Starting phenix.real_space_refine on Mon Jul 6 09:13:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y82_39030/07_2026/8y82_39030_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y82_39030/07_2026/8y82_39030.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8y82_39030/07_2026/8y82_39030_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y82_39030/07_2026/8y82_39030_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8y82_39030/07_2026/8y82_39030.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y82_39030/07_2026/8y82_39030.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.058 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 166 5.49 5 Mg 4 5.21 5 S 124 5.16 5 C 21510 2.51 5 N 5934 2.21 5 O 6776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34514 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 3659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3659 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 443} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 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: 4609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4609 Classifications: {'peptide': 576} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 552} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 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: 3659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3659 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 443} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 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: 4609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4609 Classifications: {'peptide': 576} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 552} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 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: "E" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 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: "M" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.20, per 1000 atoms: 0.24 Number of scatterers: 34514 At special positions: 0 Unit cell: (110.818, 151.341, 212.539, 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 166 15.00 Mg 4 11.99 O 6776 8.00 N 5934 7.00 C 21510 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.57 Conformation dependent library (CDL) restraints added in 1.6 seconds 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7320 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 50 sheets defined 42.1% alpha, 18.8% beta 60 base pairs and 104 stacking pairs defined. Time for finding SS restraints: 4.32 Creating SS restraints... Processing helix chain 'A' and resid 5 through 16 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: 4.111A pdb=" N CYS A 211 " --> pdb=" O GLU A 207 " (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: 3.784A 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: 3.883A 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 72 removed outlier: 3.703A pdb=" N LEU B 64 " --> pdb=" O HIS B 60 " (cutoff:3.500A) 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: 3.570A 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: 4.515A 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 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 185 through 190 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) removed outlier: 3.556A pdb=" N GLY B 209 " --> pdb=" O TYR B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 295 removed outlier: 3.607A pdb=" N SER B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) 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: 3.593A pdb=" N SER B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 429 removed outlier: 4.437A 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 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: 4.070A 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 120 through 132 Processing helix chain 'E' and resid 145 through 155 Processing helix chain 'E' and resid 168 through 176 removed outlier: 3.505A pdb=" N SER E 172 " --> pdb=" O TYR E 168 " (cutoff:3.500A) 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: 3.834A pdb=" N THR E 203 " --> pdb=" O ASP E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 219 removed outlier: 3.910A pdb=" N ILE E 217 " --> pdb=" O LEU E 213 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG E 218 " --> pdb=" O ALA E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 242 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: 3.597A 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: 3.563A 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 138 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 185 through 190 Processing helix chain 'F' and resid 193 through 208 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 242 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: 3.883A 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: 3.585A 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: 3.608A pdb=" N SER J 294 " --> pdb=" O LEU J 290 " (cutoff:3.500A) Processing helix chain 'J' and resid 312 through 322 removed outlier: 3.529A pdb=" N GLN J 317 " --> pdb=" O GLU J 313 " (cutoff:3.500A) removed outlier: 3.592A 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 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 155 removed outlier: 3.651A pdb=" N ALA M 150 " --> pdb=" O VAL M 146 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 176 Processing helix chain 'M' and resid 198 through 203 removed outlier: 3.787A 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: 3.652A 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: 4.130A 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: 3.597A 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: 3.563A 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 190 removed outlier: 4.194A pdb=" N LEU N 188 " --> pdb=" O ASN N 184 " (cutoff:3.500A) Processing helix chain 'N' and resid 192 through 208 removed outlier: 3.563A pdb=" N VAL N 196 " --> pdb=" O CYS N 192 " (cutoff:3.500A) Processing helix chain 'N' and resid 276 through 295 Processing helix chain 'N' and resid 312 through 323 removed outlier: 3.726A 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 137 through 140 Processing sheet with id=AA2, first strand: chain 'A' and resid 221 through 224 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: 6.051A pdb=" N TRP A 253 " --> pdb=" O VAL A 282 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 579 through 580 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) removed outlier: 4.206A pdb=" N HIS A 444 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing sheet with id=AA5, 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=AA6, 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: 6.751A pdb=" N CYS A 345 " --> pdb=" O GLN A 401 " (cutoff:3.500A) removed outlier: 4.675A 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: 4.424A 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=AA7, 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=AA8, 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=AA9, first strand: chain 'B' and resid 19 through 20 Processing sheet with id=AB1, first strand: chain 'B' and resid 98 through 99 removed outlier: 7.113A pdb=" N VAL B 50 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 8.466A 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=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 98 through 99 removed outlier: 7.113A pdb=" N VAL B 50 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ILE B 183 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL B 148 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 159 through 160 Processing sheet with id=AB4, first strand: chain 'E' and resid 138 through 139 removed outlier: 8.041A pdb=" N PHE E 139 " --> pdb=" O MET E 20 " (cutoff:3.500A) removed outlier: 6.050A 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: 7.706A pdb=" N SER E 224 " --> pdb=" O MET E 21 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N PHE E 23 " --> pdb=" O SER E 224 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU E 221 " --> pdb=" O TYR E 252 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N THR E 254 " --> pdb=" O LEU E 221 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL E 223 " --> pdb=" O THR E 254 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N TRP E 253 " --> pdb=" O VAL E 282 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'E' and resid 161 through 162 Processing sheet with id=AB6, first strand: chain 'E' and resid 330 through 332 removed outlier: 3.910A 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=AB6 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) removed outlier: 4.012A pdb=" N HIS E 444 " --> pdb=" O ILE E 492 " (cutoff:3.500A) Processing sheet with id=AB8, 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=AB9, 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: 4.596A pdb=" N TYR E 403 " --> pdb=" O ILE E 343 " (cutoff:3.500A) removed outlier: 6.694A 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=AC1, first strand: chain 'E' and resid 558 through 561 removed outlier: 3.615A pdb=" N ALA E 569 " --> pdb=" O CYS E 561 " (cutoff:3.500A) Processing sheet with id=AC2, 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: 3.883A 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: 6.432A 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: 5.573A pdb=" N ILE F 305 " --> pdb=" O VAL F 332 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE F 334 " --> pdb=" O ILE F 305 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LYS F 307 " --> pdb=" O ILE F 334 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 19 through 20 Processing sheet with id=AC4, first strand: chain 'F' and resid 98 through 99 removed outlier: 6.602A pdb=" N VAL F 50 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N CYS F 107 " --> pdb=" O LEU F 52 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N TYR F 54 " --> pdb=" O CYS F 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'F' and resid 98 through 99 removed outlier: 6.602A pdb=" N VAL F 50 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ARG F 51 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LEU F 147 " --> pdb=" O ARG F 51 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA F 53 " --> pdb=" O LEU F 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'F' and resid 159 through 160 removed outlier: 3.927A pdb=" N TYR F 160 " --> pdb=" O PHE F 163 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 381 through 382 Processing sheet with id=AC8, first strand: chain 'I' and resid 137 through 140 Processing sheet with id=AC9, 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=AD1, first strand: chain 'I' and resid 579 through 580 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) removed outlier: 4.206A pdb=" N HIS I 444 " --> pdb=" O ILE I 492 " (cutoff:3.500A) Processing sheet with id=AD3, 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=AD4, first strand: chain 'I' and resid 371 through 373 removed outlier: 6.899A 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: 6.751A pdb=" N CYS I 345 " --> pdb=" O GLN I 401 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLN I 401 " --> pdb=" O CYS I 345 " (cutoff:3.500A) removed outlier: 6.480A 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: 6.632A pdb=" N THR I 349 " --> pdb=" O ASN I 397 " (cutoff:3.500A) Processing sheet with id=AD5, 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=AD6, first