Starting phenix.real_space_refine on Mon Jul 6 08:52:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y80_39028/07_2026/8y80_39028.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y80_39028/07_2026/8y80_39028.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8y80_39028/07_2026/8y80_39028.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y80_39028/07_2026/8y80_39028.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8y80_39028/07_2026/8y80_39028.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y80_39028/07_2026/8y80_39028.map" } resolution = 3.38 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= 0.002 sd= 0.052 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 124 5.16 5 C 21489 2.51 5 N 5927 2.21 5 O 6765 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34473 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3655 Classifications: {'peptide': 462} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 442} Chain breaks: 5 Chain: "B" Number of atoms: 3629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3629 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 27, 'TRANS': 428} Chain breaks: 2 Chain: "C" 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: "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: 4612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4612 Classifications: {'peptide': 576} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 552} Chain breaks: 2 Chain: "F" Number of atoms: 3629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3629 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 27, 'TRANS': 428} Chain breaks: 2 Chain: "G" 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: "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: 3662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3662 Classifications: {'peptide': 463} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 443} Chain breaks: 5 Chain: "J" Number of atoms: 3629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3629 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 27, 'TRANS': 428} Chain breaks: 2 Chain: "K" 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: "L" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "M" Number of atoms: 4612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4612 Classifications: {'peptide': 576} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 552} Chain breaks: 2 Chain: "N" Number of atoms: 3629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3629 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 27, 'TRANS': 428} Chain breaks: 2 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: "C" 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: "K" 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: 8.09, per 1000 atoms: 0.23 Number of scatterers: 34473 At special positions: 0 Unit cell: (110.818, 152.168, 211.712, 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 124 16.00 P 164 15.00 Mg 4 11.99 O 6765 8.00 N 5927 7.00 C 21489 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.28 Conformation dependent library (CDL) restraints added in 1.6 seconds 7682 Ramachandran restraints generated. 3841 Oldfield, 0 Emsley, 3841 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7318 Finding SS restraints... Secondary structure from input PDB file: 154 helices and 49 sheets defined 41.8% alpha, 18.6% beta 60 base pairs and 104 stacking pairs defined. Time for finding SS restraints: 4.93 Creating SS restraints... Processing helix chain 'A' and resid 5 through 16 removed outlier: 3.792A pdb=" N ASN A 16 " --> pdb=" O HIS A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 145 through 156 removed outlier: 3.599A pdb=" N THR A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 176 Processing helix chain 'A' and resid 207 through 219 removed outlier: 4.363A pdb=" N CYS A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 242 removed outlier: 3.763A pdb=" N ASP A 242 " --> pdb=" O ARG A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 276 removed outlier: 3.785A pdb=" N GLN A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 296 Processing helix chain 'A' and resid 302 through 310 Processing helix chain 'A' and resid 355 through 367 Processing helix chain 'A' and resid 383 through 391 Processing helix chain 'A' and resid 406 through 414 Processing helix chain 'A' and resid 414 through 430 Processing helix chain 'A' and resid 458 through 466 Processing helix chain 'A' and resid 513 through 519 removed outlier: 3.884A pdb=" N ARG A 517 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N GLU A 518 " --> pdb=" O ASP A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 529 Processing helix chain 'A' and resid 532 through 549 Processing helix chain 'B' and resid 21 through 25 Processing helix chain 'B' and resid 29 through 37 Processing helix chain 'B' and resid 39 through 43 removed outlier: 3.900A pdb=" N CYS B 43 " --> pdb=" O TYR B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 59 No H-bonds generated for 'chain 'B' and resid 57 through 59' Processing helix chain 'B' and resid 60 through 71 Processing helix chain 'B' and resid 89 through 94 Processing helix chain 'B' and resid 111 through 120 removed outlier: 3.646A pdb=" N GLY B 115 " --> pdb=" O ASP B 111 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA B 118 " --> pdb=" O HIS B 114 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN B 119 " --> pdb=" O GLY B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 134 Processing helix chain 'B' and resid 135 through 137 No H-bonds generated for 'chain 'B' and resid 135 through 137' Processing helix chain 'B' and resid 151 through 157 removed outlier: 4.514A pdb=" N LYS B 156 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 174 Processing helix chain 'B' and resid 186 through 190 removed outlier: 3.815A pdb=" N ARG B 190 " --> pdb=" O ALA B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 209 removed outlier: 3.788A pdb=" N VAL B 196 " --> pdb=" O CYS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 295 Processing helix chain 'B' and resid 312 through 322 removed outlier: 3.528A pdb=" N GLN B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 429 removed outlier: 4.436A pdb=" N THR B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 459 Processing helix chain 'B' and resid 469 through 473 Processing helix chain 'E' and resid 5 through 16 removed outlier: 3.501A pdb=" N ASN E 16 " --> pdb=" O HIS E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 33 removed outlier: 3.508A pdb=" N ARG E 30 " --> pdb=" O GLY E 27 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY E 33 " --> pdb=" O ARG E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 53 Processing helix chain 'E' and resid 64 through 78 Processing helix chain 'E' and resid 88 through 98 Processing helix chain 'E' and resid 100 through 112 Processing helix chain 'E' and resid 122 through 132 removed outlier: 4.021A pdb=" N ALA E 128 " --> pdb=" O ARG E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 156 Processing helix chain 'E' and resid 168 through 177 Processing helix chain 'E' and resid 198 through 203 removed outlier: 3.787A pdb=" N GLN E 202 " --> pdb=" O PRO E 199 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR E 203 " --> pdb=" O ASP E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 219 removed outlier: 3.540A pdb=" N ARG E 218 " --> pdb=" O ALA E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 243 removed outlier: 3.588A pdb=" N GLN E 243 " --> pdb=" O ALA E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 275 removed outlier: 3.651A pdb=" N GLN E 266 " --> pdb=" O GLU E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 297 Processing helix chain 'E' and resid 302 through 310 removed outlier: 4.130A pdb=" N LYS E 308 " --> pdb=" O ALA E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 367 Processing helix chain 'E' and resid 383 through 391 removed outlier: 3.596A pdb=" N ILE E 387 " --> pdb=" O GLY E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 414 Processing helix chain 'E' and resid 414 through 430 Processing helix chain 'E' and resid 455 through 457 No H-bonds generated for 'chain 'E' and resid 455 through 457' Processing helix chain 'E' and resid 458 through 466 Processing helix chain 'E' and resid 517 through 519 No H-bonds generated for 'chain 'E' and resid 517 through 519' Processing helix chain 'E' and resid 520 through 529 Processing helix chain 'E' and resid 532 through 549 Processing helix chain 'F' and resid 21 through 25 Processing helix chain 'F' and resid 29 through 37 Processing helix chain 'F' and resid 39 through 44 Processing helix chain 'F' and resid 57 through 59 No H-bonds generated for 'chain 'F' and resid 57 through 59' Processing helix chain 'F' and resid 60 through 73 removed outlier: 3.727A pdb=" N LEU F 64 " --> pdb=" O HIS F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 95 Processing helix chain 'F' and resid 111 through 120 removed outlier: 3.564A pdb=" N GLY F 115 " --> pdb=" O ASP F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 132 Processing helix chain 'F' and resid 133 through 139 removed outlier: 4.273A pdb=" N GLN F 139 " --> pdb=" O GLY F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 157 removed outlier: 4.597A pdb=" N LYS F 156 " --> pdb=" O SER F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 174 Processing helix chain 'F' and resid 192 through 208 removed outlier: 4.401A pdb=" N VAL F 196 " --> pdb=" O CYS F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 295 Processing helix chain 'F' and resid 312 through 323 removed outlier: 3.726A pdb=" N PHE F 323 " --> pdb=" O ALA F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 429 removed outlier: 4.073A pdb=" N THR F 421 " --> pdb=" O GLY F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 443 through 459 Processing helix chain 'F' and resid 469 through 473 Processing helix chain 'I' and resid 5 through 16 Processing helix chain 'I' and resid 121 through 132 Processing helix chain 'I' and resid 145 through 156 removed outlier: 3.599A pdb=" N THR I 149 " --> pdb=" O ASP I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 176 Processing helix chain 'I' and resid 207 through 219 removed outlier: 4.133A pdb=" N CYS I 211 " --> pdb=" O GLU I 207 " (cutoff:3.500A) Processing helix chain 'I' and resid 230 through 243 removed outlier: 3.511A pdb=" N GLN I 243 " --> pdb=" O ALA I 239 " (cutoff:3.500A) Processing helix chain 'I' and resid 262 through 275 removed outlier: 3.809A pdb=" N GLN I 266 " --> pdb=" O GLU I 262 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 296 Processing helix chain 'I' and resid 302 through 310 Processing helix chain 'I' and resid 355 through 367 Processing helix chain 'I' and resid 383 through 391 Processing helix chain 'I' and resid 406 through 414 Processing helix chain 'I' and resid 414 through 430 Processing helix chain 'I' and resid 458 through 466 Processing helix chain 'I' and resid 513 through 519 removed outlier: 3.882A pdb=" N ARG I 517 " --> pdb=" O LEU I 514 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N GLU I 518 " --> pdb=" O ASP I 515 " (cutoff:3.500A) Processing helix chain 'I' and resid 520 through 529 Processing helix chain 'I' and resid 532 through 549 Processing helix chain 'J' and resid 21 through 25 Processing helix chain 'J' and resid 29 through 37 Processing helix chain 'J' and resid 39 through 43 removed outlier: 3.889A pdb=" N CYS J 43 " --> pdb=" O TYR J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 59 No H-bonds generated for 'chain 'J' and resid 57 through 59' Processing helix chain 'J' and resid 60 through 72 removed outlier: 3.704A pdb=" N LEU J 64 " --> pdb=" O HIS J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 94 Processing helix chain 'J' and resid 111 through 120 removed outlier: 3.647A pdb=" N GLY J 115 " --> pdb=" O ASP J 111 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA J 118 " --> pdb=" O HIS J 114 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN J 119 " --> pdb=" O GLY J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 134 Processing helix chain 'J' and resid 135 through 137 No H-bonds generated for 'chain 'J' and resid 135 through 137' Processing helix chain 'J' and resid 151 through 157 removed outlier: 4.515A pdb=" N LYS J 156 " --> pdb=" O SER J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 165 through 174 Processing helix chain 'J' and resid 175 through 177 No H-bonds generated for 'chain 'J' and resid 175 through 177' Processing helix chain 'J' and resid 186 through 189 Processing helix chain 'J' and resid 192 through 209 removed outlier: 3.789A pdb=" N VAL J 196 " --> pdb=" O CYS J 192 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY J 209 " --> pdb=" O TYR J 205 " (cutoff:3.500A) Processing helix chain 'J' and resid 276 through 295 removed outlier: 3.607A pdb=" N SER J 294 " --> pdb=" O LEU J 290 " (cutoff:3.500A) Processing helix chain 'J' and resid 312 through 322 removed outlier: 3.528A pdb=" N GLN J 317 " --> pdb=" O GLU J 313 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER J 322 " --> pdb=" O GLY J 318 " (cutoff:3.500A) Processing helix chain 'J' and resid 417 through 429 removed outlier: 4.438A pdb=" N THR J 421 " --> pdb=" O GLY J 417 " (cutoff:3.500A) Processing helix chain 'J' and resid 443 through 459 Processing helix chain 'J' and resid 469 through 473 Processing helix chain 'M' and resid 5 through 16 Processing helix chain 'M' and resid 27 through 31 Processing helix chain 'M' and resid 36 through 53 removed outlier: 3.595A pdb=" N LEU M 51 " --> pdb=" O ARG M 47 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 78 Processing helix chain 'M' and resid 88 through 98 Processing helix chain 'M' and resid 100 through 112 Processing helix chain 'M' and resid 120 through 132 Processing helix chain 'M' and resid 145 through 156 Processing helix chain 'M' and resid 168 through 176 Processing helix