Starting phenix.real_space_refine on Sun Jun 29 08:42:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y80_39028/06_2025/8y80_39028.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y80_39028/06_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_39028/06_2025/8y80_39028.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y80_39028/06_2025/8y80_39028.map" model { file = "/net/cci-nas-00/data/ceres_data/8y80_39028/06_2025/8y80_39028.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y80_39028/06_2025/8y80_39028.cif" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 21.71, per 1000 atoms: 0.63 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: 8.86 Conformation dependent library (CDL) restraints added in 3.9 seconds 7682 Ramachandran restraints generated. 3841 Oldfield, 0 Emsley, 3841 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7318 Finding SS restraints... Secondary structure from input PDB file: 154 helices and 49 sheets defined 41.8% alpha, 18.6% beta 60 base pairs and 104 stacking pairs defined. Time for finding SS restraints: 12.51 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: 14.88 Time building geometry restraints manager: 10.20 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: 7.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.470 Check model and map are aligned: 0.260 Set scattering table: 0.320 Process input model: 86.660 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.230 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.530 ------------------------------------------------------------------------------- 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 : 32.07 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.019 0.001 TRP A 253 HIS 0.011 0.001 HIS E 52 PHE 0.041 0.002 PHE E 247 TYR 0.021 0.001 TYR B 260 ARG 0.005 0.000 ARG B 411 Details of bonding type rmsd hydrogen bonds : bond 0.16617 ( 1468) hydrogen bonds : angle 6.83117 ( 4130) covalent geometry : bond 0.00520 (35623) covalent geometry : angle 0.85879 (49010) 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 : 3.904 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: 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: 0.5562 (t80) REVERT: A 184 LYS cc_start: 0.7774 (mttt) cc_final: 0.7543 (pttt) REVERT: A 373 THR cc_start: 0.8049 (t) cc_final: 0.7720 (m) REVERT: A 444 HIS cc_start: 0.5565 (m-70) cc_final: 0.5204 (m-70) REVERT: B 176 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8702 (mp) REVERT: E 40 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8120 (mm) REVERT: E 374 TYR cc_start: 0.5490 (t80) cc_final: 0.4981 (t80) REVERT: F 44 PHE cc_start: 0.6898 (p90) cc_final: 0.6673 (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: 0.6188 (mtt) REVERT: F 185 ASP cc_start: 0.7106 (OUTLIER) cc_final: 0.6768 (p0) REVERT: F 383 MET cc_start: 0.6999 (mmm) cc_final: 0.6755 (tpp) REVERT: F 459 THR cc_start: 0.8805 (m) cc_final: 0.8359 (p) REVERT: I 22 TRP cc_start: 0.7673 (m100) cc_final: 0.7258 (m100) REVERT: I 208 ILE cc_start: 0.7303 (mm) cc_final: 0.7079 (mm) REVERT: I 234 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.6728 (tpp) REVERT: I 495 GLU cc_start: 0.3678 (tp30) cc_final: 0.3209 (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: 0.5955 (t0) REVERT: J 376 LEU cc_start: 0.8485 (tp) cc_final: 0.8103 (tp) REVERT: M 47 ARG cc_start: 0.6919 (OUTLIER) cc_final: 0.6692 (mtp85) REVERT: M 62 ILE cc_start: 0.7972 (tp) cc_final: 0.7437 (tp) REVERT: M 374 TYR cc_start: 0.4541 (t80) cc_final: 0.3941 (t80) REVERT: M 576 ARG cc_start: 0.3987 (ttt180) cc_final: 0.3148 (ptt-90) outliers start: 134 outliers final: 63 residues processed: 1137 average time/residue: 0.5332 time to fit residues: 935.3833 Evaluate side-chains 616 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 545 time to evaluate : 4.253 ------------------------------------------------------------------------------- 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 339 optimal weight: 5.9990 chunk 304 optimal weight: 2.9990 chunk 169 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 205 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 chunk 315 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 191 optimal weight: 0.2980 chunk 234 optimal weight: 8.9990 chunk 365 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 266 GLN A 437 HIS B 60 HIS B 181 GLN B 195 ASN B 296 ASN ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN ** 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 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** I 7 ASN I 243 GLN ** I 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 ASN J 292 GLN J 296 ASN ** J 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 379 GLN J 392 GLN J 450 GLN M 123 HIS ** M 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 266 GLN N 195 ASN N 295 HIS N 296 ASN N 336 GLN N 379 GLN ** N 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.179203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.153442 restraints weight = 64819.360| |-----------------------------------------------------------------------------| r_work (start): 0.4233 rms_B_bonded: 2.67 r_work: 0.4083 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 35626 Z= 0.171 Angle : 0.703 11.730 49010 Z= 0.362 Chirality : 0.043 0.260 5476 Planarity : 0.005 0.086 5685 Dihedral : 18.187 171.744 6620 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.56 % Favored : 95.42 % Rotamer: Outliers : 6.38 % Allowed : 28.88 % Favored : 64.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.13), residues: 3841 helix: 0.65 (0.13), residues: 1477 sheet: -0.57 (0.19), residues: 754 loop : -0.74 (0.15), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 340 HIS 0.017 0.001 HIS E 52 PHE 0.028 0.002 PHE E 287 TYR 0.034 0.002 TYR I 271 ARG 0.010 0.001 ARG I 462 Details of bonding type rmsd hydrogen bonds : bond 0.05142 ( 1468) hydrogen bonds : angle 5.23251 ( 4130) covalent geometry : bond 0.00380 (35623) covalent geometry : angle 0.70257 (49010) Misc. bond : bond 0.00268 ( 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 862 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 213 poor density : 649 time to evaluate : 3.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 PHE cc_start: 0.6610 (OUTLIER) cc_final: 0.5968 (t80) REVERT: A 184 LYS cc_start: 0.7613 (mttt) cc_final: 0.7166 (ptmt) REVERT: A 331 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8377 (pt) REVERT: A 373 THR cc_start: 0.8283 (t) cc_final: 0.8030 (m) REVERT: A 532 PHE cc_start: 0.5940 (m-80) cc_final: 0.5714 (m-80) REVERT: E 16 ASN cc_start: 0.8081 (p0) cc_final: 0.7869 (p0) REVERT: E 287 PHE cc_start: 0.7255 (OUTLIER) cc_final: 0.6637 (t80) REVERT: E 352 SER cc_start: 0.4717 (OUTLIER) cc_final: 0.4440 (m) REVERT: E 521 THR cc_start: 0.7813 (p) cc_final: 0.7605 (p) REVERT: F 185 ASP cc_start: 0.7003 (OUTLIER) cc_final: 0.6689 (p0) REVERT: F 190 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.5885 (tmm160) REVERT: F 340 TRP cc_start: 0.7951 (m100) cc_final: 0.7533 (m100) REVERT: I 139 PHE cc_start: 0.7037 (OUTLIER) cc_final: 0.6048 (p90) REVERT: I 234 MET cc_start: 0.7197 (OUTLIER) cc_final: 0.6310 (ptp) REVERT: I 518 GLU cc_start: 0.7294 (pm20) cc_final: 0.6161 (tp30) REVERT: I 536 SER cc_start: 0.7918 (t) cc_final: 0.7204 (m) REVERT: J 91 GLU cc_start: 0.8374 (tp30) cc_final: 0.8011 (tp30) REVERT: J 97 PRO cc_start: 0.8941 (Cg_endo) cc_final: 0.8655 (Cg_exo) REVERT: J 178 LEU cc_start: 0.6494 (OUTLIER) cc_final: 0.6114 (pp) REVERT: J 197 MET cc_start: 0.6529 (mmm) cc_final: 0.5997 (tpp) REVERT: J 376 LEU cc_start: 0.8809 (tp) cc_final: 0.8380 (tp) REVERT: J 465 GLU cc_start: 0.6680 (mp0) cc_final: 0.6178 (mm-30) REVERT: M 94 GLU cc_start: 0.7818 (pt0) cc_final: 0.7473 (pt0) REVERT: M 359 LEU cc_start: 0.7809 (mt) cc_final: 0.7557 (mt) REVERT: M 374 TYR cc_start: 0.4806 (t80) cc_final: 0.4175 (t80) REVERT: M 514 LEU cc_start: 0.7929 (mm) cc_final: 0.7669 (mt) REVERT: M 576 ARG cc_start: 0.4102 (ttt180) cc_final: 0.3207 (ptt-90) REVERT: N 86 GLU cc_start: 0.6142 (OUTLIER) cc_final: 0.5222 (tm-30) REVERT: N 133 MET cc_start: 0.7664 (mtt) cc_final: 0.7418 (mtt) REVERT: N 190 ARG cc_start: 0.6809 (OUTLIER) cc_final: 0.6600 (tpp-160) REVERT: N 197 MET cc_start: 0.7493 (OUTLIER) cc_final: 0.7169 (mmp) REVERT: N 240 TYR cc_start: 0.6937 (m-80) cc_final: 0.6447 (m-80) REVERT: N 340 TRP cc_start: 0.8038 (m100) cc_final: 0.7416 (m100) REVERT: N 408 MET cc_start: 0.5379 (mmm) cc_final: 0.4731 (mtp) outliers start: 213 outliers final: 89 residues processed: 810 average time/residue: 0.4470 time to fit