strand: chain 'J' and resid 12 through 13 removed outlier: 6.812A 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=AD7, first strand: chain 'J' and resid 19 through 20 Processing sheet with id=AD8, first strand: chain 'J' and resid 98 through 99 removed outlier: 7.114A 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=AD8 Processing sheet with id=AD9, first strand: chain 'J' and resid 98 through 99 removed outlier: 7.114A 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=AE1, first strand: chain 'J' and resid 159 through 160 Processing sheet with id=AE2, first strand: chain 'M' and resid 138 through 140 removed outlier: 8.041A pdb=" N PHE M 139 " --> pdb=" O MET M 20 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N TRP M 22 " --> pdb=" O PHE M 139 " (cutoff:3.500A) 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: 6.740A 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) removed outlier: 6.126A pdb=" N TRP M 253 " --> pdb=" O VAL M 282 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'M' and resid 161 through 162 Processing sheet with id=AE4, first strand: chain 'M' and resid 330 through 332 removed outlier: 3.910A pdb=" N LEU M 331 " --> pdb=" O SER M 580 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER M 580 " --> pdb=" O LEU M 331 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'M' and resid 335 through 338 removed outlier: 4.631A pdb=" N LEU M 501 " --> pdb=" O VAL M 338 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS M 444 " --> pdb=" O ILE M 492 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 335 through 338 removed outlier: 4.631A pdb=" N LEU M 501 " --> pdb=" O VAL M 338 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 371 through 373 removed outlier: 6.625A 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: 4.297A pdb=" N ILE M 399 " --> pdb=" O VAL M 347 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N THR M 349 " --> pdb=" O ASN M 397 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 558 through 561 removed outlier: 3.616A pdb=" N ALA M 569 " --> pdb=" O CYS M 561 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'N' and resid 12 through 13 removed outlier: 3.990A pdb=" N SER N 12 " --> pdb=" O TYR N 366 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR N 366 " --> pdb=" O SER N 12 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU N 375 " --> pdb=" O PRO N 368 " (cutoff:3.500A) removed outlier: 6.104A 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: 6.974A 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: 3.638A pdb=" N CYS N 244 " --> pdb=" O TYR N 260 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 19 through 20 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: 8.320A pdb=" N CYS N 107 " --> pdb=" O LEU N 52 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N TYR N 54 " --> pdb=" O CYS N 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, 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: 7.688A 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=AF3 Processing sheet with id=AF4, first strand: chain 'N' and resid 159 through 160 removed outlier: 3.927A pdb=" N TYR N 160 " --> pdb=" O PHE N 163 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'N' and resid 381 through 382 1385 hydrogen bonds defined for protein. 3870 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: 8.58 Time building geometry restraints manager: 4.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5309 1.32 - 1.44: 10697 1.44 - 1.57: 19148 1.57 - 1.69: 324 1.69 - 1.82: 190 Bond restraints: 35668 Sorted by residual: bond pdb=" N PHE I 247 " pdb=" CA PHE I 247 " ideal model delta sigma weight residual 1.458 1.485 -0.028 7.40e-03 1.83e+04 1.39e+01 bond pdb=" C3' DA P 18 " pdb=" C2' DA P 18 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DA H 18 " pdb=" C2' DA H 18 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" CA SER M 167 " pdb=" CB SER M 167 " ideal model delta sigma weight residual 1.541 1.503 0.038 1.20e-02 6.94e+03 1.00e+01 bond pdb=" C PRO M 35 " pdb=" O PRO M 35 " ideal model delta sigma weight residual 1.233 1.199 0.035 1.10e-02 8.26e+03 9.91e+00 ... (remaining 35663 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 47975 2.27 - 4.54: 972 4.54 - 6.81: 104 6.81 - 9.09: 20 9.09 - 11.36: 9 Bond angle restraints: 49080 Sorted by residual: angle pdb=" N GLN N 191 " pdb=" CA GLN N 191 " pdb=" C GLN N 191 " ideal model delta sigma weight residual 110.80 122.16 -11.36 2.13e+00 2.20e-01 2.84e+01 angle pdb=" N ILE N 462 " pdb=" CA ILE N 462 " pdb=" C ILE N 462 " ideal model delta sigma weight residual 113.20 108.09 5.11 9.60e-01 1.09e+00 2.83e+01 angle pdb=" N ILE F 462 " pdb=" CA ILE F 462 " pdb=" C ILE F 462 " ideal model delta sigma weight residual 113.20 108.11 5.09 9.60e-01 1.09e+00 2.81e+01 angle pdb=" C GLN I 15 " pdb=" N ASN I 16 " pdb=" CA ASN I 16 " ideal model delta sigma weight residual 123.03 116.09 6.94 1.34e+00 5.57e-01 2.69e+01 angle pdb=" N LEU M 14 " pdb=" CA LEU M 14 " pdb=" C LEU M 14 " ideal model delta sigma weight residual 111.28 105.67 5.61 1.09e+00 8.42e-01 2.65e+01 ... (remaining 49075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 19914 35.84 - 71.68: 1210 71.68 - 107.52: 63 107.52 - 143.36: 0 143.36 - 179.20: 9 Dihedral angle restraints: 21196 sinusoidal: 9828 harmonic: 11368 Sorted by residual: dihedral pdb=" C5' AMP E 601 " pdb=" O5' AMP E 601 " pdb=" P AMP E 601 " pdb=" O3P AMP E 601 " ideal model delta sinusoidal sigma weight residual -60.00 119.20 -179.20 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" N SER E 167 " pdb=" C SER E 167 " pdb=" CA SER E 167 " pdb=" CB SER E 167 " ideal model delta harmonic sigma weight residual 122.80 133.95 -11.15 0 2.50e+00 1.60e-01 1.99e+01 dihedral pdb=" C2' AMP M 601 " pdb=" C1' AMP M 601 " pdb=" N9 AMP M 601 " pdb=" C4 AMP M 601 " ideal model delta sinusoidal sigma weight residual 91.55 168.06 -76.50 1 2.00e+01 2.50e-03 1.84e+01 ... (remaining 21193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 5153 0.095 - 0.190: 306 0.190 - 0.284: 19 0.284 - 0.379: 5 0.379 - 0.474: 3 Chirality restraints: 5486 Sorted by residual: chirality pdb=" CA ALA N 187 " pdb=" N ALA N 187 " pdb=" C ALA N 187 " pdb=" CB ALA N 187 " both_signs ideal model delta sigma weight residual False 2.48 2.01 0.47 2.00e-01 2.50e+01 5.62e+00 chirality pdb=" CA SER E 167 " pdb=" N SER E 167 " pdb=" C SER E 167 " pdb=" CB SER E 167 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.41e+00 chirality pdb=" CA ARG J 190 " pdb=" N ARG J 190 " pdb=" C ARG J 190 " pdb=" CB ARG J 190 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.46 2.00e-01 2.50e+01 5.18e+00 ... (remaining 5483 not shown) Planarity restraints: 5684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU I 14 " -0.020 2.00e-02 2.50e+03 4.16e-02 1.73e+01 pdb=" C LEU I 14 " 0.072 2.00e-02 2.50e+03 pdb=" O LEU I 14 " -0.027 2.00e-02 2.50e+03 pdb=" N GLN I 15 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER M 31 " 0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C SER M 31 " -0.059 2.00e-02 2.50e+03 pdb=" O SER M 31 " 0.022 2.00e-02 2.50e+03 pdb=" N ALA M 32 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS I 315 " 0.051 5.00e-02 4.00e+02 7.45e-02 8.88e+00 pdb=" N PRO I 316 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO I 316 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO I 316 " 0.041 5.00e-02 4.00e+02 ... (remaining 5681 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.20: 45 2.20 - 2.88: 13477 2.88 - 3.55: 50725 3.55 - 4.23: 85171 4.23 - 4.90: 144233 Nonbonded interactions: 293651 Sorted by model distance: nonbonded pdb=" OH TYR E 168 " pdb=" CB GLN M 192 " model vdw 1.526 3.440 nonbonded pdb=" OE1 GLU J 330 " pdb=" CA GLY J 414 " model vdw 1.815 3.440 nonbonded pdb=" OD2 ASP F 261 " pdb=" CG1 VAL F 463 " model vdw 1.885 3.460 nonbonded pdb=" CB GLN E 192 " pdb=" OH TYR M 168 " model vdw 1.898 3.440 nonbonded pdb=" OD2 ASP E 188 " pdb=" NH1 ARG E 190 " model vdw 1.909 3.120 ... (remaining 293646 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'I' } 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: 10.900 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: 0.050 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 38.300 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 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 : 0.005 0.410 35670 Z= 0.353 Angle : 0.729 11.358 49080 Z= 0.468 Chirality : 0.049 0.474 5486 Planarity : 0.005 0.076 5684 Dihedral : 20.404 179.197 13876 Min Nonbonded Distance : 1.526 Molprobity Statistics. All-atom Clashscore : 21.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.63 % Favored : 95.21 % Rotamer: Outliers : 1.83 % Allowed : 30.62 % Favored : 67.56 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.14), residues: 3842 helix: 0.73 (0.14), residues: 1476 sheet: -0.67 (0.20), residues: 758 loop : -0.64 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 411 TYR 0.019 0.001 TYR N 274 PHE 0.016 0.001 PHE M 287 TRP 0.015 0.001 TRP M 502 HIS 0.011 0.001 HIS M 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.27 (35668) covalent geometry : angle 0.72874 / 0.47 (49080) hydrogen bonds : bond 0.15270 / 10.05 ( 1469) hydrogen bonds : angle 6.39042 / 4.51 ( 4142) Misc. bond : bond 0.30703 / 14.80 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 822 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 761 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 LEU cc_start: 0.7792 (mm) cc_final: 0.7539 (tt) REVERT: B 100 MET cc_start: 0.6540 (mmm) cc_final: 0.5933 (tpt) REVERT: E 93 PHE cc_start: 0.8950 (OUTLIER) cc_final: 0.8169 (m-80) REVERT: I 15 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7772 (tt0) REVERT: I 390 ILE cc_start: 0.3550 (tp) cc_final: 0.3291 (tp) REVERT: J 302 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8313 (tttt) REVERT: M 30 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7571 (ttm170) REVERT: M 48 TYR cc_start: 0.6424 (t80) cc_final: 0.6076 (t80) REVERT: M 133 ASN cc_start: 0.7722 (t0) cc_final: 0.7071 (t0) REVERT: M 165 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.7218 (mm-30) REVERT: M 198 THR cc_start: 0.7157 (m) cc_final: 0.6936 (m) REVERT: M 332 ARG cc_start: 0.7614 (ttp-170) cc_final: 0.7088 (ttt180) REVERT: M 461 LEU cc_start: 0.6202 (tp) cc_final: 0.5810 (mp) REVERT: M 546 ILE cc_start: 0.7237 (mt) cc_final: 0.6661 (mt) REVERT: M 566 GLU cc_start: 0.3991 (mp0) cc_final: 0.3252 (tt0) REVERT: M 579 PHE cc_start: 0.6685 (p90) cc_final: 0.6305 (p90) REVERT: N 40 TYR cc_start: 0.7166 (t80) cc_final: 0.6874 (t80) REVERT: N 70 GLU cc_start: 0.6773 (mt-10) cc_final: 0.6511 (tt0) REVERT: N 276 SER cc_start: 0.8212 (p) cc_final: 0.8007 (m) REVERT: N 280 MET cc_start: 0.8263 (tpp) cc_final: 0.8054 (tpt) REVERT: N 376 LEU cc_start: 0.7331 (tp) cc_final: 0.7018 (tp) outliers start: 61 outliers final: 27 residues processed: 815 average time/residue: 0.2458 time to fit residues: 315.5476 Evaluate side-chains 520 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 488 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain I residue 15 GLN Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 244 ASN Chi-restraints excluded: chain I residue 265 VAL Chi-restraints excluded: chain I residue 266 GLN Chi-restraints excluded: chain I residue 269 ILE Chi-restraints excluded: chain I residue 326 LYS 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 190 ARG Chi-restraints excluded: chain J residue 302 LYS Chi-restraints excluded: chain J residue 303 ILE Chi-restraints excluded: chain M residue 30 ARG Chi-restraints excluded: chain M residue 147 ILE Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 165 GLU Chi-restraints excluded: chain M residue 189 PHE Chi-restraints excluded: chain M residue 209 HIS Chi-restraints excluded: chain M residue 211 CYS Chi-restraints excluded: chain N residue 185 ASP Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 270 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.0980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 9.9990 chunk 401 optimal weight: 10.0000 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 20.0000 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN E 83 GLN ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 114 HIS F 238 GLN ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 296 ASN F 379 GLN ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 436 ASN I 16 ASN I 18 GLN I 120 ASN I 123 HIS I 244 ASN J 60 HIS ** J 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 72 GLN M 83 GLN M 186 HIS ** M 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 533 ASN ** N 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.158982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.125942 restraints weight = 59499.775| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.62 r_work: 0.3646 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 35670 Z= 0.225 Angle : 0.697 9.771 49080 Z= 0.366 Chirality : 0.045 0.304 5486 Planarity : 0.005 0.070 5684 Dihedral : 18.092 171.123 6558 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 6.20 % Allowed : 27.92 % Favored : 65.