Starting phenix.real_space_refine on Mon Aug 25 23:10:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j7s_36047/08_2025/8j7s_36047.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j7s_36047/08_2025/8j7s_36047.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8j7s_36047/08_2025/8j7s_36047.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j7s_36047/08_2025/8j7s_36047.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j7s_36047/08_2025/8j7s_36047.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j7s_36047/08_2025/8j7s_36047.map" } resolution = 2.84 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= -0.001 sd= 0.036 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: 5 Type Number sf(0) Gaussians P 163 5.49 5 S 92 5.16 5 C 20019 2.51 5 N 5322 2.21 5 O 6216 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31812 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3634 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 22, 'TRANS': 431} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 3479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3479 Classifications: {'peptide': 418} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 406} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 399 Classifications: {'RNA': 19} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 7, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 17} Chain: "D" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 413 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "E" Number of atoms: 3636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3636 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 22, 'TRANS': 431} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 31 Chain: "F" Number of atoms: 3475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3475 Classifications: {'peptide': 418} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 406} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 399 Classifications: {'RNA': 19} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 7, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 17} Chain: "H" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 433 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "I" Number of atoms: 3633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3633 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 22, 'TRANS': 431} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 34 Chain: "J" Number of atoms: 3461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3461 Classifications: {'peptide': 418} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 406} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "K" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 399 Classifications: {'RNA': 19} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 7, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 17} Chain: "L" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 454 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "M" Number of atoms: 3629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3629 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 22, 'TRANS': 431} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 2, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 38 Chain: "N" Number of atoms: 3472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3472 Classifications: {'peptide': 418} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 406} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 6 Chain: "O" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 399 Classifications: {'RNA': 19} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 7, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 17} Chain: "P" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 497 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Residues with excluded nonbonded symmetry interactions: 16 residue: pdb=" N PHE A 238 " occ=0.23 ... (9 atoms not shown) pdb=" CZ PHE A 238 " occ=0.02 residue: pdb=" N GLY A 239 " occ=0.32 ... (2 atoms not shown) pdb=" O GLY A 239 " occ=0.20 residue: pdb=" N MET B 193 " occ=0.66 ... (6 atoms not shown) pdb=" CE MET B 193 " occ=0.35 residue: pdb=" N PRO B 195 " occ=0.13 ... (5 atoms not shown) pdb=" CD PRO B 195 " occ=0.77 residue: pdb=" N ASP B 199 " occ=0.47 ... (6 atoms not shown) pdb=" OD2 ASP B 199 " occ=0.87 residue: pdb=" N GLU B 296 " occ=0.63 ... (7 atoms not shown) pdb=" OE2 GLU B 296 " occ=0.57 residue: pdb=" N ASP B 346 " occ=0.92 ... (6 atoms not shown) pdb=" OD2 ASP B 346 " occ=0.55 residue: pdb=" N GLY B 396 " occ=0.26 ... (2 atoms not shown) pdb=" O GLY B 396 " occ=0.38 residue: pdb=" N GLY E 102 " occ=0.54 ... (2 atoms not shown) pdb=" O GLY E 102 " occ=0.07 residue: pdb=" N ALA E 237 " occ=0.11 ... (3 atoms not shown) pdb=" CB ALA E 237 " occ=0.21 residue: pdb=" N GLY E 239 " occ=0.29 ... (2 atoms not shown) pdb=" O GLY E 239 " occ=0.74 residue: pdb=" N SER F 250 " occ=0.67 ... (4 atoms not shown) pdb=" OG SER F 250 " occ=0.09 ... (remaining 4 not shown) Time building chain proxies: 8.63, per 1000 atoms: 0.27 Number of scatterers: 31812 At special positions: 0 Unit cell: (134.662, 171.291, 225.156, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 92 16.00 P 163 15.00 O 6216 8.00 N 5322 7.00 C 20019 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=0, symmetry=0 Time building additional restraints: 2.90 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 715.3 nanoseconds 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6640 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 36 sheets defined 35.4% alpha, 14.5% beta 58 base pairs and 108 stacking pairs defined. Time for finding SS restraints: 3.93 Creating SS restraints... Processing helix chain 'A' and resid 22 through 31 Processing helix chain 'A' and resid 46 through 60 Processing helix chain 'A' and resid 77 through 83 Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.652A pdb=" N ILE A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 106 Processing helix chain 'A' and resid 110 through 131 Processing helix chain 'A' and resid 206 through 214 Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 248 through 264 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.558A pdb=" N GLN A 349 " --> pdb=" O SER A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 377 Processing helix chain 'A' and resid 451 through 462 Processing helix chain 'A' and resid 477 through 491 removed outlier: 3.520A pdb=" N ARG A 481 " --> pdb=" O PRO A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'B' and resid 14 through 29 Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'B' and resid 44 through 56 Processing helix chain 'B' and resid 71 through 89 Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing helix chain 'B' and resid 123 through 139 removed outlier: 3.687A pdb=" N GLY B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 219 through 224 removed outlier: 4.057A pdb=" N PHE B 223 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR B 224 " --> pdb=" O TYR B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 233 removed outlier: 4.109A pdb=" N THR B 232 " --> pdb=" O LYS B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 247 Processing helix chain 'B' and resid 257 through 277 removed outlier: 3.664A pdb=" N MET B 277 " --> pdb=" O PHE B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 365 Processing helix chain 'B' and resid 369 through 384 removed outlier: 3.596A pdb=" N LEU B 384 " --> pdb=" O PHE B 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 17 No H-bonds generated for 'chain 'E' and resid 15 through 17' Processing helix chain 'E' and resid 22 through 30 Processing helix chain 'E' and resid 46 through 60 Processing helix chain 'E' and resid 77 through 83 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.559A pdb=" N GLY E 90 " --> pdb=" O GLU E 87 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 91' Processing helix chain 'E' and resid 97 through 106 removed outlier: 3.661A pdb=" N ILE E 101 " --> pdb=" O THR E 97 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE E 104 " --> pdb=" O ASP E 100 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 131 Processing helix chain 'E' and resid 206 through 214 Processing helix chain 'E' and resid 226 through 230 Processing helix chain 'E' and resid 248 through 264 Processing helix chain 'E' and resid 331 through 351 removed outlier: 4.239A pdb=" N GLN E 349 " --> pdb=" O SER E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 376 removed outlier: 3.614A pdb=" N VAL E 376 " --> pdb=" O ALA E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 462 Processing helix chain 'E' and resid 477 through 491 Processing helix chain 'E' and resid 502 through 506 Processing helix chain 'F' and resid 14 through 28 Processing helix chain 'F' and resid 45 through 56 Processing helix chain 'F' and resid 71 through 89 Processing helix chain 'F' and resid 109 through 113 Processing helix chain 'F' and resid 123 through 138 Processing helix chain 'F' and resid 146 through 158 removed outlier: 4.268A pdb=" N SER F 150 " --> pdb=" O ASP F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 233 removed outlier: 4.007A pdb=" N GLU F 231 " --> pdb=" O PRO F 228 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR F 232 " --> pdb=" O LYS F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 249 Processing helix chain 'F' and resid 257 through 279 removed outlier: 3.753A pdb=" N LYS F 278 " --> pdb=" O GLU F 274 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP F 279 " --> pdb=" O LEU F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 365 Processing helix chain 'F' and resid 369 through 385 removed outlier: 3.662A pdb=" N LEU F 384 " --> pdb=" O PHE F 380 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER F 385 " --> pdb=" O ILE F 381 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 31 removed outlier: 3.615A pdb=" N GLY I 26 " --> pdb=" O ASP I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 62 removed outlier: 3.897A pdb=" N LYS I 62 " --> pdb=" O ASP I 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 83 Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'I' and resid 97 through 106 removed outlier: 3.555A pdb=" N PHE I 104 " --> pdb=" O ASP I 100 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR I 106 " --> pdb=" O GLY I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 110 through 131 Processing helix chain 'I' and resid 206 through 213 Processing helix chain 'I' and resid 226 through 230 Processing helix chain 'I' and resid 248 through 264 Processing helix chain 'I' and resid 331 through 351 removed outlier: 3.685A pdb=" N GLN I 349 " --> pdb=" O SER I 345 " (cutoff:3.500A) Processing helix chain 'I' and resid 366 through 377 removed outlier: 3.729A pdb=" N VAL I 376 " --> pdb=" O ALA I 372 " (cutoff:3.500A) Processing helix chain 'I' and resid 451 through 462 Processing helix chain 'I' and resid 477 through 491 removed outlier: 3.578A pdb=" N ARG I 481 " --> pdb=" O PRO I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 502 through 506 Processing helix chain 'J' and resid 14 through 29 Processing helix chain 'J' and resid 44 through 56 Processing helix chain 'J' and resid 71 through 89 Processing helix chain 'J' and resid 109 through 113 Processing helix chain 'J' and resid 123 through 139 Processing helix chain 'J' and resid 149 through 157 removed outlier: 4.024A pdb=" N LEU J 153 " --> pdb=" O LYS J 149 " (cutoff:3.500A) Processing helix chain 'J' and resid 199 through 203 removed outlier: 3.769A pdb=" N