Starting phenix.real_space_refine on Sun Aug 9 10:24:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y82_39030/08_2026/8y82_39030_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y82_39030/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8y82_39030/08_2026/8y82_39030.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y82_39030/08_2026/8y82_39030.map" model { file = "/net/cci-nas-00/data/ceres_data/8y82_39030/08_2026/8y82_39030_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y82_39030/08_2026/8y82_39030_neut_trim.cif" } 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-2.2rc3-6140/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: 8.75, per 1000 atoms: 0.25 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: 3.06 Conformation dependent library (CDL) restraints added in 1.3 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: 5.17 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: 8.85 Time building geometry restraints manager: 4.09 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: 47853 2.27 - 4.54: 1097 4.54 - 6.81: 102 6.81 - 9.09: 19 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: 19915 35.84 - 71.68: 1209 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: 5068 0.095 - 0.190: 390 0.190 - 0.284: 20 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: 9.920 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: 0.060 Extract box with map and model: 0.690 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 38.240 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.110 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.250 ------------------------------------------------------------------------------- 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= 0.356 Angle : 0.746 11.358 49080 Z= 0.488 Chirality : 0.051 0.474 5486 Planarity : 0.005 0.076 5684 Dihedral : 20.405 179.197 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 0.00412 / 0.27 (35668) covalent geometry : angle 0.74553 / 0.49 (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 : 1.181 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: 0.7538 (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: 0.3287 (tp) REVERT: J 272 ASN cc_start: 0.5946 (p0) cc_final: 0.5528 (p0) REVERT: J 302 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8312 (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: 0.6075 (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: 0.6512 (tt0) REVERT: N 276 SER cc_start: 0.8212 (p) cc_final: 0.8008 (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: 0.2292 time to fit residues: 295.3613 Evaluate side-chains 521 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 489 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** J 60 HIS ** J 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.159186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.126619 restraints weight = 59472.960| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.54 r_work: 0.3633 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 35670 Z= 0.233 Angle : 0.694 9.560 49080 Z= 0.364 Chirality : 0.045 0.322 5486 Planarity : 0.005 0.072 5684 Dihedral : 18.000 171.380 6558 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 5.75 % Allowed : 28.58 % Favored : 65.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.14), residues: 3842 helix: 0.65 (0.13), residues: 1504 sheet: -0.69 (0.19), residues: 780 loop : -0.78 (0.16), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 411 TYR 0.032 0.002 TYR E 168 PHE 0.030 0.002 PHE J 323 TRP 0.021 0.002 TRP J 218 HIS 0.016 0.001 HIS E 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.23 (35668) covalent geometry : angle 0.69364 / 0.36 (49080) hydrogen bonds : bond 0.06008 / 3.72 ( 1469) hydrogen bonds : angle 5.24437 / 3.70 ( 4142) Misc. bond : bond 0.01679 / 0.80 ( 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 701 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 509 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASN cc_start: 0.9118 (OUTLIER) cc_final: 0.8810 (p0) REVERT: A 136 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7792 (mptp) REVERT: A 289 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8354 (tm-30) REVERT: B 100 MET cc_start: 0.7000 (mmm) cc_final: 0.6502 (mmm) REVERT: B 302 LYS cc_start: 0.8805 (ttmt) cc_final: 0.8463 (ttmm) REVERT: E 93 PHE cc_start: 0.9051 (OUTLIER) cc_final: 0.8312 (m-80) REVERT: I 206 ARG cc_start: 0.6090 (tpt90) cc_final: 0.5585 (ptt-90) REVERT: I 219 PHE cc_start: 0.8802 (OUTLIER) cc_final: 0.8007 (p90) REVERT: J 72 GLN cc_start: 0.7320 (mt0) cc_final: 0.6803 (tm-30) REVERT: J 191 GLN cc_start: 0.7238 (mt0) cc_final: 0.6397 (pp30) REVERT: J 221 ASP cc_start: 0.8559 (p0) cc_final: 0.8349 (p0) REVERT: J 224 TYR cc_start: 0.8480 (m-80) cc_final: 0.8272 (m-80) REVERT: J 323 PHE cc_start: 0.7439 (m-80) cc_final: 0.7095 (m-80) REVERT: J 375 LEU cc_start: 0.8618 (mt) cc_final: 0.8365 (mt) REVERT: M 47 ARG cc_start: 0.7974 (mtt-85) cc_final: 0.7773 (mtt-85) REVERT: M 48 TYR cc_start: 0.6861 (t80) cc_final: 0.6449 (t80) REVERT: M 133 ASN cc_start: 0.8555 (t0) cc_final: 0.7700 (t0) REVERT: M 153 ASP cc_start: 0.7780 (t70) cc_final: 0.7331 (t0) REVERT: M 268 LEU cc_start: 0.7909 (tt) cc_final: 0.7706 (mm) REVERT: M 332 ARG cc_start: 0.7938 (ttp-170) cc_final: 0.6969 (ptm-80) REVERT: M 461 LEU cc_start: 0.6223 (tp) cc_final: 0.5839 (mp) REVERT: M 497 ARG cc_start: 0.7059 (tpp-160) cc_final: 0.5119 (tpp-160) REVERT: M 531 ARG cc_start: 0.6238 (mtt180) cc_final: 0.6031 (ttp-170) REVERT: M 546 ILE cc_start: 0.7242 (mt) cc_final: 0.7006 (mt) REVERT: M 566 GLU cc_start: 0.4584 (mp0) cc_final: 0.3824 (tt0) REVERT: M 579 PHE cc_start: 0.7066 (p90) cc_final: 0.6689 (p90) REVERT: N 70 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7092 (tt0) REVERT: N 71 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7421 (mp) REVERT: N 190 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7013 (ttt-90) REVERT: N 276 SER cc_start: 0.8540 (p) cc_final: 0.8316 (m) REVERT: N 302 LYS cc_start: 0.7748 (tttm) cc_final: 0.6611 (ttmm) outliers start: 192 outliers final: 112 residues processed: 652 average time/residue: 0.2112 time to fit residues: 224.4815 Evaluate side-chains 560 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 441 time to evaluate : 1.175 ------------------------------------------------------------------------------- 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 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 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 194 ILE 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 435 ILE Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 44 PHE 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 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 160 SER 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 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 I residue 474 ILE 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 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 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 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 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: 3.9990 chunk 13 optimal weight: 0.4980 chunk 351 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 286 optimal weight: 0.8980 chunk 373 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 122 optimal weight: 7.9990 chunk 98 optimal weight: 0.0770 chunk 218 optimal weight: 6.