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.14), residues: 3842 helix: 0.64 (0.13), residues: 1504 sheet: -0.72 (0.19), residues: 784 loop : -0.79 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG I 462 TYR 0.025 0.002 TYR E 168 PHE 0.021 0.002 PHE M 91 TRP 0.017 0.002 TRP I 543 HIS 0.018 0.001 HIS E 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.22 (35668) covalent geometry : angle 0.69724 / 0.37 (49080) hydrogen bonds : bond 0.05937 / 3.69 ( 1469) hydrogen bonds : angle 5.22677 / 3.69 ( 4142) Misc. bond : bond 0.01861 / 0.91 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 507 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASN cc_start: 0.9101 (OUTLIER) cc_final: 0.8786 (p0) REVERT: A 136 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7783 (mptp) REVERT: A 289 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8355 (tm-30) REVERT: A 379 LEU cc_start: 0.7857 (mm) cc_final: 0.7631 (tp) REVERT: B 100 MET cc_start: 0.6993 (mmm) cc_final: 0.6504 (mmm) REVERT: B 302 LYS cc_start: 0.8822 (ttmt) cc_final: 0.8474 (ttmm) REVERT: E 93 PHE cc_start: 0.9049 (OUTLIER) cc_final: 0.8307 (m-80) REVERT: I 206 ARG cc_start: 0.6075 (tpt90) cc_final: 0.5590 (ptt-90) REVERT: I 219 PHE cc_start: 0.8797 (OUTLIER) cc_final: 0.7980 (p90) REVERT: I 581 LEU cc_start: 0.8025 (mp) cc_final: 0.7819 (mt) REVERT: J 40 TYR cc_start: 0.8590 (t80) cc_final: 0.8383 (t80) REVERT: J 72 GLN cc_start: 0.7349 (mt0) cc_final: 0.6843 (tm-30) REVERT: J 154 TRP cc_start: 0.7575 (m-10) cc_final: 0.7278 (m-10) REVERT: J 221 ASP cc_start: 0.8587 (p0) cc_final: 0.8375 (p0) REVERT: J 224 TYR cc_start: 0.8498 (m-80) cc_final: 0.8267 (m-80) REVERT: J 323 PHE cc_start: 0.7459 (m-80) cc_final: 0.7173 (m-80) REVERT: J 375 LEU cc_start: 0.8666 (mt) cc_final: 0.8444 (mt) REVERT: M 30 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7544 (ttm170) REVERT: M 48 TYR cc_start: 0.6916 (t80) cc_final: 0.6497 (t80) REVERT: M 133 ASN cc_start: 0.8505 (t0) cc_final: 0.7665 (t0) REVERT: M 153 ASP cc_start: 0.7791 (t70) cc_final: 0.7350 (t0) REVERT: M 268 LEU cc_start: 0.7965 (tt) cc_final: 0.7702 (mm) REVERT: M 332 ARG cc_start: 0.7948 (ttp-170) cc_final: 0.6971 (ptm-80) REVERT: M 461 LEU cc_start: 0.6219 (tp) cc_final: 0.5853 (mp) REVERT: M 497 ARG cc_start: 0.7002 (tpp-160) cc_final: 0.5081 (tpp-160) REVERT: M 546 ILE cc_start: 0.7271 (mt) cc_final: 0.7023 (mt) REVERT: M 566 GLU cc_start: 0.4566 (mp0) cc_final: 0.3811 (tt0) REVERT: M 579 PHE cc_start: 0.7134 (p90) cc_final: 0.6798 (p90) REVERT: N 70 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7117 (tt0) REVERT: N 71 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7456 (mp) REVERT: N 111 ASP cc_start: 0.7857 (p0) cc_final: 0.7633 (p0) REVERT: N 276 SER cc_start: 0.8530 (p) cc_final: 0.8290 (m) REVERT: N 279 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8459 (mt-10) REVERT: N 302 LYS cc_start: 0.7759 (tttm) cc_final: 0.6635 (ttmm) REVERT: N 465 GLU cc_start: 0.7916 (mp0) cc_final: 0.7621 (pm20) outliers start: 207 outliers final: 120 residues processed: 658 average time/residue: 0.2231 time to fit residues: 238.8752 Evaluate side-chains 569 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 442 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain E residue 11 GLN Chi-restraints excluded: chain E residue 19 HIS Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 211 CYS Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 435 ILE Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 61 MET Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 293 SER Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 15 GLN Chi-restraints excluded: chain I residue 120 ASN Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 219 PHE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 244 ASN Chi-restraints excluded: chain I residue 257 SER Chi-restraints excluded: chain I residue 261 SER Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 319 ILE Chi-restraints excluded: chain I residue 326 LYS Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 381 LEU Chi-restraints excluded: chain I residue 467 PHE Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 23 ASP Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 190 ARG Chi-restraints excluded: chain J residue 244 CYS Chi-restraints excluded: chain J residue 284 LEU Chi-restraints excluded: chain J residue 338 THR Chi-restraints excluded: chain J residue 362 ASP Chi-restraints excluded: chain J residue 407 ILE Chi-restraints excluded: chain J residue 424 SER Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 30 ARG Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain M residue 93 PHE Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 157 LYS Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 189 PHE Chi-restraints excluded: chain M residue 231 GLU Chi-restraints excluded: chain M residue 251 LEU Chi-restraints excluded: chain M residue 254 THR Chi-restraints excluded: chain M residue 267 ASP Chi-restraints excluded: chain M residue 286 THR Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 348 VAL Chi-restraints excluded: chain M residue 425 ILE Chi-restraints excluded: chain M residue 544 ILE Chi-restraints excluded: chain M residue 573 ILE Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 180 ILE Chi-restraints excluded: chain N residue 185 ASP Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 245 SER Chi-restraints excluded: chain N residue 253 THR Chi-restraints excluded: chain N residue 255 PHE Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 270 LYS Chi-restraints excluded: chain N residue 289 HIS Chi-restraints excluded: chain N residue 309 THR Chi-restraints excluded: chain N residue 329 ILE Chi-restraints excluded: chain N residue 337 SER Chi-restraints excluded: chain N residue 429 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 343 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 351 optimal weight: 0.0020 chunk 26 optimal weight: 0.9990 chunk 286 optimal weight: 0.7980 chunk 373 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 122 optimal weight: 0.4980 chunk 98 optimal weight: 0.7980 chunk 218 optimal weight: 6.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 GLN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 GLN ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 ASN F 238 GLN ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 7 ASN I 16 ASN ** I 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 166 HIS ** J 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 HIS ** M 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 119 ASN ** N 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 450 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.157764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.125766 restraints weight = 57874.044| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.64 r_work: 0.3555 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35670 Z= 0.130 Angle : 0.609 9.085 49080 Z= 0.320 Chirality : 0.042 0.351 5486 Planarity : 0.004 0.045 5684 Dihedral : 17.979 170.667 6525 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.79 % Allowed : 28.82 % Favored : 66.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.14), residues: 3842 helix: 0.84 (0.13), residues: 1500 sheet: -0.62 (0.19), residues: 800 loop : -0.78 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 47 TYR 0.025 0.002 TYR N 291 PHE 0.019 0.001 PHE J 44 TRP 0.021 0.001 TRP M 510 HIS 0.011 0.001 HIS M 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (35668) covalent geometry : angle 0.60913 / 0.32 (49080) hydrogen bonds : bond 0.05365 / 3.35 ( 1469) hydrogen bonds : angle 4.93220 / 3.48 ( 4142) Misc. bond : bond 0.01051 / 0.50 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 501 time to evaluate : 1.278 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 22 TRP cc_start: 0.8288 (m100) cc_final: 0.7846 (m100) REVERT: A 213 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7820 (mm) REVERT: A 289 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8332 (tm-30) REVERT: A 318 SER cc_start: 0.8737 (OUTLIER) cc_final: 0.8494 (m) REVERT: A 379 LEU cc_start: 0.7818 (mm) cc_final: 0.7605 (tt) REVERT: B 100 MET cc_start: 0.6677 (mmm) cc_final: 0.6285 (mmm) REVERT: B 302 LYS cc_start: 0.8870 (ttmt) cc_final: 0.8488 (ttmm) REVERT: E 16 ASN cc_start: 0.8310 (OUTLIER) cc_final: 0.8028 (p0) REVERT: E 93 PHE cc_start: 0.8995 (OUTLIER) cc_final: 0.8119 (m-80) REVERT: E 244 ASN cc_start: 0.8677 (p0) cc_final: 0.8192 (t0) REVERT: E 523 PHE cc_start: 0.7708 (t80) cc_final: 0.7504 (t80) REVERT: E 572 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7430 (pt0) REVERT: F 249 ASP cc_start: 0.7647 (t0) cc_final: 0.7437 (t0) REVERT: F 256 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7754 (tt0) REVERT: I 206 ARG cc_start: 0.5876 (tpt90) cc_final: 0.5481 (ptt-90) REVERT: I 244 ASN cc_start: 0.9143 (OUTLIER) cc_final: 0.8931 (t0) REVERT: I 374 TYR cc_start: 0.5642 (t80) cc_final: 0.5411 (t80) REVERT: I 397 ASN cc_start: 0.6165 (m-40) cc_final: 0.5830 (t0) REVERT: I 547 LEU cc_start: 0.8131 (mm) cc_final: 0.7900 (mm) REVERT: I 556 THR cc_start: 0.8140 (m) cc_final: 0.7817 (m) REVERT: J 40 TYR cc_start: 0.8575 (t80) cc_final: 0.8347 (t80) REVERT: J 72 GLN cc_start: 0.7319 (mt0) cc_final: 0.6858 (tm-30) REVERT: J 100 MET cc_start: 0.6499 (ppp) cc_final: 0.6206 (ppp) REVERT: J 154 TRP cc_start: 0.7501 (m-10) cc_final: 0.7126 (m-10) REVERT: J 192 CYS cc_start: 0.6958 (t) cc_final: 0.6725 (t) REVERT: J 375 LEU cc_start: 0.8566 (mt) cc_final: 0.8225 (mm) REVERT: M 30 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.7510 (ttm170) REVERT: M 61 ASP cc_start: 0.7756 (p0) cc_final: 0.7556 (p0) REVERT: M 133 ASN cc_start: 0.8493 (t0) cc_final: 0.7542 (t0) REVERT: M 153 ASP cc_start: 0.7765 (OUTLIER) cc_final: 0.7316 (t0) REVERT: M 268 LEU cc_start: 0.7910 (tt) cc_final: 0.7600 (mm) REVERT: M 332 ARG