Starting phenix.real_space_refine on Tue Aug 26 06:28:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y80_39028/08_2025/8y80_39028.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y80_39028/08_2025/8y80_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_2025/8y80_39028.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y80_39028/08_2025/8y80_39028.map" model { file = "/net/cci-nas-00/data/ceres_data/8y80_39028/08_2025/8y80_39028.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y80_39028/08_2025/8y80_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6.44, 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: 2.29 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 3.94 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: 6.91 Time building geometry restraints manager: 3.01 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: 48667 3.89 - 7.77: 310 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: 5169 0.111 - 0.221: 256 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: 8.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 30.590 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.090 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 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= 0.424 Angle : 0.859 19.435 49010 Z= 0.551 Chirality : 0.057 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 aren 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 covalent geometry : bond 0.00520 (35623) covalent geometry : angle 0.85879 (49010) hydrogen bonds : bond 0.16617 ( 1468) hydrogen bonds : angle 6.83117 ( 4130) Misc. bond : bond 0.28433 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7682 Ramachandran restraints generated. 3841 Oldfield, 0 Emsley, 3841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7682 Ramachandran restraints generated. 3841 Oldfield, 0 Emsley, 3841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1165 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 1031 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASN cc_start: 0.8745 (OUTLIER) cc_final: 0.8494 (p0) REVERT: A 21 MET cc_start: 0.7619 (OUTLIER) cc_final: 0.7380 (ttt) REVERT: A 143 PHE cc_start: 0.6216 (OUTLIER) cc_final: 0.5559 (t80) REVERT: A 184 LYS cc_start: 0.7774 (mttt) cc_final: 0.7544 (pttt) REVERT: A 373 THR cc_start: 0.8049 (t) cc_final: 0.7719 (m) REVERT: A 444 HIS cc_start: 0.5565 (m-70) cc_final: 0.5208 (m-70) REVERT: B 176 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8655 (mp) REVERT: E 40 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8119 (mm) REVERT: F 44 PHE cc_start: 0.6898 (p90) cc_final: 0.6670 (p90) REVERT: F 61 MET cc_start: 0.6293 (mtp) cc_final: 0.6073 (mtp) REVERT: F 133 MET cc_start: 0.6573 (mtt) cc_final: 0.6187 (mtt) REVERT: F 185 ASP cc_start: 0.7106 (OUTLIER) cc_final: 0.6765 (p0) REVERT: F 383 MET cc_start: 0.6999 (mmm) cc_final: 0.6752 (tpp) REVERT: F 459 THR cc_start: 0.8805 (m) cc_final: 0.8360 (p) REVERT: I 22 TRP cc_start: 0.7673 (m100) cc_final: 0.7256 (m100) REVERT: I 208 ILE cc_start: 0.7303 (mm) cc_final: 0.7071 (mm) REVERT: I 234 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.6732 (tpp) REVERT: I 495 GLU cc_start: 0.3678 (tp30) cc_final: 0.3227 (tp30) REVERT: I 518 GLU cc_start: 0.6639 (pm20) cc_final: 0.6124 (tp30) REVERT: J 346 ASP cc_start: 0.6238 (m-30) cc_final: 0.5958 (t0) REVERT: J 376 LEU cc_start: 0.8485 (tp) cc_final: 0.8106 (tp) REVERT: M 47 ARG cc_start: 0.6919 (OUTLIER) cc_final: 0.6689 (mtp85) REVERT: M 62 ILE cc_start: 0.7972 (tp) cc_final: 0.7438 (tp) REVERT: M 374 TYR cc_start: 0.4541 (t80) cc_final: 0.4279 (t80) REVERT: M 576 ARG cc_start: 0.3987 (ttt180) cc_final: 0.3150 (ptt-90) outliers start: 134 outliers final: 63 residues processed: 1137 average time/residue: 0.2159 time to fit residues: 379.8453 Evaluate side-chains 611 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 540 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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: 6.9990 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: 7.9990 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... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 243 GLN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN A 437 HIS B 181 GLN B 195 ASN B 296 ASN B 434 ASN ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 538 GLN ** F 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 ASN ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 177 ASN ** F 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 ASN J 181 GLN J 292 GLN J 296 ASN ** J 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 379 GLN J 392 GLN J 450 GLN M 104 GLN ** M 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 186 HIS M 266 GLN N 195 ASN ** N 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 296 ASN 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 = 0.4444 r_free = 0.4444 target = 0.170684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.143044 restraints weight = 65024.613| |-----------------------------------------------------------------------------| r_work (start): 0.4100 rms_B_bonded: 2.83 r_work: 0.3948 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 35626 Z= 0.241 Angle : 0.780 14.276 49010 Z= 0.401 Chirality : 0.046 0.249 5476 Planarity : 0.006 0.083 5685 Dihedral : 18.354 172.544 6620 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.76 % Favored : 95.21 % Rotamer: Outliers : 7.54 % Allowed : 28.28 % Favored : 64.17 % 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 aren not related in a simple way. whole: -0.53 (0.13), residues: 3841 helix: 0.42 (0.13), residues: 1454 sheet: -0.66 (0.19), residues: 730 loop : -0.79 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 298 TYR 0.044 0.003 TYR I 271 PHE 0.027 0.002 PHE E 287 TRP 0.029 0.002 TRP F 340 HIS 0.017 0.002 HIS E 52 Details of bonding type rmsd covalent geometry : bond 0.00553 (35623) covalent geometry : angle 0.78029 (49010) hydrogen bonds : bond 0.05230 ( 1468) hydrogen bonds : angle 5.34366 ( 4130) Misc. bond : bond 0.00294 ( 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 873 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 252 poor density : 621 time to evaluate : 1.185 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: 0.8014 (OUTLIER) cc_final: 0.7545 (p0) REVERT: A 143 PHE cc_start: 0.6616 (OUTLIER) cc_final: 0.5936 (t80) REVERT: A 184 LYS cc_start: 0.7817 (mttt) cc_final: 0.7209 (ptmt) REVERT: A 289 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8648 (tm-30) REVERT: A 331 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8582 (pt) REVERT: A 532 PHE cc_start: 0.6382 (m-80) cc_final: 0.6124 (m-80) REVERT: B 137 PHE cc_start: 0.7170 (m-10) cc_final: 0.6968 (m-80) REVERT: B 275 LEU cc_start: 0.8063 (mp) cc_final: 0.7324 (mp) REVERT: E 16 ASN cc_start: 0.8442 (OUTLIER) cc_final: 0.8151 (p0) REVERT: E 213 LEU cc_start: 0.8375 (mt) cc_final: 0.8085 (mt) REVERT: E 287 PHE cc_start: 0.7375 (OUTLIER) cc_final: 0.6759 (t80) REVERT: E 352 SER cc_start: 0.4711 (OUTLIER) cc_final: 0.4411 (m) REVERT: E 414 SER cc_start: 0.5448 (t) cc_final: 0.5235 (t) REVERT: E 521 THR cc_start: 0.8011 (p) cc_final: 0.7792 (p) REVERT: F 185 ASP cc_start: 0.7169 (OUTLIER) cc_final: 0.6889 (p0) REVERT: F 190 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.6031 (tmm160) REVERT: I 22 TRP cc_start: 0.8053 (m100) cc_final: 0.7753 (m100) REVERT: I 139 PHE cc_start: 0.7120 (OUTLIER) cc_final: 0.6412 (p90) REVERT: I 234 MET cc_start: 0.7185 (tpp) cc_final: 0.6632 (tpp) REVERT: I 345 CYS cc_start: 0.6304 (p) cc_final: 0.5988 (p) REVERT: I 518 GLU cc_start: 0.7530 (pm20) cc_final: 0.6404 (tp30) REVERT: J 8 LEU cc_start: 0.8139 (mt) cc_final: 0.7914 (mt) REVERT: J 178 LEU cc_start: 0.6745 (OUTLIER) cc_final: 0.6271 (pp) REVERT: J 376 LEU cc_start: 0.8945 (tp) cc_final: 0.8470 (tp) REVERT: J 465 GLU cc_start: 0.7225 (mp0) cc_final: 0.6448 (mm-30) REVERT: M 94 GLU cc_start: 0.7947 (pt0) cc_final: 0.7637 (pt0) REVERT: M 163 HIS cc_start: 0.7531 (OUTLIER) cc_final: 0.7312 (p90) REVERT: M 374 TYR cc_start: 0.4965 (t80) cc_final: 0.4044 (t80) REVERT: M 441 HIS cc_start: 0.7063 (m-70) cc_final: 0.6845 (m90) REVERT: M 514 LEU cc_start: 0.8165 (mm) cc_final: 0.7828 (mt) REVERT: M 576 ARG cc_start: 0.4255 (ttt180) cc_final: 0.3151 (ptt-90) REVERT: N 133 MET cc_start: 0.8030 (mtt) cc_final: 0.7723 (mtt) REVERT: N 158 PHE cc_start: 0.6984 (m-10) cc_final: 0.6334 (m-80) REVERT: N 197 MET cc_start: 0.7405 (OUTLIER) cc_final: 0.7104 (mmp) REVERT: N 215 LEU cc_start: 0.6617 (OUTLIER) cc_final: 0.5836 (pt) REVERT: N 218 TRP cc_start: 0.6119 (OUTLIER) cc_final: 0.5903 (m-90) REVERT: N 280 MET cc_start: 0.8436 (tpp) cc_final: 0.7990 (tpp) REVERT: N 408 MET cc_start: 0.5584 (mmm) cc_final: 0.4959 (mtp) outliers start: 252 outliers final: 112 residues processed: 802 average time/residue: 0.1800 time to fit residues: 236.9304 Evaluate side-chains 629 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 502 time to evaluate : 0.988 ------------------------------------------------------------------------------- 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 221 LEU Chi-restraints