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- 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** 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 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 119 ASN ** 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 = 0.4106 r_free = 0.4106 target = 0.157544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.125785 restraints weight = 57896.367| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.63 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: 0.8067 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35670 Z= 0.132 Angle : 0.615 9.031 49080 Z= 0.323 Chirality : 0.042 0.374 5486 Planarity : 0.004 0.048 5684 Dihedral : 17.917 170.933 6523 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 5.00 % Allowed : 28.91 % Favored : 66.09 % 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: -0.23 (0.14), residues: 3842 helix: 0.83 (0.13), residues: 1500 sheet: -0.61 (0.18), residues: 818 loop : -0.77 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 301 TYR 0.026 0.002 TYR N 291 PHE 0.019 0.001 PHE J 44 TRP 0.022 0.001 TRP M 510 HIS 0.011 0.001 HIS M 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (35668) covalent geometry : angle 0.61495 / 0.32 (49080) hydrogen bonds : bond 0.05420 / 3.38 ( 1469) hydrogen bonds : angle 4.94607 / 3.48 ( 4142) Misc. bond : bond 0.00505 / 0.26 ( 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 662 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 495 time to evaluate : 1.130 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 22 TRP cc_start: 0.8287 (m100) cc_final: 0.7837 (m100) REVERT: A 213 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7769 (mm) REVERT: A 289 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8335 (tm-30) REVERT: A 318 SER cc_start: 0.8727 (OUTLIER) cc_final: 0.8491 (m) REVERT: B 100 MET cc_start: 0.6683 (mmm) cc_final: 0.6293 (mmm) REVERT: E 93 PHE cc_start: 0.9000 (OUTLIER) cc_final: 0.8123 (m-80) REVERT: E 210 LYS cc_start: 0.8205 (tppt) cc_final: 0.7855 (mtpp) REVERT: E 234 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.8071 (tpp) REVERT: E 244 ASN cc_start: 0.8676 (p0) cc_final: 0.8195 (t0) REVERT: E 572 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7390 (pt0) REVERT: F 249 ASP cc_start: 0.7642 (t0) cc_final: 0.7434 (t0) REVERT: F 256 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7777 (tt0) REVERT: I 206 ARG cc_start: 0.5887 (tpt90) cc_final: 0.5472 (ptt-90) REVERT: I 397 ASN cc_start: 0.6112 (m-40) cc_final: 0.5818 (t0) REVERT: I 522 ASP cc_start: 0.8481 (m-30) cc_final: 0.8073 (t0) REVERT: J 72 GLN cc_start: 0.7312 (mt0) cc_final: 0.6842 (tm-30) REVERT: J 100 MET cc_start: 0.6549 (ppp) cc_final: 0.6255 (ppp) REVERT: J 192 CYS cc_start: 0.6934 (t) cc_final: 0.6705 (t) REVERT: J 375 LEU cc_start: 0.8559 (mt) cc_final: 0.8218 (mm) REVERT: M 30 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.7498 (ttm170) REVERT: M 133 ASN cc_start: 0.8481 (t0) cc_final: 0.7534 (t0) REVERT: M 153 ASP cc_start: 0.7768 (t70) cc_final: 0.7322 (t0) REVERT: M 268 LEU cc_start: 0.7900 (tt) cc_final: 0.7612 (mm) REVERT: M 332 ARG cc_start: 0.7804 (ttp-170) cc_final: 0.6978 (ptm-80) REVERT: M 497 ARG cc_start: 0.6878 (tpp-160) cc_final: 0.4873 (tpp-160) REVERT: M 546 ILE cc_start: 0.7461 (mt) cc_final: 0.7075 (mt) REVERT: M 566 GLU cc_start: 0.4787 (mp0) cc_final: 0.4075 (tt0) REVERT: N 72 GLN cc_start: 0.7885 (tp40) cc_final: 0.7641 (tp-100) REVERT: N 190 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.6601 (ttt-90) REVERT: N 197 MET cc_start: 0.7389 (mmp) cc_final: 0.6885 (mmp) REVERT: N 270 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8137 (mmmm) REVERT: N 276 SER cc_start: 0.8547 (p) cc_final: 0.8328 (m) REVERT: N 330 GLU cc_start: 0.8266 (mt-10) cc_final: 0.8058 (mt-10) outliers start: 167 outliers final: 94 residues processed: 621 average time/residue: 0.2174 time to fit residues: 222.4878 Evaluate side-chains 545 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 441 time to evaluate : 1.129 ------------------------------------------------------------------------------- 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 404 ILE Chi-restraints excluded: chain A residue 429 LEU 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 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 362 ASP Chi-restraints excluded: chain B residue 397 GLU 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 234 MET 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 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 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 293 SER Chi-restraints excluded: chain F residue 327 THR 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 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 405 ASP 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 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 117 VAL 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 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 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 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: 5.9990 chunk 165 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 307 optimal weight: 5.9990 chunk 154 optimal weight: 3.9990 chunk 225 optimal weight: 0.2980 chunk 57 optimal weight: 2.9990 chunk 138 optimal weight: 7.9990 chunk 194 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 ** 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** I 7 ASN ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 ASN ** I 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 83 GLN ** M 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 177 ASN N 289 HIS ** 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** N 450 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.155752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.124408 restraints weight = 57870.685| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.72 r_work: 0.3530 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35670 Z= 0.147 Angle : 0.601 9.434 49080 Z= 0.315 Chirality : 0.042 0.325 5486 Planarity : 0.004 0.038 5684 Dihedral : 17.830 171.064 6511 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 5.27 % Allowed : 27.89 % Favored : 66.84 % 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: -0.12 (0.14), residues: 3842 helix: 0.98 (0.14), residues: 1476 sheet: -0.55 (0.19), residues: 800 loop : -0.74 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 47 TYR 0.019 0.001 TYR I 162 PHE 0.021 0.001 PHE E 523 TRP 0.021 0.001 TRP M 510 HIS 0.009 0.001 HIS E 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (35668) covalent geometry : angle 0.60137 / 0.32 (49080) hydrogen bonds : bond 0.05199 / 3.24 ( 1469) hydrogen bonds : angle 4.81663 / 3.39 ( 4142) Misc. bond : bond 0.00131 / 0.07 ( 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 642 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 466 time to evaluate : 1.279 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: 0.8313 (m100) cc_final: 0.7848 (m100) REVERT: A 213 LEU cc_start: 0.8309 (mm) cc_final: 0.7882 (mm) REVERT: A 289 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8342 (tm-30) REVERT: A 319 ILE cc_start: 0.8436 (pt) cc_final: 0.8216 (pt) REVERT: A 379 LEU cc_start: 0.7850 (mm) cc_final: 0.7610 (tt) REVERT: A 567 PHE cc_start: 0.6456 (m-80) cc_final: 0.6221 (m-80) REVERT: B 100 MET cc_start: 0.6761 (mmm) cc_final: 0.6397 (mmm) REVERT: B 302 LYS cc_start: 0.8936 (ttmt) cc_final: 0.8521 (ttmm) REVERT: E 16 ASN cc_start: 0.8277 (OUTLIER) cc_final: 0.7914 (p0) REVERT: E 93 PHE cc_start: 0.9034 (OUTLIER) cc_final: 0.8261 (m-80) REVERT: E 132 MET cc_start: 0.8762 (ttp) cc_final: 0.8547 (ttt) REVERT: E 210 LYS cc_start: 0.8285 (tppt) cc_final: 0.7925 (mtpp) REVERT: E 234 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.8105 (tpp) REVERT: E 572 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7309 (pt0) REVERT: I 206 ARG cc_start: 0.5870 (tpt90) cc_final: 0.5544 (ptt-90) REVERT: I 397 ASN cc_start: 0.6194 (m-40) cc_final: 0.5781 (t0) REVERT: I 522 ASP cc_start: 0.8528 (m-30) cc_final: 0.8088 (t0) REVERT: I 547 LEU cc_start: 0.8188 (mm) cc_final: 0.7946 (mm) REVERT: J 72 GLN cc_start: 0.7252 (mt0) cc_final: 0.6853 (tm-30) REVERT: J 100 MET cc_start: 0.6437 (ppp) cc_final: 0.6193 (ppp) REVERT: J 192 CYS cc_start: 0.6953 (t) cc_final: 0.6696 (t) REVERT: J 375 LEU cc_start: 0.8654 (mt) cc_final: 0.8433 (mp) REVERT: J 426 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8223 (mt) REVERT: M 30 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.7492 (ttm170) REVERT: M 133 ASN cc_start: 0.8579 (t0) cc_final: 0.7680 (t0) REVERT: M 332 ARG cc_start: 0.7848 (ttp-170) cc_final: 0.7096 (ptm-80) REVERT: M 445 TYR cc_start: 0.4513 (m-80) cc_final: 0.4276 (m-80) REVERT: M 497 ARG cc_start: 0.6966 (tpp-160) cc_final: 0.4865 (tpp-160) REVERT: M 566 GLU cc_start: 0.4875 (mp0) cc_final: 0.4130 (tt0) REVERT: M 579 PHE cc_start: 0.7188 (p90) cc_final: 0.6605 (p90) REVERT: N 20 LEU cc_start: 0.7389 (tp) cc_final: 0.7117 (tt) REVERT: N 61 MET cc_start: 0.7192 (mtp) cc_final: 0.6859 (mtp) REVERT: N 190 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.6763 (ttt-90) REVERT: N 276 SER cc_start: 0.8587 (p) cc_final: 0.8349 (m) REVERT: N 430 LYS cc_start: 0.6908 (ttmm) cc_final: 0.6602 (mttm) outliers start: 176 outliers final: 119 residues processed: 596 average time/residue: 0.2137 time to fit residues: 211.9807 Evaluate side-chains 552 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 425 time to evaluate : 1.340 ------------------------------------------------------------------------------- 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 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 429 LEU 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 60 HIS Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 104 HIS 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 435 ASN 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 208 ILE Chi-restraints excluded: chain E residue 234 MET 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 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 106 ARG 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 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 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 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 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 426 LEU Chi-restraints excluded: chain J residue 473 MET 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 251 LEU 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 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 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 180 ILE Chi-restraints excluded: chain N residue 185 ASP 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 289 HIS 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: 6.9990 chunk 183 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 122 optimal weight: 0.8980 chunk 134 optimal weight: 9.9990 chunk 287 optimal weight: 3.9990 chunk 327 optimal weight: 2.9990 chunk 367 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 242 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 295 HIS ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 436 ASN ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 15 GLN I 16 ASN ** I 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 195 ASN J 296 ASN M 72 GLN ** M 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 139 GLN ** 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.150789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.119204 restraints weight = 57729.216| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.54 r_work: 0.3458 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 35670 Z= 0.200 Angle : 0.630 9.314 49080 Z= 0.328 Chirality : 0.043 0.337 5486 Planarity : 0.004 0.039 5684 Dihedral : 17.816 171.813 6503 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 6.08 % Allowed : 27.86 % Favored : 66.06 % 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: -0.21 (0.14), residues: 3842 helix: 0.90 (0.14), residues: 1472 sheet: -0.56 (0.19), residues: 800 loop : -0.81 (0.16), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 47 TYR 0.024 0.002 TYR J 40 PHE 0.024 0.002 PHE M 287 TRP 0.022 0.001 TRP M 510 HIS 0.030 0.001 HIS B 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.20 (35668) covalent geometry : angle 0.62979 / 0.33 (49080) hydrogen bonds : bond 0.05191 / 3.24 ( 1469) hydrogen bonds : angle 4.80240 / 3.39 ( 4142) Misc. bond : bond 0.00059 / 0.03 ( 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 644 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 441 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 HIS cc_start: 0.8943 (OUTLIER) cc_final: 0.8347 (p90) REVERT: A 22 TRP cc_start: 0.8336 (m100) cc_final: 0.7892 (m100) REVERT: A 136 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7790 (mptp) REVERT: A 213 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7970 (mm) REVERT: A 289 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8384 (tm-30) REVERT: A 318 SER cc_start: 0.8752 (OUTLIER) cc_final: 0.8486 (m) REVERT: B 34 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8107 (mp) REVERT: B 100 MET cc_start: 0.6752 (mmm) cc_final: 0.6461 (mmm) REVERT: E 16 ASN cc_start: 0.8343 (OUTLIER) cc_final: 0.7923 (p0) REVERT: E 93 PHE cc_start: 0.9111 (OUTLIER) cc_final: 0.8353 (m-80) REVERT: E 194 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8609 (mp) REVERT: E 210 LYS cc_start: 0.8368 (tppt) cc_final: 0.7897 (mtmm) REVERT: E 234 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.7952 (mpp) REVERT: E 572 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7212 (pt0) REVERT: F 106 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7697 (mtp180) REVERT: I 206 ARG cc_start: 0.5949 (tpt90) cc_final: 0.5598 (ptt-90) REVERT: I 397 ASN cc_start: 0.6186 (m-40) cc_final: 0.5849 (t0) REVERT: I 522 ASP cc_start: 0.8546 (m-30) cc_final: 0.8147 (t0) REVERT: I 547 LEU cc_start: 0.8306 (mm) cc_final: 0.8023 (mm) REVERT: J 72 GLN cc_start: 0.7311 (mt0) cc_final: 0.6958 (tm-30) REVERT: J 100 MET cc_start: 0.6412 (ppp) cc_final: 0.6194 (ppp) REVERT: J 192 CYS cc_start: 0.7067 (t) cc_final: 0.6805 (t) REVERT: M 61 ASP cc_start: 0.7786 (p0) cc_final: 0.7579 (p0) REVERT: M 332 ARG cc_start: 0.7854 (ttp-170) cc_final: 0.6932 (ptm-80) REVERT: M 403 TYR cc_start: 0.7123 (m-80) cc_final: 0.6921 (m-80) REVERT: M 445 TYR cc_start: 0.4623 (m-80) cc_final: 0.4375 (m-80) REVERT: M 497 ARG cc_start: 0.6992 (tpp-160) cc_final: 0.4443 (tpp-160) REVERT: M 525 ARG cc_start: 0.7606 (ttp-170) cc_final: 