cc_start: 0.7798 (ttp-170) cc_final: 0.6983 (ptm-80) REVERT: M 497 ARG cc_start: 0.6881 (tpp-160) cc_final: 0.4854 (tpp-160) REVERT: M 546 ILE cc_start: 0.7482 (mt) cc_final: 0.7098 (mt) REVERT: M 566 GLU cc_start: 0.4781 (mp0) cc_final: 0.4068 (tt0) REVERT: N 190 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.6609 (ttt-90) REVERT: N 197 MET cc_start: 0.7305 (mmp) cc_final: 0.6861 (mmp) REVERT: N 278 GLN cc_start: 0.8225 (tt0) cc_final: 0.8006 (tp40) REVERT: N 279 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8488 (mt-10) outliers start: 160 outliers final: 89 residues processed: 620 average time/residue: 0.2039 time to fit residues: 208.5038 Evaluate side-chains 537 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 437 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain E residue 11 GLN Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 572 GLU Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 61 MET Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 244 CYS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 468 ASP Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 219 PHE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 232 ASN Chi-restraints excluded: chain I residue 236 MET Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 244 ASN Chi-restraints excluded: chain I residue 286 THR Chi-restraints excluded: chain I residue 319 ILE Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 347 VAL Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 378 VAL Chi-restraints excluded: chain I residue 467 PHE Chi-restraints excluded: chain I residue 474 ILE Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 244 CYS Chi-restraints excluded: chain J residue 284 LEU Chi-restraints excluded: chain J residue 338 THR Chi-restraints excluded: chain J residue 345 VAL Chi-restraints excluded: chain J residue 362 ASP Chi-restraints excluded: chain J residue 388 GLN Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 473 MET Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 30 ARG Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 93 PHE Chi-restraints excluded: chain M residue 153 ASP Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 189 PHE Chi-restraints excluded: chain M residue 251 LEU Chi-restraints excluded: chain M residue 267 ASP Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain M residue 348 VAL Chi-restraints excluded: chain M residue 425 ILE Chi-restraints excluded: chain M residue 544 ILE Chi-restraints excluded: chain N residue 185 ASP Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 242 THR Chi-restraints excluded: chain N residue 255 PHE Chi-restraints excluded: chain N residue 309 THR Chi-restraints excluded: chain N residue 337 SER Chi-restraints excluded: chain N residue 397 GLU 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 230 optimal weight: 5.9990 chunk 370 optimal weight: 3.9990 chunk 254 optimal weight: 9.9990 chunk 165 optimal weight: 0.9980 chunk 1 optimal weight: 0.0970 chunk 307 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 225 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 138 optimal weight: 0.4980 chunk 194 optimal weight: 0.7980 overall best weight: 1.2780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 7 ASN I 15 GLN I 16 ASN ** I 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 HIS ** M 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 177 ASN ** N 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 389 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 = 0.4086 r_free = 0.4086 target = 0.155951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.124350 restraints weight = 57903.427| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.57 r_work: 0.3536 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35670 Z= 0.151 Angle : 0.605 12.035 49080 Z= 0.316 Chirality : 0.042 0.302 5486 Planarity : 0.004 0.040 5684 Dihedral : 17.883 170.651 6509 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 5.09 % Allowed : 28.10 % Favored : 66.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.14), residues: 3842 helix: 0.97 (0.14), residues: 1476 sheet: -0.56 (0.19), residues: 800 loop : -0.75 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 47 TYR 0.018 0.001 TYR N 229 PHE 0.018 0.001 PHE M 287 TRP 0.021 0.001 TRP M 510 HIS 0.008 0.001 HIS E 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (35668) covalent geometry : angle 0.60485 / 0.32 (49080) hydrogen bonds : bond 0.05153 / 3.22 ( 1469) hydrogen bonds : angle 4.83246 / 3.41 ( 4142) Misc. bond : bond 0.00066 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 461 time to evaluate : 1.246 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 22 TRP cc_start: 0.8315 (m100) cc_final: 0.7856 (m100) REVERT: A 213 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7895 (mm) REVERT: A 289 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8355 (tm-30) REVERT: A 319 ILE cc_start: 0.8458 (pt) cc_final: 0.8240 (pt) REVERT: B 100 MET cc_start: 0.6751 (mmm) cc_final: 0.6387 (mmm) REVERT: B 302 LYS cc_start: 0.8858 (ttmt) cc_final: 0.8512 (ttmm) REVERT: E 93 PHE cc_start: 0.9033 (OUTLIER) cc_final: 0.8272 (m-80) REVERT: E 132 MET cc_start: 0.8741 (ttp) cc_final: 0.8523 (ttt) REVERT: E 572 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7329 (pt0) REVERT: F 256 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7797 (tt0) REVERT: I 206 ARG cc_start: 0.5863 (tpt90) cc_final: 0.5545 (ptt-90) REVERT: I 397 ASN cc_start: 0.6259 (m-40) cc_final: 0.5848 (t0) REVERT: I 547 LEU cc_start: 0.8227 (mm) cc_final: 0.7952 (mm) REVERT: I 556 THR cc_start: 0.8203 (OUTLIER) cc_final: 0.7913 (m) REVERT: J 40 TYR cc_start: 0.8609 (t80) cc_final: 0.8388 (t80) REVERT: J 72 GLN cc_start: 0.7242 (mt0) cc_final: 0.6857 (tm-30) REVERT: J 100 MET cc_start: 0.6440 (ppp) cc_final: 0.6203 (ppp) REVERT: J 154 TRP cc_start: 0.7597 (m-10) cc_final: 0.7362 (m-10) REVERT: J 192 CYS cc_start: 0.6906 (t) cc_final: 0.6661 (t) REVERT: J 215 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8127 (mm) REVERT: J 375 LEU cc_start: 0.8649 (mt) cc_final: 0.8430 (mp) REVERT: M 30 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.7517 (ttm170) REVERT: M 61 ASP cc_start: 0.7812 (p0) cc_final: 0.7588 (p0) REVERT: M 133 ASN cc_start: 0.8580 (t0) cc_final: 0.7677 (t0) REVERT: M 332 ARG cc_start: 0.7873 (ttp-170) cc_final: 0.7145 (ptm-80) REVERT: M 445 TYR cc_start: 0.4521 (m-80) cc_final: 0.4249 (m-80) REVERT: M 497 ARG cc_start: 0.6981 (tpp-160) cc_final: 0.4880 (tpp-160) REVERT: M 508 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6946 (pm20) REVERT: M 527 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.6148 (mtt-85) REVERT: M 566 GLU cc_start: 0.4857 (mp0) cc_final: 0.4108 (tt0) REVERT: M 579 PHE cc_start: 0.7191 (p90) cc_final: 0.6619 (p90) REVERT: N 190 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.6690 (ttt-90) REVERT: N 430 LYS cc_start: 0.6919 (ttmm) cc_final: 0.6614 (mttm) outliers start: 170 outliers final: 115 residues processed: 592 average time/residue: 0.2066 time to fit residues: 203.1131 Evaluate side-chains 548 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 422 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain E residue 11 GLN Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 572 GLU Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 106 ARG Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 244 CYS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 293 SER Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 468 ASP Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 15 GLN Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 219 PHE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 232 ASN Chi-restraints excluded: chain I residue 236 MET Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 286 THR Chi-restraints excluded: chain I residue 319 ILE Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 347 VAL Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 378 VAL Chi-restraints excluded: chain I residue 467 PHE Chi-restraints excluded: chain I residue 474 ILE Chi-restraints excluded: chain I residue 556 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain J residue 244 CYS Chi-restraints excluded: chain J residue 284 LEU Chi-restraints excluded: chain J residue 345 VAL Chi-restraints excluded: chain J residue 362 ASP Chi-restraints excluded: chain J residue 388 GLN Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 473 MET Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 30 ARG Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 93 PHE Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 189 PHE Chi-restraints excluded: chain M residue 231 GLU Chi-restraints excluded: chain M residue 267 ASP Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain M residue 348 VAL Chi-restraints excluded: chain M residue 349 THR Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 425 ILE Chi-restraints excluded: chain M residue 508 GLU Chi-restraints excluded: chain M residue 527 ARG Chi-restraints excluded: chain M residue 544 ILE Chi-restraints excluded: chain M residue 573 ILE Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 119 ASN Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain N residue 180 ILE Chi-restraints excluded: chain N residue 185 ASP Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 242 THR Chi-restraints excluded: chain N residue 245 SER Chi-restraints excluded: chain N residue 255 PHE Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 337 SER Chi-restraints excluded: chain N residue 345 VAL Chi-restraints excluded: chain N residue 397 GLU 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 281 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 183 optimal weight: 3.9990 chunk 19 optimal weight: 0.0050 chunk 122 optimal weight: 0.9990 chunk 134 optimal weight: 10.0000 chunk 287 optimal weight: 0.4980 chunk 327 optimal weight: 8.9990 chunk 367 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 242 optimal weight: 6.