Starting phenix.real_space_refine on Sun Aug 9 10:06:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y80_39028/08_2026/8y80_39028.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y80_39028/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8y80_39028/08_2026/8y80_39028.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y80_39028/08_2026/8y80_39028.map" model { file = "/net/cci-nas-00/data/ceres_data/8y80_39028/08_2026/8y80_39028.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y80_39028/08_2026/8y80_39028.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6.42, per 1000 atoms: 0.19 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: 2.86 Conformation dependent library (CDL) restraints added in 1.3 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: 4.10 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: 7.59 Time building geometry restraints manager: 3.82 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: 5071 0.111 - 0.221: 354 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: 6.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 31.770 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.080 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.760 ------------------------------------------------------------------------------- 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= 0.455 Angle : 0.886 19.435 49010 Z= 0.611 Chirality : 0.061 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 0.00537 / 0.37 (35623) covalent geometry : angle 0.88630 / 0.61 (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 : 0.845 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: 0.8495 (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: 0.7543 (pttt) REVERT: A 373 THR cc_start: 0.8049 (t) cc_final: 0.7726 (m) REVERT: A 444 HIS cc_start: 0.5566 (m-70) cc_final: 0.5190 (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: 0.6764 (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: 0.3230 (tp30) REVERT: I 518 GLU cc_start: 0.6639 (pm20) cc_final: 0.6162 (tp30) REVERT: J 346 ASP cc_start: 0.6238 (m-30) cc_final: 0.5957 (t0) REVERT: J 376 LEU cc_start: 0.8485 (tp) cc_final: 0.8104 (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: 0.7437 (tp) REVERT: M 374 TYR cc_start: 0.4541 (t80) cc_final: 0.4284 (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: 0.2220 time to fit residues: 394.6221 Evaluate side-chains 612 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 541 time to evaluate : 1.117 ------------------------------------------------------------------------------- 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: 9.9990 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: 8.9990 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 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN B 296 ASN ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 HIS 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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** ** 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: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.174542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.146373 restraints weight = 65456.159| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 2.64 r_work: 0.4026 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 35626 Z= 0.241 Angle : 0.779 11.821 49010 Z= 0.413 Chirality : 0.048 0.313 5476 Planarity : 0.006 0.093 5685 Dihedral : 18.259 171.648 6620 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.71 % Favored : 95.26 % Rotamer: Outliers : 7.69 % Allowed : 28.23 % Favored : 64.08 % 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: -0.64 (0.13), residues: 3841 helix: 0.33 (0.13), residues: 1486 sheet: -0.70 (0.19), residues: 730 loop : -0.89 (0.15), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 516 TYR 0.040 0.003 TYR E 92 PHE 0.038 0.003 PHE E 287 TRP 0.020 0.002 TRP F 340 HIS 0.020 0.002 HIS E 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.24 (35623) covalent geometry : angle 0.77852 / 0.41 (49010) hydrogen bonds : bond 0.06195 / 4.16 ( 1468) hydrogen bonds : angle 5.47348 / 3.88 ( 4130) Misc. bond : bond 0.00711 / 0.35 ( 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 881 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 257 poor density : 624 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASN cc_start: 0.8290 (OUTLIER) cc_final: 0.7898 (p0) REVERT: A 143 PHE cc_start: 0.6621 (OUTLIER) cc_final: 0.5948 (t80) REVERT: A 184 LYS cc_start: 0.7700 (mttt) cc_final: 0.7187 (ptmt) REVERT: A 331 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8512 (pt) REVERT: A 373 THR cc_start: 0.8320 (t) cc_final: 0.8087 (m) REVERT: B 361 VAL cc_start: 0.7420 (OUTLIER) cc_final: 0.7199 (p) REVERT: E 16 ASN cc_start: 0.8280 (p0) cc_final: 0.8062 (p0) REVERT: E 210 LYS cc_start: 0.7446 (OUTLIER) cc_final: 0.7174 (mmtm) REVERT: E 287 PHE cc_start: 0.7188 (OUTLIER) cc_final: 0.6579 (t80) REVERT: E 352 SER cc_start: 0.4560 (OUTLIER) cc_final: 0.4261 (m) REVERT: F 133 MET cc_start: 0.6677 (mtt) cc_final: 0.6333 (mtt) REVERT: F 185 ASP cc_start: 0.7082 (OUTLIER) cc_final: 0.6773 (p0) REVERT: F 190 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.5905 (tmm160) REVERT: F 296 ASN cc_start: 0.8348 (OUTLIER) cc_final: 0.8121 (m110) REVERT: I 22 TRP cc_start: 0.8078 (m100) cc_final: 0.7622 (m100) REVERT: I 218 ARG cc_start: 0.7130 (OUTLIER) cc_final: 0.6860 (ttm170) REVERT: I 326 LYS cc_start: 0.7205 (pttm) cc_final: 0.6980 (pttp) REVERT: I 345 CYS cc_start: 0.6166 (OUTLIER) cc_final: 0.5945 (p) REVERT: I 518 GLU cc_start: 0.7360 (pm20) cc_final: 0.6169 (tp30) REVERT: I 536 SER cc_start: 0.7927 (t) cc_final: 0.7203 (m) REVERT: J 178 LEU cc_start: 0.6599 (OUTLIER) cc_final: 0.6155 (pp) REVERT: J 190 ARG cc_start: 0.7313 (OUTLIER) cc_final: 0.6722 (mmm160) REVERT: J 197 MET cc_start: 0.6535 (mmm) cc_final: 0.6148 (tpp) REVERT: J 295 HIS cc_start: 0.7661 (m90) cc_final: 0.7444 (m90) REVERT: J 376 LEU cc_start: 0.8843 (tp) cc_final: 0.8337 (tp) REVERT: J 465 GLU cc_start: 0.6857 (mp0) cc_final: 0.6248 (mm-30) REVERT: M 57 TYR cc_start: 0.7712 (t80) cc_final: 0.7453 (t80) REVERT: M 75 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.7260 (mmt) REVERT: M 94 GLU cc_start: 0.7860 (pt0) cc_final: 0.7525 (pt0) REVERT: M 143 PHE cc_start: 0.8449 (m-80) cc_final: 0.8246 (m-80) REVERT: M 331 LEU cc_start: 0.8390 (mt) cc_final: 0.8072 (mt) REVERT: M 374 TYR cc_start: 0.4932 (t80) cc_final: 0.4030 (t80) REVERT: M 514 LEU cc_start: 0.7931 (mm) cc_final: 0.7652 (mt) REVERT: M 576 ARG cc_start: 0.4118 (ttt180) cc_final: 0.3082 (ptt-90) REVERT: N 139 GLN cc_start: 0.7314 (OUTLIER) cc_final: 0.7027 (mp10) REVERT: N 240 TYR cc_start: 0.7097 (m-80) cc_final: 0.6574 (m-80) REVERT: N 340 TRP cc_start: 0.8042 (m100) cc_final: 0.7323 (m100) REVERT: N 397 GLU cc_start: 0.5100 (mp0) cc_final: 0.4703 (mp0) REVERT: N 473 MET cc_start: 0.6245 (ptt) cc_final: 0.5984 (ptt) outliers start: 257 outliers final: 117 residues processed: 811 average time/residue: 0.2035 time to fit residues: 272.0445 Evaluate side-chains 640 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 507 time to evaluate : 1.200 ------------------------------------------------------------------------------- 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 218 ARG 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 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 289 GLU 