0.7316 (ttp80) REVERT: M 579 PHE cc_start: 0.7206 (p90) cc_final: 0.6650 (p90) REVERT: N 61 MET cc_start: 0.7061 (mtp) cc_final: 0.6773 (mtp) REVERT: N 276 SER cc_start: 0.8665 (p) cc_final: 0.8321 (m) REVERT: N 301 ARG cc_start: 0.7999 (ptm-80) cc_final: 0.7660 (tpt90) REVERT: N 430 LYS cc_start: 0.7033 (ttmm) cc_final: 0.6673 (mttm) outliers start: 203 outliers final: 137 residues processed: 596 average time/residue: 0.2144 time to fit residues: 211.3301 Evaluate side-chains 564 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 415 time to evaluate : 1.213 ------------------------------------------------------------------------------- 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 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 429 LEU 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 34 LEU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 104 HIS 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 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 394 VAL 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 141 THR 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 234 MET 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 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 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 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 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 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 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 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 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 180 ILE Chi-restraints excluded: chain J residue 215 LEU 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 407 ILE Chi-restraints excluded: chain J residue 473 MET 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 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 251 LEU 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 527 ARG Chi-restraints excluded: chain M residue 544 ILE Chi-restraints excluded: chain M residue 546 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 190 ARG Chi-restraints excluded: chain N residue 228 SER 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 289 HIS 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 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: 7.9990 chunk 91 optimal weight: 10.0000 chunk 86 optimal weight: 0.6980 chunk 92 optimal weight: 20.0000 chunk 26 optimal weight: 0.1980 chunk 258 optimal weight: 3.9990 chunk 362 optimal weight: 0.9990 chunk 392 optimal weight: 2.9990 chunk 94 optimal weight: 20.0000 chunk 399 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 ASN ** F 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 436 ASN ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 15 GLN I 16 ASN ** I 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 195 ASN ** J 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 367 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 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.152266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.119519 restraints weight = 57505.269| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.59 r_work: 0.3467 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 35670 Z= 0.163 Angle : 0.614 9.885 49080 Z= 0.318 Chirality : 0.042 0.329 5486 Planarity : 0.004 0.043 5684 Dihedral : 17.790 172.427 6499 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 5.75 % Allowed : 28.31 % Favored : 65.94 % 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: -0.19 (0.14), residues: 3842 helix: 0.94 (0.14), residues: 1472 sheet: -0.56 (0.19), residues: 800 loop : -0.82 (0.16), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 47 TYR 0.020 0.002 TYR N 291 PHE 0.023 0.002 PHE E 523 TRP 0.021 0.001 TRP M 510 HIS 0.015 0.001 HIS B 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (35668) covalent geometry : angle 0.61445 / 0.32 (49080) hydrogen bonds : bond 0.05075 / 3.17 ( 1469) hydrogen bonds : angle 4.72907 / 3.34 ( 4142) Misc. bond : bond 0.00051 / 0.02 ( 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 639 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 447 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 HIS cc_start: 0.8942 (OUTLIER) cc_final: 0.8323 (p90) REVERT: A 22 TRP cc_start: 0.8332 (m100) cc_final: 0.7865 (m100) REVERT: A 136 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7779 (mptp) REVERT: A 213 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7987 (mm) REVERT: A 289 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8381 (tm-30) REVERT: A 318 SER cc_start: 0.8769 (OUTLIER) cc_final: 0.8519 (m) REVERT: A 567 PHE cc_start: 0.6489 (m-80) cc_final: 0.6237 (m-80) REVERT: B 34 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8165 (mp) REVERT: B 100 MET cc_start: 0.6736 (mmm) cc_final: 0.6466 (mmm) REVERT: E 16 ASN cc_start: 0.8143 (OUTLIER) cc_final: 0.7791 (p0) REVERT: E 93 PHE cc_start: 0.9075 (OUTLIER) cc_final: 0.8268 (m-80) REVERT: E 132 MET cc_start: 0.8802 (ttt) cc_final: 0.8568 (ttt) REVERT: E 210 LYS cc_start: 0.8307 (tppt) cc_final: 0.7841 (mtmm) REVERT: E 234 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.7944 (mpp) REVERT: E 244 ASN cc_start: 0.8642 (p0) cc_final: 0.8137 (t0) REVERT: E 572 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7277 (pt0) REVERT: F 106 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7694 (mtp180) REVERT: I 206 ARG cc_start: 0.5923 (tpt90) cc_final: 0.5562 (ptt-90) REVERT: I 310 ARG cc_start: 0.6816 (ptt-90) cc_final: 0.6450 (tpt-90) REVERT: I 397 ASN cc_start: 0.6073 (m-40) cc_final: 0.5715 (t0) REVERT: I 437 HIS cc_start: 0.7291 (p-80) cc_final: 0.6952 (p-80) REVERT: I 522 ASP cc_start: 0.8548 (m-30) cc_final: 0.8148 (t0) REVERT: I 547 LEU cc_start: 0.8298 (mm) cc_final: 0.8033 (mm) REVERT: J 40 TYR cc_start: 0.8653 (t80) cc_final: 0.8321 (t80) REVERT: J 49 GLN cc_start: 0.8273 (pm20) cc_final: 0.7919 (pt0) REVERT: J 72 GLN cc_start: 0.7253 (mt0) cc_final: 0.6759 (tm-30) REVERT: J 168 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8253 (mmm160) REVERT: J 192 CYS cc_start: 0.7039 (t) cc_final: 0.6798 (t) REVERT: J 214 LYS cc_start: 0.8675 (ttpt) cc_final: 0.7885 (mtpt) REVERT: J 440 LYS cc_start: 0.8539 (mtpp) cc_final: 0.8167 (mtpp) REVERT: M 61 ASP cc_start: 0.7830 (p0) cc_final: 0.7590 (p0) REVERT: M 332 ARG cc_start: 0.7857 (ttp-170) cc_final: 0.7038 (ptm-80) REVERT: M 381 LEU cc_start: 0.6788 (tp) cc_final: 0.6422 (tt) REVERT: M 445 TYR cc_start: 0.4734 (m-80) cc_final: 0.4505 (m-80) REVERT: M 508 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6866 (pm20) REVERT: M 525 ARG cc_start: 0.7590 (ttp-170) cc_final: 0.7307 (ttp80) REVERT: N 61 MET cc_start: 0.7086 (mtp) cc_final: 0.6829 (mtp) REVERT: N 276 SER cc_start: 0.8685 (p) cc_final: 0.8351 (m) REVERT: N 302 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7933 (tptp) outliers start: 192 outliers final: 137 residues processed: 596 average time/residue: 0.2176 time to fit residues: 214.2305 Evaluate side-chains 571 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 420 time to evaluate : 1.234 ------------------------------------------------------------------------------- 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 219 PHE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 290 MET 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 