residues: 589.0767 Evaluate side-chains 620 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 519 time to evaluate : 3.896 ------------------------------------------------------------------------------- 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 221 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 331 LEU 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 B residue 12 SER Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 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 82 LEU 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 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 287 PHE Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 490 VAL Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 560 SER Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 40 TYR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 140 LYS Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 190 ARG Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 438 LEU 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 146 VAL Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 233 VAL Chi-restraints excluded: chain I residue 234 MET Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 244 ASN Chi-restraints excluded: chain I residue 289 GLU Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 333 THR Chi-restraints excluded: chain I residue 580 SER Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain J residue 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 362 ASP Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 426 LEU Chi-restraints excluded: chain J residue 464 ASN Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain M residue 154 ILE Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 381 LEU 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 190 ARG Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 255 PHE Chi-restraints excluded: chain N residue 293 SER Chi-restraints excluded: chain N residue 370 THR 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 180 optimal weight: 3.9990 chunk 205 optimal weight: 0.5980 chunk 203 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 278 optimal weight: 10.0000 chunk 343 optimal weight: 3.9990 chunk 253 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 355 optimal weight: 3.9990 chunk 313 optimal weight: 0.5980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 HIS B 49 GLN B 184 ASN B 306 HIS B 458 GLN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 GLN ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 278 GLN ** F 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 49 GLN ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 181 GLN J 387 GLN ** M 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 191 GLN ** N 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.169499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.141711 restraints weight = 64820.207| |-----------------------------------------------------------------------------| r_work (start): 0.4090 rms_B_bonded: 2.74 r_work: 0.3943 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 35626 Z= 0.198 Angle : 0.702 11.502 49010 Z= 0.358 Chirality : 0.043 0.221 5476 Planarity : 0.005 0.059 5685 Dihedral : 18.046 172.511 6521 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 6.73 % Allowed : 27.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.13), residues: 3841 helix: 0.53 (0.13), residues: 1489 sheet: -0.61 (0.19), residues: 762 loop : -0.79 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 154 HIS 0.014 0.002 HIS N 60 PHE 0.022 0.002 PHE E 287 TYR 0.029 0.002 TYR I 271 ARG 0.008 0.001 ARG A 310 Details of bonding type rmsd hydrogen bonds : bond 0.04921 ( 1468) hydrogen bonds : angle 5.05197 ( 4130) covalent geometry : bond 0.00457 (35623) covalent geometry : angle 0.70213 (49010) Misc. bond : bond 0.00384 ( 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 800 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 225 poor density : 575 time to evaluate : 3.981 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: 0.8510 (OUTLIER) cc_final: 0.8137 (p0) REVERT: A 143 PHE cc_start: 0.6627 (OUTLIER) cc_final: 0.5968 (t80) REVERT: A 184 LYS cc_start: 0.7836 (mttt) cc_final: 0.7248 (ptmt) REVERT: A 221 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8004 (tp) REVERT: A 237 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9079 (tt) REVERT: A 278 ARG cc_start: 0.7727 (ttm110) cc_final: 0.7258 (mmp80) REVERT: A 525 ARG cc_start: 0.6875 (mmp80) cc_final: 0.6473 (mtm110) REVERT: B 328 GLU cc_start: 0.7578 (tt0) cc_final: 0.7354 (tt0) REVERT: E 16 ASN cc_start: 0.8482 (OUTLIER) cc_final: 0.8278 (p0) REVERT: E 200 ASP cc_start: 0.7791 (m-30) cc_final: 0.7470 (m-30) REVERT: E 287 PHE cc_start: 0.7722 (OUTLIER) cc_final: 0.7286 (t80) REVERT: E 352 SER cc_start: 0.4524 (OUTLIER) cc_final: 0.4219 (m) REVERT: E 448 ILE cc_start: 0.4299 (mp) cc_final: 0.4062 (mp) REVERT: F 185 ASP cc_start: 0.7185 (OUTLIER) cc_final: 0.6956 (p0) REVERT: I 22 TRP cc_start: 0.8041 (m100) cc_final: 0.7748 (m100) REVERT: I 139 PHE cc_start: 0.7264 (OUTLIER) cc_final: 0.6645 (p90) REVERT: I 341 GLN cc_start: 0.7309 (mt0) cc_final: 0.7058 (tm-30) REVERT: I 518 GLU cc_start: 0.7577 (pm20) cc_final: 0.6464 (tp30) REVERT: I 556 THR cc_start: 0.7428 (OUTLIER) cc_final: 0.7216 (m) REVERT: J 83 TYR cc_start: 0.6727 (t80) cc_final: 0.6508 (t80) REVERT: J 178 LEU cc_start: 0.6700 (OUTLIER) cc_final: 0.6205 (pp) REVERT: J 197 MET cc_start: 0.6833 (mmm) cc_final: 0.6395 (tpp) REVERT: J 465 GLU cc_start: 0.7168 (mp0) cc_final: 0.6405 (mm-30) REVERT: M 94 GLU cc_start: 0.7839 (pt0) cc_final: 0.7518 (pt0) REVERT: M 514 LEU cc_start: 0.8147 (mm) cc_final: 0.7883 (mt) REVERT: M 530 TYR cc_start: 0.5609 (m-80) cc_final: 0.5373 (m-80) REVERT: M 576 ARG cc_start: 0.4369 (ttt180) cc_final: 0.3320 (ptt-90) REVERT: N 100 MET cc_start: 0.8206 (ttm) cc_final: 0.7739 (pmm) REVERT: N 133 MET cc_start: 0.8040 (mtt) cc_final: 0.7661 (mtt) REVERT: N 158 PHE cc_start: 0.7134 (m-10) cc_final: 0.6773 (m-80) REVERT: N 197 MET cc_start: 0.7480 (OUTLIER) cc_final: 0.7198 (mpp) REVERT: N 198 TRP cc_start: 0.6101 (m100) cc_final: 0.5850 (m100) REVERT: N 299 MET cc_start: 0.7522 (ptm) cc_final: 0.7259 (ptm) REVERT: N 397 GLU cc_start: 0.5479 (mp0) cc_final: 0.4976 (mp0) outliers start: 225 outliers final: 115 residues processed: 741 average time/residue: 0.4815 time to fit residues: 585.2191 Evaluate side-chains 619 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 492 time to evaluate : 3.892 ------------------------------------------------------------------------------- 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 268 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 357 SER 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 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 A residue 583 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 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 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 308 THR Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 60 HIS Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 287 PHE Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 380 PHE 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 37 TYR Chi-restraints excluded: chain F residue 40 TYR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 140 LYS Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 185 ASP 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 16 ASN Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 139 PHE Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 143 PHE Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 233 VAL Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 265 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 556 THR Chi-restraints excluded: chain I residue 580 SER Chi-restraints excluded: chain J residue 35 SER 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 244 CYS Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 308 THR Chi-restraints excluded: chain J residue 361 VAL 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 M residue 19 HIS Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 154 ILE Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 224 SER Chi-restraints excluded: chain M residue 298 VAL Chi-restraints excluded: chain M residue 336 LEU 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 573 ILE Chi-restraints excluded: chain N residue 60 HIS Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain N residue 182 ILE Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 255 PHE Chi-restraints excluded: chain N residue 293 SER Chi-restraints excluded: chain N residue 370 THR Chi-restraints excluded: chain N residue 429 THR Chi-restraints excluded: chain N residue 466 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 115 optimal weight: 0.7980 chunk 119 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 233 optimal weight: 0.9990 chunk 324 optimal weight: 0.8980 chunk 213 optimal weight: 0.0970 chunk 343 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 385 optimal weight: 0.8980 chunk 25 optimal weight: 8.