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 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 440 ARG 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: 1.9990 chunk 25 optimal weight: 4.9990 chunk 289 optimal weight: 0.7980 chunk 290 optimal weight: 0.7980 chunk 141 optimal weight: 0.0980 chunk 205 optimal weight: 5.9990 chunk 235 optimal weight: 0.0870 chunk 227 optimal weight: 6.9990 chunk 352 optimal weight: 7.9990 chunk 262 optimal weight: 7.9990 chunk 361 optimal weight: 10.0000 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 GLN B 49 GLN B 184 ASN B 195 ASN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 HIS ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 177 ASN F 238 GLN ** F 295 HIS ** 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 82 ASN J 181 GLN J 195 ASN J 387 GLN J 392 GLN M 12 HIS ** M 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 123 HIS N 317 GLN ** N 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.174821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.148350 restraints weight = 64913.345| |-----------------------------------------------------------------------------| r_work (start): 0.4168 rms_B_bonded: 2.78 r_work: 0.4021 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 35626 Z= 0.153 Angle : 0.678 12.071 49010 Z= 0.352 Chirality : 0.043 0.320 5476 Planarity : 0.005 0.063 5685 Dihedral : 17.997 172.507 6541 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 5.87 % Allowed : 28.82 % Favored : 65.31 % 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: -0.51 (0.13), residues: 3841 helix: 0.46 (0.13), residues: 1507 sheet: -0.67 (0.19), residues: 756 loop : -0.82 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 301 TYR 0.025 0.002 TYR I 271 PHE 0.030 0.002 PHE A 532 TRP 0.019 0.001 TRP N 433 HIS 0.013 0.001 HIS E 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (35623) covalent geometry : angle 0.67755 / 0.35 (49010) hydrogen bonds : bond 0.05527 / 3.71 ( 1468) hydrogen bonds : angle 5.15372 / 3.65 ( 4130) Misc. bond : bond 0.00671 / 0.34 ( 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 769 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 573 time to evaluate : 1.037 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: 0.8292 (OUTLIER) cc_final: 0.7851 (p0) REVERT: A 21 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7674 (ttm) REVERT: A 143 PHE cc_start: 0.6560 (OUTLIER) cc_final: 0.5900 (t80) REVERT: A 184 LYS cc_start: 0.7751 (mttt) cc_final: 0.7184 (ptmt) REVERT: A 219 PHE cc_start: 0.7930 (OUTLIER) cc_final: 0.7319 (p90) REVERT: A 310 ARG cc_start: 0.7714 (ptt90) cc_final: 0.6945 (ptp-170) REVERT: A 373 THR cc_start: 0.8361 (t) cc_final: 0.8154 (m) REVERT: B 361 VAL cc_start: 0.7448 (OUTLIER) cc_final: 0.7192 (p) REVERT: E 16 ASN cc_start: 0.8269 (OUTLIER) cc_final: 0.8015 (p0) REVERT: E 200 ASP cc_start: 0.7579 (m-30) cc_final: 0.7139 (m-30) REVERT: E 287 PHE cc_start: 0.7558 (OUTLIER) cc_final: 0.7022 (t80) REVERT: E 352 SER cc_start: 0.4614 (OUTLIER) cc_final: 0.4364 (m) REVERT: E 448 ILE cc_start: 0.3958 (mp) cc_final: 0.3735 (mp) REVERT: F 133 MET cc_start: 0.7023 (mtt) cc_final: 0.6642 (mtt) REVERT: F 185 ASP cc_start: 0.7101 (OUTLIER) cc_final: 0.6837 (p0) REVERT: F 190 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.5943 (tmm160) REVERT: F 238 GLN cc_start: 0.6751 (OUTLIER) cc_final: 0.6189 (mp10) REVERT: I 16 ASN cc_start: 0.7137 (OUTLIER) cc_final: 0.6911 (p0) REVERT: I 22 TRP cc_start: 0.7935 (m100) cc_final: 0.7581 (m100) REVERT: I 139 PHE cc_start: 0.7203 (OUTLIER) cc_final: 0.6192 (p90) REVERT: I 223 VAL cc_start: 0.7209 (p) cc_final: 0.6823 (p) REVERT: I 518 GLU cc_start: 0.7355 (pm20) cc_final: 0.6217 (tp30) REVERT: I 536 SER cc_start: 0.7936 (t) cc_final: 0.7202 (m) REVERT: J 376 LEU cc_start: 0.8921 (tp) cc_final: 0.8436 (tp) REVERT: J 465 GLU cc_start: 0.6844 (mp0) cc_final: 0.6223 (mm-30) REVERT: M 94 GLU cc_start: 0.7831 (pt0) cc_final: 0.7485 (pt0) REVERT: M 374 TYR cc_start: 0.4966 (t80) cc_final: 0.3997 (t80) REVERT: M 508 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.6597 (pm20) REVERT: M 514 LEU cc_start: 0.8002 (mm) cc_final: 0.7739 (mt) REVERT: M 576 ARG cc_start: 0.4081 (ttt180) cc_final: 0.3106 (ptt-90) REVERT: N 147 LEU cc_start: 0.8420 (mt) cc_final: 0.8183 (mp) REVERT: N 197 MET cc_start: 0.7486 (OUTLIER) cc_final: 0.7209 (mpp) REVERT: N 198 TRP cc_start: 0.6022 (m100) cc_final: 0.5791 (m100) REVERT: N 218 TRP cc_start: 0.5799 (OUTLIER) cc_final: 0.5503 (m-90) REVERT: N 240 TYR cc_start: 0.7150 (m-80) cc_final: 0.6441 (m-80) REVERT: N 397 GLU cc_start: 0.5113 (mp0) cc_final: 0.4687 (mp0) outliers start: 196 outliers final: 107 residues processed: 711 average time/residue: 0.1905 time to fit residues: 224.5528 Evaluate side-chains 627 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 504 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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 255 VAL Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 333 THR 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 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 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 333 THR 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 238 GLN 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 144 ASP 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 J residue 5 LEU Chi-restraints excluded: chain J residue 82 ASN 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 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 194 ILE Chi-restraints excluded: chain M residue 224 SER Chi-restraints excluded: chain M residue 236 MET Chi-restraints excluded: chain M residue 275 LYS Chi-restraints excluded: chain M residue 298 VAL Chi-restraints excluded: chain M residue 381 LEU Chi-restraints excluded: chain M residue 417 LEU 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 132 SER 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 451 VAL 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: 4.9990 chunk 322 optimal weight: 0.9990 chunk 245 optimal weight: 6.9990 chunk 393 optimal weight: 0.9980 chunk 146 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 309 optimal weight: 0.7980 chunk 397 optimal weight: 0.3980 chunk 357 optimal weight: 0.4980 chunk 257 optimal weight: 0.8980 chunk 389 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 49 GLN B 82 ASN B 177 ASN ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 60 HIS F 139 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 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 306 HIS ** M 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 177 ASN N 317 GLN N 367 GLN ** N 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.174171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.147339 restraints weight = 64398.376| |-----------------------------------------------------------------------------| r_work (start): 0.4156 rms_B_bonded: 2.78 r_work: 0.4005 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 35626 Z= 0.141 Angle : 0.656 13.265 49010 Z= 0.338 Chirality : 0.043 0.317 5476 Planarity : 0.004 0.054 5685 Dihedral : 17.921 171.322 6520 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 5.24 % Allowed : 29.51 % Favored : 65.25 % 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: -0.47 (0.14), residues: 3841 helix: 0.57 (0.14), residues: 1485 sheet: -0.69 (0.19), residues: 782 loop : -0.84 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 