417 LEU 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 34 LEU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 104 HIS 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 251 ASP 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 394 VAL 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 16 ASN 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 208 ILE Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 234 MET 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 350 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 106 ARG Chi-restraints excluded: chain F residue 110 LEU 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 293 SER Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 436 ASN 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 236 MET 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 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 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 125 LEU Chi-restraints excluded: chain J residue 168 ARG 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 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 51 LEU Chi-restraints excluded: chain M residue 77 SER 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 231 GLU 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 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 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 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 289 HIS Chi-restraints excluded: chain N residue 302 LYS 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 394 VAL Chi-restraints excluded: chain N residue 397 GLU 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: 5.9990 chunk 72 optimal weight: 3.9990 chunk 207 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 197 optimal weight: 10.9990 chunk 129 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 189 optimal weight: 0.9980 chunk 370 optimal weight: 0.0980 chunk 367 optimal weight: 0.9980 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 ASN ** I 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 367 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 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.151081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.119780 restraints weight = 57719.155| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.43 r_work: 0.3464 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 35670 Z= 0.167 Angle : 0.618 10.627 49080 Z= 0.321 Chirality : 0.042 0.328 5486 Planarity : 0.004 0.069 5684 Dihedral : 17.760 172.733 6497 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 5.57 % Allowed : 28.85 % Favored : 65.58 % 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: 0.92 (0.14), residues: 1474 sheet: -0.56 (0.19), residues: 800 loop : -0.84 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG M 497 TYR 0.024 0.002 TYR M 271 PHE 0.023 0.002 PHE E 523 TRP 0.022 0.001 TRP M 510 HIS 0.013 0.001 HIS M 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (35668) covalent geometry : angle 0.61772 / 0.32 (49080) hydrogen bonds : bond 0.05027 / 3.13 ( 1469) hydrogen bonds : angle 4.72768 / 3.34 ( 4142) Misc. bond : bond 0.00055 / 0.03 ( 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 638 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 452 time to evaluate : 1.241 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 19 HIS cc_start: 0.8950 (OUTLIER) cc_final: 0.8380 (p90) REVERT: A 22 TRP cc_start: 0.8301 (m100) cc_final: 0.7852 (m100) REVERT: A 136 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7790 (mptp) REVERT: A 213 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7988 (mm) REVERT: A 289 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8367 (tm-30) REVERT: A 319 ILE cc_start: 0.8544 (pt) cc_final: 0.8340 (pt) REVERT: A 570 GLU cc_start: 0.7810 (pm20) cc_final: 0.7543 (tm-30) REVERT: B 34 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8230 (mp) REVERT: B 100 MET cc_start: 0.6690 (mmm) cc_final: 0.6472 (mmm) REVERT: E 93 PHE cc_start: 0.9077 (OUTLIER) cc_final: 0.8367 (m-80) REVERT: E 132 MET cc_start: 0.8756 (ttt) cc_final: 0.8506 (ttt) REVERT: E 194 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8631 (mp) REVERT: E 210 LYS cc_start: 0.8386 (tppt) cc_final: 0.7944 (mtmm) REVERT: E 234 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.7908 (mpp) REVERT: E 244 ASN cc_start: 0.8633 (p0) cc_final: 0.8143 (t0) REVERT: E 572 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7293 (pt0) REVERT: F 106 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7704 (mtp180) REVERT: I 206 ARG cc_start: 0.5951 (tpt90) cc_final: 0.5614 (ptt-90) REVERT: I 310 ARG cc_start: 0.6905 (ptt-90) cc_final: 0.6504 (tpt-90) REVERT: I 397 ASN cc_start: 0.6002 (m-40) cc_final: 0.5672 (t0) REVERT: I 437 HIS cc_start: 0.7314 (p-80) cc_final: 0.7000 (p-80) REVERT: I 522 ASP cc_start: 0.8549 (m-30) cc_final: 0.8209 (t0) REVERT: I 547 LEU cc_start: 0.8333 (mm) cc_final: 0.8125 (mm) REVERT: J 49 GLN cc_start: 0.8289 (pm20) cc_final: 0.7936 (pt0) REVERT: J 72 GLN cc_start: 0.7290 (mt0) cc_final: 0.6809 (tm-30) REVERT: J 168 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8293 (mmm160) REVERT: J 440 LYS cc_start: 0.8543 (mtpp) cc_final: 0.8236 (mtpp) REVERT: M 61 ASP cc_start: 0.7870 (p0) cc_final: 0.7633 (p0) REVERT: M 332 ARG cc_start: 0.7874 (ttp-170) cc_final: 0.7024 (ptm-80) REVERT: M 381 LEU cc_start: 0.6807 (tp) cc_final: 0.6514 (tt) REVERT: M 508 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6748 (pm20) REVERT: M 525 ARG cc_start: 0.7591 (ttp-170) cc_final: 0.7352 (ttp80) REVERT: M 579 PHE cc_start: 0.7249 (p90) cc_final: 0.6710 (p90) REVERT: N 40 TYR cc_start: 0.7866 (t80) cc_final: 0.7369 (t80) REVERT: N 61 MET cc_start: 0.7048 (mtp) cc_final: 0.6693 (mtp) REVERT: N 276 SER cc_start: 0.8674 (p) cc_final: 0.8305 (m) REVERT: N 301 ARG cc_start: 0.8167 (ptm-80) cc_final: 0.7692 (tpt170) REVERT: N 302 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7692 (tptp) outliers start: 186 outliers final: 144 residues processed: 596 average time/residue: 0.1989 time to fit residues: 196.1397 Evaluate side-chains 583 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 426 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 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 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 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 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 71 LEU Chi-restraints excluded: chain B residue 104 HIS 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 251 ASP 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 394 VAL 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 16 ASN 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 189 PHE 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 224 SER Chi-restraints excluded: chain E residue 234 MET 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 350 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 106 ARG Chi-restraints excluded: chain F residue 110 LEU 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 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 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 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 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 125 LEU 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 