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 GLN ** E 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 ASN E 365 GLN ** F 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 GLN ** F 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 386 ASN ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 ASN J 195 ASN J 306 HIS ** M 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 104 GLN M 163 HIS M 186 HIS N 82 ASN N 191 GLN N 317 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.170690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.143257 restraints weight = 64607.231| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 2.86 r_work: 0.3954 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 35626 Z= 0.137 Angle : 0.648 12.819 49010 Z= 0.325 Chirality : 0.041 0.250 5476 Planarity : 0.004 0.048 5685 Dihedral : 17.934 173.478 6501 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 5.39 % Allowed : 28.70 % Favored : 65.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.14), residues: 3841 helix: 0.70 (0.14), residues: 1488 sheet: -0.59 (0.19), residues: 772 loop : -0.76 (0.16), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP I 295 HIS 0.009 0.001 HIS E 52 PHE 0.041 0.002 PHE A 532 TYR 0.020 0.002 TYR I 271 ARG 0.010 0.001 ARG E 528 Details of bonding type rmsd hydrogen bonds : bond 0.04632 ( 1468) hydrogen bonds : angle 4.88289 ( 4130) covalent geometry : bond 0.00312 (35623) covalent geometry : angle 0.64786 (49010) Misc. bond : bond 0.00248 ( 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 738 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 558 time to evaluate : 4.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 PHE cc_start: 0.6529 (OUTLIER) cc_final: 0.5895 (t80) REVERT: A 184 LYS cc_start: 0.7854 (mttt) cc_final: 0.7256 (ptmt) REVERT: A 221 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8154 (tp) REVERT: A 237 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9069 (tt) REVERT: A 278 ARG cc_start: 0.7791 (ttm110) cc_final: 0.7444 (mmp80) REVERT: A 525 ARG cc_start: 0.6783 (mmp80) cc_final: 0.6420 (mtm110) REVERT: E 16 ASN cc_start: 0.8306 (OUTLIER) cc_final: 0.8098 (p0) REVERT: E 121 ILE cc_start: 0.7909 (OUTLIER) cc_final: 0.7705 (tp) REVERT: E 200 ASP cc_start: 0.7739 (m-30) cc_final: 0.7332 (m-30) REVERT: E 287 PHE cc_start: 0.7840 (OUTLIER) cc_final: 0.7467 (t80) REVERT: E 387 ILE cc_start: 0.7989 (mm) cc_final: 0.7568 (tp) REVERT: E 418 LYS cc_start: 0.5513 (tptm) cc_final: 0.5071 (tptm) REVERT: E 528 ARG cc_start: 0.6494 (ttm110) cc_final: 0.5436 (ttp-110) REVERT: I 22 TRP cc_start: 0.7980 (m100) cc_final: 0.7536 (m100) REVERT: I 139 PHE cc_start: 0.7267 (OUTLIER) cc_final: 0.6647 (p90) REVERT: I 234 MET cc_start: 0.6716 (tpp) cc_final: 0.6439 (ptp) REVERT: I 290 MET cc_start: 0.6839 (tmm) cc_final: 0.6576 (tmm) REVERT: I 341 GLN cc_start: 0.7526 (mt0) cc_final: 0.7255 (tm-30) REVERT: I 345 CYS cc_start: 0.6073 (p) cc_final: 0.5735 (p) REVERT: I 518 GLU cc_start: 0.7559 (pm20) cc_final: 0.6538 (tp30) REVERT: J 197 MET cc_start: 0.6909 (mmm) cc_final: 0.6492 (tpp) REVERT: J 465 GLU cc_start: 0.7046 (mp0) cc_final: 0.6304 (mm-30) REVERT: M 94 GLU cc_start: 0.7792 (pt0) cc_final: 0.7446 (pt0) REVERT: M 340 THR cc_start: 0.2553 (OUTLIER) cc_final: 0.2214 (m) REVERT: M 514 LEU cc_start: 0.8203 (mm) cc_final: 0.7918 (mt) REVERT: M 576 ARG cc_start: 0.4312 (ttt180) cc_final: 0.3269 (ptt-90) REVERT: N 100 MET cc_start: 0.8267 (ttm) cc_final: 0.7761 (ttp) REVERT: N 133 MET cc_start: 0.7963 (mtt) cc_final: 0.7508 (mtt) REVERT: N 158 PHE cc_start: 0.7310 (m-10) cc_final: 0.6718 (m-80) REVERT: N 197 MET cc_start: 0.7452 (OUTLIER) cc_final: 0.7183 (mpp) outliers start: 180 outliers final: 111 residues processed: 688 average time/residue: 0.6961 time to fit residues: 801.6961 Evaluate side-chains 623 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 503 time to evaluate : 3.547 ------------------------------------------------------------------------------- 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 221 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 543 TRP Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 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 369 LEU Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 60 HIS Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 82 LEU 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 208 ILE Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 287 PHE Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 363 ILE Chi-restraints excluded: chain E residue 380 PHE Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 490 VAL Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 560 SER Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 37 TYR Chi-restraints excluded: chain F residue 40 TYR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 140 LYS Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 336 GLN Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 16 ASN Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 19 HIS Chi-restraints excluded: chain I residue 139 PHE Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 143 PHE Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 219 PHE Chi-restraints excluded: chain I residue 233 VAL Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 281 LEU Chi-restraints excluded: chain I residue 306 ASP Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 331 LEU 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 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 251 ASP Chi-restraints excluded: chain J residue 308 THR Chi-restraints excluded: chain J residue 361 VAL 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 93 PHE Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 208 ILE Chi-restraints excluded: chain M residue 224 SER Chi-restraints excluded: chain M residue 298 VAL Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain M residue 340 THR Chi-restraints excluded: chain M residue 381 LEU Chi-restraints excluded: chain M residue 440 ARG 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 182 ILE Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 244 CYS Chi-restraints excluded: chain N residue 255 PHE Chi-restraints excluded: chain N residue 370 THR Chi-restraints excluded: chain N residue 421 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 271 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 189 optimal weight: 8.9990 chunk 256 optimal weight: 0.5980 chunk 264 optimal weight: 0.7980 chunk 239 optimal weight: 4.9990 chunk 338 optimal weight: 0.0060 chunk 353 optimal weight: 20.0000 chunk 373 optimal weight: 3.9990 chunk 327 optimal weight: 0.0670 chunk 148 optimal weight: 7.9990 overall best weight: 0.8936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 ASN ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 HIS 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 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 ASN ** J 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 317 GLN N 389 ASN N 419 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.169534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.142126 restraints weight = 64740.286| |-----------------------------------------------------------------------------| r_work (start): 0.4100 rms_B_bonded: 2.82 r_work: 0.3939 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.4953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 35626 Z= 0.140 Angle : 0.645 13.609 49010 Z= 0.322 Chirality : 0.041 0.252 5476 Planarity : 0.004 0.048 5685 Dihedral : 17.913 174.124 6497 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 5.36 % Allowed : 29.30 % Favored : 65.