51 TYR 0.041 0.002 TYR J 448 PHE 0.028 0.002 PHE M 356 TRP 0.046 0.002 TRP F 154 HIS 0.010 0.001 HIS E 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (35623) covalent geometry : angle 0.65568 / 0.34 (49010) hydrogen bonds : bond 0.05172 / 3.47 ( 1468) hydrogen bonds : angle 5.00714 / 3.54 ( 4130) Misc. bond : bond 0.00670 / 0.32 ( 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 725 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 550 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: A 16 ASN cc_start: 0.8270 (OUTLIER) cc_final: 0.7930 (p0) REVERT: A 143 PHE cc_start: 0.6476 (OUTLIER) cc_final: 0.5845 (t80) REVERT: A 184 LYS cc_start: 0.7752 (mttt) cc_final: 0.7181 (ptmt) REVERT: A 237 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.9059 (tt) REVERT: A 349 THR cc_start: 0.6881 (OUTLIER) cc_final: 0.6499 (p) REVERT: A 373 THR cc_start: 0.8363 (t) cc_final: 0.8130 (m) REVERT: A 422 GLU cc_start: 0.7139 (tp30) cc_final: 0.6594 (tp30) REVERT: B 177 ASN cc_start: 0.7563 (OUTLIER) cc_final: 0.7258 (t0) REVERT: B 361 VAL cc_start: 0.7443 (OUTLIER) cc_final: 0.7190 (p) REVERT: E 16 ASN cc_start: 0.8296 (OUTLIER) cc_final: 0.8028 (p0) REVERT: E 213 LEU cc_start: 0.8508 (mt) cc_final: 0.8056 (mt) REVERT: E 287 PHE cc_start: 0.7680 (OUTLIER) cc_final: 0.7213 (t80) REVERT: F 133 MET cc_start: 0.6950 (mtt) cc_final: 0.6453 (mtt) REVERT: I 16 ASN cc_start: 0.7128 (OUTLIER) cc_final: 0.6926 (p0) REVERT: I 22 TRP cc_start: 0.7852 (m100) cc_final: 0.7564 (m100) REVERT: I 139 PHE cc_start: 0.7207 (OUTLIER) cc_final: 0.6379 (p90) REVERT: I 234 MET cc_start: 0.6731 (tpp) cc_final: 0.6407 (ptp) REVERT: I 504 MET cc_start: 0.7468 (mmm) cc_final: 0.7256 (mmm) REVERT: I 518 GLU cc_start: 0.7424 (pm20) cc_final: 0.6245 (tp30) REVERT: I 536 SER cc_start: 0.7988 (t) cc_final: 0.7258 (m) REVERT: J 376 LEU cc_start: 0.8896 (tp) cc_final: 0.8408 (tp) REVERT: J 465 GLU cc_start: 0.6856 (mp0) cc_final: 0.6272 (mm-30) REVERT: M 94 GLU cc_start: 0.7921 (pt0) cc_final: 0.7598 (pt0) REVERT: M 374 TYR cc_start: 0.4899 (t80) cc_final: 0.4627 (t80) REVERT: M 508 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6679 (mp0) REVERT: M 514 LEU cc_start: 0.8024 (mm) cc_final: 0.7790 (mt) REVERT: M 576 ARG cc_start: 0.4113 (ttt180) cc_final: 0.3195 (ptt-90) REVERT: N 147 LEU cc_start: 0.8452 (mt) cc_final: 0.8222 (mp) REVERT: N 158 PHE cc_start: 0.6841 (m-10) cc_final: 0.6273 (m-80) REVERT: N 193 ARG cc_start: 0.6573 (OUTLIER) cc_final: 0.5854 (tpp80) REVERT: N 197 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.7142 (mpp) REVERT: N 211 ILE cc_start: 0.8169 (pt) cc_final: 0.7932 (pp) REVERT: N 240 TYR cc_start: 0.7188 (m-80) cc_final: 0.6602 (m-80) REVERT: N 288 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7271 (pt) REVERT: N 313 GLU cc_start: 0.6308 (tp30) cc_final: 0.6072 (tp30) REVERT: N 397 GLU cc_start: 0.5551 (mp0) cc_final: 0.5053 (mp0) outliers start: 175 outliers final: 100 residues processed: 677 average time/residue: 0.2075 time to fit residues: 236.5990 Evaluate side-chains 618 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 504 time to evaluate : 1.228 ------------------------------------------------------------------------------- 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 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 137 PHE Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 177 ASN 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 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 333 THR 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 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 188 LEU Chi-restraints excluded: chain F residue 247 VAL 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 144 ASP 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 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 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 221 ASP Chi-restraints excluded: chain J residue 244 CYS Chi-restraints excluded: chain J residue 287 SER 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 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 194 ILE 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 381 LEU 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 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 288 LEU Chi-restraints excluded: chain N residue 289 HIS Chi-restraints excluded: chain N residue 370 THR 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: 0.8980 chunk 218 optimal weight: 2.9990 chunk 200 optimal weight: 9.9990 chunk 285 optimal weight: 0.2980 chunk 127 optimal weight: 10.0000 chunk 69 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 273 optimal weight: 1.9990 chunk 134 optimal weight: 0.0770 chunk 233 optimal weight: 0.7980 chunk 190 optimal weight: 0.5980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 49 GLN B 177 ASN ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 HIS ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 GLN ** F 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 436 ASN ** I 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 ASN ** J 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 191 GLN N 317 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.174168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.147554 restraints weight = 64607.839| |-----------------------------------------------------------------------------| r_work (start): 0.4156 rms_B_bonded: 2.65 r_work: 0.4017 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 35626 Z= 0.134 Angle : 0.636 14.249 49010 Z= 0.329 Chirality : 0.043 0.313 5476 Planarity : 0.004 0.052 5685 Dihedral : 17.847 172.087 6499 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 5.00 % Allowed : 29.63 % Favored : 65.37 % 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: -0.38 (0.14), residues: 3841 helix: 0.65 (0.14), residues: 1475 sheet: -0.63 (0.19), residues: 784 loop : -0.80 (0.15), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 301 TYR 0.029 0.002 TYR J 448 PHE 0.023 0.002 PHE E 420 TRP 0.033 0.002 TRP I 295 HIS 0.008 0.001 HIS E 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (35623) covalent geometry : angle 0.63610 / 0.33 (49010) hydrogen bonds : bond 0.05087 / 3.41 ( 1468) hydrogen bonds : angle 4.92731 / 3.47 ( 4130) Misc. bond : bond 0.01035 / 0.49 ( 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 717 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 550 time to evaluate : 1.334 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: 0.8291 (OUTLIER) cc_final: 0.7989 (p0) REVERT: A 143 PHE cc_start: 0.6462 (OUTLIER) cc_final: 0.5843 (t80) REVERT: A 184 LYS cc_start: 0.7749 (mttt) cc_final: 0.7194 (ptmt) REVERT: A 237 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.9076 (tt) REVERT: A 278 ARG cc_start: 0.7682 (ttm110) cc_final: 0.7273 (mmp80) REVERT: A 349 THR cc_start: 0.6813 (OUTLIER) cc_final: 0.6422 (p) REVERT: A 373 THR cc_start: 0.8393 (t) cc_final: 0.8160 (m) REVERT: B 333 GLN cc_start: 0.8189 (tt0) cc_final: 0.7984 (tt0) REVERT: B 361 VAL cc_start: 0.7447 (OUTLIER) cc_final: 0.7187 (p) REVERT: E 16 ASN cc_start: 0.8223 (OUTLIER) cc_final: 0.7954 (p0) REVERT: E 287 PHE cc_start: 0.7763 (OUTLIER) cc_final: 0.7300 (t80) REVERT: E 418 LYS cc_start: 0.5449 (tptm) cc_final: 0.4787 (tptm) REVERT: I 22 TRP cc_start: 0.7804 (m100) cc_final: 0.7504 (m100) REVERT: I 139 PHE cc_start: 0.7209 (OUTLIER) cc_final: 0.6485 (p90) REVERT: I 345 