338 THR Chi-restraints excluded: chain J residue 345 VAL Chi-restraints excluded: chain J residue 388 GLN Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 424 SER Chi-restraints excluded: chain J residue 426 LEU 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 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 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 398 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 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 289 HIS Chi-restraints excluded: chain N residue 302 LYS 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 394 VAL Chi-restraints excluded: chain N residue 397 GLU Chi-restraints excluded: chain N residue 429 THR 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: 0.9990 chunk 172 optimal weight: 0.7980 chunk 264 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 322 optimal weight: 0.9990 chunk 152 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 372 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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** ** F 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 238 GLN ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 436 ASN I 7 ASN I 16 ASN ** I 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 195 ASN ** J 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 367 GLN ** 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 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.152064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.120276 restraints weight = 57627.857| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.56 r_work: 0.3477 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35670 Z= 0.143 Angle : 0.607 10.449 49080 Z= 0.315 Chirality : 0.042 0.321 5486 Planarity : 0.004 0.052 5684 Dihedral : 17.739 172.983 6497 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.97 % Allowed : 29.30 % Favored : 65.73 % 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: -0.16 (0.14), residues: 3842 helix: 0.97 (0.14), residues: 1474 sheet: -0.56 (0.19), residues: 804 loop : -0.81 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 47 TYR 0.019 0.002 TYR N 229 PHE 0.022 0.001 PHE E 287 TRP 0.026 0.001 TRP M 510 HIS 0.016 0.001 HIS B 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (35668) covalent geometry : angle 0.60664 / 0.31 (49080) hydrogen bonds : bond 0.04887 / 3.03 ( 1469) hydrogen bonds : angle 4.67158 / 3.30 ( 4142) Misc. bond : bond 0.00042 / 0.02 ( 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 625 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 459 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 HIS cc_start: 0.8923 (OUTLIER) cc_final: 0.8353 (p90) REVERT: A 22 TRP cc_start: 0.8242 (m100) cc_final: 0.7819 (m100) REVERT: A 136 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7736 (mptp) REVERT: A 213 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7974 (mm) REVERT: A 289 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8356 (tm-30) REVERT: A 319 ILE cc_start: 0.8481 (pt) cc_final: 0.8270 (pt) REVERT: A 570 GLU cc_start: 0.7833 (pm20) cc_final: 0.7530 (tm-30) REVERT: B 104 HIS cc_start: 0.7709 (OUTLIER) cc_final: 0.7335 (t70) REVERT: E 16 ASN cc_start: 0.8249 (OUTLIER) cc_final: 0.8043 (p0) REVERT: E 93 PHE cc_start: 0.9054 (OUTLIER) cc_final: 0.8299 (m-80) REVERT: E 132 MET cc_start: 0.8770 (ttt) cc_final: 0.8540 (ttt) REVERT: E 194 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8651 (mp) REVERT: E 210 LYS cc_start: 0.8364 (tppt) cc_final: 0.7959 (mtmm) REVERT: E 234 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.7855 (mpp) REVERT: E 244 ASN cc_start: 0.8622 (p0) cc_final: 0.8143 (t0) REVERT: E 572 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7310 (pt0) REVERT: F 106 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7693 (mtp180) REVERT: I 206 ARG cc_start: 0.5901 (tpt90) cc_final: 0.5598 (ptt-90) REVERT: I 310 ARG cc_start: 0.6908 (ptt-90) cc_final: 0.6517 (tpt-90) REVERT: I 397 ASN cc_start: 0.5917 (m-40) cc_final: 0.5658 (t0) REVERT: I 437 HIS cc_start: 0.7321 (p-80) cc_final: 0.7021 (p-80) REVERT: I 522 ASP cc_start: 0.8565 (m-30) cc_final: 0.8226 (t0) REVERT: I 547 LEU cc_start: 0.8431 (mm) cc_final: 0.8175 (mm) REVERT: J 49 GLN cc_start: 0.8274 (pm20) cc_final: 0.7920 (pt0) REVERT: J 72 GLN cc_start: 0.7218 (mt0) cc_final: 0.6770 (tm-30) REVERT: J 168 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8299 (mmm160) REVERT: J 440 LYS cc_start: 0.8517 (mtpp) cc_final: 0.8231 (mtpp) REVERT: M 61 ASP cc_start: 0.7880 (p0) cc_final: 0.7625 (p0) REVERT: M 332 ARG cc_start: 0.7962 (ttp-170) cc_final: 0.7148 (ptm-80) REVERT: M 381 LEU cc_start: 0.6920 (tp) cc_final: 0.6583 (tt) REVERT: M 508 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6743 (pm20) REVERT: M 525 ARG cc_start: 0.7588 (ttp-170) cc_final: 0.7350 (ttp80) REVERT: M 579 PHE cc_start: 0.7219 (p90) cc_final: 0.6720 (p90) REVERT: N 40 TYR cc_start: 0.7766 (t80) cc_final: 0.7135 (t80) REVERT: N 276 SER cc_start: 0.8665 (p) cc_final: 0.8304 (m) REVERT: N 301 ARG cc_start: 0.8164 (ptm-80) cc_final: 0.7639 (tpt170) REVERT: N 302 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7783 (tptp) outliers start: 166 outliers final: 133 residues processed: 590 average time/residue: 0.2020 time to fit residues: 196.8898 Evaluate side-chains 581 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 434 time to evaluate : 1.358 ------------------------------------------------------------------------------- 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 241 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 290 MET 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 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 71 LEU Chi-restraints excluded: chain B residue 104 HIS 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 394 VAL Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 11 GLN Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 77 SER 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 189 PHE 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 234 MET 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 350 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 106 ARG Chi-restraints excluded: chain F residue 110 LEU 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 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 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 12 SER Chi-restraints excluded: chain J residue 28 THR 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 215 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 376 LEU 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 426 LEU 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 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 527 ARG 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 178 LEU Chi-restraints excluded: chain N residue 180 ILE Chi-restraints excluded: chain N residue 185 ASP 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 289 HIS Chi-restraints excluded: chain N residue 302 LYS 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 394 VAL Chi-restraints excluded: chain N residue 397 GLU Chi-restraints excluded: chain N residue 429 THR 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: 4.9990 chunk 143 optimal weight: 0.5980 chunk 315 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 29 optimal weight: 