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 GLN ** F 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 238 GLN ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 7 ASN I 15 GLN I 16 ASN ** I 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 195 ASN ** J 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 139 GLN N 289 HIS ** N 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 389 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.155406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.125774 restraints weight = 57739.397| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 2.19 r_work: 0.3576 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35670 Z= 0.129 Angle : 0.586 9.303 49080 Z= 0.306 Chirality : 0.041 0.295 5486 Planarity : 0.004 0.040 5684 Dihedral : 17.819 171.040 6507 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 5.39 % Allowed : 27.65 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.14), residues: 3842 helix: 1.03 (0.14), residues: 1476 sheet: -0.48 (0.19), residues: 800 loop : -0.73 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 462 TYR 0.018 0.001 TYR M 271 PHE 0.022 0.001 PHE E 523 TRP 0.023 0.001 TRP M 510 HIS 0.011 0.001 HIS M 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (35668) covalent geometry : angle 0.58598 / 0.31 (49080) hydrogen bonds : bond 0.04947 / 3.08 ( 1469) hydrogen bonds : angle 4.72873 / 3.34 ( 4142) Misc. bond : bond 0.00036 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 456 time to evaluate : 1.305 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 19 HIS cc_start: 0.8870 (OUTLIER) cc_final: 0.8342 (p90) REVERT: A 22 TRP cc_start: 0.8183 (m100) cc_final: 0.7767 (m100) REVERT: A 213 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7828 (mm) REVERT: A 289 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8289 (tm-30) REVERT: A 318 SER cc_start: 0.8638 (OUTLIER) cc_final: 0.8404 (m) REVERT: A 319 ILE cc_start: 0.8418 (pt) cc_final: 0.8205 (pt) REVERT: A 567 PHE cc_start: 0.6513 (m-80) cc_final: 0.6295 (m-80) REVERT: B 100 MET cc_start: 0.6507 (mmm) cc_final: 0.6221 (mmm) REVERT: E 93 PHE cc_start: 0.8981 (OUTLIER) cc_final: 0.8247 (m-80) REVERT: E 194 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8705 (mt) REVERT: E 210 LYS cc_start: 0.8368 (tppt) cc_final: 0.7915 (mtmm) REVERT: E 244 ASN cc_start: 0.8593 (p0) cc_final: 0.8123 (t0) REVERT: E 572 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7380 (pt0) REVERT: F 106 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7638 (mtp180) REVERT: F 284 LEU cc_start: 0.9199 (mt) cc_final: 0.8887 (tp) REVERT: I 206 ARG cc_start: 0.5865 (tpt90) cc_final: 0.5595 (ptt-90) REVERT: I 397 ASN cc_start: 0.6210 (m-40) cc_final: 0.5758 (t0) REVERT: I 522 ASP cc_start: 0.8442 (m-30) cc_final: 0.8097 (t0) REVERT: I 547 LEU cc_start: 0.8287 (mm) cc_final: 0.8040 (mm) REVERT: I 556 THR cc_start: 0.8406 (OUTLIER) cc_final: 0.8148 (m) REVERT: J 40 TYR cc_start: 0.8618 (t80) cc_final: 0.8417 (t80) REVERT: J 72 GLN cc_start: 0.7278 (mt0) cc_final: 0.6948 (tm-30) REVERT: M 5 THR cc_start: 0.5807 (OUTLIER) cc_final: 0.5584 (p) REVERT: M 133 ASN cc_start: 0.8416 (t0) cc_final: 0.7480 (t0) REVERT: M 332 ARG cc_start: 0.7843 (ttp-170) cc_final: 0.7006 (ptm-80) REVERT: M 462 ARG cc_start: 0.5263 (mtp85) cc_final: 0.4710 (mpt-90) REVERT: M 508 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6780 (pm20) REVERT: M 579 PHE cc_start: 0.7169 (p90) cc_final: 0.6654 (p90) REVERT: N 197 MET cc_start: 0.7203 (mmp) cc_final: 0.6967 (mmp) REVERT: N 270 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8017 (mmmm) outliers start: 180 outliers final: 121 residues processed: 596 average time/residue: 0.2195 time to fit residues: 215.8128 Evaluate side-chains 558 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 425 time to evaluate : 1.179 ------------------------------------------------------------------------------- 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 20 MET Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain E residue 11 GLN Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 435 ILE Chi-restraints excluded: chain E residue 572 GLU Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 61 MET Chi-restraints excluded: chain F residue 106 ARG Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 244 CYS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 255 PHE Chi-restraints excluded: chain F residue 293 SER Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 219 PHE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 232 ASN Chi-restraints excluded: chain I residue 236 MET Chi-restraints excluded: chain I residue 244 ASN Chi-restraints excluded: chain I residue 319 ILE Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 347 VAL Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 378 VAL Chi-restraints excluded: chain I residue 405 ASP Chi-restraints excluded: chain I residue 467 PHE Chi-restraints excluded: chain I residue 474 ILE Chi-restraints excluded: chain I residue 556 THR Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 244 CYS Chi-restraints excluded: chain J residue 338 THR Chi-restraints excluded: chain J residue 345 VAL Chi-restraints excluded: chain J residue 362 ASP Chi-restraints excluded: chain J residue 388 GLN Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 473 MET Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 93 PHE Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 189 PHE Chi-restraints excluded: chain M residue 231 GLU Chi-restraints excluded: chain M residue 237 LEU Chi-restraints excluded: chain M residue 267 ASP Chi-restraints excluded: chain M residue 268 LEU Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain M residue 343 ILE Chi-restraints excluded: chain M residue 348 VAL Chi-restraints excluded: chain M residue 349 THR Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 425 ILE Chi-restraints excluded: chain M residue 508 GLU Chi-restraints excluded: chain M residue 544 ILE Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 119 ASN Chi-restraints excluded: chain N residue 180 ILE Chi-restraints excluded: chain N residue 185 ASP Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 242 THR Chi-restraints excluded: chain N residue 244 CYS Chi-restraints excluded: chain N residue 245 SER Chi-restraints excluded: chain N residue 255 PHE Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 270 LYS Chi-restraints excluded: chain N residue 289 HIS Chi-restraints excluded: chain N residue 309 THR Chi-restraints excluded: chain N residue 337 SER Chi-restraints excluded: chain N residue 345 VAL Chi-restraints excluded: chain N residue 397 GLU 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 372 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 258 optimal weight: 2.9990 chunk 362 optimal weight: 3.9990 chunk 392 optimal weight: 0.0060 chunk 94 optimal weight: 10.0000 chunk 399 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 overall best weight: 3.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 HIS ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 ASN E 55 GLN ** F 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 295 HIS ** F 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 436 ASN ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 ASN ** I 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 195 ASN J 296 ASN ** M 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.146922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.115540 restraints weight = 58226.190| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.55 r_work: 0.3389 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 35670 Z= 0.299 Angle : 0.716 10.266 49080 Z= 0.372 Chirality : 0.046 0.341 5486 Planarity : 0.005 0.050 5684 Dihedral : 17.890 172.881 6501 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 6.47 % Allowed : 27.23 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.14), residues: 3842 helix: 0.60 (0.13), residues: 1476 sheet: -0.76 (0.19), residues: 784 loop : -0.96 (0.16), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 529 TYR 0.022 0.002 TYR M 271 PHE 0.027 0.002 PHE E 523 TRP 0.020 0.002 TRP M 510 HIS 0.019 0.002 HIS M 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00679 / 0.30 (35668) covalent geometry : angle 0.71552 / 0.37 (49080) hydrogen bonds : bond 0.05483 / 3.44 ( 1469) hydrogen bonds : angle 4.98708 / 3.52 ( 4142) Misc. bond : bond 0.00056 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 448 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 HIS cc_start: 0.9040 (OUTLIER) cc_final: 0.8491 (p90) REVERT: A 136 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7918 (mptp) REVERT: A 213 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8043 (mm) REVERT: A 289 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8371 (tm-30) REVERT: A 318 SER cc_start: 0.8864 (OUTLIER) cc_final: 0.8622 (m) REVERT: B 34 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8149 (mp) REVERT: B 100 MET cc_start: 0.6952 (mmm) cc_final: 0.6707 (mmm) REVERT: E 132 MET cc_start: 0.8871 (ttt) cc_final: 0.8661 (ttt) REVERT: E 572 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7445 (pt0) REVERT: F 290 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9051 (mp) REVERT: F 408 MET cc_start: 0.9030 (tpp) cc_final: 0.8814 (ttm) REVERT: I 206 ARG cc_start: 0.6048 (tpt90) cc_final: 0.5651 (ptt-90) REVERT: I 229 ARG cc_start: 0.5895 (OUTLIER) cc_final: 0.5680 (ptt180) REVERT: I 310 ARG cc_start: 0.6945 (ptt-90) cc_final: 0.6550 (tpt-90) REVERT: I 397 ASN cc_start: 0.6071 (m-40) cc_final: 0.5806 (t0) REVERT: I 437 HIS cc_start: 0.7338 (p-80) cc_final: 0.7017 (p-80) REVERT: I 547 LEU cc_start: 0.8398 (mm) cc_final: 0.8099 (mm) REVERT: I 556 THR cc_start: 0.8375 (OUTLIER) cc_final: 0.8140 (m) REVERT: J 49 GLN cc_start: 0.8332 (pm20) cc_final: 0.7943 (pt0) REVERT: J 72 GLN cc_start: 0.7332 (mt0) cc_final: 0.6816 (tm-30) REVERT: J 168 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.7698 (mmm-85) REVERT: J 280 MET cc_start: 0.7273 (tpt) cc_final: 0.6013 (tpt) REVERT: M 43 ASP cc_start: 0.8902 (t70) cc_final: 0.8268 (t0) REVERT: M 88 GLU cc_start: 0.6859 (tt0) cc_final: 0.6549 (tt0) REVERT: M 332 ARG cc_start: 0.7949 (ttp-170) cc_final: 0.7123 (ptm-80) REVERT: M 381 LEU cc_start: 0.6886 (tp) cc_final: 0.6554 (tt) REVERT: M 403 TYR cc_start: 0.7115 (m-80) cc_final: 0.6905 (m-80) REVERT: M 462 ARG cc_start: 0.5188 (mtp85) cc_final: 0.4628 (mpt-90) REVERT: M 496 GLU cc_start: 0.6400 (tp30) cc_final: 0.6086 (tp30) REVERT: M 525 ARG cc_start: 0.7686 (ttp-170) cc_final: 0.7396 (ttp80) REVERT: N 61 MET cc_start: 0.7263 (OUTLIER) cc_final: 0.6915 (mtp) REVERT: N 255 PHE cc_start: 0.7148 (OUTLIER) cc_final: 0.5917 (t80) REVERT: N 270 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8077 (mmmm) REVERT: N 301 ARG cc_start: 0.8256 (ptm-80) cc_final: 0.7615 (tpt90) REVERT: N 430 LYS cc_start: 0.7372 (OUTLIER) cc_final: 0.7145 (mttm) outliers start: 216 outliers final: 146 residues processed: 616 average time/residue: 0.2119 time to fit residues: 213.7353 Evaluate side-chains 583 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 422 time to evaluate : 1.225 ------------------------------------------------------------------------------- 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 126 LEU Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain E residue 11 GLN Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 189 PHE Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 435 ILE Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 572 GLU Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 61 MET Chi-restraints excluded: chain F residue 106 ARG Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 244 CYS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 255 PHE Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 293 SER Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 219 PHE Chi-restraints excluded: chain I residue 229 ARG Chi-restraints excluded: chain I residue 232 ASN Chi-restraints excluded: chain I residue 242 ASP Chi-restraints excluded: chain I residue 244 ASN Chi-restraints excluded: chain I residue 286 THR Chi-restraints excluded: chain I residue 319 ILE Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 347 VAL Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 378 VAL Chi-restraints excluded: chain I residue 405 ASP Chi-restraints excluded: chain I residue 467 PHE Chi-restraints excluded: chain I residue 474 ILE Chi-restraints excluded: chain I residue 556 THR Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 23 ASP Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 168 ARG Chi-restraints excluded: chain J residue 192 CYS Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain J residue 276 SER Chi-restraints excluded: chain J residue 338 THR Chi-restraints excluded: chain J residue 345 VAL Chi-restraints excluded: chain J residue 362 ASP Chi-restraints excluded: chain J residue 379 GLN Chi-restraints excluded: chain J residue 388 