excluded: chain A residue 289 GLU 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 429 LEU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 511 ILE 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 12 SER 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 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 308 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain E residue 60 HIS Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 143 PHE Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 287 PHE Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 490 VAL Chi-restraints excluded: chain E residue 505 LEU 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 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 242 THR Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain I residue 16 ASN Chi-restraints excluded: chain I residue 17 SER 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 233 VAL 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 429 LEU 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 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 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 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 163 HIS Chi-restraints excluded: chain M residue 164 LEU 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 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 182 ILE Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 215 LEU Chi-restraints excluded: chain N residue 218 TRP Chi-restraints excluded: chain N residue 245 SER Chi-restraints excluded: chain N residue 255 PHE Chi-restraints excluded: chain N residue 256 GLU Chi-restraints excluded: chain N residue 293 SER Chi-restraints excluded: chain N residue 370 THR Chi-restraints excluded: chain N residue 429 THR Chi-restraints excluded: chain N residue 454 ASP Chi-restraints excluded: chain N residue 466 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 63 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 289 optimal weight: 0.9990 chunk 290 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 205 optimal weight: 0.8980 chunk 235 optimal weight: 0.0980 chunk 227 optimal weight: 0.9990 chunk 352 optimal weight: 6.9990 chunk 262 optimal weight: 10.0000 chunk 361 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 GLN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN B 49 GLN B 60 HIS B 306 HIS E 55 GLN E 83 GLN ** E 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 238 GLN ** F 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 386 ASN I 7 ASN I 243 GLN ** I 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 ASN J 195 ASN J 387 GLN M 12 HIS ** M 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 163 HIS N 82 ASN N 177 ASN N 191 GLN N 317 GLN ** N 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.171646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.144442 restraints weight = 64640.928| |-----------------------------------------------------------------------------| r_work (start): 0.4120 rms_B_bonded: 2.80 r_work: 0.3973 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.4243 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= 0.145 Angle : 0.664 13.137 49010 Z= 0.336 Chirality : 0.042 0.264 5476 Planarity : 0.005 0.118 5685 Dihedral : 18.014 172.738 6522 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 5.48 % Allowed : 29.33 % Favored : 65.19 % 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 aren not related in a simple way. whole: -0.39 (0.14), residues: 3841 helix: 0.54 (0.13), residues: 1497 sheet: -0.61 (0.19), residues: 734 loop : -0.74 (0.15), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 528 TYR 0.026 0.002 TYR J 83 PHE 0.023 0.002 PHE E 287 TRP 0.020 0.001 TRP N 433 HIS 0.012 0.001 HIS E 52 Details of bonding type rmsd covalent geometry : bond 0.00329 (35623) covalent geometry : angle 0.66430 (49010) hydrogen bonds : bond 0.04821 ( 1468) hydrogen bonds : angle 5.02498 ( 4130) Misc. bond : bond 0.00254 ( 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 746 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 563 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASN cc_start: 0.8292 (OUTLIER) cc_final: 0.8014 (p0) REVERT: A 21 MET cc_start: 0.8072 (mtm) cc_final: 0.7708 (mtm) REVERT: A 143 PHE cc_start: 0.6617 (OUTLIER) cc_final: 0.5943 (t80) REVERT: A 184 LYS cc_start: 0.7789 (mttt) cc_final: 0.7207 (ptmt) REVERT: A 219 PHE cc_start: 0.7904 (OUTLIER) cc_final: 0.7075 (p90) REVERT: A 221 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8149 (tp) REVERT: A 237 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.9068 (tt) REVERT: B 361 VAL cc_start: 0.7539 (OUTLIER) cc_final: 0.7249 (p) REVERT: E 16 ASN cc_start: 0.8340 (OUTLIER) cc_final: 0.8064 (p0) REVERT: E 213 LEU cc_start: 0.8267 (mt) cc_final: 0.7959 (mt) REVERT: E 287 PHE cc_start: 0.7715 (OUTLIER) cc_final: 0.7238 (t80) REVERT: E 387 ILE cc_start: 0.7982 (mm) cc_final: 0.7570 (tp) REVERT: E 414 SER cc_start: 0.5109 (t) cc_final: 0.4733 (p) REVERT: E 448 ILE cc_start: 0.4262 (mp) cc_final: 0.3996 (mp) REVERT: E 528 ARG cc_start: 0.6480 (ttm110) cc_final: 0.5469 (ttp80) REVERT: F 51 ARG cc_start: 0.7310 (mpp80) cc_final: 0.6871 (mtm180) REVERT: F 238 GLN cc_start: 0.6893 (OUTLIER) cc_final: 0.6333 (mp10) REVERT: I 139 PHE cc_start: 0.7398 (OUTLIER) cc_final: 0.6797 (p90) REVERT: I 234 MET cc_start: 0.6875 (tpp) cc_final: 0.6346 (ptp) REVERT: I 290 MET cc_start: 0.6911 (tmm) cc_final: 0.6564 (tmm) REVERT: I 345 CYS cc_start: 0.5966 (OUTLIER) cc_final: 0.5765 (p) REVERT: I 495 GLU cc_start: 0.3928 (tp30) cc_final: 0.3566 (tp30) REVERT: I 504 MET cc_start: 0.7280 (mmm) cc_final: 0.6732 (mmm) REVERT: I 518 GLU cc_start: 0.7583 (pm20) cc_final: 0.6322 (tp30) REVERT: I 536 SER cc_start: 0.7885 (t) cc_final: 0.7197 (m) REVERT: J 197 MET cc_start: 0.6681 (mmt) cc_final: 0.6444 (tpp) REVERT: J 234 ASN cc_start: 0.7513 (t0) cc_final: 0.7283 (t0) REVERT: J 376 LEU cc_start: 0.8945 (tp) cc_final: 0.8466 (tp) REVERT: J 465 GLU cc_start: 0.7045 (mp0) cc_final: 0.6294 (mm-30) REVERT: M 94 GLU cc_start: 0.7779 (pt0) cc_final: 0.7411 (pt0) REVERT: M 374 TYR cc_start: 0.4890 (t80) cc_final: 0.3908 (t80) REVERT: M 508 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6679 (mp0) REVERT: M 514 LEU cc_start: 0.8090 (mm) cc_final: 0.7782 (mt) REVERT: M 576 ARG cc_start: 0.4274 (ttt180) cc_final: 0.3303 (ptt-90) REVERT: N 100 MET cc_start: 0.8171 (ttm) cc_final: 0.7844 (pmm) REVERT: N 133 MET cc_start: 0.7922 (mtt) cc_final: 0.7504 (mtt) REVERT: N 158 PHE cc_start: 0.6981 (m-10) cc_final: 0.6675 (m-80) REVERT: N 197 MET cc_start: 0.7365 (OUTLIER) cc_final: 0.7128 (mpp) REVERT: N 215 LEU cc_start: 0.6643 (OUTLIER) cc_final: 0.6095 (pt) REVERT: N 240 TYR cc_start: 0.7323 (m-80) cc_final: 0.6576 (m-80) outliers start: 183 outliers final: 98 residues processed: 695 average time/residue: 0.1660 time to fit residues: 192.6668 Evaluate side-chains 620 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 508 time to evaluate : 1.077 ------------------------------------------------------------------------------- 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 221 LEU 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 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 478 VAL Chi-restraints excluded: chain A residue 543 TRP Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 166 HIS 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 303 ILE Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 60 HIS Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 119 LEU 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 282 VAL Chi-restraints excluded: chain E residue 287 PHE Chi-restraints excluded: chain E residue 298 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 363 ILE Chi-restraints excluded: chain E residue 380 PHE Chi-restraints excluded: chain E residue 417 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 139 GLN 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 211 ILE Chi-restraints excluded: chain F residue 238 GLN Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 19 HIS Chi-restraints excluded: chain I residue 139 PHE Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 143 PHE Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 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 294 ILE Chi-restraints excluded: chain I residue 301 LYS 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 345 CYS Chi-restraints excluded: chain I residue 407 ILE Chi-restraints excluded: chain I residue 417 LEU 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 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 154 ILE Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 208 ILE Chi-restraints excluded: chain M residue 224 SER Chi-restraints excluded: chain M residue 298 VAL Chi-restraints excluded: chain M residue 347 VAL 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 M residue 573 ILE 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 197 MET Chi-restraints excluded: chain N residue 215 LEU Chi-restraints excluded: chain N residue 370 THR Chi-restraints excluded: chain N residue 382 VAL Chi-restraints excluded: chain N residue 463 VAL Chi-restraints excluded: chain N residue 466 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 335 optimal weight: 9.9990 chunk 322 optimal weight: 0.5980 chunk 245 optimal weight: 9.9990 chunk 393 optimal weight: 6.9990 chunk 146 optimal weight: 0.0970 chunk 28 optimal weight: 0.9990 chunk 309 optimal weight: 5.9990 chunk 397 optimal weight: 8.9990 chunk 357 optimal weight: 0.8980 chunk 257 optimal weight: 0.5980 chunk 389 optimal weight: 7.