0.8980 chunk 94 optimal weight: 20.0000 chunk 307 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** E 16 ASN ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 ASN ** I 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 367 GLN ** 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 72 GLN N 289 HIS ** 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 = 0.4036 r_free = 0.4036 target = 0.152812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.121243 restraints weight = 57086.249| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.60 r_work: 0.3489 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 35670 Z= 0.131 Angle : 0.606 11.930 49080 Z= 0.313 Chirality : 0.042 0.314 5486 Planarity : 0.004 0.054 5684 Dihedral : 17.707 173.114 6497 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.82 % Allowed : 29.72 % Favored : 65.46 % 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: -0.14 (0.14), residues: 3842 helix: 0.97 (0.14), residues: 1490 sheet: -0.51 (0.19), residues: 804 loop : -0.81 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 47 TYR 0.019 0.001 TYR N 229 PHE 0.021 0.001 PHE E 287 TRP 0.030 0.001 TRP M 510 HIS 0.021 0.001 HIS N 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (35668) covalent geometry : angle 0.60620 / 0.31 (49080) hydrogen bonds : bond 0.04811 / 2.97 ( 1469) hydrogen bonds : angle 4.65134 / 3.28 ( 4142) Misc. bond : bond 0.00045 / 0.02 ( 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 613 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 452 time to evaluate : 1.289 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: 0.8906 (OUTLIER) cc_final: 0.8346 (p90) REVERT: A 22 TRP cc_start: 0.8175 (m100) cc_final: 0.7775 (m100) REVERT: A 136 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7707 (mptp) REVERT: A 213 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7920 (mm) REVERT: A 289 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8330 (tm-30) REVERT: A 319 ILE cc_start: 0.8420 (pt) cc_final: 0.8173 (pt) REVERT: A 567 PHE cc_start: 0.6163 (m-80) cc_final: 0.5628 (m-10) REVERT: A 570 GLU cc_start: 0.7814 (pm20) cc_final: 0.7523 (tm-30) REVERT: B 79 GLU cc_start: 0.8468 (mt-10) cc_final: 0.7769 (mm-30) REVERT: B 100 MET cc_start: 0.6512 (mmm) cc_final: 0.6033 (tpt) REVERT: E 16 ASN cc_start: 0.8088 (OUTLIER) cc_final: 0.7868 (p0) REVERT: E 93 PHE cc_start: 0.9041 (OUTLIER) cc_final: 0.8326 (m-80) REVERT: E 132 MET cc_start: 0.8742 (ttt) cc_final: 0.8484 (ttt) REVERT: E 194 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8657 (mt) REVERT: E 210 LYS cc_start: 0.8352 (tppt) cc_final: 0.7945 (mtmm) REVERT: E 234 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.7865 (mpp) REVERT: E 244 ASN cc_start: 0.8616 (p0) cc_final: 0.8117 (t0) REVERT: E 572 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7342 (pt0) REVERT: F 106 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7648 (mtp180) REVERT: I 206 ARG cc_start: 0.5871 (tpt90) cc_final: 0.5581 (ptt-90) REVERT: I 310 ARG cc_start: 0.6891 (ptt-90) cc_final: 0.6506 (tpt-90) REVERT: I 349 THR cc_start: 0.6854 (p) cc_final: 0.6652 (t) REVERT: I 437 HIS cc_start: 0.7293 (p-80) cc_final: 0.6998 (p-80) REVERT: I 522 ASP cc_start: 0.8557 (m-30) cc_final: 0.8219 (t0) REVERT: I 547 LEU cc_start: 0.8408 (mm) cc_final: 0.8168 (mm) REVERT: J 49 GLN cc_start: 0.8248 (pm20) cc_final: 0.7879 (pt0) REVERT: J 72 GLN cc_start: 0.7241 (mt0) cc_final: 0.6955 (tm-30) REVERT: J 192 CYS cc_start: 0.7240 (t) cc_final: 0.6897 (t) REVERT: J 440 LYS cc_start: 0.8486 (mtpp) cc_final: 0.8223 (mtpp) REVERT: M 6 ASP cc_start: 0.7109 (t0) cc_final: 0.6871 (m-30) REVERT: M 61 ASP cc_start: 0.7813 (p0) cc_final: 0.7586 (p0) REVERT: M 332 ARG cc_start: 0.7956 (ttp-170) cc_final: 0.7588 (ptm-80) REVERT: M 381 LEU cc_start: 0.6927 (tp) cc_final: 0.6594 (tt) REVERT: M 508 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6834 (pm20) REVERT: M 525 ARG cc_start: 0.7566 (ttp-170) cc_final: 0.7331 (ttp80) REVERT: M 579 PHE cc_start: 0.7182 (p90) cc_final: 0.6716 (p90) REVERT: N 276 SER cc_start: 0.8630 (p) cc_final: 0.8289 (m) REVERT: N 301 ARG cc_start: 0.8108 (ptm-80) cc_final: 0.7653 (tpt170) REVERT: N 302 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7606 (tptp) outliers start: 161 outliers final: 131 residues processed: 579 average time/residue: 0.2145 time to fit residues: 203.5561 Evaluate side-chains 572 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 429 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 HIS 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 161 VAL Chi-restraints excluded: chain A residue 206 ARG 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 289 GLU Chi-restraints excluded: chain A residue 290 MET 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 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 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 394 VAL 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 16 ASN Chi-restraints excluded: chain E residue 77 SER 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 189 PHE 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 224 SER Chi-restraints excluded: chain E residue 234 MET 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 350 LEU Chi-restraints excluded: chain E residue 417 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 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 110 LEU 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 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 375 THR Chi-restraints excluded: chain I residue 378 VAL Chi-restraints excluded: chain I residue 467 PHE Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain J residue 338 THR Chi-restraints excluded: chain J residue 345 VAL 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 424 SER Chi-restraints excluded: chain J residue 426 LEU 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 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 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 527 ARG 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 180 ILE Chi-restraints excluded: chain N residue 185 ASP 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 288 LEU Chi-restraints excluded: chain N residue 289 HIS Chi-restraints excluded: chain N residue 302 LYS Chi-restraints excluded: chain N residue 309 THR 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 466 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 365 optimal weight: 0.6980 chunk 372 optimal weight: 1.9990 chunk 315 optimal weight: 2.9990 chunk 258 optimal weight: 5.9990 chunk 392 optimal weight: 4.9990 chunk 69 optimal weight: 0.0570 chunk 399 optimal weight: 20.0000 chunk 75 optimal weight: 0.6980 chunk 118 optimal weight: 0.9980 chunk 277 optimal weight: 4.9990 chunk 353 optimal weight: 2.9990 overall best weight: 0.8900 ------------------------------------------------------------------------------- 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 ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 ASN I 133 ASN ** I 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 18 GLN ** M 244 ASN ** 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 = 0.4048 r_free = 0.4048 target = 0.153932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.122297 restraints weight = 57176.181| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.45 r_work: 0.3496 