CYS cc_start: 0.6078 (p) cc_final: 0.5721 (p) REVERT: I 504 MET cc_start: 0.7497 (mmm) cc_final: 0.7120 (mmm) REVERT: I 518 GLU cc_start: 0.7427 (pm20) cc_final: 0.6413 (tp30) REVERT: I 536 SER cc_start: 0.7967 (t) cc_final: 0.7260 (m) REVERT: J 178 LEU cc_start: 0.6693 (OUTLIER) cc_final: 0.6236 (pp) REVERT: J 376 LEU cc_start: 0.8902 (tp) cc_final: 0.8423 (tp) REVERT: J 465 GLU cc_start: 0.6912 (mp0) cc_final: 0.6307 (mm-30) REVERT: M 94 GLU cc_start: 0.7834 (pt0) cc_final: 0.7536 (pt0) REVERT: M 374 TYR cc_start: 0.4844 (t80) cc_final: 0.4525 (t80) REVERT: M 514 LEU cc_start: 0.8064 (mm) cc_final: 0.7811 (mt) REVERT: M 576 ARG cc_start: 0.4135 (ttt180) cc_final: 0.3220 (ptt-90) REVERT: N 29 HIS cc_start: 0.5385 (t-170) cc_final: 0.5168 (t-170) REVERT: N 147 LEU cc_start: 0.8421 (mt) cc_final: 0.8201 (mp) REVERT: N 193 ARG cc_start: 0.6678 (OUTLIER) cc_final: 0.5788 (tpp80) REVERT: N 197 MET cc_start: 0.7331 (OUTLIER) cc_final: 0.7109 (mpp) REVERT: N 288 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7177 (pt) REVERT: N 313 GLU cc_start: 0.6352 (tp30) cc_final: 0.6090 (tp30) REVERT: N 397 GLU cc_start: 0.5514 (mp0) cc_final: 0.5127 (mp0) outliers start: 167 outliers final: 115 residues processed: 669 average time/residue: 0.2172 time to fit residues: 244.0193 Evaluate side-chains 630 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 503 time to evaluate : 1.267 ------------------------------------------------------------------------------- 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 267 ASP Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 426 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 560 SER 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 137 PHE 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 19 HIS Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 60 HIS Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 190 ARG 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 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 380 PHE Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 426 LEU 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 E residue 572 GLU Chi-restraints excluded: chain F residue 40 TYR Chi-restraints excluded: chain F residue 140 LYS Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 336 GLN 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 144 ASP 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 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 J residue 5 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 148 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 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 77 SER Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 194 ILE Chi-restraints excluded: chain M residue 208 ILE Chi-restraints excluded: chain M residue 275 LYS Chi-restraints excluded: chain M residue 298 VAL Chi-restraints excluded: chain M residue 365 GLN Chi-restraints excluded: chain M residue 381 LEU 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 86 GLU Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 125 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 288 LEU Chi-restraints excluded: chain N residue 293 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 249 optimal weight: 0.9980 chunk 236 optimal weight: 6.9990 chunk 157 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 35 optimal weight: 0.3980 chunk 88 optimal weight: 0.6980 chunk 321 optimal weight: 0.7980 chunk 397 optimal weight: 0.0170 chunk 231 optimal weight: 6.9990 chunk 323 optimal weight: 2.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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 49 GLN B 434 ASN ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 175 ASN ** 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 ** I 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 297 GLN J 49 GLN ** J 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 166 HIS N 191 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.173353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.146727 restraints weight = 64337.367| |-----------------------------------------------------------------------------| r_work (start): 0.4148 rms_B_bonded: 2.65 r_work: 0.4011 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 35626 Z= 0.130 Angle : 0.634 14.846 49010 Z= 0.325 Chirality : 0.042 0.315 5476 Planarity : 0.004 0.051 5685 Dihedral : 17.841 172.481 6497 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 5.51 % Allowed : 29.21 % 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: -0.34 (0.14), residues: 3841 helix: 0.71 (0.14), residues: 1483 sheet: -0.63 (0.19), residues: 784 loop : -0.79 (0.16), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 431 TYR 0.038 0.002 TYR B 205 PHE 0.025 0.002 PHE N 158 TRP 0.045 0.002 TRP I 295 HIS 0.007 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (35623) covalent geometry : angle 0.63367 / 0.33 (49010) hydrogen bonds : bond 0.04972 / 3.34 ( 1468) hydrogen bonds : angle 4.89078 / 3.44 ( 4130) Misc. bond : bond 0.00860 / 0.41 ( 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 716 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 532 time to evaluate : 1.327 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: 0.8303 (OUTLIER) cc_final: 0.7920 (p0) REVERT: A 143 PHE cc_start: 0.6439 (OUTLIER) cc_final: 0.5825 (t80) REVERT: A 184 LYS cc_start: 0.7765 (mttt) cc_final: 0.7143 (ptmt) REVERT: A 237 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9075 (tt) REVERT: A 278 ARG cc_start: 0.7686 (ttm110) cc_final: 0.7290 (mmp80) REVERT: A 349 THR cc_start: 0.6877 (OUTLIER) cc_final: 0.6470 (p) REVERT: A 422 GLU cc_start: 0.7135 (tp30) cc_final: 0.6794 (tp30) REVERT: A 426 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7679 (mm) REVERT: B 333 GLN cc_start: 0.8176 (tt0) cc_final: 0.7890 (tt0) REVERT: B 361 VAL cc_start: 0.7457 (OUTLIER) cc_final: 0.7218 (p) REVERT: E 16 ASN cc_start: 0.8266 (OUTLIER) cc_final: 0.7996 (p0) REVERT: E 287 PHE cc_start: 0.7853 (OUTLIER) cc_final: 0.7440 (t80) REVERT: E 387 ILE cc_start: 0.8013 (mm) cc_final: 0.7583 (tp) REVERT: E 418 LYS cc_start: 0.5371 (tptm) cc_final: 0.4722 (tptm) REVERT: I 139 PHE cc_start: 0.7131 (OUTLIER) cc_final: 0.6451 (p90) REVERT: I 345 CYS cc_start: 0.5899 (p) cc_final: 0.5611 (p) REVERT: I 504 MET cc_start: 0.7472 (mmm) cc_final: 0.6987 (mmm) REVERT: I 518 GLU cc_start: 0.7471 (pm20) cc_final: 0.6232 (tp30) REVERT: I 536 SER cc_start: 0.7955 (t) cc_final: 0.7239 (m) REVERT: J 34 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7876 (mp) REVERT: J 81 THR cc_start: 0.7041 (t) cc_final: 0.6802 (m) REVERT: J 178 LEU cc_start: 0.6704 (OUTLIER) cc_final: 0.6241 (pp) REVERT: J 197 MET cc_start: 0.5354 (tpp) cc_final: 0.5153 (tpp) REVERT: J 333 GLN cc_start: 0.7357 (OUTLIER) cc_final: 0.7047 (tp-100) REVERT: J 376 LEU cc_start: 0.8874 (tp) cc_final: 0.8412 (tp) REVERT: J 465 GLU cc_start: 0.6912 (mp0) cc_final: 0.6339 (mm-30) REVERT: M 94 GLU cc_start: 0.7836 (pt0) cc_final: 0.7494 (pt0) REVERT: M 374 TYR cc_start: 0.4838 (t80) cc_final: 0.4532 (t80) REVERT: M 514 LEU cc_start: 0.8131 (mm) cc_final: 0.7873 (mt) REVERT: M 576 ARG cc_start: 0.4152 (ttt180) cc_final: 0.3234 (ptt-90) REVERT: N 86 GLU cc_start: 0.6116 (OUTLIER) cc_final: 0.5244 (tm-30) REVERT: N 197 MET cc_start: 0.7427 (OUTLIER) cc_final: 0.7183 (mpp) REVERT: N 288 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.6710 (pt) REVERT: N 292 GLN cc_start: 0.8245 (mt0) cc_final: 0.7536 (mp10) REVERT: N 313 GLU cc_start: 0.6486 (tp30) cc_final: 0.6165 (tp30) outliers start: 184 outliers final: 123 residues processed: 663 average time/residue: 0.2112 time to fit residues: 236.5790 Evaluate side-chains 631 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 493 time to evaluate : 1.246 ------------------------------------------------------------------------------- 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 315 CYS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 349 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 547 LEU Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 560 SER 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 104 HIS 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 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 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 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 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 380 PHE Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 426 LEU 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 E residue 577 THR 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 247 VAL Chi-restraints excluded: chain F residue 309 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 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 144 ASP Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain I residue 233 VAL 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 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 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 148 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 333 GLN 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 154 ILE Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 194 ILE 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 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 86 GLU 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 182 ILE Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 255 PHE Chi-restraints excluded: chain N residue 288 LEU Chi-restraints excluded: chain N residue 293 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 181 optimal weight: 0.6980 chunk 6 optimal weight: 6.9990 chunk 289 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 309 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 347 optimal weight: 5.9990 chunk 19 optimal weight: 0.1980 chunk 225 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 302 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 49 GLN B 177 ASN B 458 GLN E 175 ASN ** 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 245 ASN J 82 ASN ** J 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 244 ASN N 191 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.167979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.140609 restraints weight = 65060.764| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 2.84 r_work: 0.3917 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 35626 Z= 0.179 Angle : 0.679 13.382 49010 Z= 0.349 Chirality : 0.044 0.324 5476 Planarity : 0.004 0.052 5685 Dihedral : 17.906 173.458 6495 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 5.60 % Allowed : 29.42 % Favored : 64.98 % 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: -0.39 (0.14), residues: 3841 helix: 0.66 (0.14), residues: 1473 sheet: -0.63 (0.19), residues: 775 loop : -0.82 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 301 TYR 0.030 0.002 TYR E 402 PHE 0.023 0.002 PHE B 44 TRP 0.036 0.002 TRP M 510 HIS 0.010 0.001 HIS I 444 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 (35623) covalent geometry : angle 0.67860 / 0.35 (49010) hydrogen bonds : bond 0.04978 / 3.35 ( 1468) hydrogen bonds : angle 4.91805 / 3.46 ( 4130) Misc. bond : bond 0.02071 / 0.99 ( 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 712 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 525 time to evaluate : 1.315 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 143 PHE cc_start: 0.6489 (OUTLIER) cc_final: 0.5850 (t80) REVERT: A 184 LYS cc_start: 0.7925 (mttt) cc_final: 0.7271 (ptmt) REVERT: A 237 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9062 (tt) REVERT: A 278 ARG cc_start: 0.7916 (ttm110) cc_final: 0.7536 (mmp80) REVERT: A 422 GLU cc_start: 0.7191 (tp30) cc_final: 0.6848 (tp30) REVERT: A 426 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7793 (mm) REVERT: B 303 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8004 (tt) REVERT: B 361 VAL cc_start: 0.7604 (OUTLIER) cc_final: 0.7381 (p) REVERT: B 409 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8774 (mt) REVERT: B 448 TYR cc_start: 0.7724 (t80) cc_final: 0.7519 (t80) REVERT: E 16 ASN cc_start: 0.8473 (OUTLIER) cc_final: 0.8213 (p0) REVERT: E 200 ASP cc_start: 0.7823 (m-30) cc_final: 0.7404 (m-30) REVERT: E 287 PHE cc_start: 0.7963 (OUTLIER) cc_final: 0.7425 (t80) REVERT: E 387 ILE cc_start: 0.8043 (mm) cc_final: 0.7605 (tp) REVERT: E 418 LYS cc_start: 0.5546 (tptm) cc_final: 0.4820 (tptm) REVERT: I 139 PHE cc_start: 0.7046 (OUTLIER) cc_final: 0.6126 (p90) REVERT: I 341 GLN cc_start: 0.7002 (pm20) cc_final: 0.6621 (tm-30) REVERT: I 345 CYS cc_start: 0.5887 (p) cc_final: 0.5592 (p) REVERT: I 504 MET cc_start: 0.7493 (mmm) cc_final: 0.7121 (mmm) REVERT: I 518 GLU cc_start: 0.7580 (pm20) cc_final: 0.6406 (tp30) REVERT: J 34 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7945 (mp) REVERT: J 82 ASN cc_start: 0.6332 (OUTLIER) cc_final: 0.6130 (p0) REVERT: J 178 LEU cc_start: 0.6759 (OUTLIER) cc_final: 0.6282 (pp) REVERT: J 333 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.7208 (tp-100) REVERT: J 465 GLU cc_start: 0.7280 (mp0) cc_final: 0.6550 (mm-30) REVERT: M 94 GLU cc_start: 0.7833 (pt0) cc_final: 0.7525 (pt0) REVERT: M 374 TYR cc_start: 0.4802 (t80) cc_final: 0.4393 (t80) REVERT: M 514 LEU cc_start: 0.8149 (mm) cc_final: 0.7870 (mt) REVERT: M 530 TYR cc_start: 0.5791 (m-80) cc_final: 0.5521 (m-80) REVERT: M 576 ARG cc_start: 0.4315 (ttt180) cc_final: 0.3267 (ptt-90) REVERT: N 100 MET cc_start: 0.8196 (ttm) cc_final: 0.7918 (mpp) REVERT: N 147 LEU cc_start: 0.8515 (mt) cc_final: 0.8297 (mp) REVERT: N 193 ARG cc_start: 0.6738 (OUTLIER) cc_final: 0.5859 (tpp80) REVERT: N 197 MET cc_start: 0.7366 (OUTLIER) cc_final: 0.7132 (mpp) REVERT: N 288 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7425 (pt) REVERT: N 418 TRP cc_start: 0.6941 (m100) cc_final: 0.6600 (m100) outliers start: 187 outliers final: 133 residues processed: 657 average time/residue: 0.2118 time to fit residues: 235.4545 Evaluate side-chains 635 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 486 time to evaluate : 1.260 ------------------------------------------------------------------------------- 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 171 LEU 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 315 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 349 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 478 VAL Chi-restraints excluded: chain A residue 543 TRP Chi-restraints excluded: chain A residue 547 LEU 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 60 HIS Chi-restraints excluded: chain B residue 81 THR 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 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 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 455 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 77 SER Chi-restraints