chain 'M' and resid 198 through 203 removed outlier: 3.788A pdb=" N GLN M 202 " --> pdb=" O PRO M 199 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR M 203 " --> pdb=" O ASP M 200 " (cutoff:3.500A) Processing helix chain 'M' and resid 205 through 219 removed outlier: 3.598A pdb=" N ILE M 217 " --> pdb=" O LEU M 213 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG M 218 " --> pdb=" O ALA M 214 " (cutoff:3.500A) Processing helix chain 'M' and resid 230 through 242 Processing helix chain 'M' and resid 262 through 275 removed outlier: 3.574A pdb=" N GLN M 266 " --> pdb=" O GLU M 262 " (cutoff:3.500A) Processing helix chain 'M' and resid 286 through 297 Processing helix chain 'M' and resid 302 through 310 removed outlier: 4.129A pdb=" N LYS M 308 " --> pdb=" O ALA M 304 " (cutoff:3.500A) Processing helix chain 'M' and resid 355 through 367 Processing helix chain 'M' and resid 383 through 391 removed outlier: 3.596A pdb=" N ILE M 387 " --> pdb=" O GLY M 383 " (cutoff:3.500A) Processing helix chain 'M' and resid 406 through 414 Processing helix chain 'M' and resid 414 through 430 Processing helix chain 'M' and resid 455 through 457 No H-bonds generated for 'chain 'M' and resid 455 through 457' Processing helix chain 'M' and resid 458 through 466 Processing helix chain 'M' and resid 517 through 519 No H-bonds generated for 'chain 'M' and resid 517 through 519' Processing helix chain 'M' and resid 520 through 529 Processing helix chain 'M' and resid 532 through 549 Processing helix chain 'N' and resid 21 through 25 Processing helix chain 'N' and resid 29 through 37 Processing helix chain 'N' and resid 39 through 44 Processing helix chain 'N' and resid 57 through 59 No H-bonds generated for 'chain 'N' and resid 57 through 59' Processing helix chain 'N' and resid 60 through 73 removed outlier: 3.727A pdb=" N LEU N 64 " --> pdb=" O HIS N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 89 through 95 Processing helix chain 'N' and resid 111 through 120 removed outlier: 3.564A pdb=" N GLY N 115 " --> pdb=" O ASP N 111 " (cutoff:3.500A) Processing helix chain 'N' and resid 121 through 132 Processing helix chain 'N' and resid 133 through 138 Processing helix chain 'N' and resid 151 through 157 removed outlier: 4.596A pdb=" N LYS N 156 " --> pdb=" O SER N 153 " (cutoff:3.500A) Processing helix chain 'N' and resid 165 through 174 Processing helix chain 'N' and resid 184 through 188 Processing helix chain 'N' and resid 195 through 208 Processing helix chain 'N' and resid 276 through 295 Processing helix chain 'N' and resid 312 through 323 removed outlier: 3.727A pdb=" N PHE N 323 " --> pdb=" O ALA N 319 " (cutoff:3.500A) Processing helix chain 'N' and resid 417 through 429 removed outlier: 4.074A pdb=" N THR N 421 " --> pdb=" O GLY N 417 " (cutoff:3.500A) Processing helix chain 'N' and resid 443 through 459 Processing helix chain 'N' and resid 469 through 473 Processing sheet with id=AA1, first strand: chain 'A' and resid 161 through 162 removed outlier: 6.574A pdb=" N TYR A 162 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N MET A 20 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N PHE A 139 " --> pdb=" O MET A 20 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N TRP A 22 " --> pdb=" O PHE A 139 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU A 221 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N THR A 254 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL A 223 " --> pdb=" O THR A 254 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LEU A 251 " --> pdb=" O TYR A 280 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL A 282 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N TRP A 253 " --> pdb=" O VAL A 282 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 579 through 580 Processing sheet with id=AA3, first strand: chain 'A' and resid 335 through 338 removed outlier: 4.528A pdb=" N LEU A 501 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N HIS A 444 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 335 through 338 removed outlier: 4.528A pdb=" N LEU A 501 " --> pdb=" O VAL A 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 371 through 373 removed outlier: 6.899A pdb=" N ILE A 343 " --> pdb=" O TYR A 403 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N TYR A 403 " --> pdb=" O ILE A 343 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N CYS A 345 " --> pdb=" O GLN A 401 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLN A 401 " --> pdb=" O CYS A 345 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL A 347 " --> pdb=" O ILE A 399 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE A 399 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N THR A 349 " --> pdb=" O ASN A 397 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 558 through 561 removed outlier: 3.528A pdb=" N ALA A 569 " --> pdb=" O CYS A 561 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 12 through 13 removed outlier: 6.812A pdb=" N GLU B 373 " --> pdb=" O LEU B 369 " (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 98 through 99 removed outlier: 7.112A pdb=" N VAL B 50 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N CYS B 107 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N TYR B 54 " --> pdb=" O CYS B 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 98 through 99 removed outlier: 7.112A pdb=" N VAL B 50 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ILE B 183 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL B 148 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 159 through 160 Processing sheet with id=AB3, first strand: chain 'E' and resid 138 through 140 removed outlier: 8.094A pdb=" N PHE E 139 " --> pdb=" O MET E 20 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N TRP E 22 " --> pdb=" O PHE E 139 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N MET E 21 " --> pdb=" O VAL E 222 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N SER E 224 " --> pdb=" O MET E 21 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N PHE E 23 " --> pdb=" O SER E 224 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LEU E 221 " --> pdb=" O TYR E 252 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N THR E 254 " --> pdb=" O LEU E 221 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL E 223 " --> pdb=" O THR E 254 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 160 through 162 Processing sheet with id=AB5, first strand: chain 'E' and resid 330 through 332 removed outlier: 3.909A pdb=" N LEU E 331 " --> pdb=" O SER E 580 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER E 580 " --> pdb=" O LEU E 331 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'E' and resid 335 through 338 removed outlier: 4.631A pdb=" N LEU E 501 " --> pdb=" O VAL E 338 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N HIS E 444 " --> pdb=" O ILE E 492 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 335 through 338 removed outlier: 4.631A pdb=" N LEU E 501 " --> pdb=" O VAL E 338 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 371 through 373 removed outlier: 6.625A pdb=" N ILE E 343 " --> pdb=" O TYR E 403 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N TYR E 403 " --> pdb=" O ILE E 343 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N CYS E 345 " --> pdb=" O GLN E 401 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N GLN E 401 " --> pdb=" O CYS E 345 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL E 347 " --> pdb=" O ILE E 399 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE E 399 " --> pdb=" O VAL E 347 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR E 349 " --> pdb=" O ASN E 397 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 558 through 561 removed outlier: 3.616A pdb=" N ALA E 569 " --> pdb=" O CYS E 561 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 12 through 13 removed outlier: 3.989A pdb=" N SER F 12 " --> pdb=" O TYR F 366 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR F 366 " --> pdb=" O SER F 12 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU F 375 " --> pdb=" O PRO F 368 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU F 331 " --> pdb=" O PHE F 412 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE F 303 " --> pdb=" O GLU F 330 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL F 332 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ILE F 305 " --> pdb=" O VAL F 332 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE F 334 " --> pdb=" O ILE F 305 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LYS F 307 " --> pdb=" O ILE F 334 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 19 through 20 Processing sheet with id=AC3, first strand: chain 'F' and resid 50 through 51 removed outlier: 6.601A pdb=" N VAL F 50 " --> pdb=" O VAL F 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'F' and resid 106 through 108 removed outlier: 5.901A pdb=" N TYR F 54 " --> pdb=" O CYS F 107 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 159 through 160 removed outlier: 3.926A pdb=" N TYR F 160 " --> pdb=" O PHE F 163 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 381 through 382 Processing sheet with id=AC7, first strand: chain 'I' and resid 137 through 139 Processing sheet with id=AC8, first strand: chain 'I' and resid 221 through 224 removed outlier: 6.098A pdb=" N LEU I 251 " --> pdb=" O TYR I 280 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL I 282 " --> pdb=" O LEU I 251 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N TRP I 253 " --> pdb=" O VAL I 282 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 579 through 580 Processing sheet with id=AD1, first strand: chain 'I' and resid 335 through 338 removed outlier: 4.529A pdb=" N LEU I 501 " --> pdb=" O VAL I 338 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N HIS I 444 " --> pdb=" O ILE I 492 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 335 through 338 removed outlier: 4.529A pdb=" N LEU I 501 " --> pdb=" O VAL I 338 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 371 through 373 removed outlier: 6.898A pdb=" N ILE I 343 " --> pdb=" O TYR I 403 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N TYR I 403 " --> pdb=" O ILE I 343 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N CYS I 345 " --> pdb=" O GLN I 401 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N GLN I 401 " --> pdb=" O CYS I 345 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL I 347 " --> pdb=" O ILE I 399 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE I 399 " --> pdb=" O VAL I 347 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N THR I 349 " --> pdb=" O ASN I 397 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 558 through 561 removed outlier: 3.528A pdb=" N ALA I 569 " --> pdb=" O CYS I 561 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 12 through 13 removed outlier: 6.813A pdb=" N GLU J 373 " --> pdb=" O LEU J 369 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA J 223 " --> pdb=" O LYS J 302 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 19 through 20 Processing sheet with id=AD7, first strand: chain 'J' and resid 98 through 99 removed outlier: 7.113A pdb=" N VAL J 50 " --> pdb=" O VAL J 99 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N CYS J 107 " --> pdb=" O LEU J 52 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N TYR J 54 " --> pdb=" O CYS J 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'J' and resid 98 through 99 removed outlier: 7.113A pdb=" N VAL J 50 " --> pdb=" O VAL J 99 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ILE J 183 " --> pdb=" O LEU J 146 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL J 148 " --> pdb=" O ILE J 183 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 159 through 160 Processing sheet with id=AE1, first strand: chain 'M' and resid 20 through 24 removed outlier: 6.336A pdb=" N MET M 21 " --> pdb=" O VAL M 222 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N SER M 224 " --> pdb=" O MET M 21 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N PHE M 23 " --> pdb=" O SER M 224 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N LEU M 221 " --> pdb=" O TYR M 252 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N THR M 254 " --> pdb=" O LEU M 221 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL M 223 " --> pdb=" O THR M 254 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 161 through 162 Processing sheet with id=AE3, first strand: chain 'M' and resid 330 through 332 removed outlier: 3.911A pdb=" N LEU M 331 " --> pdb=" O SER M 580 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER M 580 " --> pdb=" O LEU M 331 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'M' and resid 335 through 338 removed outlier: 4.630A pdb=" N LEU M 501 " --> pdb=" O VAL M 338 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N HIS M 444 " --> pdb=" O ILE M 492 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 335 through 338 removed outlier: 4.630A pdb=" N LEU M 501 " --> pdb=" O VAL M 338 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 371 through 373 removed outlier: 6.624A pdb=" N ILE M 343 " --> pdb=" O TYR M 403 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N TYR M 403 " --> pdb=" O ILE M 343 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N CYS M 345 " --> pdb=" O GLN M 401 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N GLN M 401 " --> pdb=" O CYS M 345 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL M 347 " --> pdb=" O ILE M 399 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE M 399 " --> pdb=" O VAL M 347 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR M 349 " --> pdb=" O ASN M 397 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 558 through 561 removed outlier: 3.615A pdb=" N ALA M 569 " --> pdb=" O CYS M 561 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 12 through 13 removed outlier: 3.989A pdb=" N SER N 12 " --> pdb=" O TYR N 366 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR N 366 " --> pdb=" O SER N 12 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU N 375 " --> pdb=" O PRO N 368 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU N 331 " --> pdb=" O PHE N 412 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE N 303 " --> pdb=" O GLU N 330 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL N 332 " --> pdb=" O ILE N 303 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ILE N 305 " --> pdb=" O VAL N 332 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE N 334 " --> pdb=" O ILE N 305 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LYS N 307 " --> pdb=" O ILE N 334 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS N 244 " --> pdb=" O TYR N 260 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'N' and resid 19 through 20 Processing sheet with id=AF1, first strand: chain 'N' and resid 98 through 99 removed outlier: 6.602A pdb=" N VAL N 50 " --> pdb=" O VAL N 99 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N CYS N 107 " --> pdb=" O LEU N 52 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N TYR N 54 " --> pdb=" O CYS N 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'N' and resid 98 through 99 removed outlier: 6.602A pdb=" N VAL N 50 " --> pdb=" O VAL N 99 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ARG N 51 " --> pdb=" O VAL N 145 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LEU N 147 " --> pdb=" O ARG N 51 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA N 53 " --> pdb=" O LEU N 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'N' and resid 159 through 160 removed outlier: 3.928A pdb=" N TYR N 160 " --> pdb=" O PHE N 163 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'N' and resid 381 through 382 1384 hydrogen bonds defined for protein. 