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.14), residues: 3841 helix: 0.76 (0.14), residues: 1488 sheet: -0.61 (0.19), residues: 772 loop : -0.78 (0.16), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP F 154 HIS 0.009 0.001 HIS I 444 PHE 0.026 0.002 PHE M 287 TYR 0.026 0.002 TYR B 205 ARG 0.007 0.000 ARG A 310 Details of bonding type rmsd hydrogen bonds : bond 0.04531 ( 1468) hydrogen bonds : angle 4.82989 ( 4130) covalent geometry : bond 0.00322 (35623) covalent geometry : angle 0.64475 (49010) Misc. bond : bond 0.00180 ( 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 701 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 522 time to evaluate : 6.488 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: symmetry clash revert: symmetry clash REVERT: A 143 PHE cc_start: 0.6551 (OUTLIER) cc_final: 0.5885 (t80) REVERT: A 184 LYS cc_start: 0.7869 (mttt) cc_final: 0.7245 (ptmt) REVERT: A 221 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8171 (tp) REVERT: A 237 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9078 (tt) REVERT: A 278 ARG cc_start: 0.7819 (ttm110) cc_final: 0.7311 (mmp80) REVERT: A 395 GLU cc_start: 0.6933 (pt0) cc_final: 0.6280 (mm-30) REVERT: A 525 ARG cc_start: 0.6831 (mmp80) cc_final: 0.6500 (mtm110) REVERT: B 473 MET cc_start: 0.7899 (ptm) cc_final: 0.7615 (ptm) REVERT: E 387 ILE cc_start: 0.8044 (mm) cc_final: 0.7619 (tp) REVERT: E 418 LYS cc_start: 0.5613 (tptm) cc_final: 0.4873 (tptm) REVERT: E 448 ILE cc_start: 0.4674 (mp) cc_final: 0.4426 (mp) REVERT: E 528 ARG cc_start: 0.6571 (ttm110) cc_final: 0.5566 (ttp-170) REVERT: I 22 TRP cc_start: 0.7979 (m100) cc_final: 0.7529 (m100) REVERT: I 139 PHE cc_start: 0.7159 (OUTLIER) cc_final: 0.6429 (p90) REVERT: I 219 PHE cc_start: 0.5816 (OUTLIER) cc_final: 0.4883 (p90) REVERT: I 290 MET cc_start: 0.6756 (tmm) cc_final: 0.6458 (tmm) REVERT: I 341 GLN cc_start: 0.7643 (mt0) cc_final: 0.7286 (tm-30) REVERT: I 345 CYS cc_start: 0.5864 (p) cc_final: 0.5643 (p) REVERT: I 504 MET cc_start: 0.7315 (mmm) cc_final: 0.7113 (mmm) REVERT: I 518 GLU cc_start: 0.7605 (pm20) cc_final: 0.6692 (tp30) REVERT: J 34 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7933 (mp) REVERT: J 81 THR cc_start: 0.7501 (p) cc_final: 0.7231 (t) REVERT: J 197 MET cc_start: 0.6973 (mmm) cc_final: 0.6524 (tpp) REVERT: J 325 SER cc_start: 0.8605 (p) cc_final: 0.8113 (t) REVERT: J 465 GLU cc_start: 0.7105 (mp0) cc_final: 0.6353 (mm-30) REVERT: M 94 GLU cc_start: 0.7851 (pt0) cc_final: 0.7553 (pt0) REVERT: M 514 LEU cc_start: 0.8234 (mm) cc_final: 0.7953 (mt) REVERT: M 576 ARG cc_start: 0.4327 (ttt180) cc_final: 0.3314 (ptt-90) REVERT: N 133 MET cc_start: 0.7918 (mtt) cc_final: 0.7510 (mtt) REVERT: N 197 MET cc_start: 0.7443 (OUTLIER) cc_final: 0.7193 (mpp) REVERT: N 301 ARG cc_start: 0.6715 (ptm-80) cc_final: 0.6323 (ppt170) REVERT: N 389 ASN cc_start: 0.7668 (OUTLIER) cc_final: 0.7451 (p0) outliers start: 179 outliers final: 123 residues processed: 658 average time/residue: 0.4396 time to fit residues: 487.3238 Evaluate side-chains 619 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 488 time to evaluate : 3.520 ------------------------------------------------------------------------------- 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 221 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 543 TRP Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 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 373 GLU 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 82 LEU Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 205 ASP 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 242 ASP Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 267 ASP 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 333 THR 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 426 LEU Chi-restraints excluded: chain E residue 443 THR Chi-restraints excluded: chain E residue 490 VAL Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 560 SER Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 37 TYR Chi-restraints excluded: chain F residue 40 TYR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 140 LYS Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 197 MET 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 438 LEU Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 19 HIS Chi-restraints excluded: chain I residue 139 PHE Chi-restraints excluded: chain I residue 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 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 426 LEU Chi-restraints excluded: chain I residue 547 LEU Chi-restraints excluded: chain I residue 557 VAL Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 36 GLN Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 221 ASP Chi-restraints excluded: chain J residue 242 THR Chi-restraints excluded: chain J residue 244 CYS Chi-restraints excluded: chain J residue 308 THR Chi-restraints excluded: chain J residue 361 VAL 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 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 298 VAL Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain M residue 381 LEU Chi-restraints excluded: chain M residue 440 ARG 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 244 CYS Chi-restraints excluded: chain N residue 255 PHE Chi-restraints excluded: chain N residue 317 GLN Chi-restraints excluded: chain N residue 370 THR Chi-restraints excluded: chain N residue 389 ASN 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 301 optimal weight: 10.0000 chunk 358 optimal weight: 8.9990 chunk 379 optimal weight: 6.9990 chunk 252 optimal weight: 9.9990 chunk 389 optimal weight: 3.9990 chunk 349 optimal weight: 7.9990 chunk 213 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 271 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 437 HIS ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN B 181 GLN B 272 ASN ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 GLN E 16 ASN ** E 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN E 175 ASN ** E 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS F 306 HIS F 336 GLN ** 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** I 16 ASN ** I 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 ASN ** J 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 415 ASN M 12 HIS ** M 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 158 HIS ** M 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 191 GLN ** N 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 367 GLN ** N 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 434 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.153918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.125296 restraints weight = 65037.349| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 2.70 r_work: 0.3727 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.6438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.147 35626 Z= 0.358 Angle : 0.874 17.813 49010 Z= 0.448 Chirality : 0.049 0.309 5476 Planarity : 0.006 0.083 5685 Dihedral : 18.451 175.799 6495 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 20.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 7.36 % Allowed : 27.48 % Favored : 65.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.13), residues: 3841 helix: -0.09 (0.13), residues: 1476 sheet: -1.12 (0.19), residues: 780 loop : -1.22 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP I 295 HIS 0.016 0.003 HIS E 52 PHE 0.030 0.003 PHE M 219 TYR 0.037 0.003 TYR B 205 ARG 0.013 0.001 ARG M 440 Details of bonding type rmsd hydrogen bonds : bond 0.05918 ( 1468) hydrogen bonds : angle 5.49551 ( 4130) covalent geometry : bond 0.00825 (35623) covalent geometry : angle 0.87414 (49010) Misc. bond : bond 0.02208 ( 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 759 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 246 poor density : 513 time to evaluate : 3.