excluded: chain E residue 146 VAL 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 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 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 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 28 THR Chi-restraints excluded: chain F residue 37 TYR 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 247 VAL Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 336 GLN Chi-restraints excluded: chain F residue 466 ILE 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 144 ASP 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 208 ILE 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 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 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 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 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 194 ILE Chi-restraints excluded: chain M residue 208 ILE Chi-restraints excluded: chain M residue 224 SER Chi-restraints excluded: chain M residue 244 ASN 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 440 ARG 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 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 288 LEU Chi-restraints excluded: chain N residue 370 THR Chi-restraints excluded: chain N residue 451 VAL Chi-restraints excluded: chain N residue 463 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 151 optimal weight: 8.9990 chunk 269 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 210 optimal weight: 1.9990 chunk 258 optimal weight: 8.9990 chunk 310 optimal weight: 0.4980 chunk 260 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 371 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 383 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 458 GLN ** F 295 HIS ** 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 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 244 ASN N 191 GLN N 317 GLN N 419 HIS N 434 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.168149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.141147 restraints weight = 64438.720| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 2.63 r_work: 0.3940 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.5274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 35626 Z= 0.147 Angle : 0.659 15.810 49010 Z= 0.338 Chirality : 0.043 0.320 5476 Planarity : 0.004 0.049 5685 Dihedral : 17.893 173.601 6493 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 5.12 % Allowed : 29.84 % 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: -0.40 (0.14), residues: 3841 helix: 0.71 (0.14), residues: 1475 sheet: -0.77 (0.19), residues: 804 loop : -0.82 (0.16), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 332 TYR 0.027 0.002 TYR B 205 PHE 0.042 0.002 PHE I 467 TRP 0.032 0.002 TRP I 295 HIS 0.007 0.001 HIS E 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (35623) covalent geometry : angle 0.65888 / 0.34 (49010) hydrogen bonds : bond 0.04902 / 3.30 ( 1468) hydrogen bonds : angle 4.88474 / 3.43 ( 4130) Misc. bond : bond 0.00698 / 0.33 ( 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 682 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 511 time to evaluate : 1.276 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 143 PHE cc_start: 0.6461 (OUTLIER) cc_final: 0.5854 (t80) REVERT: A 184 LYS cc_start: 0.7916 (mttt) cc_final: 0.7258 (tttt) REVERT: A 237 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9049 (tt) REVERT: A 278 ARG cc_start: 0.7900 (ttm110) cc_final: 0.7445 (mmp80) REVERT: A 422 GLU cc_start: 0.7143 (tp30) cc_final: 0.6787 (tp30) REVERT: A 426 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7741 (mm) REVERT: B 361 VAL cc_start: 0.7599 (OUTLIER) cc_final: 0.7324 (p) REVERT: B 409 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8756 (mt) REVERT: B 448 TYR cc_start: 0.7722 (t80) cc_final: 0.7489 (t80) REVERT: E 16 ASN cc_start: 0.8324 (OUTLIER) cc_final: 0.8068 (p0) REVERT: E 287 PHE cc_start: 0.7899 (OUTLIER) cc_final: 0.7433 (t80) REVERT: E 387 ILE cc_start: 0.8035 (mm) cc_final: 0.7617 (tp) REVERT: E 418 LYS cc_start: 0.5527 (tptm) cc_final: 0.4830 (tptm) REVERT: I 290 MET cc_start: 0.6774 (tmm) cc_final: 0.6448 (tmm) REVERT: I 341 GLN cc_start: 0.6984 (pm20) cc_final: 0.6550 (tm-30) REVERT: I 504 MET cc_start: 0.7474 (mmm) cc_final: 0.7075 (mmm) REVERT: I 518 GLU cc_start: 0.7536 (pm20) cc_final: 0.6368 (tp30) REVERT: J 34 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7921 (mp) REVERT: J 178 LEU cc_start: 0.6710 (OUTLIER) cc_final: 0.6244 (pp) REVERT: J 333 GLN cc_start: 0.7454 (OUTLIER) cc_final: 0.7089 (tp-100) REVERT: J 465 GLU cc_start: 0.7132 (mp0) cc_final: 0.6480 (mm-30) REVERT: M 94 GLU cc_start: 0.7814 (pt0) cc_final: 0.7485 (pt0) REVERT: M 374 TYR cc_start: 0.4791 (t80) cc_final: 0.4393 (t80) REVERT: M 530 TYR cc_start: 0.5755 (m-80) cc_final: 0.5492 (m-80) REVERT: M 576 ARG cc_start: 0.4406 (ttt180) cc_final: 0.3299 (ptt-90) REVERT: N 100 MET cc_start: 0.8284 (ttm) cc_final: 0.7931 (mpp) REVERT: N 193 ARG cc_start: 0.6803 (OUTLIER) cc_final: 0.6000 (tpp-160) REVERT: N 197 MET cc_start: 0.7333 (OUTLIER) cc_final: 0.7078 (mpp) REVERT: N 272 ASN cc_start: 0.8651 (p0) cc_final: 0.8376 (p0) REVERT: N 288 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7447 (pt) outliers start: 171 outliers final: 132 residues processed: 637 average time/residue: 0.2103 time to fit residues: 226.6660 Evaluate side-chains 627 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 482 time to evaluate : 1.261 ------------------------------------------------------------------------------- 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 171 LEU Chi-restraints excluded: chain A residue 181 ILE 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 315 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 349 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 547 LEU 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 60 HIS Chi-restraints excluded: chain B residue 81 THR 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 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 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 60 HIS Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 83 GLN Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 146 VAL 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 333 THR 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 140 LYS Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 309 THR 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 16 ASN 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 144 ASP Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain I residue 233 VAL Chi-restraints excluded: chain I residue 281 LEU Chi-restraints excluded: chain I residue 294 ILE 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 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 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 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 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 194 ILE 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 440 ARG 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 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 288 LEU Chi-restraints excluded: chain N residue 293 SER Chi-restraints excluded: chain N residue 317 GLN Chi-restraints excluded: chain N residue 370 THR Chi-restraints excluded: chain N residue 382 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 369 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 183 optimal weight: 0.7980 chunk 339 optimal weight: 3.9990 chunk 142 optimal weight: 10.0000 chunk 365 optimal weight: 1.9990 chunk 151 optimal weight: 6.9990 chunk 321 optimal weight: 3.9990 chunk 229 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 197 optimal weight: 9.