3858 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 144 hydrogen bonds 272 hydrogen bond angles 0 basepair planarities 60 basepair parallelities 104 stacking parallelities Total time for adding SS restraints: 9.57 Time building geometry restraints manager: 4.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 5231 1.30 - 1.43: 10514 1.43 - 1.56: 19364 1.56 - 1.69: 324 1.69 - 1.82: 190 Bond restraints: 35623 Sorted by residual: bond pdb=" CA ALA E 240 " pdb=" C ALA E 240 " ideal model delta sigma weight residual 1.522 1.453 0.069 1.36e-02 5.41e+03 2.58e+01 bond pdb=" C ALA E 240 " pdb=" O ALA E 240 " ideal model delta sigma weight residual 1.236 1.174 0.062 1.25e-02 6.40e+03 2.46e+01 bond pdb=" C VAL N 196 " pdb=" O VAL N 196 " ideal model delta sigma weight residual 1.236 1.179 0.057 1.19e-02 7.06e+03 2.27e+01 bond pdb=" C ALA E 215 " pdb=" O ALA E 215 " ideal model delta sigma weight residual 1.237 1.184 0.053 1.17e-02 7.31e+03 2.05e+01 bond pdb=" CA LYS M 193 " pdb=" C LYS M 193 " ideal model delta sigma weight residual 1.524 1.464 0.060 1.35e-02 5.49e+03 1.98e+01 ... (remaining 35618 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.89: 48665 3.89 - 7.77: 312 7.77 - 11.66: 29 11.66 - 15.55: 2 15.55 - 19.43: 2 Bond angle restraints: 49010 Sorted by residual: angle pdb=" N ASN N 195 " pdb=" CA ASN N 195 " pdb=" C ASN N 195 " ideal model delta sigma weight residual 111.24 96.99 14.25 1.29e+00 6.01e-01 1.22e+02 angle pdb=" N HIS E 209 " pdb=" CA HIS E 209 " pdb=" C HIS E 209 " ideal model delta sigma weight residual 111.28 102.28 9.00 1.09e+00 8.42e-01 6.82e+01 angle pdb=" C GLN N 191 " pdb=" N CYS N 192 " pdb=" CA CYS N 192 " ideal model delta sigma weight residual 121.54 105.88 15.66 1.91e+00 2.74e-01 6.73e+01 angle pdb=" C ASN M 245 " pdb=" CA ASN M 245 " pdb=" CB ASN M 245 " ideal model delta sigma weight residual 111.89 122.25 -10.36 1.42e+00 4.96e-01 5.33e+01 angle pdb=" C ILE E 217 " pdb=" N ARG E 218 " pdb=" CA ARG E 218 " ideal model delta sigma weight residual 120.29 130.52 -10.23 1.42e+00 4.96e-01 5.19e+01 ... (remaining 49005 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.01: 19702 34.01 - 68.02: 1390 68.02 - 102.03: 82 102.03 - 136.04: 0 136.04 - 170.05: 8 Dihedral angle restraints: 21182 sinusoidal: 9817 harmonic: 11365 Sorted by residual: dihedral pdb=" C ASN M 245 " pdb=" N ASN M 245 " pdb=" CA ASN M 245 " pdb=" CB ASN M 245 " ideal model delta harmonic sigma weight residual -122.60 -138.25 15.65 0 2.50e+00 1.60e-01 3.92e+01 dihedral pdb=" C ASN N 195 " pdb=" N ASN N 195 " pdb=" CA ASN N 195 " pdb=" CB ASN N 195 " ideal model delta harmonic sigma weight residual -122.60 -108.32 -14.28 0 2.50e+00 1.60e-01 3.26e+01 dihedral pdb=" CA ASN I 142 " pdb=" C ASN I 142 " pdb=" N PHE I 143 " pdb=" CA PHE I 143 " ideal model delta harmonic sigma weight residual 180.00 152.05 27.95 0 5.00e+00 4.00e-02 3.12e+01 ... (remaining 21179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 5150 0.111 - 0.221: 275 0.221 - 0.332: 40 0.332 - 0.442: 9 0.442 - 0.553: 2 Chirality restraints: 5476 Sorted by residual: chirality pdb=" CA ARG N 193 " pdb=" N ARG N 193 " pdb=" C ARG N 193 " pdb=" CB ARG N 193 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.64e+00 chirality pdb=" CA ASN M 245 " pdb=" N ASN M 245 " pdb=" C ASN M 245 " pdb=" CB ASN M 245 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.19e+00 chirality pdb=" CA HIS B 60 " pdb=" N HIS B 60 " pdb=" C HIS B 60 " pdb=" CB HIS B 60 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.12e+00 ... (remaining 5473 not shown) Planarity restraints: 5685 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU N 188 " 0.031 2.00e-02 2.50e+03 6.24e-02 3.90e+01 pdb=" C LEU N 188 " -0.108 2.00e-02 2.50e+03 pdb=" O LEU N 188 " 0.041 2.00e-02 2.50e+03 pdb=" N THR N 189 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS N 192 " 0.027 2.00e-02 2.50e+03 5.39e-02 2.90e+01 pdb=" C CYS N 192 " -0.093 2.00e-02 2.50e+03 pdb=" O CYS N 192 " 0.036 2.00e-02 2.50e+03 pdb=" N ARG N 193 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG F 138 " -0.020 2.00e-02 2.50e+03 4.32e-02 1.86e+01 pdb=" C ARG F 138 " 0.075 2.00e-02 2.50e+03 pdb=" O ARG F 138 " -0.029 2.00e-02 2.50e+03 pdb=" N GLN F 139 " -0.026 2.00e-02 2.50e+03 ... (remaining 5682 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 199 2.35 - 2.99: 18536 2.99 - 3.62: 54031 3.62 - 4.26: 83727 4.26 - 4.90: 137374 Nonbonded interactions: 293867 Sorted by model distance: nonbonded pdb=" OH TYR E 168 " pdb=" N GLN M 192 " model vdw 1.710 3.120 nonbonded pdb=" NH1 ARG J 301 " pdb=" O LYS M 59 " model vdw 1.711 3.120 nonbonded pdb=" OE1 GLN B 246 " pdb=" OG SER B 287 " model vdw 1.718 3.040 nonbonded pdb=" O ASP B 249 " pdb=" NE2 HIS B 295 " model vdw 1.720 3.120 nonbonded pdb=" ND2 ASN E 120 " pdb=" OD2 ASP E 288 " model vdw 1.722 3.120 ... (remaining 293862 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'I' and resid 4 through 585) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 5 through 473) selection = chain 'J' selection = (chain 'N' and resid 5 through 473) } ncs_group { reference = (chain 'C' and resid 1 through 21) selection = chain 'G' selection = (chain 'K' and resid 1 through 21) selection = chain 'O' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' selection = chain 'P' } ncs_group { reference = chain 'E' selection = chain 'M' } 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: 9.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.540 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 39.350 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6582 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 : 0.006 0.313 35626 Z= 0.454 Angle : 0.871 19.435 49010 Z= 0.596 Chirality : 0.059 0.553 5476 Planarity : 0.006 0.099 5685 Dihedral : 20.436 170.047 13864 Min Nonbonded Distance : 1.710 Molprobity Statistics. All-atom Clashscore : 32.08 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.89 % Favored : 94.69 % Rotamer: Outliers : 4.01 % Allowed : 29.93 % Favored : 66.06 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.14), residues: 3841 helix: 0.80 (0.14), residues: 1449 sheet: -0.56 (0.20), residues: 720 loop : -0.73 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 411 TYR 0.021 0.001 TYR B 260 PHE 0.041 0.002 PHE E 247 TRP 0.019 0.001 TRP A 253 HIS 0.011 0.001 HIS E 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.37 (35623) covalent geometry : angle 0.87085 / 0.60 (49010) hydrogen bonds : bond 0.16617 / 10.92 ( 1468) hydrogen bonds : angle 6.83117 / 4.87 ( 4130) Misc. bond : bond 0.28433 / 14.25 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7682 Ramachandran restraints generated. 3841 Oldfield, 0 Emsley, 3841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7682 Ramachandran restraints generated. 3841 Oldfield, 0 Emsley, 3841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1165 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 1031 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASN cc_start: 0.8745 (OUTLIER) cc_final: 0.8494 (p0) REVERT: A 21 MET cc_start: 0.7619 (OUTLIER) cc_final: 0.7380 (ttt) REVERT: A 143 PHE cc_start: 0.6216 (OUTLIER) cc_final: 0.5559 (t80) REVERT: A 184 LYS cc_start: 0.7774 (mttt) cc_final: 0.7544 (pttt) REVERT: A 373 THR cc_start: 0.8049 (t) cc_final: 0.7719 (m) REVERT: A 444 HIS cc_start: 0.5566 (m-70) cc_final: 0.5208 (m-70) REVERT: B 176 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8655 (mp) REVERT: E 40 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8119 (mm) REVERT: F 44 PHE cc_start: 0.6898 (p90) cc_final: 0.6670 (p90) REVERT: F 61 MET cc_start: 0.6293 (mtp) cc_final: 0.6073 (mtp) REVERT: F 133 MET cc_start: 0.6573 (mtt) cc_final: 0.6187 (mtt) REVERT: F 185 ASP cc_start: 0.7106 (OUTLIER) cc_final: 0.6765 (p0) REVERT: F 383 MET cc_start: 0.6999 (mmm) cc_final: 0.6752 (tpp) REVERT: F 459 THR cc_start: 0.8804 (m) cc_final: 0.8360 (p) REVERT: I 22 TRP cc_start: 0.7673 (m100) cc_final: 0.7256 (m100) REVERT: I 208 ILE cc_start: 0.7303 (mm) cc_final: 0.7071 (mm) REVERT: I 234 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.6732 (tpp) REVERT: I 495 GLU cc_start: 0.3678 (tp30) cc_final: 0.3227 (tp30) REVERT: I 518 GLU cc_start: 0.6639 (pm20) cc_final: 0.6124 (tp30) REVERT: J 346 ASP cc_start: 0.6238 (m-30) cc_final: 0.5958 (t0) REVERT: J 376 LEU cc_start: 0.8485 (tp) cc_final: 0.8106 (tp) REVERT: M 47 ARG cc_start: 0.6919 (OUTLIER) cc_final: 0.6689 (mtp85) REVERT: M 62 ILE cc_start: 0.7972 (tp) cc_final: 0.7438 (tp) REVERT: M 374 TYR cc_start: 0.4541 (t80) cc_final: 0.4279 (t80) REVERT: M 576 ARG cc_start: 0.3986 (ttt180) cc_final: 0.3150 (ptt-90) outliers start: 134 outliers final: 63 residues processed: 1137 average time/residue: 0.2389 time to fit residues: 423.0698 Evaluate side-chains 611 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 540 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 218 ARG Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 207 LYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain E residue 58 GLN Chi-restraints excluded: chain E residue 60 HIS Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 120 ASN Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 143 PHE Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 163 HIS Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 210 LYS Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain F residue 139 GLN Chi-restraints excluded: chain F residue 140 LYS Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 190 ARG Chi-restraints excluded: chain F residue 191 GLN Chi-restraints excluded: chain I residue 139 PHE Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 234 MET Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 244 ASN Chi-restraints excluded: chain I residue 265 VAL Chi-restraints excluded: chain I residue 329 PRO Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain J residue 41 SER Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 190 ARG Chi-restraints excluded: chain J residue 303 ILE Chi-restraints excluded: chain M residue 47 ARG Chi-restraints excluded: chain M residue 49 TYR Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 147 ILE Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 153 ASP Chi-restraints excluded: chain M residue 154 ILE Chi-restraints excluded: chain M residue 155 SER Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 165 GLU Chi-restraints excluded: chain M residue 192 GLN Chi-restraints excluded: chain M residue 241 ILE Chi-restraints excluded: chain M residue 245 ASN Chi-restraints excluded: chain M residue 251 LEU Chi-restraints excluded: chain N residue 185 ASP Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 195 ASN Chi-restraints excluded: chain N residue 197 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.0870 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 8.9990 chunk 401 optimal weight: 9.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 0.9980 overall best weight: 2.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 243 GLN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 GLN A 341 GLN A 437 HIS ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 HIS B 181 GLN B 195 ASN B 296 ASN ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 538 GLN ** F 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 ASN ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 177 ASN F 278 GLN F 336 GLN ** F 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 436 ASN ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 243 GLN ** I 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 ASN J 181 GLN J 292 GLN J 296 ASN ** J 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 379 GLN ** J 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 450 GLN ** M 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 192 GLN M 266 GLN N 139 GLN N 195 ASN N 295 HIS N 296 ASN ** N 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 379 GLN ** N 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.174345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.147583 restraints weight = 65430.938| |-----------------------------------------------------------------------------| r_work (start): 0.4155 rms_B_bonded: 2.73 r_work: 0.4007 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 35626 Z= 0.237 Angle : 0.779 12.569 49010 Z= 0.413 Chirality : 0.048 0.331 5476 Planarity : 0.006 0.094 5685 Dihedral : 18.391 171.722 6620 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.74 % Favored : 95.24 % Rotamer: Outliers : 7.87 % Allowed : 27.93 % Favored : 64.