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 PHE cc_start: 0.6584 (OUTLIER) cc_final: 0.5921 (t80) REVERT: A 184 LYS cc_start: 0.8136 (mttt) cc_final: 0.7281 (tttt) REVERT: A 237 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9131 (tt) REVERT: A 278 ARG cc_start: 0.8111 (ttm110) cc_final: 0.7605 (mmp80) REVERT: A 290 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8658 (ttp) REVERT: A 525 ARG cc_start: 0.7454 (mmp80) cc_final: 0.7216 (mtm110) REVERT: B 131 GLN cc_start: 0.8081 (mt0) cc_final: 0.7734 (mm-40) REVERT: B 154 TRP cc_start: 0.7997 (m-10) cc_final: 0.7703 (m-10) REVERT: B 403 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8085 (mp) REVERT: B 448 TYR cc_start: 0.7911 (t80) cc_final: 0.7596 (t80) REVERT: E 387 ILE cc_start: 0.8294 (mm) cc_final: 0.7932 (tp) REVERT: E 418 LYS cc_start: 0.6131 (tptm) cc_final: 0.5186 (tptm) REVERT: E 514 LEU cc_start: 0.7796 (mm) cc_final: 0.7580 (mp) REVERT: E 573 ILE cc_start: 0.7674 (mp) cc_final: 0.7411 (mt) REVERT: F 290 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8814 (tt) REVERT: I 22 TRP cc_start: 0.8159 (m100) cc_final: 0.7696 (m100) REVERT: I 139 PHE cc_start: 0.7029 (OUTLIER) cc_final: 0.6707 (p90) REVERT: I 270 THR cc_start: 0.8440 (m) cc_final: 0.8164 (p) REVERT: I 341 GLN cc_start: 0.7659 (mt0) cc_final: 0.7237 (tm-30) REVERT: I 345 CYS cc_start: 0.6001 (p) cc_final: 0.5734 (p) REVERT: I 500 LYS cc_start: 0.8488 (mttt) cc_final: 0.8177 (mtpt) REVERT: I 504 MET cc_start: 0.7313 (mmm) cc_final: 0.6998 (mmm) REVERT: I 518 GLU cc_start: 0.8111 (pm20) cc_final: 0.7156 (tp30) REVERT: I 528 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.6680 (ttm170) REVERT: I 551 ILE cc_start: 0.5390 (OUTLIER) cc_final: 0.5145 (mp) REVERT: J 65 ASP cc_start: 0.6398 (OUTLIER) cc_final: 0.6110 (t70) REVERT: J 178 LEU cc_start: 0.6867 (OUTLIER) cc_final: 0.6426 (pp) REVERT: J 197 MET cc_start: 0.7540 (mmm) cc_final: 0.7086 (tpp) REVERT: J 308 THR cc_start: 0.7951 (OUTLIER) cc_final: 0.7389 (p) REVERT: J 325 SER cc_start: 0.8861 (p) cc_final: 0.8410 (t) REVERT: M 366 LYS cc_start: 0.4502 (mmtm) cc_final: 0.4217 (mmtp) REVERT: M 418 LYS cc_start: 0.5303 (tptm) cc_final: 0.4996 (tttm) REVERT: M 573 ILE cc_start: 0.4338 (OUTLIER) cc_final: 0.3893 (mt) REVERT: N 25 ARG cc_start: 0.4479 (mtt180) cc_final: 0.4000 (mtt180) REVERT: N 125 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8527 (tt) REVERT: N 193 ARG cc_start: 0.6804 (OUTLIER) cc_final: 0.5847 (tpp80) REVERT: N 197 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.7226 (mpp) REVERT: N 272 ASN cc_start: 0.8954 (p0) cc_final: 0.8714 (p0) REVERT: N 280 MET cc_start: 0.8604 (tpp) cc_final: 0.8173 (tpp) REVERT: N 285 SER cc_start: 0.9035 (p) cc_final: 0.8741 (t) outliers start: 246 outliers final: 149 residues processed: 705 average time/residue: 0.4549 time to fit residues: 529.4822 Evaluate side-chains 613 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 449 time to evaluate : 3.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 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 313 GLU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 458 GLN 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 146 VAL Chi-restraints excluded: chain E residue 205 ASP 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 242 ASP Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 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 333 THR 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 460 ASP Chi-restraints excluded: chain E residue 560 SER Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 37 TYR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 140 LYS Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 191 GLN Chi-restraints excluded: chain F residue 197 MET Chi-restraints excluded: chain F residue 221 ASP Chi-restraints excluded: chain F residue 244 CYS Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 290 LEU 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 139 PHE Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 143 PHE Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 219 PHE 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 426 LEU Chi-restraints excluded: chain I residue 528 ARG Chi-restraints excluded: chain I residue 547 LEU Chi-restraints excluded: chain I residue 551 ILE Chi-restraints excluded: chain I residue 557 VAL Chi-restraints excluded: chain I residue 559 ILE Chi-restraints excluded: chain I residue 580 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 65 ASP Chi-restraints excluded: chain J residue 104 HIS 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 196 VAL Chi-restraints excluded: chain J residue 221 ASP Chi-restraints excluded: chain J residue 229 TYR 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 308 THR Chi-restraints excluded: chain J residue 309 THR Chi-restraints excluded: chain J residue 332 VAL Chi-restraints excluded: chain J residue 334 ILE Chi-restraints excluded: chain J residue 361 VAL 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 J residue 446 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 121 ILE 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 224 SER Chi-restraints excluded: chain M residue 298 VAL Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain M residue 352 SER 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 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 193 ARG Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 245 SER Chi-restraints excluded: chain N residue 255 PHE Chi-restraints excluded: chain N residue 293 SER Chi-restraints excluded: chain N residue 370 THR Chi-restraints excluded: chain N residue 421 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 370 optimal weight: 0.6980 chunk 226 optimal weight: 7.9990 chunk 237 optimal weight: 9.9990 chunk 133 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 233 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 167 optimal weight: 0.3980 chunk 48 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 261 optimal weight: 0.0870 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN A 437 HIS B 49 GLN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN ** E 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 GLN ** F 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 379 GLN ** F 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 ASN I 209 HIS ** I 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 244 ASN M 437 HIS N 191 GLN ** N 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.160942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.133776 restraints weight = 64395.764| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 2.68 r_work: 0.3844 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.6546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35626 Z= 0.140 Angle : 0.682 15.115 49010 Z= 0.343 Chirality : 0.042 0.268 5476 Planarity : 0.004 0.055 5685 Dihedral : 18.136 174.991 6493 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.46 % Allowed : 30.62 % Favored : 64.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.13), residues: 3841 helix: 0.48 (0.13), residues: 1466 sheet: -0.83 (0.19), residues: 782 loop : -0.97 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 154 HIS 0.010 0.001 HIS A 437 PHE 0.023 0.002 PHE E 287 TYR 0.031 0.002 TYR E 402 ARG 0.013 0.001 ARG M 206 Details of bonding type rmsd hydrogen bonds : bond 0.04811 ( 1468) hydrogen bonds : angle 5.00506 ( 4130) covalent geometry : bond 0.00315 (35623) covalent geometry : angle 0.68209 (49010) Misc. bond : bond 0.00534 ( 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 677 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 528 time to evaluate : 3.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 PHE cc_start: 0.6586 (OUTLIER) cc_final: 0.5927 (t80) REVERT: A 184 LYS cc_start: 0.8003 (mttt) cc_final: 0.7203 (tttt) REVERT: A 278 ARG cc_start: 0.8051 (ttm110) cc_final: 0.7480 (mmp80) REVERT: A 341 GLN cc_start: 0.8540 (tp-100) cc_final: 0.8307 (tp-100) REVERT: A 525 ARG cc_start: 0.7227 (mmp80) cc_final: 0.6931 (mtm110) REVERT: B 131 GLN cc_start: 0.7951 (mt0) cc_final: 0.7649 (mm110) REVERT: B 448 TYR cc_start: 0.7761 (t80) cc_final: 0.7504 (t80) REVERT: E 387 ILE cc_start: 0.8213 (mm) cc_final: 0.7858 (tp) REVERT: E 414 SER cc_start: 0.5073 (t) cc_final: 0.4700 (t) REVERT: E 418 LYS cc_start: 0.5925 (tptm) cc_final: 0.4977 (tptm) REVERT: E 573 ILE cc_start: 0.7691 (mp) cc_final: 0.7350 (mt) REVERT: F 408 MET cc_start: 0.7407 (mmm) cc_final: 0.7182 (tpt) REVERT: I 22 TRP cc_start: 0.8112 (m100) cc_final: 0.7598 (m100) REVERT: I 270 THR cc_start: 0.8443 (m) cc_final: 0.8154 (p) REVERT: I 341 GLN cc_start: 0.7516 (mt0) cc_final: 0.7213 (tm-30) REVERT: I 345 CYS cc_start: 0.5775 (p) cc_final: 0.5552 (p) REVERT: I 504 MET cc_start: 0.7377 (mmm) cc_final: 0.6995 (mmm) REVERT: I 518 GLU cc_start: 0.8030 (pm20) cc_final: 0.7118 (tp30) REVERT: J 34 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8121 (mp) REVERT: J 131 GLN cc_start: 0.7692 (mt0) cc_final: 0.7425 (mm110) REVERT: J 197 MET cc_start: 0.7406 (mmm) cc_final: 0.6968 (tpp) REVERT: J 308 THR cc_start: 0.7635 (m) cc_final: 0.7295 (p) REVERT: J 320 PHE cc_start: 0.7364 (OUTLIER) cc_final: 0.6692 (m-80) REVERT: M 366 LYS cc_start: 0.4339 (mmtm) cc_final: 0.4031 (mmtp) REVERT: N 25 ARG cc_start: 0.4398 (mtt180) cc_final: 0.3984 (mtt180) REVERT: N 133 MET cc_start: 0.7675 (mtt) cc_final: 0.7384 (mtm) REVERT: N 155 LYS cc_start: 0.8291 (mmtt) cc_final: 0.8078 (tttt) REVERT: N 193 ARG cc_start: 0.6820 (OUTLIER) cc_final: 