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35670 Z= 0.132 Angle : 0.613 11.904 49080 Z= 0.316 Chirality : 0.042 0.313 5486 Planarity : 0.004 0.128 5684 Dihedral : 17.694 173.095 6497 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.52 % Allowed : 30.02 % Favored : 65.46 % 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: -0.12 (0.14), residues: 3842 helix: 0.96 (0.14), residues: 1490 sheet: -0.41 (0.19), residues: 800 loop : -0.83 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG I 462 TYR 0.020 0.001 TYR N 87 PHE 0.030 0.002 PHE F 21 TRP 0.032 0.001 TRP M 510 HIS 0.011 0.001 HIS M 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (35668) covalent geometry : angle 0.61268 / 0.32 (49080) hydrogen bonds : bond 0.04775 / 2.94 ( 1469) hydrogen bonds : angle 4.64837 / 3.28 ( 4142) Misc. bond : bond 0.00052 / 0.02 ( 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 592 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 441 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 HIS cc_start: 0.8913 (OUTLIER) cc_final: 0.8329 (p90) REVERT: A 22 TRP cc_start: 0.8161 (m100) cc_final: 0.7741 (m100) REVERT: A 136 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7675 (mptp) REVERT: A 213 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7939 (mm) REVERT: A 289 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8333 (tm-30) REVERT: A 319 ILE cc_start: 0.8369 (pt) cc_final: 0.8114 (pt) REVERT: A 518 GLU cc_start: 0.8717 (pm20) cc_final: 0.8359 (pm20) REVERT: A 567 PHE cc_start: 0.6111 (m-80) cc_final: 0.5586 (m-10) REVERT: A 570 GLU cc_start: 0.7894 (pm20) cc_final: 0.7458 (tm-30) REVERT: B 79 GLU cc_start: 0.8453 (mt-10) cc_final: 0.7750 (mm-30) REVERT: B 100 MET cc_start: 0.6479 (mmm) cc_final: 0.5994 (tpt) REVERT: B 280 MET cc_start: 0.8207 (tpp) cc_final: 0.7639 (tpp) REVERT: E 93 PHE cc_start: 0.9027 (OUTLIER) cc_final: 0.8307 (m-80) REVERT: E 132 MET cc_start: 0.8717 (ttt) cc_final: 0.8503 (ttt) REVERT: E 194 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8648 (mt) REVERT: E 234 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.7903 (mpp) REVERT: E 244 ASN cc_start: 0.8618 (p0) cc_final: 0.8118 (t0) REVERT: E 572 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7328 (pt0) REVERT: F 106 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7575 (mtp180) REVERT: I 206 ARG cc_start: 0.5894 (tpt90) cc_final: 0.5603 (ptt-90) REVERT: I 310 ARG cc_start: 0.6898 (ptt-90) cc_final: 0.6484 (tpt-90) REVERT: I 522 ASP cc_start: 0.8556 (m-30) cc_final: 0.8203 (t0) REVERT: I 547 LEU cc_start: 0.8424 (mm) cc_final: 0.8180 (mm) REVERT: J 49 GLN cc_start: 0.8248 (pm20) cc_final: 0.7855 (pt0) REVERT: J 72 GLN cc_start: 0.7231 (mt0) cc_final: 0.6752 (tm-30) REVERT: J 191 GLN cc_start: 0.7113 (mt0) cc_final: 0.6346 (pp30) REVERT: J 440 LYS cc_start: 0.8465 (mtpp) cc_final: 0.8193 (mtpp) REVERT: M 6 ASP cc_start: 0.7065 (t0) cc_final: 0.6815 (m-30) REVERT: M 381 LEU cc_start: 0.6976 (tp) cc_final: 0.6573 (tt) REVERT: M 508 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6839 (pm20) REVERT: M 525 ARG cc_start: 0.7523 (ttp-170) cc_final: 0.7311 (ttp80) REVERT: N 20 LEU cc_start: 0.7543 (tt) cc_final: 0.7183 (tt) REVERT: N 40 TYR cc_start: 0.7634 (t80) cc_final: 0.7361 (t80) REVERT: N 276 SER cc_start: 0.8640 (p) cc_final: 0.8301 (m) REVERT: N 301 ARG cc_start: 0.8168 (ptm-80) cc_final: 0.7663 (tpt170) REVERT: N 302 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7790 (tptt) outliers start: 151 outliers final: 129 residues processed: 561 average time/residue: 0.2102 time to fit residues: 195.8487 Evaluate side-chains 570 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 430 time to evaluate : 1.240 ------------------------------------------------------------------------------- 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 241 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 290 MET 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 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 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 394 VAL 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 16 ASN Chi-restraints excluded: chain E residue 77 SER 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 189 PHE Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 234 MET 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 350 LEU Chi-restraints excluded: chain E residue 417 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 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 110 LEU 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 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 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 375 THR Chi-restraints excluded: chain I residue 467 PHE Chi-restraints excluded: chain I residue 474 ILE Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain J residue 338 THR Chi-restraints excluded: chain J residue 345 VAL 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 424 SER 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 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 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 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 N residue 28 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 180 ILE Chi-restraints excluded: chain N residue 185 ASP 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 288 LEU Chi-restraints excluded: chain N residue 289 HIS Chi-restraints excluded: chain N residue 302 LYS Chi-restraints excluded: chain N residue 309 THR 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 466 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 296 optimal weight: 0.6980 chunk 169 optimal weight: 2.9990 chunk 339 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 chunk 387 optimal weight: 0.8980 chunk 153 optimal weight: 0.9980 chunk 313 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 342 optimal weight: 0.0070 chunk 188 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 437 HIS ** J 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 244 ASN ** 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 = 0.4050 r_free = 0.4050 target = 0.154224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.121673 restraints weight = 56980.254| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.68 r_work: 0.3486 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.214 35670 Z= 0.171 Angle : 0.709 59.182 49080 Z= 0.385 Chirality : 0.043 0.730 5486 Planarity : 0.004 0.121 5684 Dihedral : 17.694 173.101 6495 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.37 % Favored : 95.60 % Rotamer: Outliers : 4.37 % Allowed : 30.05 % Favored : 65.58 % Cbeta Deviations : 0.03 % 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: -0.12 (0.14), residues: 3842 helix: 0.96 (0.14), residues: 1490 sheet: -0.40 (0.19), residues: 800 loop : -0.83 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG I 462 TYR 0.017 0.001 TYR N 87 PHE 0.025 0.001 PHE F 21 TRP 0.028 0.001 TRP M 510 HIS 0.010 0.001 HIS M 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.17 (35668) covalent geometry : angle 0.70861 / 0.38 (49080) hydrogen bonds : bond 0.04797 / 2.97 ( 1469) hydrogen bonds : angle 4.65239 / 3.29 ( 4142) Misc. bond : bond 0.00048 / 0.02 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8403.11 seconds wall clock time: 145 minutes 15.78 seconds (8715.78 seconds total)