (mt) REVERT: F 348 GLU cc_start: 0.6203 (pp20) cc_final: 0.5864 (pp20) REVERT: F 356 GLU cc_start: 0.6058 (OUTLIER) cc_final: 0.5729 (mt-10) REVERT: F 453 LYS cc_start: 0.8277 (ttmm) cc_final: 0.8014 (mtmt) REVERT: I 234 HIS cc_start: 0.5848 (t-90) cc_final: 0.5516 (t70) REVERT: L 48 GLN cc_start: 0.7260 (OUTLIER) cc_final: 0.7037 (mm-40) REVERT: L 339 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7299 (mm) REVERT: M 45 PHE cc_start: 0.6166 (t80) cc_final: 0.5754 (t80) REVERT: M 261 CYS cc_start: 0.7559 (OUTLIER) cc_final: 0.7240 (m) REVERT: M 307 LYS cc_start: 0.7745 (mptt) cc_final: 0.7217 (mtpt) REVERT: N 1 MET cc_start: 0.8246 (tpp) cc_final: 0.7984 (mmm) REVERT: N 18 GLN cc_start: 0.7644 (mm-40) cc_final: 0.7427 (mm110) REVERT: N 235 LYS cc_start: 0.8610 (mttm) cc_final: 0.8290 (mttt) REVERT: N 348 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6950 (mt-10) REVERT: N 415 GLU cc_start: 0.6890 (tp30) cc_final: 0.6649 (tp30) REVERT: N 430 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7756 (mp-120) outliers start: 62 outliers final: 22 residues processed: 324 average time/residue: 0.6676 time to fit residues: 253.6812 Evaluate side-chains 302 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 269 time to evaluate : 0.984 ------------------------------------------------------------------------------- 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 391 PHE Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 364 ARG 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 E residue 393 LEU Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 143 GLU 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 L residue 48 GLN 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 32 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 145 optimal weight: 0.5980 chunk 244 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 289 optimal weight: 1.9990 chunk 176 optimal weight: 0.6980 chunk 322 optimal weight: 1.9990 chunk 271 optimal weight: 0.9980 chunk 196 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN E 320 HIS E 364 GLN ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 ASN M 318 ASN N 276 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.132519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.110759 restraints weight = 52904.834| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.75 r_work: 0.3415 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33676 Z= 0.145 Angle : 0.573 12.896 46256 Z= 0.307 Chirality : 0.043 0.217 5076 Planarity : 0.004 0.051 5264 Dihedral : 18.343 179.456 6028 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.20 % Allowed : 14.43 % 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 aren not related in a simple way. whole: -0.53 (0.14), residues: 3528 helix: 1.56 (0.16), residues: 1148 sheet: -0.27 (0.19), residues: 736 loop : -1.85 (0.14), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 257 TYR 0.018 0.001 TYR A 392 PHE 0.013 0.002 PHE L 304 TRP 0.014 0.001 TRP E 219 HIS 0.003 0.001 HIS E 160 Details of bonding type rmsd covalent geometry : bond 0.00334 (33676) covalent geometry : angle 0.57290 (46256) hydrogen bonds : bond 0.04157 ( 1235) hydrogen bonds : angle 4.54507 ( 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 359 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 289 time to evaluate : 1.111 Fit side-chains REVERT: A 28 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7286 (mm) REVERT: A 189 GLU cc_start: 0.8168 (tt0) cc_final: 0.7966 (tt0) REVERT: A 190 TYR cc_start: 0.7596 (m-10) cc_final: 0.7224 (m-10) REVERT: A 221 TYR cc_start: 0.5625 (p90) cc_final: 0.4903 (p90) REVERT: A 229 LYS cc_start: 0.6928 (ttpt) cc_final: 0.5743 (pptt) REVERT: A 391 PHE cc_start: 0.6663 (OUTLIER) cc_final: 0.4873 (t80) REVERT: B 8 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6825 (mm-30) REVERT: B 85 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8399 (mtpt) REVERT: B 364 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8476 (mtt-85) REVERT: E 86 LYS cc_start: 0.8206 (ttmm) cc_final: 0.7873 (tmmt) REVERT: E 189 GLU cc_start: 0.7412 (tt0) cc_final: 0.7112 (tt0) REVERT: E 244 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7571 (pp20) REVERT: E 393 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7582 (mt) REVERT: F 453 LYS cc_start: 0.8258 (ttmm) cc_final: 0.7997 (mtmt) REVERT: I 229 LYS cc_start: 0.7969 (mtmt) cc_final: 0.7353 (pttp) REVERT: I 234 HIS cc_start: 0.5851 (t-90) cc_final: 0.5529 (t70) REVERT: L 48 GLN cc_start: 0.7313 (OUTLIER) cc_final: 0.7079 (mm-40) REVERT: L 350 ILE cc_start: 0.6960 (OUTLIER) cc_final: 0.6288 (mp) REVERT: M 45 PHE cc_start: 0.6159 (t80) cc_final: 0.5753 (t80) REVERT: M 261 CYS cc_start: 0.7559 (OUTLIER) cc_final: 0.7220 (m) REVERT: N 1 MET cc_start: 0.8252 (tpp) cc_final: 0.8001 (mmm) REVERT: N 235 LYS cc_start: 0.8627 (mttm) cc_final: 0.8294 (mttt) REVERT: N 275 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7471 (ptt90) REVERT: N 348 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7000 (mt-10) REVERT: N 415 GLU cc_start: 0.6925 (tp30) cc_final: 0.6692 (tp30) REVERT: N 430 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7749 (mp-120) outliers start: 70 outliers final: 29 residues processed: 332 average time/residue: 0.6440 time to fit residues: 251.0144 Evaluate side-chains 316 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 274 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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 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 89 THR Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 364 ARG 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 E residue 393 LEU Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 334 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 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 10 optimal weight: 4.9990 chunk 196 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 108 optimal weight: 3.9990 chunk 135 optimal weight: 0.0570 chunk 304 optimal weight: 0.4980 chunk 14 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 319 optimal weight: 0.9980 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN E 320 HIS E 364 GLN E 370 ASN 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 = 0.3881 r_free = 0.3881 target = 0.132417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.110576 restraints weight = 53277.569| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.75 r_work: 0.3409 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33676 Z= 0.150 Angle : 0.584 13.674 46256 Z= 0.311 Chirality : 0.043 0.212 5076 Planarity : 0.004 0.051 5264 Dihedral : 18.329 179.197 6028 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.20 % Allowed : 14.84 % Favored : 82.96 % 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 aren not related in a simple way. whole: -0.53 (0.14), residues: 3528 helix: 1.55 (0.16), residues: 1148 sheet: -0.25 (0.19), residues: 736 loop : -1.84 (0.14), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 257 TYR 0.014 0.001 TYR A 221 PHE 0.018 0.002 PHE M 158 TRP 0.014 0.001 TRP I 319 HIS 0.003 0.001 HIS E 160 Details of bonding type rmsd covalent geometry : bond 0.00347 (33676) covalent geometry : angle 0.58358 (46256) hydrogen bonds : bond 0.04246 ( 1235) hydrogen bonds : angle 4.56801 ( 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 359 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 289 time to evaluate : 1.028 Fit side-chains revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7286 (mm) REVERT: A 189 GLU cc_start: 0.8165 (tt0) cc_final: 0.7963 (tt0) REVERT: A 190 TYR cc_start: 0.7567 (m-10) cc_final: 0.7195 (m-10) REVERT: A 221 TYR cc_start: 0.5621 (p90) cc_final: 0.4896 (p90) REVERT: A 229 LYS cc_start: 0.6898 (ttpt) cc_final: 0.5716 (pptt) REVERT: A 391 PHE cc_start: 0.6680 (OUTLIER) cc_final: 0.4921 (t80) REVERT: B 8 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6804 (mm-30) REVERT: B 85 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8406 (mtpt) REVERT: B 364 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8472 (mtt-85) REVERT: E 86 LYS cc_start: 0.8206 (ttmm) cc_final: 0.7868 (tmmt) REVERT: E 189 GLU cc_start: 0.7427 (tt0) cc_final: 0.6751 (tt0) REVERT: E 244 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7561 (pp20) REVERT: F 348 GLU cc_start: 0.6298 (OUTLIER) cc_final: 0.5961 (pp20) REVERT: F 356 GLU cc_start: 0.6122 (OUTLIER) cc_final: 0.5805 (mt-10) REVERT: I 234 HIS cc_start: 0.5832 (t-90) cc_final: 0.5496 (t70) REVERT: I 394 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7396 (mt-10) REVERT: L 48 GLN cc_start: 0.7337 (OUTLIER) cc_final: 0.7084 (mm-40) REVERT: L 350 ILE cc_start: 0.6969 (OUTLIER) cc_final: 0.6317 (mp) REVERT: L 435 MET cc_start: 0.7561 (OUTLIER) cc_final: 0.7244 (mtt) REVERT: M 45 PHE cc_start: 0.6161 (t80) cc_final: 0.5781 (t80) REVERT: M 261 CYS cc_start: 0.7559 (OUTLIER) cc_final: 0.7212 (m) REVERT: M 307 LYS cc_start: 0.7631 (mptt) cc_final: 0.7183 (mppt) REVERT: N 1 MET cc_start: 0.8251 (tpp) cc_final: 0.8003 (mmm) REVERT: N 235 LYS cc_start: 0.8629 (mttm) cc_final: 0.8298 (mttt) REVERT: N 275 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7470 (ptt90) REVERT: N 348 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.7008 (mt-10) REVERT: N 415 GLU cc_start: 0.6932 (tp30) cc_final: 0.6694 (tp30) REVERT: N 430 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7747 (mp-120) outliers start: 70 outliers final: 33 residues processed: 330 average time/residue: 0.6575 time to fit residues: 255.7332 Evaluate side-chains 325 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 276 time to evaluate : 1.049 ------------------------------------------------------------------------------- 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 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 89 THR Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 364 ARG 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 253 SER Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 348 GLU Chi-restraints excluded: chain F residue 356 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 204 THR 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 48 GLN Chi-restraints excluded: chain L residue 74 MET 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 435 MET Chi-restraints excluded: chain L residue 449 GLU 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 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: 4.9990 chunk 68 optimal weight: 0.9980 chunk 307 optimal weight: 0.9990 chunk 341 optimal weight: 0.0670 chunk 286 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 294 optimal weight: 5.9990 chunk 360 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 356 optimal weight: 2.9990 chunk 140 optimal weight: 0.5980 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 ASN A 370 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 = 0.3888 r_free = 0.3888 target = 0.132877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.111607 restraints weight = 52980.609| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.81 r_work: 0.3421 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1495 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= 0.141 Angle : 0.574 14.186 46256 Z= 0.307 Chirality : 0.043 0.211 5076 Planarity : 0.004 0.050 5264 Dihedral : 18.290 179.649 6028 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.08 % Allowed : 15.47 % Favored : 82.45 % 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 aren not related in a simple way. whole: -0.48 (0.14), residues: 3528 helix: 1.60 (0.16), residues: 1148 sheet: -0.21 (0.19), residues: 736 loop : -1.83 (0.14), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 257 TYR 0.019 0.001 TYR A 392 PHE 0.015 0.002 PHE M 158 TRP 0.013 0.001 TRP I 319 HIS 0.003 0.001 HIS E 160 Details of bonding type rmsd covalent geometry : bond 0.00323 (33676) covalent geometry : angle 0.57429 (46256) hydrogen bonds : bond 0.04061 ( 1235) hydrogen bonds : angle 4.50635 ( 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 356 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 290 time to evaluate : 1.045 Fit side-chains revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7260 (mm) REVERT: A 133 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6914 (mm-30) REVERT: A 189 GLU cc_start: 0.8145 (tt0) cc_final: 0.7605 (tm-30) REVERT: A 190 TYR cc_start: 0.7527 (m-10) cc_final: 0.7140 (m-10) REVERT: A 221 TYR cc_start: 0.5650 (p90) cc_final: 0.4928 (p90) REVERT: A 391 PHE cc_start: 0.6580 (OUTLIER) cc_final: 0.4838 (t80) REVERT: B 85 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8396 (mtpt) REVERT: B 364 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8476 (mtt-85) REVERT: E 86 LYS cc_start: 0.8186 (ttmm) cc_final: 0.7844 (tmmt) REVERT: E 189 GLU cc_start: 0.7408 (tt0) cc_final: 0.6689 (tt0) REVERT: E 244 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7550 (pp20) REVERT: F 348 GLU cc_start: 0.6356 (OUTLIER) cc_final: 0.6030 (pp20) REVERT: I 193 MET cc_start: 0.4429 (tmt) cc_final: 0.3750 (tmm) REVERT: I 196 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.7234 (mmpt) REVERT: I 229 LYS cc_start: 0.7965 (mtmt) cc_final: 0.7608 (pttp) REVERT: I 234 HIS cc_start: 0.5775 (t-90) cc_final: 0.5460 (t70) REVERT: L 350 ILE cc_start: 0.6938 (OUTLIER) cc_final: 0.6286 (mp) REVERT: L 435 MET cc_start: 0.7564 (OUTLIER) cc_final: 0.7220 (mtt) REVERT: M 45 PHE cc_start: 0.6098 (t80) cc_final: 0.5740 (t80) REVERT: M 261 CYS cc_start: 0.7509 (OUTLIER) cc_final: 0.7209 (m) REVERT: M 307 LYS cc_start: 0.7616 (mptt) cc_final: 0.7162 (mppt) REVERT: N 1 MET cc_start: 0.8246 (tpp) cc_final: 0.7984 (mmm) REVERT: N 235 LYS cc_start: 0.8614 (mttm) cc_final: 0.8278 (mttt) REVERT: N 243 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7576 (mtt180) REVERT: N 275 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7470 (ptt90) REVERT: N 348 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6993 (mt-10) REVERT: N 415 GLU cc_start: 0.6936 (tp30) cc_final: 0.6690 (tp30) REVERT: N 430 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7728 (mp-120) outliers start: 66 outliers final: 33 residues processed: 330 average time/residue: 0.6700 time to fit residues: 259.2305 Evaluate side-chains 328 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 280 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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 A residue 391 PHE Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 85 LYS 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 364 ARG 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 253 SER Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 348 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 196 LYS Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 316 ASP 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 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 435 MET Chi-restraints excluded: chain L residue 449 GLU 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 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 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: 3.9990 chunk 22 optimal weight: 2.9990 chunk 294 optimal weight: 5.9990 chunk 205 optimal weight: 3.9990 chunk 250 optimal weight: 0.9990 chunk 247 optimal weight: 0.0980 chunk 327 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 265 optimal weight: 1.9990 chunk 223 optimal weight: 2.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.129635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.107771 restraints weight = 52732.069| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.74 r_work: 0.3360 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1641 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= 0.263 Angle : 0.717 13.408 46256 Z= 0.379 Chirality : 0.049 0.225 5076 Planarity : 0.005 0.060 5264 Dihedral : 18.477 178.348 6028 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.55 % Allowed : 15.38 % Favored : 82.08 % 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 aren not related in a simple way. whole: -0.88 (0.14), residues: 3528 helix: 1.14 (0.15), residues: 1142 sheet: -0.40 (0.19), residues: 746 loop : -1.98 (0.14), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 257 TYR 0.023 0.002 TYR M 392 PHE 0.024 0.003 PHE I 45 TRP 0.016 0.002 TRP A 192 HIS 0.005 0.001 HIS F 251 Details of bonding type rmsd covalent geometry : bond 0.00631 (33676) covalent geometry : angle 0.71717 (46256) hydrogen bonds : bond 0.05679 ( 1235) hydrogen bonds : angle 4.89124 ( 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 369 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 288 time to evaluate : 1.212 Fit side-chains revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7281 (mm) REVERT: A 190 TYR cc_start: 0.7700 (m-10) cc_final: 0.7391 (m-10) REVERT: A 221 TYR cc_start: 0.5776 (p90) cc_final: 0.4964 (p90) REVERT: A 391 PHE cc_start: 0.7137 (OUTLIER) cc_final: 0.5607 (t80) REVERT: B 1 MET cc_start: 0.8528 (tpt) cc_final: 0.7930 (tpp) REVERT: B 8 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.6870 (mm-30) REVERT: B 85 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8465 (mtpt) REVERT: B 364 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8490 (mtt-85) REVERT: E 121 LYS cc_start: 0.7524 (OUTLIER) cc_final: 0.7191 (mtpt) REVERT: E 189 GLU cc_start: 0.7455 (tt0) cc_final: 