0.5761 (tpp-160) REVERT: N 197 MET cc_start: 0.7330 (OUTLIER) cc_final: 0.7115 (mpp) REVERT: N 221 ASP cc_start: 0.6234 (m-30) cc_final: 0.5865 (m-30) REVERT: N 272 ASN cc_start: 0.8961 (p0) cc_final: 0.8761 (p0) REVERT: N 273 PRO cc_start: 0.9232 (Cg_endo) cc_final: 0.9026 (Cg_exo) REVERT: N 285 SER cc_start: 0.9000 (p) cc_final: 0.8742 (t) outliers start: 149 outliers final: 101 residues processed: 637 average time/residue: 0.6949 time to fit residues: 748.9633 Evaluate side-chains 575 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 469 time to evaluate : 3.875 ------------------------------------------------------------------------------- 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 268 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 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 60 HIS Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 180 ILE 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 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 82 LEU Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain E residue 363 ILE Chi-restraints excluded: chain E residue 380 PHE Chi-restraints excluded: chain E residue 560 SER Chi-restraints excluded: chain F residue 37 TYR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 140 LYS Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 197 MET Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 289 HIS 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 149 THR Chi-restraints excluded: chain I residue 209 HIS Chi-restraints excluded: chain I residue 244 ASN 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 321 LEU Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 426 LEU Chi-restraints excluded: chain I residue 557 VAL Chi-restraints excluded: chain I residue 575 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 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 320 PHE Chi-restraints excluded: chain J residue 361 VAL Chi-restraints excluded: chain J residue 394 VAL 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 208 ILE Chi-restraints excluded: chain M residue 224 SER Chi-restraints excluded: chain M residue 244 ASN Chi-restraints excluded: chain M residue 298 VAL Chi-restraints excluded: chain M residue 317 VAL Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain M residue 365 GLN Chi-restraints excluded: chain M residue 440 ARG Chi-restraints excluded: chain N residue 58 THR Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 182 ILE Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 193 ARG Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 255 PHE Chi-restraints excluded: chain N residue 429 THR Chi-restraints excluded: chain N residue 463 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 30 optimal weight: 2.9990 chunk 384 optimal weight: 6.9990 chunk 202 optimal weight: 0.0170 chunk 142 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 373 optimal weight: 0.3980 chunk 188 optimal weight: 7.9990 chunk 196 optimal weight: 2.9990 chunk 350 optimal weight: 6.9990 chunk 201 optimal weight: 1.9990 chunk 184 optimal weight: 0.9990 overall best weight: 0.8822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 HIS ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN ** E 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS F 336 GLN ** F 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 387 GLN F 436 ASN ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 209 HIS I 297 GLN ** J 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 83 GLN M 134 GLN M 209 HIS M 244 ASN N 191 GLN N 317 GLN ** N 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.160632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.133739 restraints weight = 64375.605| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 2.57 r_work: 0.3861 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.6689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 35626 Z= 0.147 Angle : 0.680 14.579 49010 Z= 0.341 Chirality : 0.042 0.280 5476 Planarity : 0.004 0.050 5685 Dihedral : 17.999 175.473 6489 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.52 % Allowed : 30.65 % Favored : 64.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.14), residues: 3841 helix: 0.61 (0.14), residues: 1457 sheet: -0.78 (0.19), residues: 771 loop : -0.88 (0.15), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP I 295 HIS 0.017 0.001 HIS I 209 PHE 0.028 0.002 PHE A 420 TYR 0.032 0.002 TYR M 191 ARG 0.010 0.000 ARG M 206 Details of bonding type rmsd hydrogen bonds : bond 0.04669 ( 1468) hydrogen bonds : angle 4.93132 ( 4130) covalent geometry : bond 0.00336 (35623) covalent geometry : angle 0.67958 (49010) Misc. bond : bond 0.00470 ( 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 656 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 505 time to evaluate : 3.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 PHE cc_start: 0.6621 (OUTLIER) cc_final: 0.5946 (t80) REVERT: A 184 LYS cc_start: 0.7993 (mttt) cc_final: 0.7215 (tttt) REVERT: A 278 ARG cc_start: 0.8050 (ttm110) cc_final: 0.7518 (mmp80) REVERT: A 525 ARG cc_start: 0.7228 (mmp80) cc_final: 0.7002 (mtm110) REVERT: B 131 GLN cc_start: 0.7941 (mt0) cc_final: 0.7712 (mm110) REVERT: B 330 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6821 (mt-10) REVERT: B 448 TYR cc_start: 0.7739 (t80) cc_final: 0.7499 (t80) REVERT: E 332 ARG cc_start: 0.8038 (ttt-90) cc_final: 0.7800 (tmt170) REVERT: E 387 ILE cc_start: 0.8156 (mm) cc_final: 0.7787 (tp) REVERT: E 414 SER cc_start: 0.5076 (t) cc_final: 0.4709 (t) REVERT: E 573 ILE cc_start: 0.7801 (mp) cc_final: 0.7478 (mt) REVERT: F 284 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8024 (tt) REVERT: I 21 MET cc_start: 0.8189 (mtm) cc_final: 0.7938 (mtp) REVERT: I 22 TRP cc_start: 0.8064 (m100) cc_final: 0.7680 (m100) REVERT: I 209 HIS cc_start: 0.6811 (OUTLIER) cc_final: 0.5726 (m90) REVERT: I 270 THR cc_start: 0.8415 (m) cc_final: 0.8135 (p) REVERT: I 341 GLN cc_start: 0.7508 (mt0) cc_final: 0.7243 (tm-30) REVERT: I 345 CYS cc_start: 0.5694 (p) cc_final: 0.5459 (p) REVERT: I 500 LYS cc_start: 0.8302 (mttt) cc_final: 0.7928 (mtpt) REVERT: I 504 MET cc_start: 0.7313 (mmm) cc_final: 0.6896 (mmm) REVERT: I 518 GLU cc_start: 0.8007 (pm20) cc_final: 0.7218 (tp30) REVERT: J 16 GLU cc_start: 0.7738 (tt0) cc_final: 0.7434 (pt0) REVERT: J 34 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8104 (mp) REVERT: J 81 THR cc_start: 0.7777 (p) cc_final: 0.7570 (m) REVERT: J 92 LYS cc_start: 0.8192 (tmtt) cc_final: 0.7930 (mppt) REVERT: J 131 GLN cc_start: 0.7706 (mt0) cc_final: 0.7446 (mm110) REVERT: J 197 MET cc_start: 0.7402 (mmm) cc_final: 0.7092 (tpp) REVERT: J 308 THR cc_start: 0.7700 (m) cc_final: 0.7273 (p) REVERT: J 320 PHE cc_start: 0.7312 (OUTLIER) cc_final: 0.6599 (m-80) REVERT: M 206 ARG cc_start: 0.7678 (mmm160) cc_final: 0.7454 (mmm160) REVERT: M 366 LYS cc_start: 0.4430 (mmtm) cc_final: 0.4195 (mmtp) REVERT: M 384 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6843 (mm-30) REVERT: M 530 TYR cc_start: 0.5904 (m-80) cc_final: 0.5434 (m-80) REVERT: N 25 ARG cc_start: 0.4474 (mtt180) cc_final: 0.4076 (mtt180) REVERT: N 193 ARG cc_start: 0.6833 (OUTLIER) cc_final: 0.5902 (tpp-160) REVERT: N 221 ASP cc_start: 0.6161 (m-30) cc_final: 0.5902 (m-30) REVERT: N 272 ASN cc_start: 0.8905 (p0) cc_final: 0.8704 (p0) REVERT: N 470 ARG cc_start: 0.7786 (ptt90) cc_final: 0.7579 (ptt-90) outliers start: 151 outliers final: 113 residues processed: 624 average time/residue: 0.4504 time to fit residues: 462.7476 Evaluate side-chains 593 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 472 time to evaluate : 3.