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.13), residues: 3841 helix: 0.28 (0.13), residues: 1486 sheet: -0.72 (0.19), residues: 730 loop : -0.89 (0.15), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 516 TYR 0.042 0.003 TYR E 92 PHE 0.037 0.003 PHE E 287 TRP 0.035 0.002 TRP F 154 HIS 0.020 0.002 HIS E 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.24 (35623) covalent geometry : angle 0.77897 / 0.41 (49010) hydrogen bonds : bond 0.06082 / 4.09 ( 1468) hydrogen bonds : angle 5.46683 / 3.87 ( 4130) Misc. bond : bond 0.02147 / 1.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7682 Ramachandran restraints generated. 3841 Oldfield, 0 Emsley, 3841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7682 Ramachandran restraints generated. 3841 Oldfield, 0 Emsley, 3841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 898 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 263 poor density : 635 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASN cc_start: 0.8264 (OUTLIER) cc_final: 0.7794 (p0) REVERT: A 143 PHE cc_start: 0.6617 (OUTLIER) cc_final: 0.5945 (t80) REVERT: A 184 LYS cc_start: 0.7702 (mttt) cc_final: 0.7192 (ptmt) REVERT: A 270 THR cc_start: 0.8015 (m) cc_final: 0.7812 (p) REVERT: A 331 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8546 (pt) REVERT: A 373 THR cc_start: 0.8327 (t) cc_final: 0.8094 (m) REVERT: B 275 LEU cc_start: 0.7875 (mp) cc_final: 0.6976 (mp) REVERT: B 361 VAL cc_start: 0.7435 (OUTLIER) cc_final: 0.7215 (p) REVERT: E 16 ASN cc_start: 0.8307 (p0) cc_final: 0.8070 (p0) REVERT: E 210 LYS cc_start: 0.7362 (OUTLIER) cc_final: 0.7158 (mmtm) REVERT: E 287 PHE cc_start: 0.7174 (OUTLIER) cc_final: 0.6503 (t80) REVERT: E 352 SER cc_start: 0.4576 (OUTLIER) cc_final: 0.4276 (m) REVERT: F 133 MET cc_start: 0.6748 (mtt) cc_final: 0.6369 (mtt) REVERT: F 185 ASP cc_start: 0.7119 (OUTLIER) cc_final: 0.6811 (p0) REVERT: F 190 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.5961 (tmm160) REVERT: F 296 ASN cc_start: 0.8367 (OUTLIER) cc_final: 0.8138 (m110) REVERT: I 22 TRP cc_start: 0.8086 (m100) cc_final: 0.7611 (m100) REVERT: I 218 ARG cc_start: 0.7102 (OUTLIER) cc_final: 0.6827 (ttm170) REVERT: I 326 LYS cc_start: 0.7257 (pttm) cc_final: 0.7030 (pttp) REVERT: I 345 CYS cc_start: 0.6165 (OUTLIER) cc_final: 0.5954 (p) REVERT: I 518 GLU cc_start: 0.7375 (pm20) cc_final: 0.6185 (tp30) REVERT: I 536 SER cc_start: 0.7926 (t) cc_final: 0.7205 (m) REVERT: J 178 LEU cc_start: 0.6625 (OUTLIER) cc_final: 0.6175 (pp) REVERT: J 190 ARG cc_start: 0.7200 (OUTLIER) cc_final: 0.6692 (mmm160) REVERT: J 197 MET cc_start: 0.6606 (mmm) cc_final: 0.6235 (tpp) REVERT: J 295 HIS cc_start: 0.7690 (m90) cc_final: 0.7444 (m90) REVERT: J 376 LEU cc_start: 0.8863 (tp) cc_final: 0.8350 (tp) REVERT: J 465 GLU cc_start: 0.6894 (mp0) cc_final: 0.6266 (mm-30) REVERT: M 75 MET cc_start: 0.7732 (OUTLIER) cc_final: 0.7314 (mmt) REVERT: M 94 GLU cc_start: 0.7846 (pt0) cc_final: 0.7505 (pt0) REVERT: M 374 TYR cc_start: 0.4855 (t80) cc_final: 0.3967 (t80) REVERT: M 514 LEU cc_start: 0.7993 (mm) cc_final: 0.7748 (mt) REVERT: M 576 ARG cc_start: 0.4113 (ttt180) cc_final: 0.3071 (ptt-90) REVERT: N 133 MET cc_start: 0.7820 (mtt) cc_final: 0.7615 (mtt) REVERT: N 240 TYR cc_start: 0.7125 (m-80) cc_final: 0.6641 (m-80) REVERT: N 340 TRP cc_start: 0.8064 (m100) cc_final: 0.7341 (m100) REVERT: N 397 GLU cc_start: 0.5069 (mp0) cc_final: 0.4836 (mp0) REVERT: N 473 MET cc_start: 0.6322 (ptt) cc_final: 0.6111 (ptt) outliers start: 263 outliers final: 117 residues processed: 827 average time/residue: 0.2102 time to fit residues: 285.9178 Evaluate side-chains 644 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 512 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 60 HIS Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 143 PHE Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 190 ARG Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 210 LYS Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 287 PHE Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 490 VAL Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 560 SER Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 40 TYR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 139 GLN Chi-restraints excluded: chain F residue 140 LYS Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 190 ARG Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 139 PHE Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 143 PHE Chi-restraints excluded: chain I residue 144 ASP Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 218 ARG Chi-restraints excluded: chain I residue 233 VAL Chi-restraints excluded: chain I residue 234 MET Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 244 ASN Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 333 THR Chi-restraints excluded: chain I residue 345 CYS Chi-restraints excluded: chain I residue 580 SER Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain J residue 169 ILE Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain J residue 190 ARG Chi-restraints excluded: chain J residue 221 ASP Chi-restraints excluded: chain J residue 242 THR Chi-restraints excluded: chain J residue 244 CYS Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 334 ILE Chi-restraints excluded: chain J residue 362 ASP Chi-restraints excluded: chain J residue 369 LEU Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 426 LEU Chi-restraints excluded: chain J residue 464 ASN Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain M residue 154 ILE Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 208 ILE Chi-restraints excluded: chain M residue 381 LEU Chi-restraints excluded: chain M residue 508 GLU Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain N residue 139 GLN Chi-restraints excluded: chain N residue 182 ILE Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 255 PHE Chi-restraints excluded: chain N residue 293 SER Chi-restraints excluded: chain N residue 345 VAL Chi-restraints excluded: chain N residue 370 THR Chi-restraints excluded: chain N residue 429 THR Chi-restraints excluded: chain N residue 454 ASP Chi-restraints excluded: chain N residue 466 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 63 optimal weight: 0.2980 chunk 25 optimal weight: 4.9990 chunk 289 optimal weight: 2.9990 chunk 290 optimal weight: 0.8980 chunk 141 optimal weight: 0.0980 chunk 205 optimal weight: 9.9990 chunk 235 optimal weight: 0.0670 chunk 227 optimal weight: 10.0000 chunk 352 optimal weight: 7.9990 chunk 262 optimal weight: 7.9990 chunk 361 optimal weight: 5.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN B 184 ASN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 HIS B 458 GLN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 386 ASN I 7 ASN ** I 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 195 ASN J 387 GLN J 392 GLN M 12 HIS M 123 HIS N 177 ASN N 317 GLN ** N 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.174153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.147381 restraints weight = 64839.636| |-----------------------------------------------------------------------------| r_work (start): 0.4162 rms_B_bonded: 2.76 r_work: 0.4009 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 35626 Z= 0.155 Angle : 0.678 12.385 49010 Z= 0.352 Chirality : 0.043 0.299 5476 Planarity : 0.005 0.070 5685 Dihedral : 18.133 171.607 6537 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 5.66 % Allowed : 28.82 % Favored : 65.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.13), residues: 3841 helix: 0.42 (0.13), residues: 1507 sheet: -0.68 (0.19), residues: 732 loop : -0.85 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 313 TYR 0.036 0.002 TYR N 448 PHE 0.034 0.002 PHE A 532 TRP 0.021 0.001 TRP N 433 HIS 0.014 0.001 HIS N 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (35623) covalent geometry : angle 0.67752 / 0.35 (49010) hydrogen bonds : bond 0.05459 / 3.66 ( 1468) hydrogen bonds : angle 5.13976 / 3.64 ( 4130) Misc. bond : bond 0.00321 / 0.15 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7682 Ramachandran restraints generated. 3841 Oldfield, 0 Emsley, 3841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7682 Ramachandran restraints generated. 3841 Oldfield, 0 Emsley, 3841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 562 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASN cc_start: 0.8263 (OUTLIER) cc_final: 0.7926 (p0) REVERT: A 143 PHE cc_start: 0.6529 (OUTLIER) cc_final: 0.5853 (t80) REVERT: A 184 LYS cc_start: 0.7749 (mttt) cc_final: 0.7198 (ptmt) REVERT: A 270 THR cc_start: 0.8025 (m) cc_final: 0.7824 (p) REVERT: A 426 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7653 (mm) REVERT: B 361 VAL cc_start: 0.7446 (OUTLIER) cc_final: 0.7187 (p) REVERT: E 16 ASN cc_start: 0.8248 (OUTLIER) cc_final: 0.7979 (p0) REVERT: E 287 PHE cc_start: 0.7558 (OUTLIER) cc_final: 0.7013 (t80) REVERT: E 352 SER cc_start: 0.4667 (OUTLIER) cc_final: 0.4406 (m) REVERT: E 387 ILE cc_start: 0.7989 (mm) cc_final: 0.7561 (tp) REVERT: E 448 ILE cc_start: 0.4058 (mp) cc_final: 0.3835 (mp) REVERT: F 185 ASP cc_start: 0.7070 (OUTLIER) cc_final: 0.6805 (p0) REVERT: F 190 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.5992 (tmm160) REVERT: I 16 ASN cc_start: 0.7168 (OUTLIER) cc_final: 0.6943 (p0) REVERT: I 22 TRP cc_start: 0.7927 (m100) cc_final: 0.7597 (m100) REVERT: I 139 PHE cc_start: 0.7227 (OUTLIER) cc_final: 0.6094 (p90) REVERT: I 223 VAL cc_start: 0.7189 (p) cc_final: 0.6788 (p) REVERT: I 418 LYS cc_start: 0.6989 (tptm) cc_final: 0.6653 (tppt) REVERT: I 518 GLU cc_start: 0.7367 (pm20) cc_final: 0.6233 (tp30) REVERT: I 536 SER cc_start: 0.7954 (t) cc_final: 0.7232 (m) REVERT: J 376 LEU cc_start: 0.8890 (tp) cc_final: 0.8411 (tp) REVERT: J 465 GLU cc_start: 0.6861 (mp0) cc_final: 0.6239 (mm-30) REVERT: M 94 GLU cc_start: 0.7855 (pt0) cc_final: 0.7502 (pt0) REVERT: M 374 TYR cc_start: 0.4946 (t80) cc_final: 0.3968 (t80) REVERT: M 508 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6677 (pm20) REVERT: M 514 LEU cc_start: 0.8062 (mm) cc_final: 0.7794 (mt) REVERT: M 576 ARG cc_start: 0.4097 (ttt180) cc_final: 0.3112 (ptt-90) REVERT: N 63 LYS cc_start: 0.7912 (mttp) cc_final: 0.7665 (mttp) REVERT: N 133 MET cc_start: 0.7885 (mtt) cc_final: 0.7468 (mtt) REVERT: N 218 TRP cc_start: 0.5980 (OUTLIER) cc_final: 0.5708 (m-90) REVERT: N 397 GLU cc_start: 0.5430 (mp0) cc_final: 0.4886 (mp0) outliers start: 189 outliers final: 105 residues processed: 701 average time/residue: 0.2027 time to fit residues: 236.8909 Evaluate side-chains 621 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 503 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 543 TRP Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 60 HIS Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 143 PHE Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 190 ARG Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 287 PHE Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 490 VAL Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 560 SER Chi-restraints excluded: chain E residue 572 GLU Chi-restraints excluded: chain F residue 40 TYR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 139 GLN Chi-restraints excluded: chain F residue 140 LYS Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 190 ARG Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 289 HIS Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 16 ASN Chi-restraints excluded: chain I residue 139 PHE Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 143 PHE Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 219 PHE Chi-restraints excluded: chain I residue 233 VAL Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 244 ASN Chi-restraints excluded: chain I residue 281 LEU Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 333 THR Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 491 SER Chi-restraints excluded: chain I residue 547 LEU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain J residue 221 ASP Chi-restraints excluded: chain J residue 242 THR Chi-restraints excluded: chain J residue 244 CYS Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 288 LEU Chi-restraints excluded: chain J residue 329 ILE Chi-restraints excluded: chain J residue 362 ASP Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 426 LEU Chi-restraints excluded: chain J residue 442 LEU Chi-restraints excluded: chain J residue 464 ASN Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain M residue 154 ILE Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 224 SER Chi-restraints excluded: chain M residue 275 LYS Chi-restraints excluded: chain M residue 298 VAL Chi-restraints excluded: chain M residue 508 GLU Chi-restraints excluded: chain M residue 573 ILE Chi-restraints excluded: chain N residue 58 THR Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 182 ILE Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 218 TRP Chi-restraints excluded: chain N residue 245 SER Chi-restraints excluded: chain N residue 370 THR Chi-restraints excluded: chain N residue 466 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 335 optimal weight: 5.9990 chunk 322 optimal weight: 5.9990 chunk 245 optimal weight: 6.9990 chunk 393 optimal weight: 6.9990 chunk 146 optimal weight: 10.0000 chunk 28 optimal weight: 0.4980 chunk 309 optimal weight: 2.9990 chunk 397 optimal weight: 0.3980 chunk 357 optimal weight: 1.9990 chunk 257 optimal weight: 0.3980 chunk 389 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN B 177 ASN B 458 GLN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 GLN E 245 ASN E 365 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 GLN F 139 GLN F 238 GLN ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 GLN ** F 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 436 ASN I 245 ASN ** I 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 49 GLN J 82 ASN ** J 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 306 HIS N 317 GLN ** N 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.172964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.145737 restraints weight = 64145.651| |-----------------------------------------------------------------------------| r_work (start): 0.4139 rms_B_bonded: 2.78 r_work: 0.3998 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35626 Z= 0.146 Angle : 0.654 13.062 49010 Z= 0.338 Chirality : 0.043 0.295 5476 Planarity : 0.004 0.054 5685 Dihedral : 18.045 171.275 6517 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 5.36 % Allowed : 29.36 % Favored : 65.