GLU J 202 " --> pdb=" O ASP J 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 231 removed outlier: 3.786A pdb=" N THR J 230 " --> pdb=" O LEU J 227 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU J 231 " --> pdb=" O PRO J 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 227 through 231' Processing helix chain 'J' and resid 257 through 277 Processing helix chain 'J' and resid 353 through 365 Processing helix chain 'J' and resid 369 through 384 removed outlier: 3.512A pdb=" N TRP J 373 " --> pdb=" O TRP J 369 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU J 384 " --> pdb=" O PHE J 380 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 17 No H-bonds generated for 'chain 'M' and resid 15 through 17' Processing helix chain 'M' and resid 22 through 30 Processing helix chain 'M' and resid 46 through 60 Processing helix chain 'M' and resid 77 through 83 Processing helix chain 'M' and resid 87 through 89 No H-bonds generated for 'chain 'M' and resid 87 through 89' Processing helix chain 'M' and resid 97 through 106 removed outlier: 3.819A pdb=" N PHE M 104 " --> pdb=" O ASP M 100 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 131 removed outlier: 3.784A pdb=" N THR M 114 " --> pdb=" O THR M 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 206 through 213 Processing helix chain 'M' and resid 226 through 230 Processing helix chain 'M' and resid 248 through 264 Processing helix chain 'M' and resid 331 through 351 removed outlier: 3.708A pdb=" N GLN M 349 " --> pdb=" O SER M 345 " (cutoff:3.500A) Processing helix chain 'M' and resid 366 through 376 Processing helix chain 'M' and resid 427 through 430 Processing helix chain 'M' and resid 451 through 463 Processing helix chain 'M' and resid 477 through 491 removed outlier: 3.533A pdb=" N THR M 491 " --> pdb=" O GLY M 487 " (cutoff:3.500A) Processing helix chain 'M' and resid 502 through 506 Processing helix chain 'N' and resid 14 through 28 Processing helix chain 'N' and resid 45 through 56 Processing helix chain 'N' and resid 71 through 89 Processing helix chain 'N' and resid 123 through 138 Processing helix chain 'N' and resid 146 through 158 removed outlier: 4.144A pdb=" N SER N 150 " --> pdb=" O ASP N 146 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 233 removed outlier: 3.585A pdb=" N GLU N 231 " --> pdb=" O PRO N 228 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR N 233 " --> pdb=" O THR N 230 " (cutoff:3.500A) Processing helix chain 'N' and resid 257 through 278 removed outlier: 3.603A pdb=" N CYS N 261 " --> pdb=" O ARG N 257 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS N 262 " --> pdb=" O ASN N 258 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG N 263 " --> pdb=" O ALA N 259 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS N 278 " --> pdb=" O GLU N 274 " (cutoff:3.500A) Processing helix chain 'N' and resid 353 through 366 removed outlier: 3.600A pdb=" N LYS N 366 " --> pdb=" O ARG N 362 " (cutoff:3.500A) Processing helix chain 'N' and resid 369 through 384 removed outlier: 3.798A pdb=" N TRP N 373 " --> pdb=" O TRP N 369 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 removed outlier: 6.337A pdb=" N LYS A 2 " --> pdb=" O LYS B 411 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 5 through 6 removed outlier: 4.925A pdb=" N VAL A 412 " --> pdb=" O PHE A 419 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N PHE A 419 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER A 417 " --> pdb=" O ASN A 414 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ILE A 443 " --> pdb=" O SER A 389 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N SER A 389 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ILE A 445 " --> pdb=" O THR A 387 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N THR A 387 " --> pdb=" O ILE A 445 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL A 357 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL A 386 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE A 359 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ILE A 388 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ALA A 361 " --> pdb=" O ILE A 388 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA4, first strand: chain 'A' and resid 92 through 95 removed outlier: 6.439A pdb=" N GLY A 42 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ILE A 142 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE A 44 " --> pdb=" O ILE A 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 397 through 398 Processing sheet with id=AA6, first strand: chain 'A' and resid 425 through 426 removed outlier: 3.753A pdb=" N THR A 431 " --> pdb=" O VAL A 426 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 31 through 33 removed outlier: 6.571A pdb=" N LYS B 4 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LEU B 61 " --> pdb=" O LYS B 4 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N PHE B 6 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL B 63 " --> pdb=" O PHE B 6 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N SER B 8 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N ILE B 118 " --> pdb=" O ILE B 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 175 through 179 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 175 through 179 current: chain 'B' and resid 291 through 294 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 291 through 294 current: chain 'B' and resid 318 through 328 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 334 through 344 current: chain 'B' and resid 400 through 404 Processing sheet with id=AA9, first strand: chain 'B' and resid 208 through 209 Processing sheet with id=AB1, first strand: chain 'E' and resid 2 through 3 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 2 through 3 current: chain 'F' and resid 169 through 179 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 169 through 179 current: chain 'F' and resid 291 through 294 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 291 through 294 current: chain 'F' and resid 318 through 328 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 334 through 344 current: chain 'F' and resid 400 through 412 Processing sheet with id=AB2, first strand: chain 'E' and resid 5 through 6 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 5 through 6 current: chain 'E' and resid 297 through 305 removed outlier: 3.751A pdb=" N LEU E 305 " --> pdb=" O VAL E 312 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL E 312 " --> pdb=" O LEU E 305 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 312 through 313 current: chain 'E' and resid 382 through 389 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 382 through 389 current: chain 'E' and resid 417 through 420 Processing sheet with id=AB3, first strand: chain 'E' and resid 18 through 20 removed outlier: 3.534A pdb=" N GLN E 18 " --> pdb=" O PHE E 14 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 94 through 95 removed outlier: 7.863A pdb=" N LYS E 94 " --> pdb=" O SER E 41 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL E 43 " --> pdb=" O LYS E 94 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLY E 42 " --> pdb=" O PHE E 140 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ILE E 142 " --> pdb=" O GLY E 42 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE E 44 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N TRP E 139 " --> pdb=" O GLN E 222 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N PHE E 224 " --> pdb=" O TRP E 139 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N VAL E 141 " --> pdb=" O PHE E 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'E' and resid 425 through 426 Processing sheet with id=AB6, first strand: chain 'F' and resid 32 through 33 removed outlier: 7.115A pdb=" N LYS F 4 " --> pdb=" O CYS F 58 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N PHE F 60 " --> pdb=" O LYS F 4 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N PHE F 6 " --> pdb=" O PHE F 60 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N LEU F 62 " --> pdb=" O PHE F 6 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N SER F 8 " --> pdb=" O LEU F 62 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N SER F 64 " --> pdb=" O SER F 8 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ILE F 95 " --> pdb=" O CYS F 58 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N PHE F 60 " --> pdb=" O ILE F 95 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LEU F 97 " --> pdb=" O PHE F 60 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU F 62 " --> pdb=" O LEU F 97 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N ILE F 118 " --> pdb=" O ILE F 94 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 208 through 209 Processing sheet with id=AB8, first strand: chain 'I' and resid 2 through 3 removed outlier: 5.800A pdb=" N LYS I 2 " --> pdb=" O LYS J 411 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 5 through 6 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 5 through 6 current: chain 'I' and resid 297 through 305 removed outlier: 3.631A pdb=" N VAL I 312 " --> pdb=" O LEU I 305 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 312 through 313 current: chain 'I' and resid 382 through 389 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 382 through 389 current: chain 'I' and resid 417 through 420 Processing sheet with id=AC1, first strand: chain 'I' and resid 19 through 20 removed outlier: 3.544A pdb=" N LYS I 270 " --> pdb=" O LEU I 13 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 92 through 95 removed outlier: 6.044A pdb=" N GLY I 42 " --> pdb=" O PHE I 140 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ILE I 142 " --> pdb=" O GLY I 42 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE I 44 " --> pdb=" O ILE I 142 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TRP I 139 " --> pdb=" O GLN I 222 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N PHE I 224 " --> pdb=" O TRP I 139 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL I 141 " --> pdb=" O PHE I 224 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 425 through 426 removed outlier: 3.579A pdb=" N THR I 431 " --> pdb=" O VAL I 426 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 31 through 33 removed outlier: 6.997A pdb=" N LYS J 4 " --> pdb=" O LYS J 59 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N LEU J 61 " --> pdb=" O LYS J 4 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N PHE J 6 " --> pdb=" O LEU J 61 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N VAL J 63 " --> pdb=" O PHE J 6 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N SER J 8 " --> pdb=" O VAL J 63 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N ILE J 95 " --> pdb=" O CYS J 58 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N PHE J 60 " --> pdb=" O ILE J 95 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LEU J 97 " --> pdb=" O PHE J 60 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU J 62 " --> pdb=" O LEU J 97 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 175 through 177 Processing sheet with id=AC6, first strand: chain 'J' and resid 208 through 209 removed outlier: 4.096A pdb=" N VAL J 208 " --> pdb=" O CYS J 215 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N CYS J 215 " --> pdb=" O VAL J 208 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 283 through 286 Processing sheet with id=AC8, first strand: chain 'J' and resid 390 through 394 Processing sheet with id=AC9, first strand: chain 'M' and resid 2 through 3 