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 60 HIS ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 GLN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 HIS E 245 ASN E 365 GLN ** F 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 GLN ** F 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 436 ASN I 16 ASN I 297 GLN J 82 ASN J 306 HIS ** M 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 191 GLN N 317 GLN N 367 GLN N 419 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.171375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.144138 restraints weight = 64231.011| |-----------------------------------------------------------------------------| r_work (start): 0.4122 rms_B_bonded: 2.74 r_work: 0.3980 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.4632 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= 0.134 Angle : 0.642 13.291 49010 Z= 0.324 Chirality : 0.041 0.245 5476 Planarity : 0.004 0.051 5685 Dihedral : 17.890 173.887 6502 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 5.12 % Allowed : 29.24 % Favored : 65.64 % 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 aren not related in a simple way. whole: -0.38 (0.14), residues: 3841 helix: 0.64 (0.14), residues: 1487 sheet: -0.66 (0.19), residues: 774 loop : -0.77 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 115 TYR 0.022 0.002 TYR J 83 PHE 0.045 0.002 PHE A 532 TRP 0.042 0.002 TRP F 154 HIS 0.010 0.001 HIS E 52 Details of bonding type rmsd covalent geometry : bond 0.00303 (35623) covalent geometry : angle 0.64209 (49010) hydrogen bonds : bond 0.04588 ( 1468) hydrogen bonds : angle 4.85868 ( 4130) Misc. bond : bond 0.00687 ( 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 731 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 560 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASN cc_start: 0.8265 (OUTLIER) cc_final: 0.8060 (p0) REVERT: A 143 PHE cc_start: 0.6580 (OUTLIER) cc_final: 0.5947 (t80) REVERT: A 184 LYS cc_start: 0.7822 (mttt) cc_final: 0.7236 (ptmt) REVERT: A 237 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9081 (tt) REVERT: A 278 ARG cc_start: 0.7701 (ttm110) cc_final: 0.7389 (mmp80) REVERT: B 361 VAL cc_start: 0.7502 (OUTLIER) cc_final: 0.7231 (p) REVERT: E 213 LEU cc_start: 0.8407 (mt) cc_final: 0.8024 (mt) REVERT: E 287 PHE cc_start: 0.7821 (OUTLIER) cc_final: 0.7466 (t80) REVERT: E 387 ILE cc_start: 0.8028 (mm) cc_final: 0.7596 (tp) REVERT: E 414 SER cc_start: 0.5533 (t) cc_final: 0.5192 (p) REVERT: E 418 LYS cc_start: 0.5481 (tptm) cc_final: 0.4814 (tptm) REVERT: E 448 ILE cc_start: 0.4445 (mp) cc_final: 0.4185 (mp) REVERT: E 528 ARG cc_start: 0.6465 (ttm110) cc_final: 0.5443 (ttp80) REVERT: I 139 PHE cc_start: 0.7389 (OUTLIER) cc_final: 0.6880 (p90) REVERT: I 234 MET cc_start: 0.6789 (tpp) cc_final: 0.6421 (ptp) REVERT: I 290 MET cc_start: 0.6856 (tmm) cc_final: 0.6561 (tmm) REVERT: I 341 GLN cc_start: 0.7014 (pm20) cc_final: 0.6712 (tm-30) REVERT: I 345 CYS cc_start: 0.5971 (OUTLIER) cc_final: 0.5616 (p) REVERT: I 504 MET cc_start: 0.7189 (mmm) cc_final: 0.6542 (mmm) REVERT: I 518 GLU cc_start: 0.7610 (pm20) cc_final: 0.6501 (tp30) REVERT: I 536 SER cc_start: 0.7882 (t) cc_final: 0.7177 (m) REVERT: J 234 ASN cc_start: 0.7594 (t0) cc_final: 0.7336 (t0) REVERT: J 465 GLU cc_start: 0.7092 (mp0) cc_final: 0.6375 (mm-30) REVERT: M 94 GLU cc_start: 0.7801 (pt0) cc_final: 0.7457 (pt0) REVERT: M 374 TYR cc_start: 0.4880 (t80) cc_final: 0.4527 (t80) REVERT: M 508 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6705 (mp0) REVERT: M 514 LEU cc_start: 0.8186 (mm) cc_final: 0.7915 (mt) REVERT: M 576 ARG cc_start: 0.4215 (ttt180) cc_final: 0.3242 (ptt-90) REVERT: N 133 MET cc_start: 0.7792 (mtt) cc_final: 0.7425 (mtt) REVERT: N 158 PHE cc_start: 0.7079 (m-10) cc_final: 0.6727 (m-80) REVERT: N 197 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.7213 (mpp) outliers start: 171 outliers final: 100 residues processed: 683 average time/residue: 0.1729 time to fit residues: 197.4002 Evaluate side-chains 606 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 497 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 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 B residue 81 THR Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 166 HIS 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 303 ILE Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 60 HIS Chi-restraints excluded: chain E residue 121 ILE 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 282 VAL Chi-restraints excluded: chain E residue 287 PHE Chi-restraints excluded: chain E residue 298 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 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 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 337 SER Chi-restraints excluded: chain F residue 438 LEU 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 139 PHE Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 143 PHE Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 219 PHE Chi-restraints excluded: chain I residue 233 VAL Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 281 LEU Chi-restraints excluded: chain I residue 289 GLU 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 345 CYS Chi-restraints excluded: chain I residue 407 ILE Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 557 VAL Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 221 ASP Chi-restraints excluded: chain J residue 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 466 ILE Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 298 VAL Chi-restraints excluded: chain M residue 440 ARG Chi-restraints excluded: chain M residue 508 GLU Chi-restraints excluded: chain M residue 573 ILE Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 182 ILE Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 245 SER Chi-restraints excluded: chain N residue 370 THR Chi-restraints excluded: chain N residue 382 VAL Chi-restraints excluded: chain N residue 421 THR Chi-restraints excluded: chain N residue 429 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: 0.0970 chunk 218 optimal weight: 8.9990 chunk 200 optimal weight: 6.9990 chunk 285 optimal weight: 4.9990 chunk 127 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 273 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 233 optimal weight: 6.9990 chunk 190 optimal weight: 0.0050 overall best weight: 1.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 HIS B 60 HIS ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 ASN E 175 ASN F 60 HIS ** F 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 278 GLN F 336 GLN ** F 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 436 ASN ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 244 ASN N 191 GLN N 317 GLN N 419 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.163221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.135570 restraints weight = 64658.236| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 2.69 r_work: 0.3864 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.5391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 35626 Z= 0.202 Angle : 0.693 14.426 49010 Z= 0.348 Chirality : 0.043 0.246 5476 Planarity : 0.005 0.051 5685 Dihedral : 17.966 175.910 6495 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 6.41 % Allowed : 28.20 % Favored : 65.40 % 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 aren not related in a simple way. whole: -0.52 (0.13), residues: 3841 helix: 0.55 (0.14), residues: 1470 sheet: -0.74 (0.19), residues: 780 loop : -0.87 (0.15), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 32 TYR 0.022 0.002 TYR B 87 PHE 0.022 0.002 PHE E 189 TRP 0.031 0.002 TRP I 295 HIS 0.011 0.002 HIS E 52 Details of bonding type rmsd covalent geometry : bond 0.00473 (35623) covalent geometry : angle 0.69302 (49010) hydrogen bonds : bond 0.04748 ( 1468) hydrogen bonds : angle 4.93933 ( 4130) Misc. bond : bond 0.00639 ( 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 740 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 214 poor density : 526 time to evaluate : 1.111 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: 0.8444 (OUTLIER) cc_final: 0.8210 (p0) REVERT: A 143 PHE cc_start: 0.6559 (OUTLIER) cc_final: 0.5899 (t80) REVERT: A 184 LYS cc_start: 0.7892 (mttt) cc_final: 0.7236 (tttt) REVERT: A 237 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9081 (tt) REVERT: A 278 ARG cc_start: 0.7917 (ttm110) cc_final: 0.7560 (mmp80) REVERT: B 131 GLN cc_start: 0.7751 (mt0) cc_final: 0.7422 (mm-40) REVERT: B 409 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8723 (mt) REVERT: B 