GLN Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 407 ILE Chi-restraints excluded: chain J residue 473 MET Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 77 SER Chi-restraints excluded: chain M residue 82 LEU 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 189 PHE Chi-restraints excluded: chain M residue 231 GLU Chi-restraints excluded: chain M residue 267 ASP Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 343 ILE Chi-restraints excluded: chain M residue 348 VAL Chi-restraints excluded: chain M residue 349 THR Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 398 SER Chi-restraints excluded: chain M residue 425 ILE Chi-restraints excluded: chain M residue 544 ILE Chi-restraints excluded: chain M residue 573 ILE Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 119 ASN Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain N residue 180 ILE Chi-restraints excluded: chain N residue 185 ASP Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 242 THR Chi-restraints excluded: chain N residue 244 CYS Chi-restraints excluded: chain N residue 255 PHE Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 270 LYS Chi-restraints excluded: chain N residue 289 HIS Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain N residue 293 SER Chi-restraints excluded: chain N residue 309 THR Chi-restraints excluded: chain N residue 337 SER Chi-restraints excluded: chain N residue 345 VAL Chi-restraints excluded: chain N residue 381 SER Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain N residue 397 GLU Chi-restraints excluded: chain N residue 430 LYS 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 276 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 207 optimal weight: 4.9990 chunk 91 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 197 optimal weight: 10.0000 chunk 129 optimal weight: 9.9990 chunk 73 optimal weight: 0.7980 chunk 189 optimal weight: 2.9990 chunk 370 optimal weight: 0.6980 chunk 367 optimal weight: 0.7980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 ASN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 238 GLN ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 ASN I 133 ASN ** I 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 141 HIS ** N 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 386 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 = 0.4006 r_free = 0.4006 target = 0.150242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.118423 restraints weight = 57742.043| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.55 r_work: 0.3448 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35670 Z= 0.154 Angle : 0.626 8.945 49080 Z= 0.326 Chirality : 0.042 0.311 5486 Planarity : 0.004 0.043 5684 Dihedral : 17.825 172.674 6499 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 5.09 % Allowed : 29.21 % Favored : 65.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.14), residues: 3842 helix: 0.83 (0.14), residues: 1472 sheet: -0.67 (0.19), residues: 784 loop : -0.89 (0.16), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 410 TYR 0.021 0.002 TYR N 40 PHE 0.025 0.002 PHE E 523 TRP 0.022 0.001 TRP M 510 HIS 0.015 0.001 HIS M 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (35668) covalent geometry : angle 0.62615 / 0.33 (49080) hydrogen bonds : bond 0.05063 / 3.15 ( 1469) hydrogen bonds : angle 4.79921 / 3.40 ( 4142) Misc. bond : bond 0.00016 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 445 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 HIS cc_start: 0.8950 (OUTLIER) cc_final: 0.8370 (p90) REVERT: A 136 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7832 (mptp) REVERT: A 213 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7996 (mm) REVERT: A 289 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8359 (tm-30) REVERT: A 318 SER cc_start: 0.8840 (OUTLIER) cc_final: 0.8592 (m) REVERT: A 504 MET cc_start: 0.8636 (mmm) cc_final: 0.7926 (mmm) REVERT: B 34 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8191 (mp) REVERT: B 100 MET cc_start: 0.6757 (mmm) cc_final: 0.6546 (mmm) REVERT: E 93 PHE cc_start: 0.9091 (OUTLIER) cc_final: 0.8314 (m-80) REVERT: E 132 MET cc_start: 0.8822 (ttt) cc_final: 0.8579 (ttt) REVERT: E 244 ASN cc_start: 0.8631 (p0) cc_final: 0.8140 (t0) REVERT: E 572 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7388 (pt0) REVERT: F 106 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7757 (mtp180) REVERT: F 408 MET cc_start: 0.8981 (tpp) cc_final: 0.8706 (ttm) REVERT: F 440 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.7099 (tmtt) REVERT: I 206 ARG cc_start: 0.5946 (tpt90) cc_final: 0.5588 (ptt-90) REVERT: I 310 ARG cc_start: 0.6905 (ptt-90) cc_final: 0.6505 (tpt-90) REVERT: I 397 ASN cc_start: 0.6164 (m-40) cc_final: 0.5764 (t0) REVERT: I 437 HIS cc_start: 0.7324 (p-80) cc_final: 0.7011 (p-80) REVERT: I 522 ASP cc_start: 0.8556 (m-30) cc_final: 0.8176 (t0) REVERT: I 547 LEU cc_start: 0.8365 (mm) cc_final: 0.8070 (mm) REVERT: I 556 THR cc_start: 0.8420 (OUTLIER) cc_final: 0.8201 (m) REVERT: J 49 GLN cc_start: 0.8270 (pm20) cc_final: 0.7892 (pt0) REVERT: J 72 GLN cc_start: 0.7309 (mt0) cc_final: 0.6826 (tm-30) REVERT: J 168 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8275 (mmm160) REVERT: M 43 ASP cc_start: 0.8847 (t70) cc_final: 0.8273 (t0) REVERT: M 284 THR cc_start: 0.8556 (p) cc_final: 0.8309 (t) REVERT: M 332 ARG cc_start: 0.7895 (ttp-170) cc_final: 0.7041 (ptm-80) REVERT: M 381 LEU cc_start: 0.6929 (tp) cc_final: 0.6640 (tt) REVERT: M 462 ARG cc_start: 0.5096 (mtp85) cc_final: 0.4529 (mpt-90) REVERT: M 496 GLU cc_start: 0.6302 (tp30) cc_final: 0.5955 (tp30) REVERT: M 508 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6891 (pm20) REVERT: M 525 ARG cc_start: 0.7589 (ttp-170) cc_final: 0.7348 (ttp80) REVERT: N 61 MET cc_start: 0.7236 (mtp) cc_final: 0.6891 (mtp) REVERT: N 70 GLU cc_start: 0.7461 (tt0) cc_final: 0.6831 (tt0) REVERT: N 270 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.8005 (mmmm) REVERT: N 301 ARG cc_start: 0.8228 (ptm-80) cc_final: 0.7560 (tpt90) REVERT: N 430 LYS cc_start: 0.7273 (OUTLIER) cc_final: 0.7009 (ttmt) outliers start: 170 outliers final: 130 residues processed: 580 average time/residue: 0.2168 time to fit residues: 207.0739 Evaluate side-chains 563 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 418 time to evaluate : 1.411 ------------------------------------------------------------------------------- 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 126 LEU Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 478 VAL 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 18 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain E residue 11 GLN Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 211 CYS Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 435 ILE Chi-restraints excluded: chain E residue 572 GLU Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 61 MET Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 106 ARG Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 244 CYS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 255 PHE Chi-restraints excluded: chain F residue 293 SER Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain F residue 440 LYS Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 468 ASP Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 219 PHE Chi-restraints excluded: chain I residue 232 ASN Chi-restraints excluded: chain I residue 244 ASN Chi-restraints excluded: chain I residue 319 ILE Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 347 VAL Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 378 VAL Chi-restraints excluded: chain I residue 467 PHE Chi-restraints excluded: chain I residue 474 ILE Chi-restraints excluded: chain I residue 556 THR Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 168 ARG Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain J residue 345 VAL Chi-restraints excluded: chain J residue 362 ASP Chi-restraints excluded: chain J residue 379 GLN Chi-restraints excluded: chain J residue 388 GLN Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 473 MET Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 82 LEU 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 189 PHE Chi-restraints excluded: chain M residue 231 GLU Chi-restraints excluded: chain M residue 237 LEU Chi-restraints excluded: chain M residue 254 THR Chi-restraints excluded: chain M residue 267 ASP Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain M residue 343 ILE Chi-restraints excluded: chain M residue 348 VAL Chi-restraints excluded: chain M residue 349 THR Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 425 ILE Chi-restraints excluded: chain M residue 508 GLU Chi-restraints excluded: chain M residue 544 ILE Chi-restraints excluded: chain M residue 573 ILE Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 119 ASN Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain N residue 180 ILE Chi-restraints excluded: chain N residue 185 ASP Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 242 THR Chi-restraints excluded: chain N residue 244 CYS Chi-restraints excluded: chain N residue 255 PHE Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 270 LYS Chi-restraints excluded: chain N residue 289 HIS Chi-restraints excluded: chain N residue 309 THR Chi-restraints excluded: chain N residue 330 GLU Chi-restraints excluded: chain N residue 337 SER Chi-restraints excluded: chain N residue 345 VAL Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain N residue 397 GLU Chi-restraints excluded: chain N residue 429 THR Chi-restraints excluded: chain N residue 430 LYS Chi-restraints excluded: chain N residue 466 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 361 optimal weight: 4.9990 chunk 172 optimal weight: 0.8980 chunk 264 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 322 optimal weight: 1.9990 chunk 152 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 372 optimal weight: 7.9990 chunk 164 optimal weight: 0.9980 chunk 183 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 15 GLN I 16 ASN ** I 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 289 HIS ** N 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.149816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.118881 restraints weight = 57679.962| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.57 r_work: 0.3430 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 35670 Z= 0.178 Angle : 0.631 10.956 49080 Z= 0.326 Chirality : 0.043 0.306 5486 Planarity : 0.004 0.049 5684 Dihedral : 17.753 172.818 6499 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.82 % Favored : 95.16 % Rotamer: Outliers : 5.51 % Allowed : 28.73 % Favored : 65.