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 2 through 3 current: chain 'N' and resid 169 through 179 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 169 through 179 current: chain 'N' and resid 318 through 328 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 334 through 344 current: chain 'N' and resid 400 through 412 Processing sheet with id=AD1, first strand: chain 'M' and resid 5 through 6 Processing sheet with id=AD2, first strand: chain 'M' and resid 18 through 20 removed outlier: 3.619A pdb=" N GLN M 18 " --> pdb=" O PHE M 14 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 91 through 95 removed outlier: 7.132A pdb=" N SER M 41 " --> pdb=" O THR M 92 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N LYS M 94 " --> pdb=" O SER M 41 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL M 43 " --> pdb=" O LYS M 94 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLY M 42 " --> pdb=" O PHE M 140 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE M 142 " --> pdb=" O GLY M 42 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE M 44 " --> pdb=" O ILE M 142 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N TRP M 139 " --> pdb=" O GLN M 222 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N PHE M 224 " --> pdb=" O TRP M 139 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL M 141 " --> pdb=" O PHE M 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'M' and resid 278 through 287 removed outlier: 3.614A pdb=" N VAL M 312 " --> pdb=" O LEU M 305 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 312 through 313 current: chain 'M' and resid 382 through 389 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 382 through 389 current: chain 'M' and resid 441 through 447 Processing sheet with id=AD5, first strand: chain 'M' and resid 425 through 426 removed outlier: 3.670A pdb=" N THR M 431 " --> pdb=" O VAL M 426 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 32 through 33 removed outlier: 6.300A pdb=" N ILE N 5 " --> pdb=" O TRP N 33 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LYS N 4 " --> pdb=" O LYS N 59 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N LEU N 61 " --> pdb=" O LYS N 4 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N PHE N 6 " --> pdb=" O LEU N 61 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N VAL N 63 " --> pdb=" O PHE N 6 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N SER N 8 " --> pdb=" O VAL N 63 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ILE N 95 " --> pdb=" O CYS N 58 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N PHE N 60 " --> pdb=" O ILE N 95 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LEU N 97 " --> pdb=" O PHE N 60 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU N 62 " --> pdb=" O LEU N 97 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 164 through 165 Processing sheet with id=AD8, first strand: chain 'N' and resid 208 through 209 Processing sheet with id=AD9, first strand: chain 'N' and resid 283 through 286 996 hydrogen bonds defined for protein. 2796 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 140 hydrogen bonds 280 hydrogen bond angles 0 basepair planarities 58 basepair parallelities 108 stacking parallelities Total time for adding SS restraints: 6.63 Time building geometry restraints manager: 3.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9154 1.34 - 1.46: 7889 1.46 - 1.58: 15426 1.58 - 1.70: 319 1.70 - 1.82: 140 Bond restraints: 32928 Sorted by residual: bond pdb=" CB PRO M 378 " pdb=" CG PRO M 378 " ideal model delta sigma weight residual 1.492 1.666 -0.174 5.00e-02 4.00e+02 1.21e+01 bond pdb=" C2' U K 1 " pdb=" O2' U K 1 " ideal model delta sigma weight residual 1.412 1.381 0.031 1.50e-02 4.44e+03 4.19e+00 bond pdb=" C2' U C 1 " pdb=" O2' U C 1 " ideal model delta sigma weight residual 1.412 1.441 -0.029 1.50e-02 4.44e+03 3.76e+00 bond pdb=" CG1 ILE J 265 " pdb=" CD1 ILE J 265 " ideal model delta sigma weight residual 1.513 1.457 0.056 3.90e-02 6.57e+02 2.05e+00 bond pdb=" CB GLU E 415 " pdb=" CG GLU E 415 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.78e+00 ... (remaining 32923 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 44894 2.94 - 5.88: 278 5.88 - 8.83: 43 8.83 - 11.77: 8 11.77 - 14.71: 5 Bond angle restraints: 45228 Sorted by residual: angle pdb=" CA PRO M 378 " pdb=" N PRO M 378 " pdb=" CD PRO M 378 " ideal model delta sigma weight residual 112.00 97.29 14.71 1.40e+00 5.10e-01 1.10e+02 angle pdb=" C3' U C 1 " pdb=" C2' U C 1 " pdb=" O2' U C 1 " ideal model delta sigma weight residual 114.60 106.38 8.22 1.50e+00 4.44e-01 3.00e+01 angle pdb=" CB MET A 1 " pdb=" CG MET A 1 " pdb=" SD MET A 1 " ideal model delta sigma weight residual 112.70 125.85 -13.15 3.00e+00 1.11e-01 1.92e+01 angle pdb=" CA GLU J 274 " pdb=" CB GLU J 274 " pdb=" CG GLU J 274 " ideal model delta sigma weight residual 114.10 122.35 -8.25 2.00e+00 2.50e-01 1.70e+01 angle pdb=" CB ARG B 257 " pdb=" CG ARG B 257 " pdb=" CD ARG B 257 " ideal model delta sigma weight residual 111.30 120.60 -9.30 2.30e+00 1.89e-01 1.63e+01 ... (remaining 45223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.89: 18175 33.89 - 67.78: 1284 67.78 - 101.66: 77 101.66 - 135.55: 1 135.55 - 169.44: 11 Dihedral angle restraints: 19548 sinusoidal: 9278 harmonic: 10270 Sorted by residual: dihedral pdb=" O4' U K 15 " pdb=" C1' U K 15 " pdb=" N1 U K 15 " pdb=" C2 U K 15 " ideal model delta sinusoidal sigma weight residual -160.00 9.44 -169.44 1 1.50e+01 4.44e-03 8.46e+01 dihedral pdb=" O4' U C 15 " pdb=" C1' U C 15 " pdb=" N1 U C 15 " pdb=" C2 U C 15 " ideal model delta sinusoidal sigma weight residual -160.00 6.92 -166.92 1 1.50e+01 4.44e-03 8.42e+01 dihedral pdb=" O4' U G 15 " pdb=" C1' U G 15 " pdb=" N1 U G 15 " pdb=" C2 U G 15 " ideal model delta sinusoidal sigma weight residual 200.00 44.25 155.75 1 1.50e+01 4.44e-03 8.16e+01 ... (remaining 19545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 4304 0.060 - 0.119: 615 0.119 - 0.179: 53 0.179 - 0.238: 5 0.238 - 0.298: 3 Chirality restraints: 4980 Sorted by residual: chirality pdb=" C2' U C 1 " pdb=" C3' U C 1 " pdb=" O2' U C 1 " pdb=" C1' U C 1 " both_signs ideal model delta sigma weight residual False -2.52 -2.82 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CG LEU J 264 " pdb=" CB LEU J 264 " pdb=" CD1 LEU J 264 " pdb=" CD2 LEU J 264 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CB ILE N 323 " pdb=" CA ILE N 323 " pdb=" CG1 ILE N 323 " pdb=" CG2 ILE N 323 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 4977 not shown) Planarity restraints: 5118 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR M 377 " -0.085 5.00e-02 4.00e+02 1.19e-01 2.25e+01 pdb=" N PRO M 378 " 0.204 5.00e-02 4.00e+02 pdb=" CA PRO M 378 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO M 378 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E 392 " 0.043 5.00e-02 4.00e+02 6.63e-02 7.02e+00 pdb=" N PRO E 393 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO E 393 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO E 393 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 181 " 0.040 5.00e-02 4.00e+02 6.06e-02 5.88e+00 pdb=" N PRO B 182 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 182 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 182 " 0.034 5.00e-02 4.00e+02 ... (remaining 5115 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1649 2.72 - 3.26: 30702 3.26 - 3.81: 54655 3.81 - 4.35: 67581 4.35 - 4.90: 109555 Nonbonded interactions: 264142 Sorted by model distance: nonbonded pdb=" OH TYR J 221 " pdb=" O TYR J 233 " model vdw 2.173 3.040 nonbonded pdb=" OH TYR N 221 " pdb=" O TYR N 233 " model vdw 2.197 3.040 nonbonded pdb=" OE2 GLU J 281 " pdb=" OH TYR J 383 " model vdw 2.212 3.040 nonbonded pdb=" OG1 THR E 463 " pdb=" O ASP E 474 " model vdw 2.216 3.040 nonbonded pdb=" N GLU E 99 " pdb=" OE1 GLU E 99 " model vdw 2.218 3.120 ... (remaining 264137 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 136 or (resid 137 and (name N or name CA or name \ C or name O or name CB )) or resid 138 through 306 or (resid 307 and (name N or \ name CA or name C or name O or name CB )) or resid 308 or (resid 309 and (name \ N or name CA or name C or name O or name CB )) or resid 310 through 321 or (resi \ d 322 and (name N or name CA or name C or name O or name CB )) or resid 323 thro \ ugh 399 or (resid 400 and (name N or name CA or name C or name O or name CB )) o \ r resid 401 through 506)) selection = (chain 'E' and (resid 1 through 136 or (resid 137 and (name N or name CA or name \ C or name O or name CB )) or resid 138 through 257 or (resid 258 through 260 an \ d (name N or name CA or name C or name O or name CB )) or resid 261 through 306 \ or (resid 307 and (name N or name CA or name C or name O or name CB )) or resid \ 308 or (resid 309 and (name N or name CA or name C or name O or name CB )) or re \ sid 310 through 321 or (resid 322 and (name N or name CA or name C or name O or \ name CB )) or resid 323 through 399 or (resid 400 and (name N or name CA or name \ C or name O or name CB )) or resid 401 through 506)) selection = (chain 'I' and (resid 1 through 132 or (resid 133 and (name N or name CA or name \ C or name O or name CB )) or resid 134 through 257 or (resid 258 through 260 an \ d (name N or name CA or name C or name O or name CB )) or resid 261 through 306 \ or (resid 307 and (name N or name CA or name C or name O or name CB )) or resid \ 308 through 321 or (resid 322 and (name N or name CA or name C or name O or name \ CB )) or resid 323 through 399 or (resid 400 and (name N or name CA or name C o \ r name O or name CB )) or resid 401 through 506)) selection = (chain 'M' and (resid 1 through 132 or (resid 133 and (name N or name CA or name \ C or name O or name CB )) or resid 134 through 136 or (resid 137 and (name N or \ name CA or name C or name O or name CB )) or resid 138 through 257 or (resid 25 \ 8 through 260 and (name N or name CA or name C or name O or name CB )) or resid \ 261 through 308 or (resid 309 and (name N or name CA or name C or name O or name \ CB )) or resid 310 through 506)) } ncs_group { reference = (chain 'B' and (resid 1 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 108 or (resid 109 and (name N or \ name CA or name C or name O or name CB )) or resid 110 through 125 or (resid 126 \ and (name N or name CA or name C or name O or name CB )) or resid 127 through 1 \ 64 or (resid 165 and (name N or name CA or name C or name O or name CB )) or res \ id 166 through 220 or (resid 221 and (name N or name CA or name C or name O or n \ ame CB )) or resid 222 through 316 or (resid 317 and (name N or name CA or name \ C or name O or name CB )) or resid 318 through 370 or (resid 371 and (name N or \ name CA or name C or name O or name CB )) or resid 372 through 415 or (resid 416 \ and (name N or name CA or name C or name O or name CB )) or resid 417 through 4 \ 18)) selection = (chain 'F' and (resid 1 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 99 or (resid 100 and (name N or nam \ e CA or name C or name O or name CB )) or resid 101 through 108 or (resid 109 an \ d (name N or name CA or name C or name O or name CB )) or resid 110 through 125 \ or (resid 126 and (name N or name CA or name C or name O or name CB )) or resid \ 127 through 147 or (resid 148 and (name N or name CA or name C or name O or name \ CB )) or resid 149 through 164 or (resid 165 and (name N or name CA or name C o \ r name O or name CB )) or resid 166 through 316 or (resid 317 and (name N or nam \ e CA or name C or name O or name CB )) or resid 