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 130 LEU 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 268 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 415 THR 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 58 THR Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 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 330 GLU 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 82 LEU 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 242 ASP Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 267 ASP 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 560 SER Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 37 TYR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 140 LYS Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 197 MET Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 289 HIS Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 436 ASN Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain I residue 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 209 HIS Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 244 ASN Chi-restraints excluded: chain I residue 281 LEU Chi-restraints excluded: chain I residue 286 THR 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 417 LEU Chi-restraints excluded: chain I residue 426 LEU Chi-restraints excluded: chain I residue 528 ARG Chi-restraints excluded: chain I residue 547 LEU Chi-restraints excluded: chain I residue 557 VAL Chi-restraints excluded: chain I residue 583 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 104 HIS Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 221 ASP Chi-restraints excluded: chain J residue 244 CYS Chi-restraints excluded: chain J residue 320 PHE Chi-restraints excluded: chain J residue 361 VAL Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 34 LEU 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 208 ILE Chi-restraints excluded: chain M residue 224 SER Chi-restraints excluded: chain M residue 298 VAL Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 365 GLN Chi-restraints excluded: chain M residue 381 LEU Chi-restraints excluded: chain M residue 384 GLU 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 147 LEU Chi-restraints excluded: chain N residue 182 ILE Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 193 ARG Chi-restraints excluded: chain N residue 244 CYS Chi-restraints excluded: chain N residue 255 PHE Chi-restraints excluded: chain N residue 429 THR Chi-restraints excluded: chain N residue 463 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 229 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 390 optimal weight: 10.0000 chunk 235 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 112 optimal weight: 0.4980 chunk 343 optimal weight: 9.9990 chunk 373 optimal weight: 0.0070 chunk 142 optimal weight: 6.9990 chunk 314 optimal weight: 0.0980 chunk 54 optimal weight: 1.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 HIS ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 GLN E 55 GLN ** E 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 367 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** I 15 GLN I 209 HIS ** J 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.161473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.134580 restraints weight = 64305.236| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 2.63 r_work: 0.3862 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.6802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 35626 Z= 0.141 Angle : 0.674 14.965 49010 Z= 0.338 Chirality : 0.042 0.289 5476 Planarity : 0.004 0.048 5685 Dihedral : 17.927 175.928 6486 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 4.22 % Allowed : 30.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.14), residues: 3841 helix: 0.65 (0.14), residues: 1461 sheet: -0.72 (0.19), residues: 770 loop : -0.84 (0.15), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 154 HIS 0.029 0.001 HIS A 437 PHE 0.023 0.002 PHE M 287 TYR 0.029 0.001 TYR M 191 ARG 0.008 0.000 ARG M 206 Details of bonding type rmsd hydrogen bonds : bond 0.04645 ( 1468) hydrogen bonds : angle 4.88886 ( 4130) covalent geometry : bond 0.00326 (35623) covalent geometry : angle 0.67382 (49010) Misc. bond : bond 0.00434 ( 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 639 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 498 time to evaluate : 3.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 PHE cc_start: 0.6570 (OUTLIER) cc_final: 0.5893 (t80) REVERT: A 184 LYS cc_start: 0.7990 (mttt) cc_final: 0.7183 (tttt) REVERT: A 278 ARG cc_start: 0.8082 (ttm110) cc_final: 0.7506 (mmp80) REVERT: A 480 ASN cc_start: 0.7164 (m-40) cc_final: 0.6938 (m-40) REVERT: A 525 ARG cc_start: 0.7247 (mmp80) cc_final: 0.6980 (mtm110) REVERT: B 107 CYS cc_start: 0.6603 (OUTLIER) cc_final: 0.5607 (t) REVERT: B 131 GLN cc_start: 0.7999 (mt0) cc_final: 0.7677 (mm-40) REVERT: B 330 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6747 (mt-10) REVERT: B 448 TYR cc_start: 0.7733 (t80) cc_final: 0.7484 (t80) REVERT: E 387 ILE cc_start: 0.8134 (mm) cc_final: 0.7763 (tp) REVERT: E 414 SER cc_start: 0.5181 (t) cc_final: 0.4835 (t) REVERT: E 573 ILE cc_start: 0.7806 (mp) cc_final: 0.7492 (mt) REVERT: I 21 MET cc_start: 0.8150 (mtm) cc_final: 0.7824 (mtp) REVERT: I 22 TRP cc_start: 0.8042 (m100) cc_final: 0.7715 (m100) REVERT: I 226 TYR cc_start: 0.5847 (t80) cc_final: 0.5595 (t80) REVERT: I 270 THR cc_start: 0.8458 (m) cc_final: 0.8165 (p) REVERT: I 341 GLN cc_start: 0.7577 (mt0) cc_final: 0.7195 (tm-30) REVERT: I 504 MET cc_start: 0.7258 (mmm) cc_final: 0.6749 (mmm) REVERT: I 518 GLU cc_start: 0.7993 (pm20) cc_final: 0.7209 (tp30) REVERT: J 16 GLU cc_start: 0.7805 (tt0) cc_final: 0.7487 (pt0) REVERT: J 34 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8086 (mp) REVERT: J 81 THR cc_start: 0.7857 (p) cc_final: 0.7656 (m) REVERT: J 92 LYS cc_start: 0.8148 (tmtt) cc_final: 0.7882 (mppt) REVERT: J 131 GLN cc_start: 0.7718 (mt0) cc_final: 0.7439 (mm110) REVERT: J 197 MET cc_start: 0.7474 (mmm) cc_final: 0.7082 (tpp) REVERT: J 308 THR cc_start: 0.7725 (m) cc_final: 0.7270 (p) REVERT: J 320 PHE cc_start: 0.7337 (OUTLIER) cc_final: 0.6627 (m-80) REVERT: J 373 GLU cc_start: 0.8181 (tp30) cc_final: 0.7610 (tp30) REVERT: M 366 LYS cc_start: 0.4356 (mmtm) cc_final: 0.4118 (mmtp) REVERT: M 384 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6935 (mm-30) REVERT: M 530 TYR cc_start: 0.6002 (m-80) cc_final: 0.5455 (m-80) REVERT: N 25 ARG cc_start: 0.4690 (mtt180) cc_final: 0.4153 (mtt180) REVERT: N 191 GLN cc_start: 0.8278 (mm110) cc_final: 0.7954 (mm-40) REVERT: N 221 ASP cc_start: 0.6213 (m-30) cc_final: 0.5932 (m-30) REVERT: N 261 ASP cc_start: 0.7763 (t0) cc_final: 0.7553 (p0) REVERT: N 272 ASN cc_start: 0.8923 (p0) cc_final: 0.8710 (p0) REVERT: N 280 MET cc_start: 0.8437 (tpp) cc_final: 0.8161 (tpp) REVERT: N 330 GLU cc_start: 0.7746 (mp0) cc_final: 0.7511 (mp0) outliers start: 141 outliers final: 115 residues processed: 603 average time/residue: 0.4585 time to fit residues: 453.7858 Evaluate side-chains 595 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 474 time to evaluate : 3.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 130 LEU 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 268 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 429 LEU 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 60 HIS Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 104 HIS 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 284 LEU Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 373 GLU 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 82 LEU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 267 ASP 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 560 SER Chi-restraints excluded: chain F residue 37 TYR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 140 LYS Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 197 MET Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 289 HIS Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain I residue 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 209 HIS Chi-restraints excluded: chain I residue 219 PHE Chi-restraints excluded: chain I residue 231 GLU Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 244 ASN Chi-restraints excluded: chain I residue 281 LEU Chi-restraints excluded: chain I residue 286 THR 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 417 LEU Chi-restraints excluded: chain I residue 426 LEU Chi-restraints excluded: chain I residue 528 ARG Chi-restraints excluded: chain I residue 583 VAL Chi-restraints excluded: chain J residue 34 LEU 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 320 PHE Chi-restraints excluded: chain J residue 361 VAL Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 77 SER Chi-restraints excluded: chain M residue 93 PHE Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 144 ASP Chi-restraints excluded: chain M residue 163 HIS 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 336 LEU Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 365 GLN Chi-restraints excluded: chain M residue 381 LEU Chi-restraints excluded: chain M residue 384 GLU Chi-restraints excluded: chain M residue 557 VAL Chi-restraints excluded: chain M residue 579 PHE Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 244 CYS Chi-restraints excluded: chain N residue 255 PHE Chi-restraints excluded: chain N residue 429 THR Chi-restraints excluded: chain N residue 463 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 275 optimal weight: 0.9990 chunk 51 optimal weight: 0.0770 chunk 231 optimal weight: 6.9990 chunk 14 optimal weight: 0.0170 chunk 397 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 377 optimal weight: 5.9990 chunk 233 optimal weight: 0.9990 chunk 379 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 HIS ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 GLN E 55 GLN ** E 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 289 HIS F 367 GLN F 436 ASN ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 244 ASN N 367 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.162641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.135337 restraints weight = 63848.737| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 2.71 r_work: 0.3868 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.6915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 35626 Z= 0.135 Angle : 0.678 15.231 49010 Z= 0.338 Chirality : 0.042 0.297 5476 Planarity : 0.004 0.066 5685 Dihedral : 17.859 175.423 6486 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.68 % Allowed : 31.58 % Favored : 64.