448 TYR cc_start: 0.7808 (t80) cc_final: 0.7524 (t80) REVERT: E 121 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7827 (tp) REVERT: E 387 ILE cc_start: 0.8080 (mm) cc_final: 0.7662 (tp) REVERT: E 414 SER cc_start: 0.5596 (t) cc_final: 0.4964 (t) REVERT: E 418 LYS cc_start: 0.5779 (tptm) cc_final: 0.5034 (tptm) REVERT: E 573 ILE cc_start: 0.6669 (mp) cc_final: 0.6372 (mt) REVERT: F 220 LYS cc_start: 0.6562 (mmtt) cc_final: 0.5870 (ptpp) REVERT: I 22 TRP cc_start: 0.7932 (m100) cc_final: 0.7666 (m100) REVERT: I 234 MET cc_start: 0.6892 (tpp) cc_final: 0.6613 (tpp) REVERT: I 270 THR cc_start: 0.8239 (m) cc_final: 0.8007 (p) REVERT: I 341 GLN cc_start: 0.6963 (pm20) cc_final: 0.6651 (tm-30) REVERT: I 345 CYS cc_start: 0.5491 (OUTLIER) cc_final: 0.5282 (p) REVERT: I 504 MET cc_start: 0.7320 (mmm) cc_final: 0.6764 (mmm) REVERT: I 518 GLU cc_start: 0.7768 (pm20) cc_final: 0.6846 (tp30) REVERT: I 551 ILE cc_start: 0.5441 (OUTLIER) cc_final: 0.5207 (mp) REVERT: J 16 GLU cc_start: 0.7762 (tt0) cc_final: 0.7418 (pt0) REVERT: J 154 TRP cc_start: 0.7601 (m-10) cc_final: 0.7353 (m-10) REVERT: J 178 LEU cc_start: 0.6685 (OUTLIER) cc_final: 0.6244 (pp) REVERT: M 374 TYR cc_start: 0.5039 (t80) cc_final: 0.4531 (t80) REVERT: M 530 TYR cc_start: 0.5929 (m-80) cc_final: 0.5616 (m-80) REVERT: N 100 MET cc_start: 0.8332 (ttm) cc_final: 0.8019 (mpp) REVERT: N 133 MET cc_start: 0.7988 (mtt) cc_final: 0.7573 (mtm) REVERT: N 197 MET cc_start: 0.7400 (OUTLIER) cc_final: 0.7117 (mpp) REVERT: N 222 GLU cc_start: 0.6630 (OUTLIER) cc_final: 0.6314 (pm20) REVERT: N 301 ARG cc_start: 0.6933 (ptm-80) cc_final: 0.6531 (ppt170) outliers start: 214 outliers final: 139 residues processed: 679 average time/residue: 0.1655 time to fit residues: 190.3489 Evaluate side-chains 621 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 472 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 543 TRP Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 166 HIS 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 303 ILE 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 B residue 409 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 60 HIS Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 190 ARG Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 363 ILE Chi-restraints excluded: chain E residue 380 PHE Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 560 SER Chi-restraints excluded: chain E residue 561 CYS Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 127 ASP 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 180 ILE Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 245 SER Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 289 HIS Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 143 PHE Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 219 PHE Chi-restraints excluded: chain I residue 233 VAL Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 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 345 CYS Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 547 LEU Chi-restraints excluded: chain I residue 551 ILE Chi-restraints excluded: chain I residue 580 SER Chi-restraints excluded: chain I residue 583 VAL Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 83 TYR 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 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 309 THR Chi-restraints excluded: chain J residue 374 CYS 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 109 LEU Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 144 ASP 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 244 ASN Chi-restraints excluded: chain M residue 298 VAL Chi-restraints excluded: chain M residue 402 TYR Chi-restraints excluded: chain M residue 440 ARG Chi-restraints excluded: chain M residue 557 VAL Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 182 ILE Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 222 GLU Chi-restraints excluded: chain N residue 244 CYS Chi-restraints excluded: chain N residue 245 SER Chi-restraints excluded: chain N residue 293 SER Chi-restraints excluded: chain N residue 336 GLN Chi-restraints excluded: chain N residue 370 THR Chi-restraints excluded: chain N residue 382 VAL Chi-restraints excluded: chain N residue 429 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: 5.9990 chunk 236 optimal weight: 10.0000 chunk 157 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 35 optimal weight: 0.4980 chunk 88 optimal weight: 2.9990 chunk 321 optimal weight: 0.9990 chunk 397 optimal weight: 10.0000 chunk 231 optimal weight: 5.9990 chunk 323 optimal weight: 0.4980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 16 ASN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 HIS B 60 HIS ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 ASN ** F 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 GLN ** F 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 436 ASN ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 209 HIS J 49 GLN M 18 GLN ** M 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 244 ASN N 191 GLN N 317 GLN N 389 ASN N 419 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.164127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.136454 restraints weight = 64061.371| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 2.72 r_work: 0.3883 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.5690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35626 Z= 0.150 Angle : 0.655 14.161 49010 Z= 0.328 Chirality : 0.042 0.260 5476 Planarity : 0.004 0.049 5685 Dihedral : 17.893 176.456 6491 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 5.24 % Allowed : 29.75 % Favored : 65.01 % 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 aren not related in a simple way. whole: -0.41 (0.14), residues: 3841 helix: 0.64 (0.14), residues: 1480 sheet: -0.73 (0.19), residues: 804 loop : -0.77 (0.16), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 576 TYR 0.019 0.002 TYR J 87 PHE 0.023 0.002 PHE E 287 TRP 0.040 0.002 TRP I 295 HIS 0.009 0.001 HIS I 444 Details of bonding type rmsd covalent geometry : bond 0.00343 (35623) covalent geometry : angle 0.65549 (49010) hydrogen bonds : bond 0.04552 ( 1468) hydrogen bonds : angle 4.83802 ( 4130) Misc. bond : bond 0.00630 ( 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 689 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 514 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASN cc_start: 0.8124 (OUTLIER) cc_final: 0.7894 (p0) REVERT: A 143 PHE cc_start: 0.6510 (OUTLIER) cc_final: 0.5880 (t80) REVERT: A 184 LYS cc_start: 0.7894 (mttt) cc_final: 0.7184 (tttt) REVERT: A 237 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9109 (tt) REVERT: A 278 ARG cc_start: 0.7987 (ttm110) cc_final: 0.7417 (mmp80) REVERT: A 345 CYS cc_start: 0.7798 (p) cc_final: 0.7535 (p) REVERT: B 131 GLN cc_start: 0.7754 (mt0) cc_final: 0.7410 (mm-40) REVERT: B 133 MET cc_start: 0.7558 (mtm) cc_final: 0.7317 (mtp) REVERT: B 448 TYR cc_start: 0.7813 (t80) cc_final: 0.7547 (t80) REVERT: E 121 ILE cc_start: 0.8015 (OUTLIER) cc_final: 0.7805 (tp) REVERT: E 387 ILE cc_start: 0.8091 (mm) cc_final: 0.7698 (tp) REVERT: E 414 SER cc_start: 0.5414 (t) cc_final: 0.4797 (t) REVERT: E 418 LYS cc_start: 0.5686 (tptm) cc_final: 0.5000 (tptm) REVERT: E 556 THR cc_start: 0.7147 (OUTLIER) cc_final: 0.6688 (p) REVERT: E 558 ASN cc_start: 0.6972 (OUTLIER) cc_final: 0.6493 (m-40) REVERT: E 573 ILE cc_start: 0.6815 (mp) cc_final: 0.6417 (mt) REVERT: I 22 TRP cc_start: 0.7925 (m100) cc_final: 0.7672 (m100) REVERT: I 227 SER cc_start: 0.6853 (p) cc_final: 0.6621 (m) REVERT: I 234 MET cc_start: 0.6798 (tpp) cc_final: 0.6540 (tpp) REVERT: I 270 THR cc_start: 0.8279 (m) cc_final: 0.8039 (p) REVERT: I 341 GLN cc_start: 0.6974 (pm20) cc_final: 0.6692 (tm-30) REVERT: I 345 CYS cc_start: 0.5667 (OUTLIER) cc_final: 0.5440 (p) REVERT: I 504 MET cc_start: 0.7355 (mmm) cc_final: 0.6714 (mmm) REVERT: I 518 GLU cc_start: 0.7768 (pm20) cc_final: 0.6934 (tp30) REVERT: I 528 ARG cc_start: 0.6865 (OUTLIER) cc_final: 0.6370 (ttm170) REVERT: J 16 GLU cc_start: 0.7756 (tt0) cc_final: 0.7501 (pt0) REVERT: J 154 TRP cc_start: 0.7621 (m-10) cc_final: 0.7392 (m-10) REVERT: M 374 TYR cc_start: 0.5052 (t80) cc_final: 0.4470 (t80) REVERT: M 514 LEU cc_start: 0.8207 (mm) cc_final: 0.7907 (mt) REVERT: M 530 TYR cc_start: 0.5841 (m-80) cc_final: 0.5571 (m-80) REVERT: N 100 MET cc_start: 0.8360 (ttm) cc_final: 0.7982 (mpp) REVERT: N 133 MET cc_start: 0.7838 (mtt) cc_final: 0.7430 (mtm) REVERT: N 193 ARG cc_start: 0.6779 (OUTLIER) cc_final: 0.6030 (tpp-160) REVERT: N 197 MET cc_start: 0.7412 (OUTLIER) cc_final: 0.7107 (mpp) REVERT: N 222 GLU cc_start: 0.6595 (OUTLIER) cc_final: 0.6198 (pm20) REVERT: N 272 ASN cc_start: 0.8806 (p0) cc_final: 0.8530 (p0) REVERT: N 301 ARG cc_start: 0.6920 (ptm-80) cc_final: 0.6481 (ppt170) outliers start: 175 outliers final: 124 residues processed: 646 average time/residue: 0.1684 time to fit residues: 183.0667 Evaluate side-chains 601 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 466 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 543 TRP Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 