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.14), residues: 3841 helix: 0.56 (0.14), residues: 1485 sheet: -0.63 (0.19), residues: 772 loop : -0.87 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 115 TYR 0.045 0.002 TYR J 448 PHE 0.025 0.002 PHE I 9 TRP 0.031 0.002 TRP F 154 HIS 0.010 0.001 HIS E 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (35623) covalent geometry : angle 0.65406 / 0.34 (49010) hydrogen bonds : bond 0.05118 / 3.43 ( 1468) hydrogen bonds : angle 4.99866 / 3.54 ( 4130) Misc. bond : bond 0.01089 / 0.52 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7682 Ramachandran restraints generated. 3841 Oldfield, 0 Emsley, 3841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7682 Ramachandran restraints generated. 3841 Oldfield, 0 Emsley, 3841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 733 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 554 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASN cc_start: 0.8412 (OUTLIER) cc_final: 0.8101 (p0) REVERT: A 143 PHE cc_start: 0.6415 (OUTLIER) cc_final: 0.5784 (t80) REVERT: A 184 LYS cc_start: 0.7792 (mttt) cc_final: 0.7149 (ptmt) REVERT: A 219 PHE cc_start: 0.7840 (OUTLIER) cc_final: 0.6993 (p90) REVERT: A 237 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9059 (tt) REVERT: A 270 THR cc_start: 0.8133 (m) cc_final: 0.7898 (p) REVERT: A 349 THR cc_start: 0.6894 (OUTLIER) cc_final: 0.6510 (p) REVERT: A 444 HIS cc_start: 0.5982 (m90) cc_final: 0.5725 (m170) REVERT: B 361 VAL cc_start: 0.7476 (OUTLIER) cc_final: 0.7215 (p) REVERT: E 16 ASN cc_start: 0.8344 (OUTLIER) cc_final: 0.8074 (p0) REVERT: E 213 LEU cc_start: 0.8523 (mt) cc_final: 0.8076 (mt) REVERT: E 287 PHE cc_start: 0.7707 (OUTLIER) cc_final: 0.7229 (t80) REVERT: E 352 SER cc_start: 0.4563 (OUTLIER) cc_final: 0.4363 (m) REVERT: E 387 ILE cc_start: 0.8007 (mm) cc_final: 0.7565 (tp) REVERT: E 418 LYS cc_start: 0.5308 (tptm) cc_final: 0.4669 (tptm) REVERT: F 238 GLN cc_start: 0.6841 (OUTLIER) cc_final: 0.6263 (mp10) REVERT: I 22 TRP cc_start: 0.7939 (m100) cc_final: 0.7666 (m100) REVERT: I 139 PHE cc_start: 0.7168 (OUTLIER) cc_final: 0.6321 (p90) REVERT: I 223 VAL cc_start: 0.7064 (OUTLIER) cc_final: 0.6735 (p) REVERT: I 504 MET cc_start: 0.7471 (mmm) cc_final: 0.7186 (mmm) REVERT: I 518 GLU cc_start: 0.7478 (pm20) cc_final: 0.6277 (tp30) REVERT: I 536 SER cc_start: 0.7849 (t) cc_final: 0.7136 (m) REVERT: J 34 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7788 (mp) REVERT: J 178 LEU cc_start: 0.6712 (OUTLIER) cc_final: 0.6256 (pp) REVERT: J 197 MET cc_start: 0.6657 (mmt) cc_final: 0.6452 (tpp) REVERT: J 376 LEU cc_start: 0.8961 (tp) cc_final: 0.8457 (tp) REVERT: J 465 GLU cc_start: 0.7065 (mp0) cc_final: 0.6394 (mm-30) REVERT: M 57 TYR cc_start: 0.7749 (t80) cc_final: 0.7523 (t80) REVERT: M 94 GLU cc_start: 0.7997 (pt0) cc_final: 0.7675 (pt0) REVERT: M 374 TYR cc_start: 0.4841 (t80) cc_final: 0.4544 (t80) REVERT: M 508 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.6655 (mp0) REVERT: M 514 LEU cc_start: 0.8105 (mm) cc_final: 0.7833 (mt) REVERT: M 576 ARG cc_start: 0.4143 (ttt180) cc_final: 0.3142 (ptt-90) REVERT: N 63 LYS cc_start: 0.8044 (mttp) cc_final: 0.7782 (mttp) REVERT: N 133 MET cc_start: 0.8032 (mtt) cc_final: 0.7543 (mtt) REVERT: N 158 PHE cc_start: 0.6946 (m-10) cc_final: 0.6329 (m-80) REVERT: N 197 MET cc_start: 0.7382 (OUTLIER) cc_final: 0.7157 (mpp) REVERT: N 211 ILE cc_start: 0.8278 (pt) cc_final: 0.8029 (pp) REVERT: N 288 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7468 (pt) REVERT: N 367 GLN cc_start: 0.6482 (pt0) cc_final: 0.6085 (pm20) REVERT: N 397 GLU cc_start: 0.5518 (mp0) cc_final: 0.5141 (mp0) outliers start: 179 outliers final: 107 residues processed: 684 average time/residue: 0.1893 time to fit residues: 218.0384 Evaluate side-chains 632 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 508 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 543 TRP Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 60 HIS Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 287 PHE Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 380 PHE Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 490 VAL Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 560 SER Chi-restraints excluded: chain E residue 572 GLU Chi-restraints excluded: chain F residue 40 TYR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 140 LYS Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 238 GLN Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain I residue 139 PHE Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 143 PHE Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 219 PHE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 233 VAL Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 281 LEU Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 333 THR Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 580 SER Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain J residue 221 ASP Chi-restraints excluded: chain J residue 242 THR Chi-restraints excluded: chain J residue 244 CYS Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 329 ILE Chi-restraints excluded: chain J residue 362 ASP Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 426 LEU Chi-restraints excluded: chain J residue 442 LEU Chi-restraints excluded: chain J residue 464 ASN Chi-restraints excluded: chain J residue 466 ILE Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 77 SER Chi-restraints excluded: chain M residue 93 PHE Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 154 ILE Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 208 ILE Chi-restraints excluded: chain M residue 224 SER Chi-restraints excluded: chain M residue 275 LYS Chi-restraints excluded: chain M residue 298 VAL Chi-restraints excluded: chain M residue 508 GLU Chi-restraints excluded: chain M residue 573 ILE Chi-restraints excluded: chain N residue 58 THR Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 182 ILE Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 288 LEU Chi-restraints excluded: chain N residue 370 THR Chi-restraints excluded: chain N residue 463 VAL Chi-restraints excluded: chain N residue 466 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 118 optimal weight: 1.9990 chunk 218 optimal weight: 7.9990 chunk 200 optimal weight: 9.9990 chunk 285 optimal weight: 0.5980 chunk 127 optimal weight: 9.9990 chunk 69 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 273 optimal weight: 10.0000 chunk 134 optimal weight: 9.9990 chunk 233 optimal weight: 6.9990 chunk 190 optimal weight: 9.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 HIS ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 ASN B 458 GLN E 58 GLN ** E 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 HIS ** F 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 238 GLN ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 GLN ** F 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 436 ASN I 16 ASN ** I 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 49 GLN J 82 ASN ** J 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 191 GLN N 317 GLN N 367 GLN N 419 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.165874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.138465 restraints weight = 64467.112| |-----------------------------------------------------------------------------| r_work (start): 0.4044 rms_B_bonded: 2.78 r_work: 0.3890 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.4854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 35626 Z= 0.214 Angle : 0.695 12.339 49010 Z= 0.362 Chirality : 0.045 0.316 5476 Planarity : 0.005 0.051 5685 Dihedral : 18.103 172.544 6499 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 6.29 % Allowed : 28.67 % Favored : 65.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.13), residues: 3841 helix: 0.44 (0.13), residues: 1482 sheet: -0.82 (0.19), residues: 770 loop : -0.98 (0.15), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 51 TYR 0.029 0.002 TYR J 448 PHE 0.020 0.002 PHE A 219 TRP 0.039 0.002 TRP I 295 HIS 0.009 0.002 HIS E 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.21 (35623) covalent geometry : angle 0.69463 / 0.36 (49010) hydrogen bonds : bond 0.05235 / 3.50 ( 1468) hydrogen bonds : angle 5.05249 / 3.57 ( 4130) Misc. bond : bond 0.01224 / 0.58 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7682 Ramachandran restraints generated. 3841 Oldfield, 0 Emsley, 3841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7682 Ramachandran restraints generated. 3841 Oldfield, 0 Emsley, 3841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 542 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASN cc_start: 0.8437 (OUTLIER) cc_final: 0.8176 (p0) REVERT: A 143 PHE cc_start: 0.6465 (OUTLIER) cc_final: 0.5856 (t80) REVERT: A 184 LYS cc_start: 0.7902 (mttt) cc_final: 0.7234 (tttt) REVERT: A 218 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.7049 (mtp-110) REVERT: A 237 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.9043 (tt) REVERT: A 278 ARG cc_start: 0.7917 (ttm110) cc_final: 0.7529 (mmp80) REVERT: A 480 ASN cc_start: 0.7184 (m-40) cc_final: 0.6971 (m-40) REVERT: B 131 GLN cc_start: 0.7597 (mt0) cc_final: 0.7278 (mm-40) REVERT: B 409 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8773 (mt) REVERT: B 448 TYR cc_start: 0.7788 (t80) cc_final: 0.7548 (t80) REVERT: E 16 ASN cc_start: 0.8507 (OUTLIER) cc_final: 0.8254 (p0) REVERT: E 121 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7774 (tp) REVERT: E 287 PHE cc_start: 0.7973 (OUTLIER) cc_final: 0.7573 (t80) REVERT: E 352 SER cc_start: 0.4431 (OUTLIER) cc_final: 0.4230 (m) REVERT: E 387 ILE cc_start: 0.8046 (mm) cc_final: 0.7594 (tp) REVERT: E 418 LYS cc_start: 0.5646 (tptm) cc_final: 0.4910 (tptm) REVERT: E 448 ILE cc_start: 0.4373 (mp) cc_final: 0.4152 (mp) REVERT: I 22 TRP cc_start: 0.7992 (m100) cc_final: 0.7596 (m100) REVERT: I 139 PHE cc_start: 0.7254 (OUTLIER) cc_final: 0.6699 (p90) REVERT: I 445 TYR cc_start: 0.6877 (m-80) cc_final: 0.6653 (m-80) REVERT: I 504 MET cc_start: 0.7487 (mmm) cc_final: 0.7092 (mmm) REVERT: I 518 GLU cc_start: 0.7599 (pm20) cc_final: 0.6532 (tp30) REVERT: J 34 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7895 (mp) REVERT: J 178 LEU cc_start: 0.6741 (OUTLIER) cc_final: 0.6236 (pp) REVERT: J 197 MET cc_start: 0.7265 (mmt) cc_final: 0.7049 (tpp) REVERT: J 465 GLU cc_start: 0.7317 (mp0) cc_final: 0.6538 (mm-30) REVERT: M 94 GLU cc_start: 0.7851 (pt0) cc_final: 0.7500 (pt0) REVERT: M 374 TYR cc_start: 0.4947 (t80) cc_final: 0.4555 (t80) REVERT: M 508 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6843 (mp0) REVERT: M 514 LEU cc_start: 0.8077 (mm) cc_final: 0.7798 (mt) REVERT: M 530 TYR cc_start: 0.5739 (m-80) cc_final: 0.5511 (m-80) REVERT: N 133 MET cc_start: 0.8054 (mtt) cc_final: 0.7597 (mtt) REVERT: N 193 ARG cc_start: 0.6699 (OUTLIER) cc_final: 0.5731 (tpp-160) REVERT: N 197 MET cc_start: 0.7489 (OUTLIER) cc_final: 0.7255 (mpp) REVERT: N 222 GLU cc_start: 0.6519 (OUTLIER) cc_final: 0.6287 (pm20) outliers start: 210 outliers final: 140 residues processed: 698 average time/residue: 0.1961 time to fit residues: 228.0309 Evaluate side-chains 651 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 495 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 218 ARG Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 543 TRP Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 60 HIS Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 190 ARG Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 287 PHE Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 380 PHE Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 435 ILE Chi-restraints excluded: chain E residue 443 THR Chi-restraints excluded: chain E residue 490 VAL Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 560 SER Chi-restraints excluded: chain F residue 40 TYR Chi-restraints excluded: chain F residue 140 LYS Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 245 SER Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 19 HIS Chi-restraints excluded: chain I residue 139 PHE Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 143 PHE Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 233 VAL Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 281 LEU Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 333 THR Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 426 LEU Chi-restraints excluded: chain I residue 547 LEU Chi-restraints excluded: chain I residue 557 VAL Chi-restraints excluded: chain I residue 580 SER Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain J residue 221 ASP Chi-restraints excluded: chain J residue 242 THR Chi-restraints excluded: chain J residue 244 CYS Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 329 ILE Chi-restraints excluded: chain J residue 362 ASP Chi-restraints excluded: chain J residue 378 THR Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 426 LEU Chi-restraints excluded: chain J residue 442 LEU Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 63 ASN Chi-restraints excluded: chain M residue 77 SER Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 154 ILE Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain M residue 224 SER Chi-restraints excluded: chain M residue 298 VAL Chi-restraints excluded: chain M residue 365 GLN Chi-restraints excluded: chain M residue 402 TYR Chi-restraints excluded: chain M residue 440 ARG Chi-restraints excluded: chain M residue 508 GLU Chi-restraints excluded: chain M residue 573 ILE Chi-restraints excluded: chain N residue 41 SER Chi-restraints excluded: chain N residue 58 THR Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 182 ILE Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 193 ARG Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 222 GLU Chi-restraints excluded: chain N residue 293 SER Chi-restraints excluded: chain N residue 336 GLN Chi-restraints excluded: chain N residue 370 THR Chi-restraints excluded: chain N residue 421 THR Chi-restraints excluded: chain N residue 463 VAL Chi-restraints excluded: chain N residue 466 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 249 optimal weight: 0.9980 chunk 236 optimal weight: 1.9990 chunk 157 optimal weight: 0.4980 chunk 40 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 35 optimal weight: 0.0570 chunk 88 optimal weight: 0.6980 chunk 321 optimal weight: 0.7980 chunk 397 optimal weight: 5.9990 chunk 231 optimal weight: 6.9990 chunk 323 optimal weight: 0.