318 through 370 or (resid 371 an \ d (name N or name CA or name C or name O or name CB )) or resid 372 through 415 \ or (resid 416 and (name N or name CA or name C or name O or name CB )) or resid \ 417 through 418)) selection = (chain 'J' and (resid 1 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 147 or (resid 148 and (name N or \ name CA or name C or name O or name CB )) or resid 149 through 220 or (resid 221 \ and (name N or name CA or name C or name O or name CB )) or resid 222 through 3 \ 16 or (resid 317 and (name N or name CA or name C or name O or name CB )) or res \ id 318 through 370 or (resid 371 and (name N or name CA or name C or name O or n \ ame CB )) or resid 372 through 418)) selection = (chain 'N' and (resid 1 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 108 or (resid 109 and (name N or na \ me CA or name C or name O or name CB )) or resid 110 through 125 or (resid 126 a \ nd (name N or name CA or name C or name O or name CB )) or resid 127 through 147 \ or (resid 148 and (name N or name CA or name C or name O or name CB )) or resid \ 149 through 164 or (resid 165 and (name N or name CA or name C or name O or nam \ e CB )) or resid 166 through 220 or (resid 221 and (name N or name CA or name C \ or name O or name CB )) or resid 222 through 415 or (resid 416 and (name N or na \ me CA or name C or name O or name CB )) or resid 417 through 418)) } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' selection = chain 'O' } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 8 through 27) selection = (chain 'L' and resid 8 through 27) } 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=0.01 max=1.00 mean=0.91 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: 4.030 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: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 33.090 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 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 : 0.003 0.174 32928 Z= 0.141 Angle : 0.659 14.711 45228 Z= 0.345 Chirality : 0.042 0.298 4980 Planarity : 0.004 0.119 5118 Dihedral : 20.376 169.439 12908 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.90 % Favored : 93.07 % Rotamer: Outliers : 4.65 % Allowed : 29.35 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.14), residues: 3464 helix: 0.84 (0.16), residues: 1132 sheet: -0.84 (0.21), residues: 590 loop : -1.83 (0.14), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG B 257 TYR 0.020 0.001 TYR A 411 PHE 0.023 0.001 PHE N 17 TRP 0.039 0.001 TRP F 219 HIS 0.007 0.001 HIS N 340 Details of bonding type rmsd covalent geometry : bond 0.00322 (32928) covalent geometry : angle 0.65875 (45228) hydrogen bonds : bond 0.14421 ( 1136) hydrogen bonds : angle 6.03803 ( 3076) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 294 time to evaluate : 1.121 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 358 PHE cc_start: 0.8636 (m-80) cc_final: 0.8432 (m-10) REVERT: A 484 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7448 (OUTLIER) REVERT: B 167 LYS cc_start: 0.7632 (OUTLIER) cc_final: 0.7351 (mtmm) REVERT: B 227 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8178 (mt) REVERT: F 309 MET cc_start: 0.5347 (tmm) cc_final: 0.5113 (tmm) REVERT: J 287 MET cc_start: 0.5705 (mmp) cc_final: 0.5465 (mmm) REVERT: M 399 THR cc_start: 0.7072 (OUTLIER) cc_final: 0.6652 (p) REVERT: N 223 PHE cc_start: 0.4722 (m-80) cc_final: 0.4437 (m-10) outliers start: 143 outliers final: 74 residues processed: 424 average time/residue: 0.5746 time to fit residues: 295.3158 Evaluate side-chains 249 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 172 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 303 MET Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 486 ILE Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 191 ASN Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 413 ASN Chi-restraints excluded: chain F residue 414 VAL Chi-restraints excluded: chain I residue 16 HIS Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 219 ILE Chi-restraints excluded: chain I residue 221 THR Chi-restraints excluded: chain I residue 232 ARG Chi-restraints excluded: chain I residue 255 THR Chi-restraints excluded: chain I residue 257 SER Chi-restraints excluded: chain I residue 274 VAL Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain I residue 387 THR Chi-restraints excluded: chain I residue 399 THR Chi-restraints excluded: chain I residue 413 VAL Chi-restraints excluded: chain I residue 498 THR Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 112 ILE Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 318 ASN Chi-restraints excluded: chain J residue 324 SER Chi-restraints excluded: chain J residue 415 SER Chi-restraints excluded: chain M residue 41 SER Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain M residue 399 THR Chi-restraints excluded: chain M residue 422 THR Chi-restraints excluded: chain M residue 423 VAL Chi-restraints excluded: chain M residue 470 CYS Chi-restraints excluded: chain M residue 486 ILE Chi-restraints excluded: chain M residue 498 THR Chi-restraints excluded: chain N residue 40 ASP Chi-restraints excluded: chain N residue 389 THR Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 414 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.2980 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 4.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 HIS ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 217 HIS ** F 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 129 ASN ** I 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 155 GLN ** J 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 357 GLN ** J 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 160 HIS ** N 314 GLN ** 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 = 0.4255 r_free = 0.4255 target = 0.085059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.066427 restraints weight = 143167.268| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 4.05 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3690 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3690 r_free = 0.3690 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 355 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3613 r_free = 0.3613 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1059 | |-----------------------------------------------------------------------------| r_final: 0.3613 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 32928 Z= 0.198 Angle : 0.667 10.882 45228 Z= 0.351 Chirality : 0.043 0.317 4980 Planarity : 0.004 0.065 5118 Dihedral : 18.720 169.877 6021 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.96 % Favored : 92.93 % Rotamer: Outliers : 6.44 % Allowed : 27.01 % Favored : 66.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.14), residues: 3464 helix: 0.97 (0.16), residues: 1160 sheet: -0.86 (0.21), residues: 604 loop : -1.71 (0.14), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 257 TYR 0.018 0.001 TYR J 221 PHE 0.022 0.002 PHE A 304 TRP 0.022 0.001 TRP F 219 HIS 0.019 0.001 HIS J 188 Details of bonding type rmsd covalent geometry : bond 0.00432 (32928) covalent geometry : angle 0.66672 (45228) hydrogen bonds : bond 0.04529 ( 1136) hydrogen bonds : angle 4.93276 ( 3076) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 195 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASP cc_start: 0.9184 (m-30) cc_final: 0.8938 (m-30) REVERT: A 85 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8725 (mtmp) REVERT: B 86 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8812 (mtmm) REVERT: B 138 GLN cc_start: 0.6247 (OUTLIER) cc_final: 0.5777 (mp10) REVERT: B 183 GLU cc_start: 0.9421 (pm20) cc_final: 0.9166 (tp30) REVERT: B 205 PHE cc_start: 0.8518 (OUTLIER) cc_final: 0.8269 (t80) REVERT: B 295 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7467 (mt) REVERT: B 301 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8325 (pp20) REVERT: B 309 MET cc_start: 0.7524 (tmm) cc_final: 0.7315 (tmm) REVERT: E 118 VAL cc_start: 0.9294 (t) cc_final: 0.8977 (p) REVERT: E 207 HIS cc_start: 0.8614 (OUTLIER) cc_final: 0.8295 (t-170) REVERT: F 132 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9201 (mp) REVERT: F 133 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8739 (mm-30) REVERT: F 193 MET cc_start: 0.7415 (tpp) cc_final: 0.7205 (mmm) REVERT: I 85 LYS cc_start: 0.8998 (mmtp) cc_final: 0.8618 (mmmm) REVERT: J 4 LYS cc_start: 0.9268 (OUTLIER) cc_final: 0.9024 (mptt) REVERT: J 313 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7754 (mmmt) REVERT: J 384 LEU cc_start: 0.8914 (pt) cc_final: 0.8309 (tp) REVERT: M 234 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.8376 (m-80) REVERT: N 126 ARG cc_start: 0.8792 (tpp-160) cc_final: 0.8588 (mmp80) REVERT: N 335 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8620 (tm) outliers start: 198 outliers final: 65 residues processed: 376 average time/residue: 0.5721 time to fit residues: 264.1512 Evaluate side-chains 252 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 175 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 205 PHE Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 207 HIS Chi-restraints excluded: chain E residue 298 CYS Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 234 HIS Chi-restraints excluded: chain F residue 271 LYS Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 391 PHE Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain I residue 16 HIS Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 150 TYR Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 255 THR Chi-restraints excluded: chain I residue 274 VAL Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain I residue 390 LYS Chi-restraints excluded: chain I residue 463 THR Chi-restraints excluded: chain J residue 4 LYS Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 204 THR Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 313 LYS Chi-restraints excluded: chain J residue 318 ASN Chi-restraints excluded: chain J residue 391 PHE Chi-restraints excluded: chain J residue 403 VAL Chi-restraints excluded: chain M residue 41 SER Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 234 PHE Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain M residue 365 PHE Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 423 VAL Chi-restraints excluded: chain M residue 460 LEU Chi-restraints excluded: chain M residue 463 THR Chi-restraints excluded: chain N residue 34 CYS Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 160 HIS Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain N residue 335 LEU Chi-restraints excluded: chain N residue 401 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 111 optimal weight: 8.9990 chunk 99 optimal weight: 9.9990 chunk 321 optimal weight: 4.9990 chunk 210 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 282 optimal weight: 6.9990 chunk 227 optimal weight: 0.8980 chunk 155 optimal weight: 10.0000 chunk 157 optimal weight: 0.1980 chunk 126 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 ASN ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 HIS ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 GLN I 61 GLN I 251 HIS ** I 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 66 ASN M 468 ASN N 15 ASN N 160 HIS N 314 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.075057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.057099 restraints weight = 142390.929| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 4.16 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3614 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3614 r_free = 0.3614 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1059 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3609 r_free = 0.3609 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1081 | |-----------------------------------------------------------------------------| r_final: 0.3609 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32928 Z= 0.128 Angle : 0.632 16.520 45228 Z= 0.327 Chirality : 0.042 0.306 4980 Planarity : 0.004 0.066 5118 Dihedral : 18.630 172.091 5951 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.18 % Favored : 93.74 % Rotamer: Outliers : 5.11 % Allowed : 27.56 % Favored : 67.