60 HIS Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 164 LEU 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 282 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 363 ILE Chi-restraints excluded: chain E residue 380 PHE Chi-restraints excluded: chain E residue 384 GLU Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 556 THR Chi-restraints excluded: chain E residue 558 ASN Chi-restraints excluded: chain E residue 560 SER 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 F residue 285 SER Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 438 LEU 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 146 VAL Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 209 HIS Chi-restraints excluded: chain I residue 219 PHE Chi-restraints excluded: chain I residue 233 VAL Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 281 LEU Chi-restraints excluded: chain I residue 294 ILE Chi-restraints excluded: chain I residue 306 ASP Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 345 CYS Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 528 ARG Chi-restraints excluded: chain I residue 547 LEU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 221 ASP Chi-restraints excluded: chain J residue 242 THR Chi-restraints excluded: chain J residue 244 CYS Chi-restraints excluded: chain J residue 302 LYS Chi-restraints excluded: chain J residue 334 ILE Chi-restraints excluded: chain J residue 374 CYS Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 442 LEU Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 93 PHE Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 144 ASP Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain M residue 298 VAL Chi-restraints excluded: chain M residue 402 TYR Chi-restraints excluded: chain M residue 440 ARG Chi-restraints excluded: chain M residue 573 ILE Chi-restraints excluded: chain N residue 58 THR Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 182 ILE Chi-restraints excluded: chain N residue 193 ARG Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 222 GLU Chi-restraints excluded: chain N residue 244 CYS Chi-restraints excluded: chain N residue 245 SER Chi-restraints excluded: chain N residue 293 SER 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 Chi-restraints excluded: chain N residue 429 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: 0.3980 chunk 6 optimal weight: 5.9990 chunk 289 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 309 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 347 optimal weight: 5.9990 chunk 19 optimal weight: 0.0770 chunk 225 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 302 optimal weight: 3.9990 overall best weight: 1.2140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN A 437 HIS B 60 HIS ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 GLN ** F 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 15 GLN I 209 HIS ** M 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 244 ASN N 191 GLN N 317 GLN ** N 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 434 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.163302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.136304 restraints weight = 64700.092| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 2.89 r_work: 0.3859 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.5943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 35626 Z= 0.153 Angle : 0.660 14.731 49010 Z= 0.329 Chirality : 0.042 0.260 5476 Planarity : 0.004 0.055 5685 Dihedral : 17.875 177.146 6491 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 5.81 % Allowed : 29.09 % Favored : 65.10 % 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 aren not related in a simple way. whole: -0.38 (0.14), residues: 3841 helix: 0.68 (0.14), residues: 1480 sheet: -0.70 (0.19), residues: 780 loop : -0.81 (0.15), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG M 206 TYR 0.018 0.001 TYR B 240 PHE 0.022 0.002 PHE E 287 TRP 0.053 0.002 TRP F 154 HIS 0.020 0.001 HIS I 209 Details of bonding type rmsd covalent geometry : bond 0.00356 (35623) covalent geometry : angle 0.65964 (49010) hydrogen bonds : bond 0.04547 ( 1468) hydrogen bonds : angle 4.81591 ( 4130) Misc. bond : bond 0.00339 ( 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 693 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 499 time to evaluate : 1.082 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: 0.6516 (OUTLIER) cc_final: 0.5884 (t80) REVERT: A 184 LYS cc_start: 0.7911 (mttt) cc_final: 0.7204 (tttt) REVERT: A 237 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9139 (tt) REVERT: A 278 ARG cc_start: 0.8023 (ttm110) cc_final: 0.7423 (mmp80) REVERT: B 107 CYS cc_start: 0.6750 (OUTLIER) cc_final: 0.5691 (t) REVERT: B 131 GLN cc_start: 0.7824 (mt0) cc_final: 0.7446 (mm-40) REVERT: B 448 TYR cc_start: 0.7811 (t80) cc_final: 0.7585 (t80) REVERT: E 121 ILE cc_start: 0.8003 (OUTLIER) cc_final: 0.7799 (tp) REVERT: E 387 ILE cc_start: 0.8132 (mm) cc_final: 0.7740 (tp) REVERT: E 414 SER cc_start: 0.5464 (t) cc_final: 0.4879 (t) REVERT: E 418 LYS cc_start: 0.5617 (tptm) cc_final: 0.4994 (tptm) REVERT: E 573 ILE cc_start: 0.6877 (mp) cc_final: 0.6516 (mt) REVERT: F 70 GLU cc_start: 0.7252 (mt-10) cc_final: 0.7012 (mt-10) REVERT: F 220 LYS cc_start: 0.6674 (mmtt) cc_final: 0.6043 (ptpp) REVERT: I 22 TRP cc_start: 0.7974 (m100) cc_final: 0.7657 (m100) REVERT: I 234 MET cc_start: 0.6804 (tpp) cc_final: 0.6556 (tpp) REVERT: I 270 THR cc_start: 0.8310 (m) cc_final: 0.8055 (p) REVERT: I 341 GLN cc_start: 0.7027 (pm20) cc_final: 0.6729 (tm-30) REVERT: I 345 CYS cc_start: 0.5797 (OUTLIER) cc_final: 0.5536 (p) REVERT: I 388 ARG cc_start: 0.7405 (mmt180) cc_final: 0.7116 (mmm160) REVERT: I 504 MET cc_start: 0.7410 (mmm) cc_final: 0.6694 (mmm) REVERT: I 518 GLU cc_start: 0.7779 (pm20) cc_final: 0.6907 (tp30) REVERT: I 528 ARG cc_start: 0.6965 (OUTLIER) cc_final: 0.6579 (ttm170) REVERT: J 16 GLU cc_start: 0.7816 (tt0) cc_final: 0.7581 (pt0) REVERT: J 131 GLN cc_start: 0.7690 (mt0) cc_final: 0.7373 (mm110) REVERT: J 154 TRP cc_start: 0.7741 (m-10) cc_final: 0.7518 (m-10) REVERT: J 320 PHE cc_start: 0.7278 (OUTLIER) cc_final: 0.6667 (m-80) REVERT: J 333 GLN cc_start: 0.7465 (OUTLIER) cc_final: 0.6948 (tp-100) REVERT: M 374 TYR cc_start: 0.5096 (t80) cc_final: 0.4438 (t80) REVERT: M 418 LYS cc_start: 0.5224 (tptm) cc_final: 0.4974 (tttm) REVERT: M 530 TYR cc_start: 0.5923 (m-80) cc_final: 0.5580 (m-10) REVERT: N 100 MET cc_start: 0.8331 (ttm) cc_final: 0.7960 (mpp) REVERT: N 133 MET cc_start: 0.7822 (mtt) cc_final: 0.7598 (mtt) REVERT: N 197 MET cc_start: 0.7340 (OUTLIER) cc_final: 0.7083 (mpp) REVERT: N 222 GLU cc_start: 0.6608 (OUTLIER) cc_final: 0.6368 (pm20) REVERT: N 261 ASP cc_start: 0.7671 (t0) cc_final: 0.7444 (p0) REVERT: N 272 ASN cc_start: 0.8867 (p0) cc_final: 0.8594 (p0) REVERT: N 377 TRP cc_start: 0.5067 (m-90) cc_final: 0.4667 (m-10) outliers start: 194 outliers final: 134 residues processed: 648 average time/residue: 0.1681 time to fit residues: 183.0207 Evaluate side-chains 609 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 465 time to evaluate : 1.229 ------------------------------------------------------------------------------- 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 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 289 GLU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 543 TRP Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 128 LYS 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 166 HIS Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 60 HIS Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 164 LEU 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 282 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain E residue 363 ILE Chi-restraints excluded: chain E residue 380 PHE Chi-restraints excluded: chain E residue 384 GLU Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 560 SER Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 140 LYS Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 245 SER Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 289 HIS Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 438 LEU 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 209 HIS Chi-restraints excluded: chain I residue 219 PHE 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 345 CYS Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 528 ARG 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 50 VAL Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 221 ASP Chi-restraints excluded: chain J residue 242 THR Chi-restraints excluded: chain J residue 244 CYS Chi-restraints excluded: chain J residue 309 THR Chi-restraints excluded: chain J residue 320 PHE Chi-restraints excluded: chain J residue 333 GLN Chi-restraints excluded: chain J residue 334 ILE Chi-restraints excluded: chain J residue 374 CYS Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 442 LEU Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 63 ASN Chi-restraints excluded: chain M residue 77 SER Chi-restraints excluded: chain M residue 93 PHE Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 