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 HIS ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 HIS ** F 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 GLN ** F 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 436 ASN I 16 ASN I 297 GLN I 341 GLN ** J 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 186 HIS N 191 GLN N 317 GLN N 389 ASN N 419 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.168117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.140561 restraints weight = 63929.513| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 2.73 r_work: 0.3928 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.5059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 35626 Z= 0.140 Angle : 0.663 20.093 49010 Z= 0.342 Chirality : 0.043 0.300 5476 Planarity : 0.004 0.083 5685 Dihedral : 18.034 172.665 6497 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 5.30 % Allowed : 29.78 % Favored : 64.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.14), residues: 3841 helix: 0.64 (0.14), residues: 1481 sheet: -0.75 (0.19), residues: 786 loop : -0.91 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 431 TYR 0.024 0.002 TYR J 448 PHE 0.019 0.002 PHE E 287 TRP 0.036 0.002 TRP M 510 HIS 0.010 0.001 HIS E 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (35623) covalent geometry : angle 0.66255 / 0.34 (49010) hydrogen bonds : bond 0.05026 / 3.36 ( 1468) hydrogen bonds : angle 4.96686 / 3.49 ( 4130) Misc. bond : bond 0.02194 / 1.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7682 Ramachandran restraints generated. 3841 Oldfield, 0 Emsley, 3841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7682 Ramachandran restraints generated. 3841 Oldfield, 0 Emsley, 3841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 529 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASN cc_start: 0.8323 (OUTLIER) cc_final: 0.8066 (p0) REVERT: A 143 PHE cc_start: 0.6445 (OUTLIER) cc_final: 0.5833 (t80) REVERT: A 184 LYS cc_start: 0.7892 (mttt) cc_final: 0.7232 (tttt) REVERT: A 237 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.9065 (tt) REVERT: A 278 ARG cc_start: 0.7887 (ttm110) cc_final: 0.7407 (mmp80) REVERT: A 395 GLU cc_start: 0.6813 (pt0) cc_final: 0.6244 (mm-30) REVERT: E 16 ASN cc_start: 0.8326 (OUTLIER) cc_final: 0.8102 (p0) REVERT: E 287 PHE cc_start: 0.7914 (OUTLIER) cc_final: 0.7540 (t80) REVERT: E 352 SER cc_start: 0.4482 (OUTLIER) cc_final: 0.4278 (m) REVERT: E 387 ILE cc_start: 0.8039 (mm) cc_final: 0.7606 (tp) REVERT: E 418 LYS cc_start: 0.5534 (tptm) cc_final: 0.4847 (tptm) REVERT: F 408 MET cc_start: 0.7310 (mmm) cc_final: 0.7034 (tpt) REVERT: I 22 TRP cc_start: 0.7983 (m100) cc_final: 0.7725 (m100) REVERT: I 139 PHE cc_start: 0.7345 (OUTLIER) cc_final: 0.6927 (p90) REVERT: I 219 PHE cc_start: 0.6145 (OUTLIER) cc_final: 0.5532 (p90) REVERT: I 504 MET cc_start: 0.7439 (mmm) cc_final: 0.7006 (mmm) REVERT: I 518 GLU cc_start: 0.7528 (pm20) cc_final: 0.6458 (tp30) REVERT: J 34 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7896 (mp) REVERT: J 333 GLN cc_start: 0.7417 (OUTLIER) cc_final: 0.7099 (tp-100) REVERT: J 465 GLU cc_start: 0.7212 (mp0) cc_final: 0.6446 (mm-30) REVERT: M 94 GLU cc_start: 0.7811 (pt0) cc_final: 0.7511 (pt0) REVERT: M 374 TYR cc_start: 0.4859 (t80) cc_final: 0.4469 (t80) REVERT: M 514 LEU cc_start: 0.8162 (mm) cc_final: 0.7894 (mt) REVERT: M 530 TYR cc_start: 0.5711 (m-80) cc_final: 0.5454 (m-80) REVERT: M 576 ARG cc_start: 0.4754 (ttt-90) cc_final: 0.2921 (ptt-90) REVERT: N 133 MET cc_start: 0.7910 (mtt) cc_final: 0.7463 (mtt) REVERT: N 193 ARG cc_start: 0.6779 (OUTLIER) cc_final: 0.5920 (tpp80) REVERT: N 197 MET cc_start: 0.7412 (OUTLIER) cc_final: 0.7169 (mpp) outliers start: 177 outliers final: 125 residues processed: 655 average time/residue: 0.1861 time to fit residues: 206.3601 Evaluate side-chains 627 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 490 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 543 TRP Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 60 HIS Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 83 GLN Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 190 ARG Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 287 PHE Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 380 PHE Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 435 ILE Chi-restraints excluded: chain E residue 490 VAL Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 560 SER Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 40 TYR Chi-restraints excluded: chain F residue 140 LYS Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 221 ASP Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 289 HIS Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 19 HIS Chi-restraints excluded: chain I residue 139 PHE Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 143 PHE Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 219 PHE Chi-restraints excluded: chain I residue 233 VAL Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 281 LEU Chi-restraints excluded: chain I residue 306 ASP Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 333 THR Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 583 VAL Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 221 ASP Chi-restraints excluded: chain J residue 244 CYS Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 329 ILE Chi-restraints excluded: chain J residue 333 GLN Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 426 LEU Chi-restraints excluded: chain J residue 442 LEU Chi-restraints excluded: chain J residue 464 ASN Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 93 PHE Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 208 ILE Chi-restraints excluded: chain M residue 224 SER Chi-restraints excluded: chain M residue 298 VAL Chi-restraints excluded: chain M residue 365 GLN Chi-restraints excluded: chain M residue 402 TYR Chi-restraints excluded: chain M residue 557 VAL Chi-restraints excluded: chain M residue 573 ILE Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 182 ILE Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 193 ARG Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 317 GLN Chi-restraints excluded: chain N residue 370 THR Chi-restraints excluded: chain N residue 382 VAL Chi-restraints excluded: chain N residue 463 VAL Chi-restraints excluded: chain N residue 466 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 181 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 289 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 309 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 347 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 225 optimal weight: 5.9990 chunk 27 optimal weight: 0.0870 chunk 302 optimal weight: 0.8980 overall best weight: 1.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 HIS ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 GLN ** F 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 ASN J 82 ASN ** J 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 158 HIS N 191 GLN N 419 HIS N 434 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.164656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.137050 restraints weight = 64609.091| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 2.82 r_work: 0.3852 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.5391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 35626 Z= 0.182 Angle : 0.673 15.277 49010 Z= 0.347 Chirality : 0.044 0.307 5476 Planarity : 0.004 0.051 5685 Dihedral : 18.054 173.588 6495 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 6.02 % Allowed : 29.51 % Favored : 64.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.14), residues: 3841 helix: 0.64 (0.14), residues: 1469 sheet: -0.90 (0.19), residues: 798 loop : -0.96 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 362 TYR 0.030 0.002 TYR B 205 PHE 0.022 0.002 PHE I 139 TRP 0.049 0.002 TRP I 295 HIS 0.019 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (35623) covalent geometry : angle 0.67340 / 0.35 (49010) hydrogen bonds : bond 0.05030 / 3.38 ( 1468) hydrogen bonds : angle 4.96032 / 3.48 ( 4130) Misc. bond : bond 0.00623 / 0.30 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7682 Ramachandran restraints generated. 3841 Oldfield, 0 Emsley, 3841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7682 Ramachandran restraints generated. 3841 Oldfield, 0 Emsley, 3841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 201 poor density : 513 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASN cc_start: 0.8442 (OUTLIER) cc_final: 0.8183 (p0) REVERT: A 143 PHE cc_start: 0.6460 (OUTLIER) cc_final: 0.5819 (t80) REVERT: A 184 LYS cc_start: 0.7900 (mttt) cc_final: 0.7203 (tttt) REVERT: A 218 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.6985 (mtp-110) REVERT: A 237 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9063 (tt) REVERT: A 278 ARG cc_start: 0.7993 (ttm110) cc_final: 0.7497 (mmp80) REVERT: A 345 CYS cc_start: 0.7796 (p) cc_final: 0.7532 (p) REVERT: A 395 GLU cc_start: 0.6926 (pt0) cc_final: 0.6207 (mm-30) REVERT: A 480 ASN cc_start: 0.7182 (m-40) cc_final: 0.6958 (m-40) REVERT: B 107 CYS cc_start: 0.6393 (OUTLIER) cc_final: 0.5810 (t) REVERT: B 131 GLN cc_start: 0.7721 (mt0) cc_final: 0.7349 (mm-40) REVERT: B 375 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8338 (mp) REVERT: B 448 TYR cc_start: 0.7808 (t80) cc_final: 0.7549 (t80) REVERT: E 16 ASN cc_start: 0.8486 (OUTLIER) cc_final: 0.8263 (p0) REVERT: E 121 ILE cc_start: 0.8020 (OUTLIER) cc_final: 0.7792 (tp) REVERT: E 352 SER cc_start: 0.4720 (OUTLIER) cc_final: 0.4443 (m) REVERT: E 387 ILE cc_start: 0.8110 (mm) cc_final: 0.7690 (tp) REVERT: E 418 LYS cc_start: 0.5662 (tptm) cc_final: 0.4981 (tptm) REVERT: I 22 TRP cc_start: 0.7954 (m100) cc_final: 0.7649 (m100) REVERT: I 345 CYS cc_start: 0.5644 (p) cc_final: 0.5415 (p) REVERT: I 504 MET cc_start: 0.7382 (mmm) cc_final: 0.6985 (mmm) REVERT: I 518 GLU cc_start: 0.7664 (pm20) cc_final: 0.6653 (tp30) REVERT: J 34 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7981 (mp) REVERT: J 81 THR cc_start: 0.7570 (p) cc_final: 0.7292 (m) REVERT: J 280 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.6300 (ttm) REVERT: J 304 PHE cc_start: 0.7728 (m-80) cc_final: 0.7504 (m-80) REVERT: J 315 GLU cc_start: 0.7188 (tt0) cc_final: 0.6091 (tm-30) REVERT: J 333 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.7133 (tp-100) REVERT: J 465 GLU cc_start: 0.7370 (mp0) cc_final: 0.6540 (mm-30) REVERT: M 94 GLU cc_start: 0.7858 (pt0) cc_final: 0.7531 (pt0) REVERT: M 374 TYR cc_start: 0.4988 (t80) cc_final: 0.4480 (t80) REVERT: M 508 GLU cc_start: 0.6818 (OUTLIER) cc_final: 0.6608 (pm20) REVERT: M 514 LEU cc_start: 0.8109 (mm) cc_final: 0.7816 (mt) REVERT: M 530 TYR cc_start: 0.5886 (m-80) cc_final: 0.5595 (m-80) REVERT: N 133 MET cc_start: 0.8033 (mtt) cc_final: 0.7574 (mtt) REVERT: N 193 ARG cc_start: 0.6816 (OUTLIER) cc_final: 0.6002 (tpp-160) REVERT: N 197 MET cc_start: 0.7432 (OUTLIER) cc_final: 0.7156 (mpp) outliers start: 201 outliers final: 151 residues processed: 661 average time/residue: 0.1960 time to fit residues: 218.9499 Evaluate side-chains 646 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 480 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 218 ARG Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 543 TRP Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 60 HIS Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 190 ARG Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 380 PHE Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 435 ILE Chi-restraints excluded: chain E residue 560 SER Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 140 LYS Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 221 ASP Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 19 HIS Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 143 PHE Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 219 PHE Chi-restraints excluded: chain I residue 233 VAL Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 281 LEU Chi-restraints excluded: chain I residue 306 ASP Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 333 THR Chi-restraints excluded: chain I residue 426 LEU Chi-restraints excluded: chain I residue 547 LEU Chi-restraints excluded: chain I residue 557 VAL Chi-restraints excluded: chain I residue 580 SER Chi-restraints excluded: chain I residue 583 VAL Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 221 ASP