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.14), residues: 3464 helix: 1.27 (0.16), residues: 1152 sheet: -0.78 (0.21), residues: 620 loop : -1.66 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J 19 TYR 0.020 0.001 TYR N 293 PHE 0.019 0.001 PHE E 104 TRP 0.019 0.001 TRP F 219 HIS 0.005 0.001 HIS E 207 Details of bonding type rmsd covalent geometry : bond 0.00279 (32928) covalent geometry : angle 0.63212 (45228) hydrogen bonds : bond 0.03843 ( 1136) hydrogen bonds : angle 4.66074 ( 3076) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 196 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASP cc_start: 0.9194 (m-30) cc_final: 0.8841 (m-30) REVERT: B 138 GLN cc_start: 0.5936 (OUTLIER) cc_final: 0.5504 (mp10) REVERT: B 183 GLU cc_start: 0.9450 (pm20) cc_final: 0.9204 (pm20) REVERT: B 185 LEU cc_start: 0.9577 (OUTLIER) cc_final: 0.9333 (tt) REVERT: B 193 MET cc_start: 0.7338 (OUTLIER) cc_final: 0.6794 (tpt) REVERT: B 205 PHE cc_start: 0.8539 (OUTLIER) cc_final: 0.8297 (t80) REVERT: B 295 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7420 (mt) REVERT: B 309 MET cc_start: 0.7245 (tmm) cc_final: 0.6970 (tmm) REVERT: B 323 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8712 (mm) REVERT: B 395 MET cc_start: 0.9282 (mmm) cc_final: 0.9029 (tpt) REVERT: E 118 VAL cc_start: 0.9225 (t) cc_final: 0.8852 (p) REVERT: E 207 HIS cc_start: 0.8510 (OUTLIER) cc_final: 0.8193 (t-170) REVERT: E 304 PHE cc_start: 0.7724 (t80) cc_final: 0.7453 (t80) REVERT: E 426 VAL cc_start: 0.7953 (t) cc_final: 0.7707 (t) REVERT: E 435 MET cc_start: 0.8656 (mmm) cc_final: 0.8342 (mtt) REVERT: F 129 LYS cc_start: 0.8987 (mmmm) cc_final: 0.8629 (mmtm) REVERT: F 132 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9059 (mp) REVERT: F 133 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8737 (mm-30) REVERT: F 193 MET cc_start: 0.7466 (tpp) cc_final: 0.7239 (mmm) REVERT: I 1 MET cc_start: 0.7310 (mmm) cc_final: 0.7087 (tpp) REVERT: I 74 MET cc_start: 0.8555 (pp-130) cc_final: 0.8134 (ppp) REVERT: I 85 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8550 (mmmm) REVERT: I 267 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8187 (ptpp) REVERT: I 422 THR cc_start: 0.9060 (p) cc_final: 0.8750 (m) REVERT: I 485 LYS cc_start: 0.8257 (mmmt) cc_final: 0.7852 (mttt) REVERT: J 4 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.8991 (mptt) REVERT: J 234 HIS cc_start: 0.8614 (p90) cc_final: 0.8349 (p90) REVERT: J 266 VAL cc_start: 0.9303 (t) cc_final: 0.9076 (p) REVERT: J 313 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7675 (mmmt) REVERT: J 318 ASN cc_start: 0.8987 (OUTLIER) cc_final: 0.8765 (m-40) REVERT: J 384 LEU cc_start: 0.8849 (pt) cc_final: 0.8193 (tp) REVERT: M 48 GLN cc_start: 0.8683 (mp10) cc_final: 0.8378 (pm20) REVERT: N 167 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8158 (tmmm) REVERT: N 335 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8665 (tm) outliers start: 157 outliers final: 65 residues processed: 333 average time/residue: 0.5096 time to fit residues: 208.8248 Evaluate side-chains 243 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 163 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 205 PHE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 207 HIS Chi-restraints excluded: chain E residue 298 CYS Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 234 HIS Chi-restraints excluded: chain F residue 271 LYS Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 391 PHE Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain I residue 16 HIS Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain I residue 103 LYS Chi-restraints excluded: chain I residue 150 TYR Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 267 LYS Chi-restraints excluded: chain I residue 274 VAL Chi-restraints excluded: chain I residue 281 LEU Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain I residue 390 LYS Chi-restraints excluded: chain I residue 463 THR Chi-restraints excluded: chain I residue 489 ILE Chi-restraints excluded: chain J residue 4 LYS Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 297 LYS Chi-restraints excluded: chain J residue 313 LYS Chi-restraints excluded: chain J residue 318 ASN Chi-restraints excluded: chain J residue 391 PHE Chi-restraints excluded: chain J residue 403 VAL Chi-restraints excluded: chain M residue 41 SER Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain M residue 350 ILE Chi-restraints excluded: chain M residue 365 PHE Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 423 VAL Chi-restraints excluded: chain M residue 460 LEU Chi-restraints excluded: chain M residue 463 THR Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 167 LYS Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 335 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 335 optimal weight: 20.0000 chunk 161 optimal weight: 10.0000 chunk 348 optimal weight: 10.0000 chunk 276 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 169 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 0.0980 chunk 320 optimal weight: 1.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 GLN A 360 HIS ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 HIS B 226 HIS ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 430 GLN F 357 GLN ** I 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 314 GLN M 468 ASN N 160 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.071558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.053511 restraints weight = 144729.795| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 3.73 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3536 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3536 r_free = 0.3536 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1081 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3532 r_free = 0.3532 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1126 | |-----------------------------------------------------------------------------| r_final: 0.3532 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 32928 Z= 0.241 Angle : 0.678 14.883 45228 Z= 0.353 Chirality : 0.044 0.270 4980 Planarity : 0.004 0.060 5118 Dihedral : 18.732 174.864 5939 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.13 % Favored : 92.75 % Rotamer: Outliers : 6.05 % Allowed : 27.56 % Favored : 66.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.14), residues: 3464 helix: 0.88 (0.15), residues: 1192 sheet: -0.76 (0.21), residues: 632 loop : -1.78 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 19 TYR 0.017 0.001 TYR N 293 PHE 0.017 0.002 PHE I 14 TRP 0.013 0.002 TRP F 219 HIS 0.010 0.001 HIS N 160 Details of bonding type rmsd covalent geometry : bond 0.00532 (32928) covalent geometry : angle 0.67780 (45228) hydrogen bonds : bond 0.04456 ( 1136) hydrogen bonds : angle 4.76474 ( 3076) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 170 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASP cc_start: 0.9177 (m-30) cc_final: 0.8807 (m-30) REVERT: A 85 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8856 (mtmp) REVERT: A 216 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8736 (ptpp) REVERT: B 137 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8927 (pttm) REVERT: B 138 GLN cc_start: 0.6357 (OUTLIER) cc_final: 0.5591 (mp10) REVERT: B 183 GLU cc_start: 0.9478 (pm20) cc_final: 0.9204 (pm20) REVERT: B 193 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.7023 (tpt) REVERT: B 205 PHE cc_start: 0.8562 (OUTLIER) cc_final: 0.8300 (t80) REVERT: B 295 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7533 (mt) REVERT: B 301 GLU cc_start: 0.9082 (OUTLIER) cc_final: 0.8677 (pp20) REVERT: B 309 MET cc_start: 0.7367 (tmm) cc_final: 0.7129 (tmm) REVERT: B 323 ILE cc_start: 0.9122 (OUTLIER) cc_final: 0.8841 (mm) REVERT: B 335 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8657 (tm) REVERT: E 118 VAL cc_start: 0.9222 (t) cc_final: 0.8839 (p) REVERT: E 207 HIS cc_start: 0.8588 (OUTLIER) cc_final: 0.8254 (t-170) REVERT: E 430 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8280 (mm-40) REVERT: E 453 LYS cc_start: 0.9358 (OUTLIER) cc_final: 0.9097 (mmmm) REVERT: F 132 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9141 (mp) REVERT: F 133 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8766 (mm-30) REVERT: F 309 MET cc_start: 0.6708 (tmm) cc_final: 0.6449 (tmm) REVERT: I 7 ILE cc_start: 0.7870 (OUTLIER) cc_final: 0.7573 (pt) REVERT: I 70 ILE cc_start: 0.8937 (mp) cc_final: 0.8488 (tt) REVERT: I 85 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8696 (mmmm) REVERT: I 207 HIS cc_start: 0.8866 (OUTLIER) cc_final: 0.8564 (t-170) REVERT: I 370 TRP cc_start: 0.8631 (OUTLIER) cc_final: 0.7800 (t60) REVERT: J 4 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.8978 (mptt) REVERT: J 266 VAL cc_start: 0.9297 (t) cc_final: 0.9094 (p) REVERT: J 313 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7869 (tptp) REVERT: J 384 LEU cc_start: 0.8796 (pt) cc_final: 0.8246 (tp) REVERT: M 7 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8455 (mm) REVERT: M 48 GLN cc_start: 0.8832 (mp10) cc_final: 0.8604 (pm20) REVERT: M 57 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7449 (tm) REVERT: M 234 PHE cc_start: 0.8953 (OUTLIER) cc_final: 0.8556 (m-80) REVERT: N 167 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8338 (tmmm) REVERT: N 193 MET cc_start: 0.7474 (OUTLIER) cc_final: 0.7105 (tpt) REVERT: N 335 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8985 (tm) outliers start: 186 outliers final: 69 residues processed: 339 average time/residue: 0.5268 time to fit residues: 219.8586 Evaluate side-chains 249 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 154 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 205 PHE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 207 HIS Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 430 GLN Chi-restraints excluded: chain E residue 453 LYS Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 234 HIS Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 391 PHE Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 16 HIS Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain I residue 103 LYS Chi-restraints excluded: chain I residue 150 TYR Chi-restraints excluded: chain I residue 207 HIS Chi-restraints excluded: chain I residue 208 ASP Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 274 VAL Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 370 TRP Chi-restraints excluded: chain I residue 463 THR Chi-restraints excluded: chain I residue 489 ILE Chi-restraints excluded: chain J residue 4 LYS Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 185 LEU Chi-restraints excluded: chain J residue 198 PHE Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 313 LYS Chi-restraints excluded: chain J residue 391 PHE Chi-restraints excluded: chain J residue 403 