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.14), residues: 3842 helix: 0.85 (0.14), residues: 1474 sheet: -0.67 (0.19), residues: 804 loop : -0.89 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 344 TYR 0.024 0.002 TYR N 229 PHE 0.025 0.002 PHE E 523 TRP 0.027 0.001 TRP M 510 HIS 0.013 0.001 HIS M 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 (35668) covalent geometry : angle 0.63078 / 0.33 (49080) hydrogen bonds : bond 0.05001 / 3.11 ( 1469) hydrogen bonds : angle 4.75086 / 3.37 ( 4142) Misc. bond : bond 0.00014 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 445 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 HIS cc_start: 0.8963 (OUTLIER) cc_final: 0.8379 (p90) REVERT: A 22 TRP cc_start: 0.8345 (m100) cc_final: 0.7939 (m100) REVERT: A 136 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7873 (mptp) REVERT: A 213 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7970 (mm) REVERT: A 289 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8362 (tm-30) REVERT: A 318 SER cc_start: 0.8859 (OUTLIER) cc_final: 0.8617 (m) REVERT: B 34 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8228 (mp) REVERT: B 100 MET cc_start: 0.6790 (mmm) cc_final: 0.6585 (mmm) REVERT: B 280 MET cc_start: 0.7912 (tpp) cc_final: 0.7599 (tpp) REVERT: E 93 PHE cc_start: 0.9108 (OUTLIER) cc_final: 0.8337 (m-80) REVERT: E 132 MET cc_start: 0.8851 (ttt) cc_final: 0.8612 (ttt) REVERT: E 244 ASN cc_start: 0.8667 (p0) cc_final: 0.8176 (t0) REVERT: E 572 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7404 (pt0) REVERT: F 106 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7707 (mtp180) REVERT: F 408 MET cc_start: 0.8996 (tpp) cc_final: 0.8720 (ttm) REVERT: F 440 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.7061 (tmtt) REVERT: I 206 ARG cc_start: 0.5903 (tpt90) cc_final: 0.5588 (ptt-90) REVERT: I 310 ARG cc_start: 0.6952 (ptt-90) cc_final: 0.6573 (tpt-90) REVERT: I 397 ASN cc_start: 0.6151 (m-40) cc_final: 0.5795 (t0) REVERT: I 437 HIS cc_start: 0.7311 (p-80) cc_final: 0.7020 (p-80) REVERT: I 547 LEU cc_start: 0.8392 (mm) cc_final: 0.8174 (mm) REVERT: I 556 THR cc_start: 0.8475 (OUTLIER) cc_final: 0.8256 (m) REVERT: J 49 GLN cc_start: 0.8307 (pm20) cc_final: 0.7926 (pt0) REVERT: J 72 GLN cc_start: 0.7274 (mt0) cc_final: 0.6841 (tm-30) REVERT: J 168 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8307 (mmm160) REVERT: M 43 ASP cc_start: 0.8840 (t70) cc_final: 0.8288 (t0) REVERT: M 332 ARG cc_start: 0.7922 (ttp-170) cc_final: 0.7563 (ptm-80) REVERT: M 381 LEU cc_start: 0.7141 (tp) cc_final: 0.6802 (tt) REVERT: M 462 ARG cc_start: 0.5147 (mtp85) cc_final: 0.4658 (mpt-90) REVERT: M 496 GLU cc_start: 0.6258 (tp30) cc_final: 0.5973 (tp30) REVERT: M 508 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.7004 (pm20) REVERT: M 525 ARG cc_start: 0.7583 (ttp-170) cc_final: 0.7341 (ttp80) REVERT: N 61 MET cc_start: 0.7318 (mtp) cc_final: 0.7035 (mtp) REVERT: N 76 THR cc_start: 0.8198 (m) cc_final: 0.7950 (p) REVERT: N 197 MET cc_start: 0.7775 (mmp) cc_final: 0.7545 (mmt) REVERT: N 270 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7963 (mmmm) REVERT: N 301 ARG cc_start: 0.8324 (ptm-80) cc_final: 0.7651 (tpt90) REVERT: N 430 LYS cc_start: 0.7238 (OUTLIER) cc_final: 0.7010 (ttmt) outliers start: 184 outliers final: 140 residues processed: 597 average time/residue: 0.2254 time to fit residues: 220.9452 Evaluate side-chains 584 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 429 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 478 VAL 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 18 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 11 GLN Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 189 PHE Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 211 CYS Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 435 ILE Chi-restraints excluded: chain E residue 572 GLU Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 61 MET Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 106 ARG Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 244 CYS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 255 PHE Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 293 SER Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain F residue 440 LYS Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 468 ASP Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 15 GLN Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 219 PHE Chi-restraints excluded: chain I residue 232 ASN Chi-restraints excluded: chain I residue 244 ASN Chi-restraints excluded: chain I residue 347 VAL Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 378 VAL Chi-restraints excluded: chain I residue 467 PHE Chi-restraints excluded: chain I residue 474 ILE Chi-restraints excluded: chain I residue 556 THR Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 23 ASP Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 168 ARG Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain J residue 276 SER Chi-restraints excluded: chain J residue 345 VAL Chi-restraints excluded: chain J residue 362 ASP Chi-restraints excluded: chain J residue 379 GLN Chi-restraints excluded: chain J residue 388 GLN Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 473 MET Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 90 SER 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 189 PHE Chi-restraints excluded: chain M residue 237 LEU Chi-restraints excluded: chain M residue 254 THR Chi-restraints excluded: chain M residue 267 ASP Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain M residue 317 VAL Chi-restraints excluded: chain M residue 343 ILE Chi-restraints excluded: chain M residue 348 VAL Chi-restraints excluded: chain M residue 349 THR Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 425 ILE Chi-restraints excluded: chain M residue 508 GLU Chi-restraints excluded: chain M residue 544 ILE Chi-restraints excluded: chain M residue 573 ILE Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 119 ASN Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain N residue 180 ILE Chi-restraints excluded: chain N residue 185 ASP Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 241 THR Chi-restraints excluded: chain N residue 242 THR Chi-restraints excluded: chain N residue 244 CYS Chi-restraints excluded: chain N residue 255 PHE Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 270 LYS Chi-restraints excluded: chain N residue 289 HIS Chi-restraints excluded: chain N residue 309 THR Chi-restraints excluded: chain N residue 330 GLU Chi-restraints excluded: chain N residue 337 SER Chi-restraints excluded: chain N residue 345 VAL Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain N residue 397 GLU Chi-restraints excluded: chain N residue 429 THR Chi-restraints excluded: chain N residue 430 LYS Chi-restraints excluded: chain N residue 466 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 376 optimal weight: 0.0980 chunk 143 optimal weight: 4.9990 chunk 315 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 307 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 13 optimal weight: 0.0570 chunk 97 optimal weight: 0.9980 overall best weight: 1.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 16 ASN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 ASN ** I 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 166 HIS ** J 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 289 HIS ** N 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.152103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.119894 restraints weight = 56935.841| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.63 r_work: 0.3462 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 35670 Z= 0.141 Angle : 0.622 11.618 49080 Z= 0.320 Chirality : 0.042 0.304 5486 Planarity : 0.004 0.137 5684 Dihedral : 17.711 173.110 6497 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.42 % Favored : 95.55 % Rotamer: Outliers : 4.76 % Allowed : 29.21 % Favored : 66.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.14), residues: 3842 helix: 0.90 (0.14), residues: 1474 sheet: -0.57 (0.19), residues: 800 loop : -0.82 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 332 TYR 0.023 0.001 TYR N 229 PHE 0.021 0.001 PHE E 287 TRP 0.030 0.001 TRP E 84 HIS 0.019 0.001 HIS N 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (35668) covalent geometry : angle 0.62246 / 0.32 (49080) hydrogen bonds : bond 0.04903 / 3.04 ( 1469) hydrogen bonds : angle 4.69210 / 3.33 ( 4142) Misc. bond : bond 0.00017 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 444 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 HIS cc_start: 0.8928 (OUTLIER) cc_final: 0.8339 (p90) REVERT: A 22 TRP cc_start: 0.8333 (m100) cc_final: 0.7956 (m100) REVERT: A 136 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7713 (mptp) REVERT: A 213 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7921 (mm) REVERT: A 289 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8347 (tm-30) REVERT: A 318 SER cc_start: 0.8852 (OUTLIER) cc_final: 0.8604 (m) REVERT: A 570 GLU cc_start: 0.7760 (pm20) cc_final: 0.7496 (tm-30) REVERT: B 280 MET cc_start: 0.7893 (tpp) cc_final: 0.7585 (tpp) REVERT: E 93 PHE cc_start: 0.9083 (OUTLIER) cc_final: 0.8256 (m-80) REVERT: E 244 ASN cc_start: 0.8650 (p0) cc_final: 0.8166 (t0) REVERT: E 572 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7379 (pt0) REVERT: F 21 PHE cc_start: 0.7995 (m-10) cc_final: 0.7778 (m-10) REVERT: F 106 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7723 (mtp180) REVERT: F 408 MET cc_start: 0.8988 (tpp) cc_final: 0.8689 (ttm) REVERT: I 206 ARG cc_start: 0.5866 (tpt90) cc_final: 0.5579 (ptt-90) REVERT: I 310 ARG cc_start: 0.6982 (ptt-90) cc_final: 0.6621 (tpt-90) REVERT: I 397 ASN cc_start: 0.6185 (m-40) cc_final: 0.5785 (t0) REVERT: I 547 LEU cc_start: 0.8463 (mm) cc_final: 0.8217 (mm) REVERT: I 556 THR cc_start: 0.8573 (OUTLIER) cc_final: 0.8372 (m) REVERT: J 49 GLN cc_start: 0.8270 (pm20) cc_final: 0.7856 (pt0) REVERT: J 72 GLN cc_start: 0.7271 (mt0) cc_final: 0.6842 (tm-30) REVERT: J 165 LEU cc_start: 0.7180 (tp) cc_final: 0.6942 (tt) REVERT: J 168 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8327 (mmm160) REVERT: J 376 LEU cc_start: 0.9010 (tt) cc_final: 0.8619 (tt) REVERT: M 43 ASP cc_start: 0.8737 (t70) cc_final: 0.8312 (t0) REVERT: M 381 LEU cc_start: 0.7132 (tp) cc_final: 0.6808 (tt) REVERT: M 403 TYR cc_start: 0.6293 (OUTLIER) cc_final: 0.5563 (t80) REVERT: M 462 ARG cc_start: 0.5138 (mtp85) cc_final: 0.4717 (mpt-90) REVERT: M 496 GLU cc_start: 0.6120 (tp30) cc_final: 0.5864 (tp30) REVERT: M 508 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.7052 (mp0) REVERT: M 525 ARG cc_start: 0.7545 (ttp-170) cc_final: 0.7328 (ttp80) REVERT: N 61 MET cc_start: 0.7344 (mtp) cc_final: 0.7064 (mtp) REVERT: N 76 THR cc_start: 0.8186 (m) cc_final: 0.7946 (p) REVERT: N 270 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7864 (mmmm) REVERT: N 301 ARG cc_start: 0.8325 (ptm-80) cc_final: 0.7630 (tpt90) REVERT: N 430 LYS cc_start: 0.7175 (OUTLIER) cc_final: 0.6965 (ttmt) outliers start: 159 outliers final: 128 residues processed: 573 average time/residue: 0.2201 time to fit residues: 206.2665 Evaluate side-chains 568 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 426 time to evaluate : 1.179 ------------------------------------------------------------------------------- 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 126 LEU Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 478 VAL 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 18 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 11 GLN Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 189 PHE Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 211 CYS Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 435 ILE Chi-restraints excluded: chain E residue 572 GLU Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 61 MET Chi-restraints excluded: chain F residue 106 ARG Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 244 CYS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 255 PHE Chi-restraints excluded: chain F residue 293 SER Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 468 ASP Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 219 PHE Chi-restraints excluded: chain I residue 232 ASN Chi-restraints excluded: chain I residue 244 ASN Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 347 