144 ASP Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain M residue 294 ILE Chi-restraints excluded: chain M residue 298 VAL Chi-restraints excluded: chain M residue 402 TYR Chi-restraints excluded: chain M residue 440 ARG Chi-restraints excluded: chain M residue 557 VAL Chi-restraints excluded: chain N residue 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 147 LEU Chi-restraints excluded: chain N residue 182 ILE Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 222 GLU Chi-restraints excluded: chain N residue 244 CYS Chi-restraints excluded: chain N residue 245 SER Chi-restraints excluded: chain N residue 293 SER Chi-restraints excluded: chain N residue 336 GLN Chi-restraints excluded: chain N residue 370 THR Chi-restraints excluded: chain N residue 382 VAL Chi-restraints excluded: chain N residue 429 THR Chi-restraints excluded: chain N residue 463 VAL Chi-restraints excluded: chain N residue 466 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 151 optimal weight: 5.9990 chunk 269 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 210 optimal weight: 2.9990 chunk 258 optimal weight: 2.9990 chunk 310 optimal weight: 2.9990 chunk 260 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 371 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 383 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 HIS B 60 HIS ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 158 HIS ** M 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 244 ASN N 191 GLN ** N 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 317 GLN ** N 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.157087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.129634 restraints weight = 64742.913| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 2.48 r_work: 0.3794 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.6594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 35626 Z= 0.241 Angle : 0.744 14.681 49010 Z= 0.375 Chirality : 0.044 0.266 5476 Planarity : 0.005 0.054 5685 Dihedral : 18.013 177.583 6487 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 5.84 % Allowed : 29.12 % 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 aren not related in a simple way. whole: -0.71 (0.13), residues: 3841 helix: 0.45 (0.14), residues: 1468 sheet: -0.92 (0.19), residues: 802 loop : -0.99 (0.15), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG M 206 TYR 0.027 0.002 TYR M 191 PHE 0.028 0.002 PHE I 139 TRP 0.040 0.002 TRP F 154 HIS 0.033 0.002 HIS I 209 Details of bonding type rmsd covalent geometry : bond 0.00554 (35623) covalent geometry : angle 0.74353 (49010) hydrogen bonds : bond 0.04926 ( 1468) hydrogen bonds : angle 5.02937 ( 4130) Misc. bond : bond 0.00354 ( 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 692 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 497 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 PHE cc_start: 0.6631 (OUTLIER) cc_final: 0.5951 (t80) REVERT: A 184 LYS cc_start: 0.8062 (mttt) cc_final: 0.7257 (tttt) REVERT: A 237 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9141 (tt) REVERT: A 278 ARG cc_start: 0.8201 (ttm110) cc_final: 0.7692 (mmp80) REVERT: A 305 ILE cc_start: 0.7983 (mt) cc_final: 0.7715 (tp) REVERT: B 107 CYS cc_start: 0.6940 (OUTLIER) cc_final: 0.5672 (t) REVERT: B 131 GLN cc_start: 0.7986 (mt0) cc_final: 0.7731 (mm-40) REVERT: B 154 TRP cc_start: 0.7928 (m-10) cc_final: 0.7649 (m-10) REVERT: B 240 TYR cc_start: 0.7005 (m-80) cc_final: 0.6744 (m-80) REVERT: B 263 ARG cc_start: 0.5468 (OUTLIER) cc_final: 0.5133 (ptm160) REVERT: B 448 TYR cc_start: 0.7888 (t80) cc_final: 0.7571 (t80) REVERT: E 83 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7374 (tp-100) REVERT: E 296 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7776 (ttm-80) REVERT: E 387 ILE cc_start: 0.8198 (mm) cc_final: 0.7851 (tp) REVERT: E 573 ILE cc_start: 0.7702 (mp) cc_final: 0.7352 (mt) REVERT: I 22 TRP cc_start: 0.8015 (m100) cc_final: 0.7696 (m100) REVERT: I 270 THR cc_start: 0.8437 (m) cc_final: 0.8143 (p) REVERT: I 341 GLN cc_start: 0.7024 (pm20) cc_final: 0.6806 (tm-30) REVERT: I 345 CYS cc_start: 0.5639 (OUTLIER) cc_final: 0.5365 (p) REVERT: I 388 ARG cc_start: 0.7455 (mmt180) cc_final: 0.7216 (mmm160) REVERT: I 518 GLU cc_start: 0.8014 (pm20) cc_final: 0.7248 (tp30) REVERT: I 528 ARG cc_start: 0.7178 (OUTLIER) cc_final: 0.6902 (ttm170) REVERT: J 16 GLU cc_start: 0.7943 (tt0) cc_final: 0.7688 (pt0) REVERT: J 92 LYS cc_start: 0.8159 (tmtt) cc_final: 0.7849 (mppt) REVERT: J 131 GLN cc_start: 0.7860 (mt0) cc_final: 0.7548 (mm110) REVERT: J 154 TRP cc_start: 0.8025 (m-10) cc_final: 0.7708 (m-10) REVERT: J 178 LEU cc_start: 0.6721 (OUTLIER) cc_final: 0.6354 (pp) REVERT: J 320 PHE cc_start: 0.7382 (OUTLIER) cc_final: 0.6678 (m-80) REVERT: J 333 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.7101 (tp-100) REVERT: M 374 TYR cc_start: 0.5300 (t80) cc_final: 0.4564 (t80) REVERT: M 530 TYR cc_start: 0.6034 (m-80) cc_final: 0.5813 (m-80) REVERT: N 25 ARG cc_start: 0.5003 (mtt180) cc_final: 0.4382 (mtt180) REVERT: N 100 MET cc_start: 0.8363 (ttm) cc_final: 0.8063 (mpp) REVERT: N 133 MET cc_start: 0.8048 (mtt) cc_final: 0.7817 (mtt) REVERT: N 191 GLN cc_start: 0.8266 (mm110) cc_final: 0.7922 (mm-40) REVERT: N 193 ARG cc_start: 0.6846 (OUTLIER) cc_final: 0.6006 (tpp-160) REVERT: N 197 MET cc_start: 0.7385 (OUTLIER) cc_final: 0.7095 (mpp) REVERT: N 221 ASP cc_start: 0.6250 (m-30) cc_final: 0.5977 (m-30) REVERT: N 222 GLU cc_start: 0.6680 (OUTLIER) cc_final: 0.6332 (pm20) REVERT: N 272 ASN cc_start: 0.8940 (p0) cc_final: 0.8700 (p0) REVERT: N 280 MET cc_start: 0.8686 (tpp) cc_final: 0.7978 (tpp) REVERT: N 301 ARG cc_start: 0.6972 (ptm-80) cc_final: 0.6643 (ppt170) REVERT: N 367 GLN cc_start: 0.7132 (pt0) cc_final: 0.6804 (pm20) outliers start: 195 outliers final: 141 residues processed: 643 average time/residue: 0.1892 time to fit residues: 201.2051 Evaluate side-chains 610 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 455 time to evaluate : 1.228 ------------------------------------------------------------------------------- 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 227 SER Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 478 VAL 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 93 VAL Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 263 ARG 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 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 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 164 LEU 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 282 VAL Chi-restraints excluded: chain E residue 296 ARG 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 350 LEU Chi-restraints excluded: chain E residue 363 ILE Chi-restraints excluded: chain E residue 380 PHE Chi-restraints excluded: chain E residue 384 GLU Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 560 SER Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 140 LYS Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 197 MET Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 289 HIS Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 431 VAL Chi-restraints excluded: chain F residue 438 LEU 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 146 VAL Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 231 GLU 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 345 CYS Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 528 ARG Chi-restraints excluded: chain I residue 551 ILE Chi-restraints excluded: chain I residue 559 ILE Chi-restraints excluded: chain I residue 583 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 50 VAL 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 309 THR Chi-restraints excluded: chain J residue 320 PHE Chi-restraints excluded: chain J residue 332 VAL Chi-restraints excluded: chain J residue 333 GLN Chi-restraints excluded: chain J residue 334 ILE Chi-restraints excluded: chain J residue 374 CYS Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 442 LEU Chi-restraints excluded: chain J residue 466 ILE Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 63 ASN Chi-restraints excluded: chain M residue 77 SER Chi-restraints excluded: chain M residue 93 PHE Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 144 ASP Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain M residue 208 ILE Chi-restraints excluded: chain M residue 244 ASN Chi-restraints excluded: chain M residue 294 ILE Chi-restraints excluded: chain M residue 298 VAL Chi-restraints excluded: chain M residue 402 TYR Chi-restraints excluded: chain M residue 440 ARG Chi-restraints excluded: chain M residue 490 VAL Chi-restraints excluded: chain M residue 557 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 58 THR Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 193 ARG Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 222 GLU Chi-restraints excluded: chain N residue 244 CYS Chi-restraints excluded: chain N residue 245 SER Chi-restraints excluded: chain N residue 293 SER 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 429 THR Chi-restraints excluded: chain N residue 463 VAL Chi-restraints excluded: chain N residue 466 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 369 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 183 optimal weight: 3.9990 chunk 339 optimal weight: 5.9990 chunk 142 optimal weight: 10.0000 chunk 365 optimal weight: 3.9990 chunk 151 optimal weight: 9.9990 chunk 321 optimal weight: 0.5980 chunk 229 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 197 optimal weight: 6.