VAL Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 41 SER Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 234 PHE Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain M residue 350 ILE Chi-restraints excluded: chain M residue 365 PHE Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 423 VAL Chi-restraints excluded: chain M residue 460 LEU Chi-restraints excluded: chain M residue 463 THR Chi-restraints excluded: chain M residue 470 CYS Chi-restraints excluded: chain N residue 167 LYS Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 335 LEU Chi-restraints excluded: chain N residue 401 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 201 optimal weight: 2.9990 chunk 156 optimal weight: 20.0000 chunk 163 optimal weight: 0.7980 chunk 68 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 321 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 chunk 296 optimal weight: 7.9990 chunk 120 optimal weight: 2.9990 chunk 273 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 267 GLN N 160 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.071332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.053277 restraints weight = 145803.566| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 3.76 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3532 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3532 r_free = 0.3532 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1126 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1179 | |-----------------------------------------------------------------------------| r_final: 0.3528 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 32928 Z= 0.204 Angle : 0.670 12.963 45228 Z= 0.344 Chirality : 0.043 0.324 4980 Planarity : 0.004 0.061 5118 Dihedral : 18.767 176.898 5935 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.99 % Favored : 92.90 % Rotamer: Outliers : 5.63 % Allowed : 28.25 % Favored : 66.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.14), residues: 3464 helix: 0.92 (0.15), residues: 1192 sheet: -0.68 (0.22), residues: 608 loop : -1.73 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG J 19 TYR 0.013 0.001 TYR N 293 PHE 0.025 0.002 PHE A 304 TRP 0.013 0.001 TRP E 370 HIS 0.008 0.001 HIS N 160 Details of bonding type rmsd covalent geometry : bond 0.00454 (32928) covalent geometry : angle 0.66968 (45228) hydrogen bonds : bond 0.04131 ( 1136) hydrogen bonds : angle 4.68631 ( 3076) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 162 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASP cc_start: 0.9182 (m-30) cc_final: 0.8773 (m-30) REVERT: A 40 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8179 (mttp) REVERT: A 352 GLU cc_start: 0.9102 (OUTLIER) cc_final: 0.8843 (pm20) REVERT: B 138 GLN cc_start: 0.6366 (OUTLIER) cc_final: 0.5666 (mp10) REVERT: B 183 GLU cc_start: 0.9501 (pm20) cc_final: 0.9231 (pm20) REVERT: B 193 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7515 (tpt) REVERT: B 295 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7527 (mt) REVERT: B 309 MET cc_start: 0.7287 (tmm) cc_final: 0.7062 (tmm) REVERT: B 323 ILE cc_start: 0.9145 (OUTLIER) cc_final: 0.8850 (mm) REVERT: B 335 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8670 (tm) REVERT: B 395 MET cc_start: 0.9284 (mmm) cc_final: 0.9077 (tpt) REVERT: E 118 VAL cc_start: 0.9209 (t) cc_final: 0.8830 (p) REVERT: E 207 HIS cc_start: 0.8641 (OUTLIER) cc_final: 0.8310 (t-170) REVERT: E 453 LYS cc_start: 0.9360 (OUTLIER) cc_final: 0.9084 (mmmm) REVERT: F 126 ARG cc_start: 0.8713 (tpp-160) cc_final: 0.8446 (tpp-160) REVERT: F 309 MET cc_start: 0.6695 (tmm) cc_final: 0.6488 (tmm) REVERT: I 85 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8523 (mmmm) REVERT: I 370 TRP cc_start: 0.8645 (OUTLIER) cc_final: 0.7832 (t60) REVERT: J 234 HIS cc_start: 0.8747 (p90) cc_final: 0.8467 (p90) REVERT: J 266 VAL cc_start: 0.9289 (t) cc_final: 0.9044 (p) REVERT: J 297 LYS cc_start: 0.6288 (OUTLIER) cc_final: 0.5924 (mptm) REVERT: J 384 LEU cc_start: 0.8887 (pt) cc_final: 0.8290 (tp) REVERT: M 57 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7414 (tm) REVERT: M 234 PHE cc_start: 0.8936 (OUTLIER) cc_final: 0.8536 (m-80) REVERT: N 167 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8364 (tmmm) REVERT: N 335 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8997 (tm) outliers start: 173 outliers final: 77 residues processed: 318 average time/residue: 0.4778 time to fit residues: 191.4080 Evaluate side-chains 252 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 159 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 207 HIS Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 453 LYS Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 234 HIS Chi-restraints excluded: chain F residue 271 LYS Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain I residue 16 HIS Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain I residue 103 LYS Chi-restraints excluded: chain I residue 150 TYR Chi-restraints excluded: chain I residue 208 ASP Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 274 VAL Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 370 TRP Chi-restraints excluded: chain I residue 437 VAL Chi-restraints excluded: chain I residue 463 THR Chi-restraints excluded: chain I residue 489 ILE Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 198 PHE Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 297 LYS Chi-restraints excluded: chain J residue 318 ASN Chi-restraints excluded: chain J residue 391 PHE Chi-restraints excluded: chain J residue 403 VAL Chi-restraints excluded: chain M residue 41 SER Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 234 PHE Chi-restraints excluded: chain M residue 350 ILE Chi-restraints excluded: chain M residue 365 PHE Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 423 VAL Chi-restraints excluded: chain M residue 460 LEU Chi-restraints excluded: chain M residue 463 THR Chi-restraints excluded: chain M residue 470 CYS Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain N residue 167 LYS Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 335 LEU Chi-restraints excluded: chain N residue 380 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 139 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 249 optimal weight: 10.0000 chunk 346 optimal weight: 9.9990 chunk 142 optimal weight: 0.7980 chunk 234 optimal weight: 0.9980 chunk 198 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 210 optimal weight: 0.8980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 468 ASN N 160 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.072009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.053944 restraints weight = 143490.288| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 3.77 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3558 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3558 r_free = 0.3558 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1179 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3556 r_free = 0.3556 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1225 | |-----------------------------------------------------------------------------| r_final: 0.3556 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32928 Z= 0.148 Angle : 0.667 15.655 45228 Z= 0.336 Chirality : 0.043 0.356 4980 Planarity : 0.004 0.059 5118 Dihedral : 18.734 179.578 5931 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.61 % Favored : 93.27 % Rotamer: Outliers : 5.04 % Allowed : 28.67 % Favored : 66.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.14), residues: 3464 helix: 1.05 (0.15), residues: 1192 sheet: -0.57 (0.22), residues: 608 loop : -1.69 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG M 232 TYR 0.023 0.001 TYR F 225 PHE 0.024 0.001 PHE A 304 TRP 0.014 0.001 TRP F 219 HIS 0.007 0.001 HIS N 160 Details of bonding type rmsd covalent geometry : bond 0.00329 (32928) covalent geometry : angle 0.66670 (45228) hydrogen bonds : bond 0.03820 ( 1136) hydrogen bonds : angle 4.60457 ( 3076) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 171 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASP cc_start: 0.9176 (m-30) cc_final: 0.8736 (m-30) REVERT: A 40 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8237 (mttp) REVERT: A 327 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8433 (tm-30) REVERT: A 364 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7641 (mpp80) REVERT: A 484 ASP cc_start: 0.8718 (t70) cc_final: 0.8479 (t0) REVERT: B 138 GLN cc_start: 0.6218 (OUTLIER) cc_final: 0.5995 (mp10) REVERT: B 183 GLU cc_start: 0.9540 (pm20) cc_final: 0.9249 (pm20) REVERT: B 193 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7524 (tpt) REVERT: B 205 PHE cc_start: 0.8710 (OUTLIER) cc_final: 0.8386 (t80) REVERT: B 215 CYS cc_start: 0.7854 (m) cc_final: 0.6906 (m) REVERT: B 295 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7193 (mt) REVERT: B 309 MET cc_start: 0.7218 (tmm) cc_final: 0.6951 (tmm) REVERT: B 323 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8847 (mm) REVERT: B 335 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8659 (tm) REVERT: E 41 SER cc_start: 0.7760 (OUTLIER) cc_final: 0.7516 (p) REVERT: E 207 HIS cc_start: 0.8597 (OUTLIER) cc_final: 0.8312 (t-170) REVERT: E 435 MET cc_start: 0.8507 (mmm) cc_final: 0.8165 (mtt) REVERT: E 453 LYS cc_start: 0.9332 (OUTLIER) cc_final: 0.9038 (mmmm) REVERT: F 129 LYS cc_start: 0.8918 (tppt) cc_final: 0.8700 (tppt) REVERT: F 133 GLU cc_start: 0.9125 (mm-30) cc_final: 0.8846 (mm-30) REVERT: F 193 MET cc_start: 0.7552 (tpp) cc_final: 0.7235 (tpp) REVERT: I 85 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8441 (mmmm) REVERT: I 207 HIS cc_start: 0.8856 (OUTLIER) cc_final: 0.8511 (t-170) REVERT: I 278 VAL cc_start: 0.9130 (OUTLIER) cc_final: 0.8727 (p) REVERT: I 370 TRP cc_start: 0.8603 (OUTLIER) cc_final: 0.7789 (t60) REVERT: I 457 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8885 (ttmm) REVERT: J 234 HIS cc_start: 0.8979 (p90) cc_final: 0.8722 (p90) REVERT: J 266 VAL cc_start: 0.9221 (t) cc_final: 0.8994 (p) REVERT: J 297 LYS cc_start: 0.6254 (OUTLIER) cc_final: 0.5819 (mptm) REVERT: J 395 MET cc_start: 0.7886 (pmm) cc_final: 0.3007 (tmt) REVERT: M 48 GLN cc_start: 0.8839 (mp10) cc_final: 0.8589 (pm20) REVERT: M 56 TYR cc_start: 0.8384 (t80) cc_final: 0.7940 (t80) REVERT: M 234 PHE cc_start: 0.8922 (OUTLIER) cc_final: 0.8531 (m-80) REVERT: M 258 THR cc_start: 0.9292 (m) cc_final: 0.8926 (t) REVERT: N 167 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8570 (tmmm) REVERT: N 193 MET cc_start: 0.7600 (tpt) cc_final: 0.7273 (tpt) REVERT: N 335 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8986 (tm) outliers start: 155 outliers final: 69 residues processed: 312 average time/residue: 0.5323 time to fit residues: 206.5010 Evaluate side-chains 251 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 161 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 205 PHE Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 207 HIS Chi-restraints excluded: chain E residue 348 GLU Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 453 LYS Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 234 HIS Chi-restraints excluded: chain F residue 271 LYS Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain I residue 150 TYR Chi-restraints excluded: chain I residue 207 HIS Chi-restraints excluded: chain I residue 208 ASP Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 274 VAL Chi-restraints excluded: chain I residue 278 VAL Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 370 TRP Chi-restraints excluded: chain I residue 374 LEU Chi-restraints excluded: chain I residue 457 LYS Chi-restraints excluded: chain I residue 463 THR Chi-restraints excluded: chain I residue 489 ILE Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 191 ASN Chi-restraints excluded: chain J residue 198 PHE Chi-restraints excluded: chain J residue 297 LYS Chi-restraints excluded: chain J residue 318 ASN Chi-restraints excluded: chain J residue 391 PHE Chi-restraints excluded: chain J residue 403 VAL Chi-restraints excluded: chain M residue 41 SER Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 234 PHE Chi-restraints excluded: chain M residue 350 ILE Chi-restraints excluded: chain M residue 365 PHE Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 423 VAL Chi-restraints excluded: chain M residue 460 LEU Chi-restraints excluded: chain M residue 463 THR Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 40 ASP Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 167 LYS Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 335 LEU Chi-restraints excluded: chain N residue 401 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 26 optimal weight: 0.9990 chunk 271 optimal weight: 10.0000 chunk 138 optimal weight: 2.9990 chunk 314 optimal weight: 0.0070 chunk 48 optimal weight: 0.9980 chunk 240 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 236 optimal weight: 0.9990 chunk 186 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 overall best weight: 1.