Chi-restraints excluded: chain J residue 242 THR Chi-restraints excluded: chain J residue 244 CYS Chi-restraints excluded: chain J residue 280 MET Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 333 GLN Chi-restraints excluded: chain J residue 378 THR Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 426 LEU Chi-restraints excluded: chain J residue 442 LEU Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 63 ASN Chi-restraints excluded: chain M residue 77 SER Chi-restraints excluded: chain M residue 93 PHE Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 154 ILE Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain M residue 208 ILE Chi-restraints excluded: chain M residue 224 SER Chi-restraints excluded: chain M residue 298 VAL Chi-restraints excluded: chain M residue 340 THR Chi-restraints excluded: chain M residue 365 GLN Chi-restraints excluded: chain M residue 402 TYR Chi-restraints excluded: chain M residue 440 ARG Chi-restraints excluded: chain M residue 508 GLU Chi-restraints excluded: chain M residue 557 VAL Chi-restraints excluded: chain N residue 41 SER Chi-restraints excluded: chain N residue 58 THR Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 182 ILE Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 193 ARG Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 218 TRP Chi-restraints excluded: chain N residue 255 PHE Chi-restraints excluded: chain N residue 370 THR Chi-restraints excluded: chain N residue 382 VAL Chi-restraints excluded: chain N residue 421 THR Chi-restraints excluded: chain N residue 463 VAL Chi-restraints excluded: chain N residue 466 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 151 optimal weight: 4.9990 chunk 269 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 210 optimal weight: 1.9990 chunk 258 optimal weight: 7.9990 chunk 310 optimal weight: 0.7980 chunk 260 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 371 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 383 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 16 ASN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 HIS B 49 GLN ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 GLN ** F 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 436 ASN I 16 ASN I 209 HIS ** J 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 191 GLN N 419 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.163051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.135721 restraints weight = 64561.114| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 2.91 r_work: 0.3849 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.5694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 35626 Z= 0.180 Angle : 0.677 14.146 49010 Z= 0.348 Chirality : 0.044 0.310 5476 Planarity : 0.004 0.047 5685 Dihedral : 18.059 174.436 6493 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 5.87 % Allowed : 30.20 % Favored : 63.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.14), residues: 3841 helix: 0.60 (0.14), residues: 1467 sheet: -0.92 (0.19), residues: 798 loop : -1.01 (0.15), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 301 TYR 0.024 0.002 TYR B 205 PHE 0.027 0.002 PHE E 420 TRP 0.039 0.002 TRP I 295 HIS 0.011 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (35623) covalent geometry : angle 0.67682 / 0.35 (49010) hydrogen bonds : bond 0.05032 / 3.38 ( 1468) hydrogen bonds : angle 4.98517 / 3.50 ( 4130) Misc. bond : bond 0.00541 / 0.26 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7682 Ramachandran restraints generated. 3841 Oldfield, 0 Emsley, 3841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7682 Ramachandran restraints generated. 3841 Oldfield, 0 Emsley, 3841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 506 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASN cc_start: 0.8371 (OUTLIER) cc_final: 0.8138 (p0) REVERT: A 143 PHE cc_start: 0.6440 (OUTLIER) cc_final: 0.5798 (t80) REVERT: A 184 LYS cc_start: 0.7904 (mttt) cc_final: 0.7250 (tttt) REVERT: A 218 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.6908 (mtp-110) REVERT: A 237 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9119 (tt) REVERT: A 278 ARG cc_start: 0.8035 (ttm110) cc_final: 0.7518 (mmp80) REVERT: A 345 CYS cc_start: 0.7876 (p) cc_final: 0.7619 (p) REVERT: B 107 CYS cc_start: 0.6610 (OUTLIER) cc_final: 0.5829 (t) REVERT: B 131 GLN cc_start: 0.7850 (mt0) cc_final: 0.7470 (mm-40) REVERT: B 448 TYR cc_start: 0.7840 (t80) cc_final: 0.7574 (t80) REVERT: E 16 ASN cc_start: 0.8437 (OUTLIER) cc_final: 0.8111 (p0) REVERT: E 352 SER cc_start: 0.4788 (OUTLIER) cc_final: 0.4517 (m) REVERT: E 387 ILE cc_start: 0.8119 (mm) cc_final: 0.7711 (tp) REVERT: E 418 LYS cc_start: 0.5692 (tptm) cc_final: 0.4936 (tptm) REVERT: E 573 ILE cc_start: 0.6881 (mp) cc_final: 0.6568 (mt) REVERT: I 22 TRP cc_start: 0.7948 (m100) cc_final: 0.7723 (m100) REVERT: I 270 THR cc_start: 0.8261 (m) cc_final: 0.8010 (p) REVERT: I 345 CYS cc_start: 0.5758 (p) cc_final: 0.5506 (p) REVERT: I 468 LYS cc_start: 0.6072 (mmtt) cc_final: 0.5412 (mtmm) REVERT: I 504 MET cc_start: 0.7503 (mmm) cc_final: 0.7038 (mmm) REVERT: I 518 GLU cc_start: 0.7724 (pm20) cc_final: 0.6746 (tp30) REVERT: J 34 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7993 (mp) REVERT: J 81 THR cc_start: 0.7617 (p) cc_final: 0.7360 (m) REVERT: J 178 LEU cc_start: 0.6698 (OUTLIER) cc_final: 0.6304 (pp) REVERT: J 192 CYS cc_start: 0.7469 (t) cc_final: 0.7022 (t) REVERT: J 197 MET cc_start: 0.7611 (mmt) cc_final: 0.7011 (tpp) REVERT: J 320 PHE cc_start: 0.7258 (OUTLIER) cc_final: 0.6651 (m-80) REVERT: J 333 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.7102 (tp-100) REVERT: M 94 GLU cc_start: 0.7844 (pt0) cc_final: 0.7505 (pt0) REVERT: M 374 TYR cc_start: 0.5022 (t80) cc_final: 0.4430 (t80) REVERT: M 514 LEU cc_start: 0.8134 (mm) cc_final: 0.7808 (mt) REVERT: M 530 TYR cc_start: 0.5970 (m-80) cc_final: 0.5689 (m-10) REVERT: N 133 MET cc_start: 0.7991 (mtt) cc_final: 0.7561 (mtt) REVERT: N 193 ARG cc_start: 0.6782 (OUTLIER) cc_final: 0.5905 (tpp-160) REVERT: N 197 MET cc_start: 0.7370 (OUTLIER) cc_final: 0.7121 (mpp) REVERT: N 221 ASP cc_start: 0.6016 (m-30) cc_final: 0.5675 (m-30) REVERT: N 261 ASP cc_start: 0.7710 (t0) cc_final: 0.7425 (p0) REVERT: N 272 ASN cc_start: 0.8849 (p0) cc_final: 0.8578 (p0) REVERT: N 301 ARG cc_start: 0.6785 (ptm-80) cc_final: 0.6431 (ppt170) outliers start: 196 outliers final: 156 residues processed: 648 average time/residue: 0.2006 time to fit residues: 217.7089 Evaluate side-chains 650 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 481 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 218 ARG Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 543 TRP Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 60 HIS Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 83 GLN Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 190 ARG Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 380 PHE Chi-restraints excluded: chain E residue 384 GLU Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 435 ILE Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 560 SER Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 140 LYS Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 19 HIS Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 143 PHE Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 209 HIS Chi-restraints excluded: chain I residue 219 PHE Chi-restraints excluded: chain I residue 233 VAL Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 281 LEU Chi-restraints excluded: chain I residue 306 ASP Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 333 THR Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 426 LEU Chi-restraints excluded: chain I residue 547 LEU Chi-restraints excluded: chain I residue 559 ILE Chi-restraints excluded: chain I residue 580 SER Chi-restraints excluded: chain I residue 583 VAL Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain J residue 104 HIS Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain J residue 221 ASP Chi-restraints excluded: chain J residue 242 THR Chi-restraints excluded: chain J residue 244 CYS Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 303 ILE Chi-restraints excluded: chain J residue 320 PHE Chi-restraints excluded: chain J residue 333 GLN Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 426 LEU Chi-restraints excluded: chain J residue 442 LEU Chi-restraints excluded: chain J residue 464 ASN Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 63 ASN Chi-restraints excluded: chain M residue 77 SER Chi-restraints excluded: chain M residue 93 PHE Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 154 ILE Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain M residue 208 ILE Chi-restraints excluded: chain M residue 224 SER Chi-restraints excluded: chain M residue 298 VAL Chi-restraints excluded: chain M residue 340 THR Chi-restraints excluded: chain M residue 365 GLN Chi-restraints excluded: chain M residue 401 GLN Chi-restraints excluded: chain M residue 402 TYR Chi-restraints excluded: chain M residue 440 ARG Chi-restraints excluded: chain M residue 557 VAL Chi-restraints excluded: chain N residue 41 SER Chi-restraints excluded: chain N residue 58 THR Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 182 ILE Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 193 ARG Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 218 TRP Chi-restraints excluded: chain N residue 293 SER Chi-restraints excluded: chain N residue 370 THR Chi-restraints excluded: chain N residue 382 VAL Chi-restraints excluded: chain N residue 463 VAL Chi-restraints excluded: chain N residue 466 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 369 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 183 optimal weight: 0.7980 chunk 339 optimal weight: 6.9990 chunk 142 optimal weight: 0.4980 chunk 365 optimal weight: 0.9990 chunk 151 optimal weight: 8.9990 chunk 321 optimal weight: 7.9990 chunk 229 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 197 optimal weight: 10.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 HIS B 177 ASN ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 GLN ** F 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 GLN F 367 GLN ** F 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 436 ASN I 16 ASN J 82 ASN ** J 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 191 GLN N 419 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.164334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.136888 restraints weight = 64059.130| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 2.80 r_work: 0.3872 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.5828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 35626 Z= 0.143 Angle : 0.670 14.948 49010 Z= 0.341 Chirality : 0.043 0.301 5476 Planarity : 0.004 0.048 5685 Dihedral : 18.024 174.395 6493 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 5.21 % Allowed : 30.98 % Favored : 63.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.14), residues: 3841 helix: 0.67 (0.14), residues: 1465 sheet: -0.83 (0.19), residues: 782 loop : -0.94 (0.15), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG M 206 TYR 0.030 0.002 TYR B 205 PHE 0.034 0.002 PHE E 420 TRP 0.059 0.002 TRP M 510 HIS 0.030 0.001 HIS I 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (35623) covalent geometry : angle 0.67022 / 0.34 (49010) hydrogen bonds : bond 0.04995 / 3.35 ( 1468) hydrogen bonds : angle 4.93717 / 3.46 ( 4130) Misc. bond : bond 0.00481 / 0.23 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7682 Ramachandran restraints generated. 3841 Oldfield, 0 Emsley, 3841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7682 Ramachandran restraints generated. 3841 Oldfield, 0 Emsley, 3841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 500 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 PHE cc_start: 0.6436 (OUTLIER) cc_final: 0.5824 (t80) REVERT: A 184 LYS cc_start: 0.7885 (mttt) cc_final: 0.7222 (tttt) REVERT: A 218 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.6862 (mtp-110) REVERT: A 237 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9094 (tt) REVERT: A 278 ARG cc_start: 0.8016 (ttm110) cc_final: 0.7529 (mmp80) REVERT: A 345 CYS cc_start: 0.7758 (p) cc_final: 0.7512 (p) REVERT: A 445 TYR cc_start: 0.7940 (m-80) cc_final: 0.7680 (m-80) REVERT: B 107 CYS cc_start: 0.6605 (OUTLIER) cc_final: 0.5851 (t) REVERT: B 131 GLN cc_start: 0.7805 (mt0) cc_final: 0.7440 (mm-40) REVERT: B 448 TYR cc_start: 0.7767 (t80) cc_final: 0.7547 (t80) REVERT: E 16 ASN cc_start: 0.8374 (OUTLIER) cc_final: 0.8155 (p0) REVERT: E 290 MET cc_start: 0.8088 (ttp) cc_final: 0.7883 (ttp) REVERT: E 352 SER cc_start: 0.4891 (OUTLIER) cc_final: 0.4620 (m) REVERT: E 387 ILE cc_start: 0.8109 (mm) cc_final: 0.7710 (tp) REVERT: E 414 SER cc_start: 0.5149 (t) cc_final: 0.4727 (t) REVERT: E 418 LYS cc_start: 0.5672 (tptm) cc_final: 0.4949 (tptm) REVERT: E 573 ILE cc_start: 0.6954 (mp) cc_final: 0.6650 (mt) REVERT: F 70 GLU cc_start: 0.7265 (mt-10) cc_final: 0.6912 (mt-10) REVERT: I 14 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8769 (mt) REVERT: I 22 TRP cc_start: 0.8022 (m100) cc_final: 0.7590 (m100) REVERT: I 139 PHE cc_start: 0.6707 (OUTLIER) cc_final: 0.6436 (p90) REVERT: I 209 HIS cc_start: 0.6289 (OUTLIER) cc_final: 0.5498 (m-70) REVERT: I 226 TYR cc_start: 0.5740 (t80) cc_final: 0.5511 (t80) REVERT: I 270 THR cc_start: 0.8242 (m) cc_final: 0.7982 (p) REVERT: I 290 MET cc_start: 0.6700 (tmm) cc_final: 0.6453 (tmm) REVERT: I 504 MET cc_start: 0.7461 (mmm) cc_final: 0.6942 (mmm) REVERT: I 518 GLU cc_start: 0.7712 (pm20) cc_final: 0.6835 (tp30) REVERT: I 528 ARG cc_start: 0.6943 (OUTLIER) cc_final: 0.6640 (ttm170) REVERT: J 34 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8003 (mp) REVERT: J 81 THR cc_start: 0.7658 (p) cc_final: 0.7444 (m) REVERT: J 192 CYS cc_start: 0.7406 (t) cc_final: 0.6947 (t) REVERT: J 197 MET cc_start: 0.7631 (mmt) cc_final: 0.7098 (tpp) REVERT: J 320 PHE cc_start: 0.7209 (OUTLIER) cc_final: 0.6601 (m-80) REVERT: J 333 GLN cc_start: 0.7495 (OUTLIER) cc_final: 0.7036 (tp-100) REVERT: J 376 LEU cc_start: 0.8992 (tt) cc_final: 0.8739 (tt) REVERT: M 94 GLU cc_start: 0.7785 (pt0) cc_final: 0.7505 (pt0) REVERT: M 374 TYR cc_start: 0.5056 (t80) cc_final: 0.4445 (t80) REVERT: M 418 LYS cc_start: 0.5190 (tptm) cc_final: 0.4926 (tttm) REVERT: M 514 LEU cc_start: 0.8158 (mm) cc_final: 0.7868 (mt) REVERT: M 530 TYR cc_start: 0.5840 (m-80) cc_final: 0.5615 (m-10) REVERT: N 133 MET cc_start: 0.7867 (mtt) cc_final: 0.7444 (mtt) REVERT: N 193 ARG cc_start: 0.6806 (OUTLIER) cc_final: 0.5939 (tpp-160) REVERT: N 197 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.7128 (mpp) REVERT: N 222 GLU cc_start: 0.6173 (pm20) cc_final: 0.5901 (pm20) REVERT: N 261 ASP cc_start: 0.7619 (t0) cc_final: 0.7362 (p0) REVERT: N 272 ASN cc_start: 0.8802 (p0) cc_final: 0.8514 (p0) outliers start: 174 outliers final: 133 residues processed: 630 average time/residue: 0.1891 time to fit residues: 199.8303 Evaluate side-chains 618 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 470 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 218 ARG Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 543 TRP Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 60 HIS Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 83 GLN Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 190 ARG Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 287 PHE Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 380 PHE Chi-restraints excluded: chain E residue 384 GLU Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 435 ILE Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 560 SER Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 140 LYS Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 436 ASN Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 19 HIS Chi-restraints excluded: chain I residue 139 PHE Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 143 PHE Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 209 HIS Chi-restraints excluded: chain I residue 219 PHE Chi-restraints excluded: chain I residue 233 VAL Chi-restraints excluded: chain I residue 244 ASN Chi-restraints excluded: chain I residue 281 LEU Chi-restraints excluded: chain I residue 306 ASP Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 333 THR Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 426 LEU Chi-restraints excluded: chain I residue 528 ARG Chi-restraints excluded: chain I residue 547 LEU Chi-restraints excluded: chain I residue 583 VAL Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain J residue 104 HIS Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 221 ASP Chi-restraints excluded: chain J residue 242 THR Chi-restraints excluded: chain J residue 244 CYS Chi-restraints excluded: chain J residue 303 ILE Chi-restraints excluded: chain J residue 320 PHE Chi-restraints excluded: chain J residue 333 GLN Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 442 LEU Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 77 SER Chi-restraints excluded: chain M residue 93 PHE Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 154 ILE Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain M residue 208 ILE Chi-restraints excluded: chain M residue 224 SER Chi-restraints excluded: chain M residue 298 VAL Chi-restraints excluded: chain M residue 331 LEU Chi-restraints excluded: chain M residue 340 THR Chi-restraints excluded: chain M residue 365 GLN Chi-restraints excluded: chain M residue 401 GLN Chi-restraints excluded: chain M residue 402 TYR Chi-restraints excluded: chain M residue 557 VAL Chi-restraints excluded: chain N residue 58 THR Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 182 ILE Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 193 ARG Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 255 PHE Chi-restraints excluded: chain N residue 370 THR Chi-restraints excluded: chain N residue 382 VAL Chi-restraints excluded: chain N residue 463 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 131 optimal weight: 1.9990 chunk 182 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 223 optimal weight: 20.0000 chunk 2 optimal weight: 6.9990 chunk 325 optimal weight: 0.1980 chunk 228 optimal weight: 6.9990 chunk 391 optimal weight: 2.9990 chunk 280 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 HIS ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 GLN ** F 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 ASN ** I 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 191 GLN N 367 GLN ** N 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.163079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.136041 restraints weight = 64354.479| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 2.66 r_work: 0.3870 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.6016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 35626 Z= 0.163 Angle : 0.686 16.278 49010 Z= 0.350 Chirality : 0.044 0.300 5476 Planarity : 0.004 0.057 5685 Dihedral : 18.029 174.862 6489 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 5.03 % Allowed : 31.25 % Favored : 63.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.14), residues: 3841 helix: 0.63 (0.14), residues: 1465 sheet: -0.86 (0.19), residues: 794 loop : -0.94 (0.15), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 332 TYR 0.048 0.002 TYR B 205 PHE 0.031 0.002 PHE E 420 TRP 0.050 0.002 TRP M 510 HIS 0.006 0.001 HIS I 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (35623) covalent geometry : angle 0.68584 / 0.35 (49010) hydrogen bonds : bond 0.04964 / 3.35 ( 1468) hydrogen bonds : angle 4.95913 / 3.48 ( 4130) Misc. bond : bond 0.00578 / 0.28 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7682 Ramachandran restraints generated. 3841 Oldfield, 0 Emsley, 3841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7682 Ramachandran restraints generated. 3841 Oldfield, 0 Emsley, 3841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 491 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 PHE cc_start: 0.6441 (OUTLIER) cc_final: 0.5840 (t80) REVERT: A 184 LYS cc_start: 0.7910 (mttt) cc_final: 0.7222 (tttt) REVERT: A 218 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.6849 (mtp-110) REVERT: A 237 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9118 (tt) REVERT: A 278 ARG cc_start: 0.8007 (ttm110) cc_final: 0.7520 (mmp80) REVERT: A 345 CYS cc_start: 0.7736 (p) cc_final: 0.7518 (p) REVERT: B 107 CYS cc_start: 0.6623 (OUTLIER) cc_final: 0.5660 (t) REVERT: B 131 GLN cc_start: 0.7791 (mt0) cc_final: 0.7466 (mm-40) REVERT: B 448 TYR cc_start: 0.7832 (t80) cc_final: 0.7580 (t80) REVERT: E 16 ASN cc_start: 0.8405 (OUTLIER) cc_final: 0.8126 (p0) REVERT: E 352 SER cc_start: 0.4799 (OUTLIER) cc_final: 0.4594 (m) REVERT: E 387 ILE cc_start: 0.8115 (mm) cc_final: 0.7702 (tp) REVERT: E 414 SER cc_start: 0.5152 (t) cc_final: 0.4774 (t) REVERT: E 418 LYS cc_start: 0.5684 (tptm) cc_final: 0.4928 (tptm) REVERT: E 514 LEU cc_start: 0.7749 (mm) cc_final: 0.7544 (mp) REVERT: E 573 ILE cc_start: 0.7138 (mp) cc_final: 0.6736 (mt) REVERT: I 14 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8745 (mt) REVERT: I 22 TRP cc_start: 0.8042 (m100) cc_final: 0.7568 (m100) REVERT: I 139 PHE cc_start: 0.6562 (OUTLIER) cc_final: 0.6313 (p90) REVERT: I 226 TYR cc_start: 0.5861 (t80) cc_final: 0.5641 (t80) REVERT: I 270 THR cc_start: 0.8259 (m) cc_final: 0.8006 (p) REVERT: I 290 MET cc_start: 0.6720 (tmm) cc_final: 0.6454 (tmm) REVERT: I 504 MET cc_start: 0.7395 (mmm) cc_final: 0.6868 (mmm) REVERT: I 518 GLU cc_start: 0.7743 (pm20) cc_final: 0.6889 (tp30) REVERT: I 528 ARG cc_start: 0.6972 (OUTLIER) cc_final: 0.6721 (ttm170) REVERT: J 34 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8034 (mp) REVERT: J 81 THR cc_start: 0.7575 (p) cc_final: 0.7331 (m) REVERT: J 131 GLN cc_start: 0.7669 (mt0) cc_final: 0.7363 (mm110) REVERT: J 154 TRP cc_start: 0.7754 (m-10) cc_final: 0.7491 (m-10) REVERT: J 181 GLN cc_start: 0.7581 (tm130) cc_final: 0.7080 (tp40) REVERT: J 320 PHE cc_start: 0.7212 (OUTLIER) cc_final: 0.6604 (m-80) REVERT: J 333 GLN cc_start: 0.7476 (OUTLIER) cc_final: 0.7053 (tp-100) REVERT: M 94 GLU cc_start: 0.7853 (pt0) cc_final: 0.7533 (pt0) REVERT: M 374 TYR cc_start: 0.5088 (t80) cc_final: 0.4436 (t80) REVERT: M 418 LYS cc_start: 0.5169 (tptm) cc_final: 0.4925 (tttm) REVERT: M 514 LEU cc_start: 0.8186 (mm) cc_final: 0.7922 (mt) REVERT: M 530 TYR cc_start: 0.5901 (m-80) cc_final: 0.5631 (m-10) REVERT: N 133 MET cc_start: 0.7900 (mtt) cc_final: 0.7461 (mtt) REVERT: N 155 LYS cc_start: 0.8199 (mmtt) cc_final: 0.7972 (tttt) REVERT: N 193 ARG cc_start: 0.6741 (OUTLIER) cc_final: 0.5861 (tpp-160) REVERT: N 197 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.7105 (mpp) REVERT: N 222 GLU cc_start: 0.6131 (pm20) cc_final: 0.5799 (pm20) REVERT: N 261 ASP cc_start: 0.7624 (t0) cc_final: 0.7357 (p0) REVERT: N 272 ASN cc_start: 0.8821 (p0) cc_final: 0.8531 (p0) REVERT: N 301 ARG cc_start: 0.6790 (ptm-80) cc_final: 0.6377 (ppt170) outliers start: 168 outliers final: 135 residues processed: 619 average time/residue: 0.1939 time to fit residues: 200.3425 Evaluate side-chains 618 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 469 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 218 ARG Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 543 TRP Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 60 HIS Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 83 GLN Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 190 ARG Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 380 PHE Chi-restraints excluded: chain E residue 384 GLU Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 435 ILE Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 560 SER Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 140 LYS Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 19 HIS Chi-restraints excluded: chain I residue 139 PHE Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 143 PHE Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 219 PHE Chi-restraints excluded: chain I residue 233 VAL Chi-restraints excluded: chain I residue 244 ASN Chi-restraints excluded: chain I residue 281 LEU Chi-restraints excluded: chain I residue 306 ASP Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 333 THR Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 426 LEU Chi-restraints excluded: chain I residue 528 ARG Chi-restraints excluded: chain I residue 547 LEU Chi-restraints excluded: chain I residue 583 VAL Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain J residue 104 HIS Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 221 ASP Chi-restraints excluded: chain J residue 242 THR Chi-restraints excluded: chain J residue 244 CYS Chi-restraints excluded: chain J residue 303 ILE Chi-restraints excluded: chain J residue 320 PHE Chi-restraints excluded: chain J residue 333 GLN Chi-restraints excluded: chain J residue 374 CYS Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 442 LEU Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 77 SER Chi-restraints excluded: chain M residue 93 PHE Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 154 ILE Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain M residue 208 ILE Chi-restraints excluded: chain M residue 224 SER Chi-restraints excluded: chain M residue 298 VAL Chi-restraints excluded: chain M residue 340 THR Chi-restraints excluded: chain M residue 365 GLN Chi-restraints excluded: chain M residue 401 GLN Chi-restraints excluded: chain M residue 402 TYR Chi-restraints excluded: chain M residue 557 VAL Chi-restraints excluded: chain M residue 573 ILE Chi-restraints excluded: chain N residue 58 THR Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 182 ILE Chi-restraints excluded: chain N residue 193 ARG Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 255 PHE Chi-restraints excluded: chain N residue 293 SER Chi-restraints excluded: chain N residue 370 THR Chi-restraints excluded: chain N residue 382 VAL Chi-restraints excluded: chain N residue 463 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 4 optimal weight: 0.6980 chunk 322 optimal weight: 1.9990 chunk 384 optimal weight: 1.9990 chunk 378 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 383 optimal weight: 0.8980 chunk 208 optimal weight: 2.9990 chunk 253 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 HIS B 60 HIS ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 436 ASN I 15 GLN I 16 ASN I 209 HIS J 82 ASN ** J 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 244 ASN M 437 HIS N 82 ASN N 191 GLN ** N 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 419 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.162480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.135518 restraints weight = 64177.790| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 2.67 r_work: 0.3861 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.6230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 35626 Z= 0.158 Angle : 0.686 14.940 49010 Z= 0.352 Chirality : 0.044 0.300 5476 Planarity : 0.004 0.068 5685 Dihedral : 18.001 175.446 6487 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 4.94 % Allowed : 31.46 % Favored : 63.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.14), residues: 3841 helix: 0.61 (0.14), residues: 1465 sheet: -0.89 (0.19), residues: 781 loop : -0.94 (0.15), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 332 TYR 0.041 0.002 TYR B 205 PHE 0.029 0.002 PHE E 420 TRP 0.072 0.002 TRP M 510 HIS 0.016 0.001 HIS M 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (35623) covalent geometry : angle 0.68606 / 0.35 (49010) hydrogen bonds : bond 0.04973 / 3.36 ( 1468) hydrogen bonds : angle 4.98192 / 3.50 ( 4130) Misc. bond : bond 0.00457 / 0.22 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8800.32 seconds wall clock time: 152 minutes 18.90 seconds (9138.90 seconds total)