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 HIS B 49 GLN ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS ** F 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 367 GLN ** F 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 436 ASN ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 244 ASN M 437 HIS ** N 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 317 GLN ** N 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.157956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.130821 restraints weight = 64366.238| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 2.49 r_work: 0.3811 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.6858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 35626 Z= 0.191 Angle : 0.706 15.219 49010 Z= 0.353 Chirality : 0.043 0.269 5476 Planarity : 0.004 0.050 5685 Dihedral : 17.990 177.479 6485 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.23 % Favored : 94.74 % Rotamer: Outliers : 5.21 % Allowed : 29.84 % Favored : 64.95 % 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 aren not related in a simple way. whole: -0.65 (0.14), residues: 3841 helix: 0.51 (0.14), residues: 1462 sheet: -0.93 (0.19), residues: 801 loop : -0.94 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 516 TYR 0.025 0.002 TYR M 49 PHE 0.030 0.002 PHE E 287 TRP 0.038 0.002 TRP F 154 HIS 0.031 0.001 HIS A 437 Details of bonding type rmsd covalent geometry : bond 0.00439 (35623) covalent geometry : angle 0.70581 (49010) hydrogen bonds : bond 0.04765 ( 1468) hydrogen bonds : angle 4.93968 ( 4130) Misc. bond : bond 0.00293 ( 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 656 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 482 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 PHE cc_start: 0.6608 (OUTLIER) cc_final: 0.5923 (t80) REVERT: A 184 LYS cc_start: 0.8072 (mttt) cc_final: 0.7209 (tttt) REVERT: A 237 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9127 (tt) REVERT: A 278 ARG cc_start: 0.8197 (ttm110) cc_final: 0.7675 (mmp80) REVERT: A 305 ILE cc_start: 0.7905 (mt) cc_final: 0.7667 (tp) REVERT: A 332 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7940 (ttt-90) REVERT: B 107 CYS cc_start: 0.6876 (OUTLIER) cc_final: 0.6062 (t) REVERT: B 131 GLN cc_start: 0.8048 (mt0) cc_final: 0.7708 (mm-40) REVERT: B 240 TYR cc_start: 0.7069 (m-80) cc_final: 0.6818 (m-80) REVERT: B 263 ARG cc_start: 0.5414 (OUTLIER) cc_final: 0.5083 (ptm160) REVERT: B 448 TYR cc_start: 0.7819 (t80) cc_final: 0.7532 (t80) REVERT: E 83 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7294 (tp-100) REVERT: E 387 ILE cc_start: 0.8220 (mm) cc_final: 0.7885 (tp) REVERT: E 573 ILE cc_start: 0.7713 (mp) cc_final: 0.7408 (mt) REVERT: I 22 TRP cc_start: 0.8111 (m100) cc_final: 0.7542 (m100) REVERT: I 270 THR cc_start: 0.8470 (m) cc_final: 0.8183 (p) REVERT: I 290 MET cc_start: 0.6827 (tmm) cc_final: 0.6539 (tmm) REVERT: I 388 ARG cc_start: 0.7602 (mmt180) cc_final: 0.7332 (mmm160) REVERT: I 500 LYS cc_start: 0.8229 (mttm) cc_final: 0.7922 (mtpt) REVERT: I 504 MET cc_start: 0.6931 (OUTLIER) cc_final: 0.6276 (mmm) REVERT: I 518 GLU cc_start: 0.7994 (pm20) cc_final: 0.7288 (tp30) REVERT: J 16 GLU cc_start: 0.7887 (tt0) cc_final: 0.7625 (pt0) REVERT: J 65 ASP cc_start: 0.6282 (OUTLIER) cc_final: 0.6077 (t70) REVERT: J 92 LYS cc_start: 0.8113 (tmtt) cc_final: 0.7854 (mppt) REVERT: J 154 TRP cc_start: 0.7959 (m-10) cc_final: 0.7682 (m-10) REVERT: J 178 LEU cc_start: 0.6647 (OUTLIER) cc_final: 0.6339 (pp) REVERT: J 251 ASP cc_start: 0.8464 (OUTLIER) cc_final: 0.8129 (m-30) REVERT: J 320 PHE cc_start: 0.7314 (OUTLIER) cc_final: 0.6664 (m-80) REVERT: J 333 GLN cc_start: 0.7552 (OUTLIER) cc_final: 0.7119 (tt0) REVERT: J 367 GLN cc_start: 0.8430 (tm-30) cc_final: 0.8159 (tm-30) REVERT: M 206 ARG cc_start: 0.7788 (mmm160) cc_final: 0.7488 (mmm160) REVERT: M 374 TYR cc_start: 0.5301 (t80) cc_final: 0.4495 (t80) REVERT: M 530 TYR cc_start: 0.5995 (m-80) cc_final: 0.5793 (m-80) REVERT: N 25 ARG cc_start: 0.5215 (mtt180) cc_final: 0.4521 (mtt180) REVERT: N 100 MET cc_start: 0.8201 (ttm) cc_final: 0.7918 (mpp) REVERT: N 133 MET cc_start: 0.7952 (mtt) cc_final: 0.7732 (mtt) REVERT: N 191 GLN cc_start: 0.8250 (mm110) cc_final: 0.7923 (mm-40) REVERT: N 193 ARG cc_start: 0.6898 (OUTLIER) cc_final: 0.5989 (tpp-160) REVERT: N 197 MET cc_start: 0.7345 (OUTLIER) cc_final: 0.7123 (mpp) REVERT: N 221 ASP cc_start: 0.6150 (m-30) cc_final: 0.5896 (m-30) REVERT: N 222 GLU cc_start: 0.6649 (OUTLIER) cc_final: 0.6380 (pm20) REVERT: N 261 ASP cc_start: 0.7704 (t0) cc_final: 0.7441 (p0) outliers start: 174 outliers final: 133 residues processed: 618 average time/residue: 0.1731 time to fit residues: 177.3114 Evaluate side-chains 608 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 460 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 227 SER Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 539 ILE 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 49 GLN Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 263 ARG Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 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 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 208 ILE Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain E residue 363 ILE Chi-restraints excluded: chain E residue 380 PHE Chi-restraints excluded: chain E residue 384 GLU Chi-restraints excluded: chain E residue 473 TYR Chi-restraints excluded: chain E residue 550 SER Chi-restraints excluded: chain E residue 560 SER 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 197 MET Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 289 HIS Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 431 VAL Chi-restraints excluded: chain F residue 436 ASN Chi-restraints excluded: chain F residue 438 LEU 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 146 VAL Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 219 PHE 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 417 LEU Chi-restraints excluded: chain I residue 504 MET Chi-restraints excluded: chain I residue 528 ARG Chi-restraints excluded: chain I residue 583 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 65 ASP 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 251 ASP Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 309 THR Chi-restraints excluded: chain J residue 320 PHE Chi-restraints excluded: chain J residue 332 VAL Chi-restraints excluded: chain J residue 333 GLN Chi-restraints excluded: chain J residue 334 ILE Chi-restraints excluded: chain J residue 374 CYS Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 63 ASN Chi-restraints excluded: chain M residue 77 SER Chi-restraints excluded: chain M residue 93 PHE Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 144 ASP Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain M residue 208 ILE Chi-restraints excluded: chain M residue 224 SER Chi-restraints excluded: chain M residue 244 ASN Chi-restraints excluded: chain M residue 294 ILE Chi-restraints excluded: chain M residue 298 VAL Chi-restraints excluded: chain M residue 440 ARG Chi-restraints excluded: chain M residue 557 VAL Chi-restraints excluded: chain M residue 573 ILE Chi-restraints excluded: chain N residue 58 THR Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 193 ARG Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 222 GLU Chi-restraints excluded: chain N residue 244 CYS Chi-restraints excluded: chain N residue 245 SER Chi-restraints excluded: chain N residue 293 SER Chi-restraints excluded: chain N residue 317 GLN Chi-restraints excluded: chain N residue 327 THR Chi-restraints excluded: chain N residue 336 GLN Chi-restraints excluded: chain N residue 370 THR Chi-restraints excluded: chain N residue 429 THR Chi-restraints excluded: chain N residue 463 VAL Chi-restraints excluded: chain N residue 466 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 131 optimal weight: 0.1980 chunk 182 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 12 optimal weight: 0.0470 chunk 223 optimal weight: 20.0000 chunk 2 optimal weight: 3.9990 chunk 325 optimal weight: 3.9990 chunk 228 optimal weight: 10.0000 chunk 391 optimal weight: 2.9990 chunk 280 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.6082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 ASN ** E 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 GLN F 379 GLN ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 209 HIS ** M 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 317 GLN N 367 GLN ** N 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.158026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.131072 restraints weight = 64297.590| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 