0.7078 (tt0) REVERT: E 223 PHE cc_start: 0.6068 (OUTLIER) cc_final: 0.4535 (p90) REVERT: E 244 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7559 (pp20) REVERT: F 348 GLU cc_start: 0.6571 (OUTLIER) cc_final: 0.6226 (pp20) REVERT: F 356 GLU cc_start: 0.6110 (OUTLIER) cc_final: 0.5806 (mt-10) REVERT: I 143 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7257 (tp30) REVERT: I 193 MET cc_start: 0.4602 (tmt) cc_final: 0.4334 (tmm) REVERT: I 234 HIS cc_start: 0.5964 (t-90) cc_final: 0.5658 (t70) REVERT: I 277 MET cc_start: 0.7465 (mmt) cc_final: 0.7260 (mmm) REVERT: I 394 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7401 (mt-10) REVERT: L 400 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.6851 (mt-10) REVERT: M 370 ASN cc_start: 0.7447 (t0) cc_final: 0.7199 (t0) REVERT: N 235 LYS cc_start: 0.8659 (mttm) cc_final: 0.8295 (mttt) REVERT: N 275 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7454 (ptt90) REVERT: N 348 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7154 (mt-10) REVERT: N 415 GLU cc_start: 0.7169 (tp30) cc_final: 0.6913 (tp30) REVERT: N 430 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7829 (mp-120) REVERT: N 443 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8807 (mp) outliers start: 81 outliers final: 37 residues processed: 338 average time/residue: 0.6735 time to fit residues: 265.8439 Evaluate side-chains 334 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 280 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 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 89 THR Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 403 TYR 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 121 LYS Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 348 GLU Chi-restraints excluded: chain F residue 356 GLU 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 143 GLU Chi-restraints excluded: chain I residue 204 THR 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 74 MET 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 369 GLU Chi-restraints excluded: chain L residue 391 THR Chi-restraints excluded: chain L residue 400 GLU Chi-restraints excluded: chain L residue 449 GLU 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 57 LEU 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 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: 1.9990 chunk 203 optimal weight: 0.7980 chunk 265 optimal weight: 1.9990 chunk 133 optimal weight: 0.3980 chunk 65 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 149 optimal weight: 0.5980 chunk 119 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 336 optimal weight: 1.9990 chunk 359 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN E 320 HIS E 364 GLN ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 ASN M 102 GLN 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 = 0.3879 r_free = 0.3879 target = 0.132316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.110466 restraints weight = 53073.776| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.77 r_work: 0.3407 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1524 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= 0.144 Angle : 0.595 15.836 46256 Z= 0.317 Chirality : 0.044 0.331 5076 Planarity : 0.004 0.055 5264 Dihedral : 18.329 179.117 6028 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.70 % Allowed : 16.60 % Favored : 81.70 % 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 aren not related in a simple way. whole: -0.61 (0.14), residues: 3528 helix: 1.49 (0.16), residues: 1144 sheet: -0.28 (0.19), residues: 734 loop : -1.91 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 257 TYR 0.023 0.001 TYR A 392 PHE 0.028 0.002 PHE F 14 TRP 0.015 0.001 TRP M 319 HIS 0.004 0.001 HIS E 160 Details of bonding type rmsd covalent geometry : bond 0.00329 (33676) covalent geometry : angle 0.59494 (46256) hydrogen bonds : bond 0.04175 ( 1235) hydrogen bonds : angle 4.59570 ( 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 337 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 283 time to evaluate : 1.084 Fit side-chains revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7318 (mm) REVERT: A 133 GLU cc_start: 0.7454 (mp0) cc_final: 0.7085 (mm-30) REVERT: A 190 TYR cc_start: 0.7703 (m-10) cc_final: 0.7445 (m-10) REVERT: A 221 TYR cc_start: 0.5810 (p90) cc_final: 0.4835 (p90) REVERT: A 391 PHE cc_start: 0.6871 (OUTLIER) cc_final: 0.5217 (t80) REVERT: B 8 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.6846 (mm-30) REVERT: B 364 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8475 (mtt-85) REVERT: E 86 LYS cc_start: 0.8157 (ttmm) cc_final: 0.7849 (tmmt) REVERT: E 189 GLU cc_start: 0.7412 (tt0) cc_final: 0.7051 (tt0) REVERT: E 244 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7585 (pp20) REVERT: E 257 ARG cc_start: 0.7391 (mmm-85) cc_final: 0.6904 (mmp80) REVERT: F 278 VAL cc_start: 0.7437 (t) cc_final: 0.7222 (t) REVERT: F 348 GLU cc_start: 0.6420 (OUTLIER) cc_final: 0.6074 (pp20) REVERT: F 356 GLU cc_start: 0.6085 (OUTLIER) cc_final: 0.5853 (mt-10) REVERT: I 122 MET cc_start: 0.7485 (ptm) cc_final: 0.7211 (ptm) REVERT: I 193 MET cc_start: 0.4455 (tmt) cc_final: 0.3770 (tmm) REVERT: I 229 LYS cc_start: 0.8147 (mtmt) cc_final: 0.7409 (pttp) REVERT: I 234 HIS cc_start: 0.5802 (t-90) cc_final: 0.5552 (t70) REVERT: I 394 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7386 (mt-10) REVERT: M 261 CYS cc_start: 0.7570 (OUTLIER) cc_final: 0.7222 (m) REVERT: M 307 LYS cc_start: 0.7675 (mptt) cc_final: 0.7221 (mtpt) REVERT: N 235 LYS cc_start: 0.8632 (mttm) cc_final: 0.8296 (mttt) REVERT: N 275 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7452 (ptt90) REVERT: N 348 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7054 (mt-10) REVERT: N 415 GLU cc_start: 0.6979 (tp30) cc_final: 0.6743 (tp30) REVERT: N 430 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7753 (mp-120) REVERT: N 443 ILE cc_start: 0.8979 (OUTLIER) cc_final: 0.8748 (mp) outliers start: 54 outliers final: 35 residues processed: 316 average time/residue: 0.6786 time to fit residues: 251.0328 Evaluate side-chains 326 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 278 time to evaluate : 0.993 ------------------------------------------------------------------------------- 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 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 364 ARG Chi-restraints excluded: chain B residue 415 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 253 SER Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 348 GLU Chi-restraints excluded: chain F residue 356 GLU 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 157 ILE Chi-restraints excluded: chain I residue 204 THR 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 74 MET 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 369 GLU Chi-restraints excluded: chain L residue 391 THR Chi-restraints excluded: chain L residue 449 GLU 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 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 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: 2.9990 chunk 108 optimal weight: 3.9990 chunk 234 optimal weight: 0.0970 chunk 243 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 173 optimal weight: 0.9980 chunk 213 optimal weight: 1.9990 chunk 334 optimal weight: 3.9990 chunk 278 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN E 320 HIS E 364 GLN ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 ASN M 102 GLN N 18 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.129963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.108022 restraints weight = 53140.536| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.76 r_work: 0.3366 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 33676 Z= 0.240 Angle : 0.700 14.451 46256 Z= 0.370 Chirality : 0.048 0.318 5076 Planarity : 0.005 0.061 5264 Dihedral : 18.445 178.451 6028 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 2.14 % Allowed : 16.19 % Favored : 81.67 % 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 aren not related in a simple way. whole: -0.88 (0.14), residues: 3528 helix: 1.17 (0.16), residues: 1142 sheet: -0.39 (0.19), residues: 744 loop : -2.01 (0.14), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 257 TYR 0.023 0.002 TYR M 392 PHE 0.028 0.003 PHE F 14 TRP 0.014 0.002 TRP I 319 HIS 0.005 0.001 HIS F 251 Details of bonding type rmsd covalent geometry : bond 0.00572 (33676) covalent geometry : angle 0.70011 (46256) hydrogen bonds : bond 0.05428 ( 1235) hydrogen bonds : angle 4.85439 ( 3533) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11461.29 seconds wall clock time: 195 minutes 37.99 seconds (11737.99 seconds total)