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 F 336 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** ** J 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 158 HIS M 244 ASN 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 = 0.4367 r_free = 0.4367 target = 0.163587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.136283 restraints weight = 64369.348| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 2.67 r_work: 0.3867 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.5655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 35626 Z= 0.206 Angle : 0.710 14.558 49010 Z= 0.365 Chirality : 0.045 0.333 5476 Planarity : 0.005 0.057 5685 Dihedral : 17.960 174.426 6489 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 5.21 % Allowed : 30.23 % Favored : 64.56 % 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: -0.59 (0.14), residues: 3841 helix: 0.52 (0.14), residues: 1476 sheet: -0.85 (0.19), residues: 778 loop : -0.90 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 525 TYR 0.038 0.002 TYR E 402 PHE 0.034 0.002 PHE E 458 TRP 0.050 0.002 TRP F 154 HIS 0.008 0.001 HIS E 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.21 (35623) covalent geometry : angle 0.70956 / 0.37 (49010) hydrogen bonds : bond 0.05116 / 3.45 ( 1468) hydrogen bonds : angle 4.99251 / 3.51 ( 4130) Misc. bond : bond 0.00314 / 0.15 ( 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 680 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 506 time to evaluate : 1.150 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 143 PHE cc_start: 0.6467 (OUTLIER) cc_final: 0.5856 (t80) REVERT: A 184 LYS cc_start: 0.7963 (mttt) cc_final: 0.7280 (tttt) REVERT: A 237 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9089 (tt) REVERT: A 278 ARG cc_start: 0.8018 (ttm110) cc_final: 0.7544 (mmp80) REVERT: A 345 CYS cc_start: 0.7683 (p) cc_final: 0.7460 (p) REVERT: B 131 GLN cc_start: 0.7794 (mt0) cc_final: 0.7475 (mm-40) REVERT: B 448 TYR cc_start: 0.7789 (t80) cc_final: 0.7565 (t80) REVERT: E 16 ASN cc_start: 0.8485 (OUTLIER) cc_final: 0.8227 (p0) REVERT: E 287 PHE cc_start: 0.7923 (OUTLIER) cc_final: 0.7511 (t80) REVERT: E 387 ILE cc_start: 0.8063 (mm) cc_final: 0.7630 (tp) REVERT: E 418 LYS cc_start: 0.5629 (tptm) cc_final: 0.4888 (tptm) REVERT: E 573 ILE cc_start: 0.6782 (mp) cc_final: 0.6455 (mt) REVERT: I 270 THR cc_start: 0.8258 (m) cc_final: 0.8018 (p) REVERT: I 290 MET cc_start: 0.6797 (tmm) cc_final: 0.6421 (tmm) REVERT: I 341 GLN cc_start: 0.7008 (pm20) cc_final: 0.6595 (tm-30) REVERT: I 504 MET cc_start: 0.7469 (mmm) cc_final: 0.7074 (mmm) REVERT: I 518 GLU cc_start: 0.7686 (pm20) cc_final: 0.6483 (tp30) REVERT: J 34 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7957 (mp) REVERT: J 65 ASP cc_start: 0.5916 (OUTLIER) cc_final: 0.5654 (t70) REVERT: J 81 THR cc_start: 0.7444 (p) cc_final: 0.7184 (m) REVERT: J 178 LEU cc_start: 0.6719 (OUTLIER) cc_final: 0.6208 (pp) REVERT: J 320 PHE cc_start: 0.7211 (OUTLIER) cc_final: 0.6648 (m-80) REVERT: J 333 GLN cc_start: 0.7558 (OUTLIER) cc_final: 0.7161 (tp-100) REVERT: J 465 GLU cc_start: 0.7374 (mp0) cc_final: 0.6615 (mm-30) REVERT: M 94 GLU cc_start: 0.7879 (pt0) cc_final: 0.7532 (pt0) REVERT: M 374 TYR cc_start: 0.5017 (t80) cc_final: 0.4488 (t80) REVERT: M 418 LYS cc_start: 0.5151 (tptm) cc_final: 0.4877 (tttm) REVERT: M 514 LEU cc_start: 0.8249 (mm) cc_final: 0.7935 (mt) REVERT: M 530 TYR cc_start: 0.5929 (m-80) cc_final: 0.5717 (m-80) REVERT: N 100 MET cc_start: 0.8305 (ttm) cc_final: 0.7932 (mpp) REVERT: N 193 ARG cc_start: 0.6829 (OUTLIER) cc_final: 0.5925 (tpp-160) REVERT: N 197 MET cc_start: 0.7364 (OUTLIER) cc_final: 0.7094 (mpp) REVERT: N 222 GLU cc_start: 0.6097 (pm20) cc_final: 0.5865 (pm20) REVERT: N 272 ASN cc_start: 0.8783 (p0) cc_final: 0.8506 (p0) REVERT: N 285 SER cc_start: 0.8917 (p) cc_final: 0.8662 (t) REVERT: N 288 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7595 (pt) outliers start: 174 outliers final: 140 residues processed: 637 average time/residue: 0.2109 time to fit residues: 227.3656 Evaluate side-chains 625 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 473 time to evaluate : 1.251 ------------------------------------------------------------------------------- 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 171 LEU 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 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 391 PHE Chi-restraints excluded: chain A residue 404 ILE 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 547 LEU 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 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 282 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 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 60 HIS 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 114 SER Chi-restraints excluded: chain E residue 146 VAL 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 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 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 505 LEU Chi-restraints excluded: chain E residue 560 SER Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 37 TYR 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 180 ILE 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 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 144 ASP 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 208 ILE 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 286 THR 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 65 ASP 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 242 THR Chi-restraints excluded: chain J residue 244 CYS Chi-restraints excluded: chain J residue 287 SER 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 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 194 ILE Chi-restraints excluded: chain M residue 208 ILE Chi-restraints excluded: chain M residue 224 SER Chi-restraints excluded: chain M residue 244 ASN 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 440 ARG 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 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 288 LEU Chi-restraints excluded: chain N residue 293 SER Chi-restraints excluded: chain N residue 316 ILE Chi-restraints excluded: chain N residue 317 GLN Chi-restraints excluded: chain N residue 336 GLN Chi-restraints excluded: chain N residue 370 THR Chi-restraints excluded: chain N residue 382 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 131 optimal weight: 6.9990 chunk 182 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 12 optimal weight: 0.0070 chunk 223 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 325 optimal weight: 0.0270 chunk 228 optimal weight: 8.9990 chunk 391 optimal weight: 1.9990 chunk 280 optimal weight: 0.0040 chunk 21 optimal weight: 2.9990 overall best weight: 0.3268 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 HIS ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 GLN ** F 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 186 HIS M 244 ASN N 191 GLN N 419 