VAL Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 467 PHE Chi-restraints excluded: chain I residue 474 ILE Chi-restraints excluded: chain I residue 556 THR Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 168 ARG Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain J residue 276 SER Chi-restraints excluded: chain J residue 362 ASP Chi-restraints excluded: chain J residue 379 GLN Chi-restraints excluded: chain J residue 388 GLN Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 473 MET Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 77 SER Chi-restraints excluded: chain M residue 82 LEU 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 189 PHE Chi-restraints excluded: chain M residue 267 ASP Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain M residue 317 VAL Chi-restraints excluded: chain M residue 343 ILE Chi-restraints excluded: chain M residue 348 VAL Chi-restraints excluded: chain M residue 349 THR Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 403 TYR Chi-restraints excluded: chain M residue 425 ILE Chi-restraints excluded: chain M residue 508 GLU Chi-restraints excluded: chain M residue 544 ILE Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 119 ASN Chi-restraints excluded: chain N residue 180 ILE Chi-restraints excluded: chain N residue 185 ASP Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 241 THR Chi-restraints excluded: chain N residue 242 THR Chi-restraints excluded: chain N residue 244 CYS Chi-restraints excluded: chain N residue 255 PHE Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 270 LYS Chi-restraints excluded: chain N residue 288 LEU Chi-restraints excluded: chain N residue 289 HIS Chi-restraints excluded: chain N residue 309 THR Chi-restraints excluded: chain N residue 330 GLU Chi-restraints excluded: chain N residue 337 SER Chi-restraints excluded: chain N residue 345 VAL Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain N residue 397 GLU Chi-restraints excluded: chain N residue 429 THR Chi-restraints excluded: chain N residue 430 LYS Chi-restraints excluded: chain N residue 466 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 365 optimal weight: 8.9990 chunk 372 optimal weight: 0.6980 chunk 315 optimal weight: 0.9990 chunk 258 optimal weight: 2.9990 chunk 392 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 399 optimal weight: 20.0000 chunk 75 optimal weight: 0.5980 chunk 118 optimal weight: 0.8980 chunk 277 optimal weight: 0.9990 chunk 353 optimal weight: 10.0000 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 ASN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 ASN I 437 HIS ** I 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.151974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.120856 restraints weight = 57123.447| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.38 r_work: 0.3467 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.159 35670 Z= 0.166 Angle : 0.718 59.200 49080 Z= 0.389 Chirality : 0.043 0.560 5486 Planarity : 0.004 0.102 5684 Dihedral : 17.714 173.116 6497 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.45 % Favored : 95.52 % Rotamer: Outliers : 4.55 % Allowed : 29.48 % Favored : 65.97 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.14), residues: 3842 helix: 0.90 (0.14), residues: 1474 sheet: -0.56 (0.19), residues: 800 loop : -0.82 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 332 TYR 0.063 0.002 TYR N 87 PHE 0.021 0.001 PHE E 287 TRP 0.025 0.001 TRP E 84 HIS 0.122 0.002 HIS N 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (35668) covalent geometry : angle 0.71781 / 0.39 (49080) hydrogen bonds : bond 0.04911 / 3.05 ( 1469) hydrogen bonds : angle 4.69628 / 3.33 ( 4142) Misc. bond : bond 0.00009 / 0.00 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 425 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASN cc_start: 0.8953 (OUTLIER) cc_final: 0.8278 (p0) REVERT: A 19 HIS cc_start: 0.8936 (OUTLIER) cc_final: 0.8375 (p90) REVERT: A 22 TRP cc_start: 0.8330 (m100) cc_final: 0.7946 (m100) REVERT: A 136 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7704 (mptp) REVERT: A 213 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7903 (mm) REVERT: A 289 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8335 (tm-30) REVERT: A 318 SER cc_start: 0.8838 (OUTLIER) cc_final: 0.8596 (m) REVERT: A 570 GLU cc_start: 0.7764 (pm20) cc_final: 0.7495 (tm-30) REVERT: B 280 MET cc_start: 0.7879 (tpp) cc_final: 0.7565 (tpp) REVERT: E 93 PHE cc_start: 0.9076 (OUTLIER) cc_final: 0.8261 (m-80) REVERT: E 244 ASN cc_start: 0.8639 (p0) cc_final: 0.8173 (t0) REVERT: E 572 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7373 (pt0) REVERT: F 106 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7723 (mtp180) REVERT: F 408 MET cc_start: 0.8960 (tpp) cc_final: 0.8651 (ttm) REVERT: I 206 ARG cc_start: 0.5869 (tpt90) cc_final: 0.5587 (ptt-90) REVERT: I 310 ARG cc_start: 0.6975 (ptt-90) cc_final: 0.6616 (tpt-90) REVERT: I 397 ASN cc_start: 0.6199 (m-40) cc_final: 0.5782 (t0) REVERT: I 547 LEU cc_start: 0.8469 (mm) cc_final: 0.8218 (mm) REVERT: I 556 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8369 (m) REVERT: J 49 GLN cc_start: 0.8260 (pm20) cc_final: 0.7858 (pt0) REVERT: J 72 GLN cc_start: 0.7261 (mt0) cc_final: 0.6834 (tm-30) REVERT: J 165 LEU cc_start: 0.7158 (tp) cc_final: 0.6929 (tt) REVERT: J 168 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8318 (mmm160) REVERT: J 376 LEU cc_start: 0.9001 (tt) cc_final: 0.8605 (tt) REVERT: M 43 ASP cc_start: 0.8740 (t70) cc_final: 0.8331 (t0) REVERT: M 53 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.6869 (mt-10) REVERT: M 381 LEU cc_start: 0.7131 (tp) cc_final: 0.6809 (tt) REVERT: M 403 TYR cc_start: 0.6307 (OUTLIER) cc_final: 0.5570 (t80) REVERT: M 462 ARG cc_start: 0.5116 (mtp85) cc_final: 0.4703 (mpt-90) REVERT: M 496 GLU cc_start: 0.6106 (tp30) cc_final: 0.5852 (tp30) REVERT: M 508 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.7042 (mp0) REVERT: M 525 ARG cc_start: 0.7545 (ttp-170) cc_final: 0.7329 (ttp80) REVERT: N 61 MET cc_start: 0.7309 (mtp) cc_final: 0.7030 (mtp) REVERT: N 76 THR cc_start: 0.8176 (m) cc_final: 0.7936 (p) REVERT: N 270 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7875 (mmmm) REVERT: N 301 ARG cc_start: 0.8305 (ptm-80) cc_final: 0.7627 (tpt90) REVERT: N 430 LYS cc_start: 0.7165 (OUTLIER) cc_final: 0.6960 (ttmt) outliers start: 152 outliers final: 133 residues processed: 548 average time/residue: 0.2152 time to fit residues: 195.4911 Evaluate side-chains 571 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 422 time to evaluate : 1.242 ------------------------------------------------------------------------------- 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 126 LEU Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 11 GLN Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 189 PHE Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 211 CYS Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 435 ILE Chi-restraints excluded: chain E residue 572 GLU Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 61 MET Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 106 ARG Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 244 CYS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 255 PHE Chi-restraints excluded: chain F residue 293 SER Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 468 ASP Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 219 PHE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 232 ASN Chi-restraints excluded: chain I residue 244 ASN Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 347 VAL Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 467 PHE Chi-restraints excluded: chain I residue 474 ILE Chi-restraints excluded: chain I residue 556 THR Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 168 ARG Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain J residue 276 SER Chi-restraints excluded: chain J residue 362 ASP Chi-restraints excluded: chain J residue 379 GLN Chi-restraints excluded: chain J residue 388 GLN Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 473 MET Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 53 GLU Chi-restraints excluded: chain M residue 77 SER Chi-restraints excluded: chain M residue 82 LEU 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 189 PHE Chi-restraints excluded: chain M residue 254 THR Chi-restraints excluded: chain M residue 267 ASP Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain M residue 317 VAL Chi-restraints excluded: chain M residue 319 ILE Chi-restraints excluded: chain M residue 343 ILE Chi-restraints excluded: chain M residue 348 VAL Chi-restraints excluded: chain M residue 349 THR Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 403 TYR Chi-restraints excluded: chain M residue 425 ILE Chi-restraints excluded: chain M residue 508 GLU Chi-restraints excluded: chain M residue 544 ILE Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 119 ASN Chi-restraints excluded: chain N residue 180 ILE Chi-restraints excluded: chain N residue 185 ASP Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 241 THR Chi-restraints excluded: chain N residue 242 THR Chi-restraints excluded: chain N residue 244 CYS Chi-restraints excluded: chain N residue 255 PHE Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 270 LYS Chi-restraints excluded: chain N residue 288 LEU Chi-restraints excluded: chain N residue 309 THR Chi-restraints excluded: chain N residue 330 GLU Chi-restraints excluded: chain N residue 337 SER Chi-restraints excluded: chain N residue 345 VAL Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain N residue 397 GLU Chi-restraints excluded: chain N residue 429 THR Chi-restraints excluded: chain N residue 430 LYS Chi-restraints excluded: chain N residue 466 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 296 optimal weight: 0.9990 chunk 169 optimal weight: 0.9980 chunk 339 optimal weight: 6.9990 chunk 219 optimal weight: 7.9990 chunk 387 optimal weight: 0.9980 chunk 153 optimal weight: 0.8980 chunk 313 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 342 optimal weight: 0.0370 chunk 188 optimal weight: 0.1980 chunk 98 optimal weight: 0.9980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 ASN ** I 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.150992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.119254 restraints weight = 57238.969| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.56 r_work: 0.3463 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.159 35670 Z= 0.166 Angle : 0.718 59.200 49080 Z= 0.389 Chirality : 0.043 0.560 5486 Planarity : 0.004 0.102 5684 Dihedral : 17.714 173.116 6497 Min Nonbonded Distance : 1.501 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.45 % Favored : 95.52 % Rotamer: Outliers : 4.49 % Allowed : 29.57 % Favored : 65.94 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.14), residues: 3842 helix: 0.90 (0.14), residues: 1474 sheet: -0.56 (0.19), residues: 800 loop : -0.82 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 332 TYR 0.063 0.002 TYR N 87 PHE 0.021 0.001 PHE E 287 TRP 0.025 0.001 TRP E 84 HIS 0.122 0.002 HIS N 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (35668) covalent geometry : angle 0.71782 / 0.39 (49080) hydrogen bonds : bond 0.04911 / 3.05 ( 1469) hydrogen bonds : angle 4.69628 / 3.33 ( 4142) Misc. bond : bond 0.00009 / 0.00 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8877.87 seconds wall clock time: 153 minutes 29.29 seconds (9209.29 seconds total)