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.14), residues: 3841 helix: 0.67 (0.14), residues: 1465 sheet: -0.65 (0.19), residues: 775 loop : -0.87 (0.15), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 543 HIS 0.030 0.001 HIS I 209 PHE 0.022 0.002 PHE M 287 TYR 0.027 0.001 TYR M 191 ARG 0.010 0.000 ARG N 470 Details of bonding type rmsd hydrogen bonds : bond 0.04615 ( 1468) hydrogen bonds : angle 4.86160 ( 4130) covalent geometry : bond 0.00311 (35623) covalent geometry : angle 0.67762 (49010) Misc. bond : bond 0.00399 ( 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 614 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 491 time to evaluate : 3.936 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 143 PHE cc_start: 0.6556 (OUTLIER) cc_final: 0.5863 (t80) REVERT: A 184 LYS cc_start: 0.8007 (mttt) cc_final: 0.7192 (tttt) REVERT: A 229 ARG cc_start: 0.7633 (ptt-90) cc_final: 0.7419 (ptt-90) REVERT: A 278 ARG cc_start: 0.8069 (ttm110) cc_final: 0.7438 (mmp80) REVERT: A 480 ASN cc_start: 0.7125 (m-40) cc_final: 0.6902 (m-40) REVERT: B 60 HIS cc_start: 0.7818 (OUTLIER) cc_final: 0.7346 (m-70) REVERT: B 131 GLN cc_start: 0.7961 (mt0) cc_final: 0.7605 (mm-40) REVERT: B 448 TYR cc_start: 0.7709 (t80) cc_final: 0.7474 (t80) REVERT: E 387 ILE cc_start: 0.8167 (mm) cc_final: 0.7753 (tp) REVERT: E 414 SER cc_start: 0.5185 (t) cc_final: 0.4832 (t) REVERT: E 573 ILE cc_start: 0.7826 (mp) cc_final: 0.7504 (mt) REVERT: F 51 ARG cc_start: 0.7724 (mpp80) cc_final: 0.7317 (mtm180) REVERT: I 209 HIS cc_start: 0.6752 (OUTLIER) cc_final: 0.6147 (m-70) REVERT: I 226 TYR cc_start: 0.5869 (t80) cc_final: 0.5664 (t80) REVERT: I 270 THR cc_start: 0.8479 (m) cc_final: 0.8180 (p) REVERT: I 341 GLN cc_start: 0.7524 (mt0) cc_final: 0.7076 (tm-30) REVERT: I 504 MET cc_start: 0.7190 (mmm) cc_final: 0.6749 (mmm) REVERT: I 518 GLU cc_start: 0.7983 (pm20) cc_final: 0.7360 (tp30) REVERT: J 16 GLU cc_start: 0.7862 (tt0) cc_final: 0.7625 (pt0) REVERT: J 34 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8073 (mp) REVERT: J 92 LYS cc_start: 0.8175 (tmtt) cc_final: 0.7810 (mppt) REVERT: J 131 GLN cc_start: 0.7740 (mt0) cc_final: 0.7453 (mm110) REVERT: J 197 MET cc_start: 0.7434 (mmm) cc_final: 0.7173 (tpp) REVERT: J 308 THR cc_start: 0.7753 (m) cc_final: 0.7273 (p) REVERT: J 320 PHE cc_start: 0.7310 (OUTLIER) cc_final: 0.6569 (m-80) REVERT: J 373 GLU cc_start: 0.8164 (tp30) cc_final: 0.7550 (tp30) REVERT: M 99 ASP cc_start: 0.7317 (t0) cc_final: 0.7107 (t0) REVERT: M 359 LEU cc_start: 0.7727 (mt) cc_final: 0.7417 (mt) REVERT: M 366 LYS cc_start: 0.4310 (mmtm) cc_final: 0.4077 (mmtp) REVERT: M 384 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6808 (mm-30) REVERT: M 530 TYR cc_start: 0.5951 (m-80) cc_final: 0.5388 (m-80) REVERT: M 548 PHE cc_start: 0.5511 (m-10) cc_final: 0.5120 (m-80) REVERT: N 25 ARG cc_start: 0.4877 (mtt180) cc_final: 0.4271 (mtt180) REVERT: N 191 GLN cc_start: 0.8241 (mm110) cc_final: 0.7925 (mm-40) REVERT: N 221 ASP cc_start: 0.6238 (m-30) cc_final: 0.5953 (m-30) REVERT: N 280 MET cc_start: 0.8348 (tpp) cc_final: 0.8133 (tpp) REVERT: N 330 GLU cc_start: 0.7672 (mp0) cc_final: 0.7440 (mp0) outliers start: 123 outliers final: 106 residues processed: 584 average time/residue: 0.4895 time to fit residues: 473.7302 Evaluate side-chains 575 residues out of total 3341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 463 time to evaluate : 3.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 429 LEU 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 60 HIS Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 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 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 82 LEU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 267 ASP 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 560 SER Chi-restraints excluded: chain F residue 37 TYR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 140 LYS Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 197 MET Chi-restraints excluded: chain F residue 289 HIS Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 436 ASN Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain 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 209 HIS Chi-restraints excluded: chain I residue 219 PHE Chi-restraints excluded: chain I residue 244 ASN Chi-restraints excluded: chain I residue 286 THR 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 417 LEU Chi-restraints excluded: chain I residue 426 LEU Chi-restraints excluded: chain I residue 528 ARG Chi-restraints excluded: chain I residue 583 VAL Chi-restraints excluded: chain J residue 34 LEU 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 244 CYS Chi-restraints excluded: chain J residue 320 PHE Chi-restraints excluded: chain J residue 361 VAL Chi-restraints excluded: chain J residue 394 VAL 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 163 HIS Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 208 ILE Chi-restraints excluded: chain M residue 244 ASN Chi-restraints excluded: chain M residue 298 VAL Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 365 GLN Chi-restraints excluded: chain M residue 381 LEU Chi-restraints excluded: chain M residue 384 GLU Chi-restraints excluded: chain M residue 557 VAL Chi-restraints excluded: chain M residue 579 PHE Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 244 CYS Chi-restraints excluded: chain N residue 255 PHE Chi-restraints excluded: chain N residue 429 THR Chi-restraints excluded: chain N residue 463 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 336 optimal weight: 6.9990 chunk 340 optimal weight: 0.0010 chunk 158 optimal weight: 0.0980 chunk 178 optimal weight: 0.0370 chunk 151 optimal weight: 3.9990 chunk 211 optimal weight: 5.9990 chunk 327 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 388 optimal weight: 6.9990 chunk 262 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 overall best weight: 1.4268 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 HIS ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 GLN ** E 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN ** E 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 244 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.162361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.135770 restraints weight = 64367.149| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 2.62 r_work: 0.3872 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.6928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.238 35626 Z= 0.234 Angle : 0.864 59.178 49010 Z= 0.479 Chirality : 0.053 1.943 5476 Planarity : 0.005 0.158 5685 Dihedral : 17.867 175.465 6484 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.95 % Allowed : 31.46 % Favored : 64.59 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.14), residues: 3841 helix: 0.67 (0.14), residues: 1461 sheet: -0.64 (0.19), residues: 775 loop : -0.88 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.085 0.002 TRP B 154 HIS 0.246 0.003 HIS F 289 PHE 0.060 0.002 PHE B 304 TYR 0.058 0.002 TYR M 74 ARG 0.023 0.001 ARG E 332 Details of bonding type rmsd hydrogen bonds : bond 0.04621 ( 1468) hydrogen bonds : angle 4.86156 ( 4130) covalent geometry : bond 0.00514 (35623) covalent geometry : angle 0.86354 (49010) Misc. bond : bond 0.00397 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20429.56 seconds wall clock time: 362 minutes 45.05 seconds (21765.05 seconds total)