2.50 r_work: 0.3816 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.7015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 35626 Z= 0.177 Angle : 0.710 15.383 49010 Z= 0.355 Chirality : 0.043 0.272 5476 Planarity : 0.004 0.060 5685 Dihedral : 17.957 177.559 6485 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.42 % Favored : 94.56 % Rotamer: Outliers : 4.79 % Allowed : 30.35 % Favored : 64.86 % 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 aren not related in a simple way. whole: -0.63 (0.14), residues: 3841 helix: 0.52 (0.14), residues: 1470 sheet: -0.87 (0.19), residues: 783 loop : -0.95 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 206 TYR 0.019 0.002 TYR M 191 PHE 0.029 0.002 PHE E 287 TRP 0.037 0.002 TRP F 154 HIS 0.008 0.001 HIS M 163 Details of bonding type rmsd covalent geometry : bond 0.00412 (35623) covalent geometry : angle 0.70963 (49010) hydrogen bonds : bond 0.04717 ( 1468) hydrogen bonds : angle 4.92137 ( 4130) Misc. bond : bond 0.00273 ( 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 638 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 478 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 PHE cc_start: 0.6538 (OUTLIER) cc_final: 0.5883 (t80) REVERT: A 184 LYS cc_start: 0.8092 (mttt) cc_final: 0.7207 (tttt) REVERT: A 237 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9135 (tt) REVERT: A 278 ARG cc_start: 0.8245 (ttm110) cc_final: 0.7686 (mmp80) REVERT: A 305 ILE cc_start: 0.7914 (mt) cc_final: 0.7668 (tp) REVERT: A 332 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7932 (ttt-90) REVERT: B 107 CYS cc_start: 0.6768 (OUTLIER) cc_final: 0.5592 (t) REVERT: B 131 GLN cc_start: 0.8060 (mt0) cc_final: 0.7719 (mm-40) REVERT: B 240 TYR cc_start: 0.7087 (m-80) cc_final: 0.6843 (m-80) REVERT: B 334 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.8112 (mm) REVERT: B 448 TYR cc_start: 0.7795 (t80) cc_final: 0.7522 (t80) REVERT: E 83 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7381 (tp-100) REVERT: E 387 ILE cc_start: 0.8287 (mm) cc_final: 0.7913 (tp) REVERT: E 536 SER cc_start: 0.7663 (t) cc_final: 0.7376 (p) REVERT: E 573 ILE cc_start: 0.7816 (mp) cc_final: 0.7530 (mt) REVERT: F 44 PHE cc_start: 0.6763 (p90) cc_final: 0.6561 (p90) REVERT: I 22 TRP cc_start: 0.8064 (m100) cc_final: 0.7425 (m100) REVERT: I 270 THR cc_start: 0.8561 (m) cc_final: 0.8271 (p) REVERT: I 290 MET cc_start: 0.6796 (tmm) cc_final: 0.6494 (tmm) REVERT: I 388 ARG cc_start: 0.7579 (mmt180) cc_final: 0.7369 (mmt180) REVERT: I 500 LYS cc_start: 0.8246 (mttm) cc_final: 0.7918 (mtpt) REVERT: I 518 GLU cc_start: 0.8039 (pm20) cc_final: 0.7383 (tp30) REVERT: J 16 GLU cc_start: 0.7884 (tt0) cc_final: 0.7644 (pt0) REVERT: J 65 ASP cc_start: 0.6359 (OUTLIER) cc_final: 0.6129 (t70) REVERT: J 154 TRP cc_start: 0.7992 (m-10) cc_final: 0.7727 (m-10) REVERT: J 178 LEU cc_start: 0.6727 (OUTLIER) cc_final: 0.6430 (pp) REVERT: J 251 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.8000 (m-30) REVERT: J 320 PHE cc_start: 0.7313 (OUTLIER) cc_final: 0.6663 (m-80) REVERT: J 333 GLN cc_start: 0.7521 (OUTLIER) cc_final: 0.7002 (tp-100) REVERT: J 367 GLN cc_start: 0.8353 (tm-30) cc_final: 0.8140 (tm-30) REVERT: M 206 ARG cc_start: 0.7790 (mmm160) cc_final: 0.7515 (mmm160) REVERT: M 374 TYR cc_start: 0.5405 (t80) cc_final: 0.4534 (t80) REVERT: N 25 ARG cc_start: 0.5421 (mtt180) cc_final: 0.4676 (mtt180) REVERT: N 32 ARG cc_start: 0.7563 (ttp80) cc_final: 0.7084 (ptp90) REVERT: N 100 MET cc_start: 0.8205 (ttm) cc_final: 0.7905 (mpp) REVERT: N 133 MET cc_start: 0.7958 (mtt) cc_final: 0.7730 (mtt) REVERT: N 191 GLN cc_start: 0.8226 (mm110) cc_final: 0.7947 (mm-40) REVERT: N 193 ARG cc_start: 0.6872 (OUTLIER) cc_final: 0.5878 (tpp-160) REVERT: N 197 MET cc_start: 0.7346 (OUTLIER) cc_final: 0.7138 (mpp) REVERT: N 221 ASP cc_start: 0.6278 (m-30) cc_final: 0.5985 (m-30) REVERT: N 222 GLU cc_start: 0.6690 (OUTLIER) cc_final: 0.6368 (pm20) outliers start: 160 outliers final: 131 residues processed: 606 average time/residue: 0.1713 time to fit residues: 170.8358 Evaluate side-chains 598 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 453 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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 227 SER Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 539 ILE 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 49 GLN Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 188 LEU 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 334 ILE Chi-restraints excluded: chain B residue 361 VAL 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 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 208 ILE Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain E residue 363 ILE Chi-restraints excluded: chain E residue 380 PHE Chi-restraints excluded: chain E residue 384 GLU Chi-restraints excluded: chain E residue 473 TYR Chi-restraints excluded: chain E residue 550 SER 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 188 LEU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 289 HIS Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 431 VAL Chi-restraints excluded: chain F residue 438 LEU 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 146 VAL Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 219 PHE Chi-restraints excluded: chain I residue 281 LEU Chi-restraints excluded: chain I residue 286 THR 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 417 LEU Chi-restraints excluded: chain I residue 528 ARG Chi-restraints excluded: chain I residue 583 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 65 ASP 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 251 ASP Chi-restraints excluded: chain J residue 309 THR Chi-restraints excluded: chain J residue 320 PHE Chi-restraints excluded: chain J residue 332 VAL Chi-restraints excluded: chain J residue 333 GLN Chi-restraints excluded: chain J residue 334 ILE Chi-restraints excluded: chain J residue 374 CYS Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 63 ASN Chi-restraints excluded: chain M residue 77 SER Chi-restraints excluded: chain M residue 93 PHE Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 144 ASP Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain M residue 208 ILE Chi-restraints excluded: chain M residue 224 SER Chi-restraints excluded: chain M residue 244 ASN Chi-restraints excluded: chain M residue 294 ILE Chi-restraints excluded: chain M residue 298 VAL Chi-restraints excluded: chain M residue 440 ARG Chi-restraints excluded: chain M residue 490 VAL Chi-restraints excluded: chain M residue 557 VAL Chi-restraints excluded: chain M residue 573 ILE Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 193 ARG Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 222 GLU Chi-restraints excluded: chain N residue 244 CYS Chi-restraints excluded: chain N residue 245 SER Chi-restraints excluded: chain N residue 293 SER Chi-restraints excluded: chain N residue 299 MET Chi-restraints excluded: chain N residue 327 THR Chi-restraints excluded: chain N residue 336 GLN Chi-restraints excluded: chain N residue 370 THR Chi-restraints excluded: chain N residue 429 THR Chi-restraints excluded: chain N residue 463 VAL Chi-restraints excluded: chain N residue 466 ILE 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: 0.8980 chunk 384 optimal weight: 0.9980 chunk 378 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 128 optimal weight: 7.9990 chunk 383 optimal weight: 0.9990 chunk 208 optimal weight: 0.6980 chunk 253 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 ASN ** E 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 379 GLN F 436 ASN ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 387 GLN M 18 GLN ** M 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 317 GLN ** N 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.159706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.132577 restraints weight = 64023.052| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 2.67 r_work: 0.3840 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.7111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 35626 Z= 0.145 Angle : 0.693 15.641 49010 Z= 0.346 Chirality : 0.042 0.310 5476 Planarity : 0.004 0.072 5685 Dihedral : 17.896 177.106 6485 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.00 % Favored : 94.98 % Rotamer: Outliers : 4.46 % Allowed : 30.56 % 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 aren not related in a simple way. whole: -0.48 (0.14), residues: 3841 helix: 0.72 (0.14), residues: 1450 sheet: -0.69 (0.20), residues: 745 loop : -1.00 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 206 TYR 0.032 0.002 TYR M 530 PHE 0.027 0.002 PHE E 287 TRP 0.037 0.002 TRP A 543 HIS 0.007 0.001 HIS M 163 Details of bonding type rmsd covalent geometry : bond 0.00335 (35623) covalent geometry : angle 0.69292 (49010) hydrogen bonds : bond 0.04646 ( 1468) hydrogen bonds : angle 4.87337 ( 4130) Misc. bond : bond 0.00254 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7327.21 seconds wall clock time: 127 minutes 0.73 seconds (7620.73 seconds total)