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.163931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.136712 restraints weight = 64423.363| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 2.56 r_work: 0.3877 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.5697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.324 35626 Z= 0.221 Angle : 0.802 59.200 49010 Z= 0.430 Chirality : 0.047 0.864 5476 Planarity : 0.005 0.092 5685 Dihedral : 17.967 174.219 6489 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 4.73 % Allowed : 31.04 % Favored : 64.23 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.14), residues: 3841 helix: 0.54 (0.14), residues: 1476 sheet: -0.86 (0.19), residues: 778 loop : -0.91 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.044 0.001 ARG M 206 TYR 0.059 0.002 TYR M 191 PHE 0.040 0.002 PHE E 458 TRP 0.051 0.002 TRP F 154 HIS 0.031 0.002 HIS M 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.22 (35623) covalent geometry : angle 0.80195 / 0.43 (49010) hydrogen bonds : bond 0.05062 / 3.41 ( 1468) hydrogen bonds : angle 4.99919 / 3.52 ( 4130) Misc. bond : bond 0.00306 / 0.15 ( 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 634 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 476 time to evaluate : 1.330 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 143 PHE cc_start: 0.6412 (OUTLIER) cc_final: 0.5815 (t80) REVERT: A 184 LYS cc_start: 0.7978 (mttt) cc_final: 0.7270 (tttt) REVERT: A 237 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9077 (tt) REVERT: A 278 ARG cc_start: 0.7977 (ttm110) cc_final: 0.7532 (mmp80) REVERT: A 345 CYS cc_start: 0.7746 (p) cc_final: 0.7510 (p) REVERT: B 131 GLN cc_start: 0.7784 (mt0) cc_final: 0.7465 (mm-40) REVERT: B 448 TYR cc_start: 0.7806 (t80) cc_final: 0.7560 (t80) REVERT: E 16 ASN cc_start: 0.8464 (OUTLIER) cc_final: 0.8203 (p0) REVERT: E 287 PHE cc_start: 0.7910 (OUTLIER) cc_final: 0.7504 (t80) REVERT: E 387 ILE cc_start: 0.8070 (mm) cc_final: 0.7645 (tp) REVERT: E 418 LYS cc_start: 0.5575 (tptm) cc_final: 0.4849 (tptm) REVERT: E 573 ILE cc_start: 0.6759 (mp) cc_final: 0.6433 (mt) REVERT: I 270 THR cc_start: 0.8272 (m) cc_final: 0.8029 (p) REVERT: I 290 MET cc_start: 0.6790 (tmm) cc_final: 0.6418 (tmm) REVERT: I 341 GLN cc_start: 0.7053 (pm20) cc_final: 0.6606 (tm-30) REVERT: I 504 MET cc_start: 0.7498 (mmm) cc_final: 0.7060 (mmm) REVERT: I 518 GLU cc_start: 0.7669 (pm20) cc_final: 0.6446 (tp30) REVERT: J 34 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7946 (mp) REVERT: J 81 THR cc_start: 0.7425 (p) cc_final: 0.7144 (m) REVERT: J 178 LEU cc_start: 0.6755 (OUTLIER) cc_final: 0.6288 (pp) REVERT: J 320 PHE cc_start: 0.7223 (OUTLIER) cc_final: 0.6660 (m-80) REVERT: J 333 GLN cc_start: 0.7522 (OUTLIER) cc_final: 0.7141 (tp-100) REVERT: J 465 GLU cc_start: 0.7388 (mp0) cc_final: 0.6628 (mm-30) REVERT: M 94 GLU cc_start: 0.7881 (pt0) cc_final: 0.7534 (pt0) REVERT: M 244 ASN cc_start: 0.7964 (OUTLIER) cc_final: 0.7255 (p0) REVERT: M 374 TYR cc_start: 0.4986 (t80) cc_final: 0.4464 (t80) REVERT: M 514 LEU cc_start: 0.8301 (mm) cc_final: 0.8003 (mt) REVERT: M 530 TYR cc_start: 0.5923 (m-80) cc_final: 0.5706 (m-80) REVERT: N 100 MET cc_start: 0.8315 (ttm) cc_final: 0.7908 (mpp) REVERT: N 193 ARG cc_start: 0.6762 (OUTLIER) cc_final: 0.5844 (tpp-160) REVERT: N 197 MET cc_start: 0.7322 (OUTLIER) cc_final: 0.7067 (mpp) REVERT: N 272 ASN cc_start: 0.8778 (p0) cc_final: 0.8505 (p0) REVERT: N 285 SER cc_start: 0.8921 (p) cc_final: 0.8650 (t) outliers start: 158 outliers final: 138 residues processed: 591 average time/residue: 0.2106 time to fit residues: 211.2950 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 : 1.245 ------------------------------------------------------------------------------- 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 171 LEU 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 315 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain A residue 404 ILE 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 547 LEU 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 58 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 139 GLN 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 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 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 60 HIS Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 83 GLN Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 146 VAL 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 252 TYR 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 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 505 LEU Chi-restraints excluded: chain E residue 560 SER Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 37 TYR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 71 LEU 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 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 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 144 ASP 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 208 ILE 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 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 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 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 194 ILE Chi-restraints excluded: chain M residue 224 SER Chi-restraints excluded: chain M residue 244 ASN 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 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 71 LEU Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain N residue 125 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 316 ILE Chi-restraints excluded: chain N residue 370 THR Chi-restraints excluded: chain N residue 382 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 4 optimal weight: 0.9980 chunk 322 optimal weight: 1.9990 chunk 384 optimal weight: 0.6980 chunk 378 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 383 optimal weight: 1.9990 chunk 208 optimal weight: 8.9990 chunk 253 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 HIS ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 GLN ** F 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 191 GLN N 317 GLN N 419 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.163817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.136795 restraints weight = 64117.551| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 2.56 r_work: 0.3875 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.5701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.324 35626 Z= 0.221 Angle : 0.801 57.880 49010 Z= 0.430 Chirality : 0.047 0.855 5476 Planarity : 0.005 0.092 5685 Dihedral : 17.952 174.219 6487 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 19.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 4.52 % Allowed : 31.25 % Favored : 64.23 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.14), residues: 3841 helix: 0.54 (0.14), residues: 1476 sheet: -0.86 (0.19), residues: 778 loop : -0.91 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.044 0.001 ARG M 206 TYR 0.059 0.002 TYR M 191 PHE 0.040 0.002 PHE E 458 TRP 0.051 0.002 TRP F 154 HIS 0.031 0.002 HIS M 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.22 (35623) covalent geometry : angle 0.80087 / 0.43 (49010) hydrogen bonds : bond 0.05062 / 3.41 ( 1468) hydrogen bonds : angle 4.99919 / 3.52 ( 4130) Misc. bond : bond 0.00306 / 0.15 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8978.44 seconds wall clock time: 155 minutes 21.89 seconds (9321.89 seconds total)