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 329 HIS ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 468 ASN N 160 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.072122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.054004 restraints weight = 144140.160| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 4.17 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3556 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3556 r_free = 0.3556 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1225 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3554 r_free = 0.3554 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1301 | |-----------------------------------------------------------------------------| r_final: 0.3554 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32928 Z= 0.142 Angle : 0.674 14.780 45228 Z= 0.337 Chirality : 0.043 0.366 4980 Planarity : 0.004 0.066 5118 Dihedral : 18.685 177.770 5926 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.50 % Favored : 93.42 % Rotamer: Outliers : 4.56 % Allowed : 29.71 % Favored : 65.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.14), residues: 3464 helix: 1.18 (0.16), residues: 1176 sheet: -0.62 (0.21), residues: 648 loop : -1.68 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG J 19 TYR 0.015 0.001 TYR B 221 PHE 0.023 0.001 PHE A 304 TRP 0.030 0.001 TRP B 219 HIS 0.008 0.001 HIS N 160 Details of bonding type rmsd covalent geometry : bond 0.00316 (32928) covalent geometry : angle 0.67446 (45228) hydrogen bonds : bond 0.03704 ( 1136) hydrogen bonds : angle 4.54923 ( 3076) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 175 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASP cc_start: 0.9214 (m-30) cc_final: 0.8731 (m-30) REVERT: A 40 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8234 (mttp) REVERT: A 327 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.8407 (tm-30) REVERT: A 484 ASP cc_start: 0.8680 (t70) cc_final: 0.8441 (t0) REVERT: B 138 GLN cc_start: 0.6141 (OUTLIER) cc_final: 0.5871 (mp10) REVERT: B 183 GLU cc_start: 0.9521 (pm20) cc_final: 0.9221 (pm20) REVERT: B 193 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7631 (tpt) REVERT: B 205 PHE cc_start: 0.8806 (OUTLIER) cc_final: 0.8477 (t80) REVERT: B 215 CYS cc_start: 0.7730 (m) cc_final: 0.6611 (m) REVERT: B 295 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7424 (mt) REVERT: B 309 MET cc_start: 0.7219 (OUTLIER) cc_final: 0.6956 (tmm) REVERT: B 323 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8866 (mm) REVERT: B 335 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8770 (tm) REVERT: B 411 LYS cc_start: 0.9233 (tmmt) cc_final: 0.9023 (tmmm) REVERT: E 41 SER cc_start: 0.7831 (OUTLIER) cc_final: 0.7629 (p) REVERT: E 207 HIS cc_start: 0.8562 (OUTLIER) cc_final: 0.8289 (t-170) REVERT: E 435 MET cc_start: 0.8645 (mmm) cc_final: 0.8271 (mtt) REVERT: E 453 LYS cc_start: 0.9310 (OUTLIER) cc_final: 0.9020 (mmmm) REVERT: F 91 ASP cc_start: 0.7876 (t0) cc_final: 0.7432 (t0) REVERT: F 133 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8855 (mm-30) REVERT: F 193 MET cc_start: 0.7588 (tpp) cc_final: 0.7112 (tpp) REVERT: F 309 MET cc_start: 0.6335 (tmm) cc_final: 0.6082 (tmm) REVERT: I 33 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.9065 (tp) REVERT: I 85 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8512 (mmmm) REVERT: I 207 HIS cc_start: 0.8859 (OUTLIER) cc_final: 0.8533 (t-170) REVERT: I 278 VAL cc_start: 0.9193 (OUTLIER) cc_final: 0.8816 (p) REVERT: I 370 TRP cc_start: 0.8595 (OUTLIER) cc_final: 0.7795 (t60) REVERT: I 457 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8878 (ttmm) REVERT: I 485 LYS cc_start: 0.8375 (mmmt) cc_final: 0.8082 (mttt) REVERT: J 234 HIS cc_start: 0.8853 (OUTLIER) cc_final: 0.8565 (p90) REVERT: J 266 VAL cc_start: 0.9197 (t) cc_final: 0.8990 (p) REVERT: J 297 LYS cc_start: 0.6216 (OUTLIER) cc_final: 0.5815 (mptm) REVERT: J 394 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7126 (pm20) REVERT: J 395 MET cc_start: 0.7581 (pmm) cc_final: 0.2638 (tmt) REVERT: M 7 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8421 (mm) REVERT: M 47 LYS cc_start: 0.9399 (mmmm) cc_final: 0.8843 (mmtm) REVERT: M 48 GLN cc_start: 0.8770 (mp10) cc_final: 0.8563 (pm20) REVERT: M 56 TYR cc_start: 0.8398 (t80) cc_final: 0.7976 (t80) REVERT: M 258 THR cc_start: 0.9324 (m) cc_final: 0.8937 (t) REVERT: N 137 LYS cc_start: 0.9064 (tmtt) cc_final: 0.8683 (tmmt) REVERT: N 167 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8494 (tmmm) REVERT: N 223 PHE cc_start: 0.6075 (m-10) cc_final: 0.5286 (m-10) outliers start: 140 outliers final: 68 residues processed: 298 average time/residue: 0.4707 time to fit residues: 176.4737 Evaluate side-chains 254 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 163 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 205 PHE Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 207 HIS Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 453 LYS Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 234 HIS Chi-restraints excluded: chain F residue 271 LYS Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain I residue 150 TYR Chi-restraints excluded: chain I residue 207 HIS Chi-restraints excluded: chain I residue 208 ASP Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 278 VAL Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 370 TRP Chi-restraints excluded: chain I residue 374 LEU Chi-restraints excluded: chain I residue 437 VAL Chi-restraints excluded: chain I residue 457 LYS Chi-restraints excluded: chain I residue 463 THR Chi-restraints excluded: chain I residue 489 ILE Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 191 ASN Chi-restraints excluded: chain J residue 198 PHE Chi-restraints excluded: chain J residue 234 HIS Chi-restraints excluded: chain J residue 297 LYS Chi-restraints excluded: chain J residue 318 ASN Chi-restraints excluded: chain J residue 391 PHE Chi-restraints excluded: chain J residue 394 GLU Chi-restraints excluded: chain J residue 403 VAL Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 41 SER Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 350 ILE Chi-restraints excluded: chain M residue 365 PHE Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 423 VAL Chi-restraints excluded: chain M residue 459 ILE Chi-restraints excluded: chain M residue 460 LEU Chi-restraints excluded: chain M residue 463 THR Chi-restraints excluded: chain M residue 470 CYS Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 40 ASP Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 167 LYS Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 377 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 348 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 152 optimal weight: 10.0000 chunk 208 optimal weight: 7.9990 chunk 333 optimal weight: 6.9990 chunk 236 optimal weight: 2.9990 chunk 346 optimal weight: 5.9990 chunk 210 optimal weight: 6.9990 chunk 200 optimal weight: 4.9990 chunk 284 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 HIS B 226 HIS ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 ASN B 267 GLN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** E 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 430 GLN F 314 GLN I 209 GLN ** I 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 367 ASN M 205 GLN ** N 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 160 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.068167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.049908 restraints weight = 150013.274| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 4.18 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3426 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1301 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3424 r_free = 0.3424 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1335 | |-----------------------------------------------------------------------------| r_final: 0.3424 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.076 32928 Z= 0.413 Angle : 0.849 15.489 45228 Z= 0.437 Chirality : 0.050 0.375 4980 Planarity : 0.005 0.057 5118 Dihedral : 19.000 178.169 5925 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.66 % Favored : 91.22 % Rotamer: Outliers : 4.65 % Allowed : 30.17 % Favored : 65.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.57 (0.14), residues: 3464 helix: 0.31 (0.15), residues: 1188 sheet: -1.66 (0.21), residues: 618 loop : -1.79 (0.14), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 19 TYR 0.017 0.002 TYR N 293 PHE 0.041 0.003 PHE E 224 TRP 0.032 0.002 TRP B 219 HIS 0.011 0.002 HIS A 16 Details of bonding type rmsd covalent geometry : bond 0.00912 (32928) covalent geometry : angle 0.84946 (45228) hydrogen bonds : bond 0.05495 ( 1136) hydrogen bonds : angle 5.16457 ( 3076) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 152 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8205 (mttp) REVERT: A 327 GLN cc_start: 0.9070 (OUTLIER) cc_final: 0.8341 (tm-30) REVERT: B 181 PHE cc_start: 0.8661 (OUTLIER) cc_final: 0.8409 (t80) REVERT: B 183 GLU cc_start: 0.9528 (pm20) cc_final: 0.9167 (pm20) REVERT: B 193 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.7744 (tpt) REVERT: B 198 PHE cc_start: 0.7725 (OUTLIER) cc_final: 0.7228 (t80) REVERT: B 295 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7864 (mt) REVERT: B 309 MET cc_start: 0.7308 (tmm) cc_final: 0.7061 (tmm) REVERT: B 335 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8857 (tm) REVERT: E 118 VAL cc_start: 0.9279 (t) cc_final: 0.8942 (p) REVERT: E 430 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8338 (mm-40) REVERT: E 435 MET cc_start: 0.8674 (mmm) cc_final: 0.8321 (mtt) REVERT: E 453 LYS cc_start: 0.9400 (OUTLIER) cc_final: 0.9180 (mmmm) REVERT: E 471 ILE cc_start: 0.7240 (OUTLIER) cc_final: 0.6812 (pp) REVERT: I 70 ILE cc_start: 0.9101 (mp) cc_final: 0.8562 (tt) REVERT: I 85 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8653 (mmmm) REVERT: I 278 VAL cc_start: 0.9260 (OUTLIER) cc_final: 0.8793 (p) REVERT: I 370 TRP cc_start: 0.8723 (OUTLIER) cc_final: 0.7843 (t60) REVERT: I 457 LYS cc_start: 0.9152 (OUTLIER) cc_final: 0.8846 (mtmm) REVERT: J 142 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8273 (tmtt) REVERT: J 297 LYS cc_start: 0.6122 (OUTLIER) cc_final: 0.5639 (mptm) REVERT: J 309 MET cc_start: 0.7422 (tpt) cc_final: 0.6907 (tmm) REVERT: J 394 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7221 (pm20) REVERT: J 395 MET cc_start: 0.7535 (pmm) cc_final: 0.2606 (tmt) REVERT: M 41 SER cc_start: 0.8675 (OUTLIER) cc_final: 0.8371 (p) REVERT: M 47 LYS cc_start: 0.9428 (mmmm) cc_final: 0.8991 (mmtm) REVERT: M 205 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.7421 (tp40) REVERT: M 234 PHE cc_start: 0.8991 (t80) cc_final: 0.8506 (m-10) REVERT: N 167 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8321 (tmmm) REVERT: N 223 PHE cc_start: 0.6199 (m-10) cc_final: 0.5519 (m-10) outliers start: 143 outliers final: 70 residues processed: 279 average time/residue: 0.4666 time to fit residues: 164.5651 Evaluate side-chains 230 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 140 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 207 HIS Chi-restraints excluded: chain E residue 208 ASP Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 430 GLN Chi-restraints excluded: chain E residue 453 LYS Chi-restraints excluded: chain E residue 471 ILE Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 234 HIS Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain I residue 150 TYR Chi-restraints excluded: chain I residue 208 ASP Chi-restraints excluded: chain I residue 223 ILE Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 255 THR Chi-restraints excluded: chain I residue 274 VAL Chi-restraints excluded: chain I residue 278 VAL Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 370 TRP Chi-restraints excluded: chain I residue 437 VAL Chi-restraints excluded: chain I residue 457 LYS Chi-restraints excluded: chain I residue 463 THR Chi-restraints excluded: chain I residue 489 ILE Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 142 LYS Chi-restraints excluded: chain J residue 198 PHE Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 297 LYS Chi-restraints excluded: chain J residue 318 ASN Chi-restraints excluded: chain J residue 394 GLU Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 403 VAL Chi-restraints excluded: chain M residue 41 SER Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 205 GLN Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 303 MET Chi-restraints excluded: chain M residue 350 ILE Chi-restraints excluded: chain M residue 358 PHE Chi-restraints excluded: chain M residue 365 PHE Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 405 ILE Chi-restraints excluded: chain M residue 423 VAL Chi-restraints excluded: chain M residue 460 LEU Chi-restraints excluded: chain M residue 463 THR Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 160 HIS Chi-restraints excluded: chain N residue 167 LYS Chi-restraints excluded: chain N residue 239 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 43 optimal weight: 0.6980 chunk 231 optimal weight: 0.9990 chunk 179 optimal weight: 0.9990 chunk 334 optimal weight: 7.9990 chunk 278 optimal weight: 2.9990 chunk 345 optimal weight: 8.9990 chunk 143 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 192 optimal weight: 0.9980 chunk 330 optimal weight: 10.0000 chunk 297 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 ASN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 HIS ** J 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 468 ASN N 160 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.071217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.053142 restraints weight = 143446.006| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 3.75 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3545 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3545 r_free = 0.3545 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1335 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3543 r_free = 0.3543 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1361 | |-----------------------------------------------------------------------------| r_final: 0.3543 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 32928 Z= 0.141 Angle : 0.722 14.609 45228 Z= 0.360 Chirality : 0.044 0.398 4980 Planarity : 0.004 0.052 5118 Dihedral : 18.859 177.757 5924 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.24 % Favored : 93.65 % Rotamer: Outliers : 2.96 % Allowed : 31.83 % Favored : 65.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.14), residues: 3464 helix: 0.84 (0.15), residues: 1206 sheet: -1.04 (0.21), residues: 640 loop : -1.76 (0.15), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 19 TYR 0.028 0.001 TYR F 225 PHE 0.017 0.001 PHE F 205 TRP 0.033 0.001 TRP B 219 HIS 0.016 0.001 HIS N 160 Details of bonding type rmsd covalent geometry : bond 0.00311 (32928) covalent geometry : angle 0.72194 (45228) hydrogen bonds : bond 0.03816 ( 1136) hydrogen bonds : angle 4.74534 ( 3076) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 169 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASP cc_start: 0.9059 (m-30) cc_final: 0.8608 (m-30) REVERT: A 40 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8382 (mttp) REVERT: A 327 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8384 (tm-30) REVERT: A 484 ASP cc_start: 0.8757 (t70) cc_final: 0.8513 (t0) REVERT: B 183 GLU cc_start: 0.9488 (pm20) cc_final: 0.9042 (pm20) REVERT: B 193 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7690 (tpt) REVERT: B 198 PHE cc_start: 0.7758 (OUTLIER) cc_final: 0.7243 (t80) REVERT: B 205 PHE cc_start: 0.8981 (OUTLIER) cc_final: 0.8592 (t80) REVERT: B 215 CYS cc_start: 0.8326 (m) cc_final: 0.7119 (m) REVERT: B 295 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7500 (mt) REVERT: B 309 MET cc_start: 0.7452 (OUTLIER) cc_final: 0.6752 (tmm) REVERT: B 335 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8848 (tm) REVERT: B 395 MET cc_start: 0.8945 (tpt) cc_final: 0.8654 (OUTLIER) REVERT: E 56 TYR cc_start: 0.8271 (t80) cc_final: 0.8036 (t80) REVERT: E 435 MET cc_start: 0.8680 (mmm) cc_final: 0.8359 (mtt) REVERT: E 471 ILE cc_start: 0.7320 (OUTLIER) cc_final: 0.6893 (pp) REVERT: F 129 LYS cc_start: 0.8653 (tppt) cc_final: 0.7334 (tppt) REVERT: F 133 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8156 (mm-30) REVERT: F 277 MET cc_start: 0.8866 (mmp) cc_final: 0.8633 (mmp) REVERT: F 309 MET cc_start: 0.6398 (tmm) cc_final: 0.6080 (tmm) REVERT: I 33 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.9057 (tp) REVERT: I 85 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8732 (tppp) REVERT: I 370 TRP cc_start: 0.8711 (OUTLIER) cc_final: 0.8016 (t60) REVERT: I 457 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8855 (ttmm) REVERT: J 234 HIS cc_start: 0.8718 (p90) cc_final: 0.8447 (p90) REVERT: J 297 LYS cc_start: 0.6265 (OUTLIER) cc_final: 0.5870 (mptm) REVERT: J 309 MET cc_start: 0.7371 (tpt) cc_final: 0.6884 (tmm) REVERT: J 384 LEU cc_start: 0.9182 (pt) cc_final: 0.8646 (tp) REVERT: J 394 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7272 (pm20) REVERT: J 395 MET cc_start: 0.7677 (pmm) cc_final: 0.2947 (tmt) REVERT: M 41 SER cc_start: 0.8590 (OUTLIER) cc_final: 0.8301 (p) REVERT: N 167 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8625 (tmmm) REVERT: N 176 LEU cc_start: 0.7705 (mm) cc_final: 0.7259 (mm) REVERT: N 193 MET cc_start: 0.7415 (tpt) cc_final: 0.7212 (tpt) REVERT: N 223 PHE cc_start: 0.6272 (m-10) cc_final: 0.5593 (m-10) outliers start: 91 outliers final: 53 residues processed: 249 average time/residue: 0.5573 time to fit residues: 172.3144 Evaluate side-chains 220 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 151 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 205 PHE Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 471 ILE Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 234 HIS Chi-restraints excluded: chain F residue 271 LYS Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain I residue 150 TYR Chi-restraints excluded: chain I residue 208 ASP Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 370 TRP Chi-restraints excluded: chain I residue 437 VAL Chi-restraints excluded: chain I residue 457 LYS Chi-restraints excluded: chain I residue 463 THR Chi-restraints excluded: chain I residue 489 ILE Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 198 PHE Chi-restraints excluded: chain J residue 204 THR Chi-restraints excluded: chain J residue 297 LYS Chi-restraints excluded: chain J residue 394 GLU Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 403 VAL Chi-restraints excluded: chain M residue 41 SER Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 350 ILE Chi-restraints excluded: chain M residue 365 PHE Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 423 VAL Chi-restraints excluded: chain M residue 460 LEU Chi-restraints excluded: chain M residue 463 THR Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 167 LYS Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 380 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 189 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 308 optimal weight: 3.9990 chunk 212 optimal weight: 0.0980 chunk 352 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 171 optimal weight: 4.9990 chunk 348 optimal weight: 10.0000 chunk 314 optimal weight: 4.9990 chunk 221 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 ASN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 446 ASN ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 160 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.070174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.052104 restraints weight = 145361.005| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 3.98 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3504 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1361 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3502 r_free = 0.3502 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1395 | |-----------------------------------------------------------------------------| r_final: 0.3502 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 32928 Z= 0.197 Angle : 0.735 14.209 45228 Z= 0.367 Chirality : 0.045 0.393 4980 Planarity : 0.004 0.052 5118 Dihedral : 18.829 179.271 5924 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.90 % Favored : 92.98 % Rotamer: Outliers : 2.73 % Allowed : 32.22 % Favored : 65.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.14), residues: 3464 helix: 0.79 (0.15), residues: 1206 sheet: -1.10 (0.21), residues: 640 loop : -1.76 (0.15), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 19 TYR 0.014 0.001 TYR I 403 PHE 0.035 0.002 PHE E 224 TRP 0.029 0.001 TRP B 219 HIS 0.008 0.001 HIS N 160 Details of bonding type rmsd covalent geometry : bond 0.00442 (32928) covalent geometry : angle 0.73496 (45228) hydrogen bonds : bond 0.04070 ( 1136) hydrogen bonds : angle 4.77835 ( 3076) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 155 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASP cc_start: 0.9040 (m-30) cc_final: 0.8589 (m-30) REVERT: A 40 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8388 (mttp) REVERT: A 327 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.8336 (tm-30) REVERT: A 352 GLU cc_start: 0.9179 (OUTLIER) cc_final: 0.8842 (pm20) REVERT: A 364 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7454 (mtm110) REVERT: A 484 ASP cc_start: 0.8773 (t70) cc_final: 0.8543 (OUTLIER) REVERT: B 183 GLU cc_start: 0.9501 (pm20) cc_final: 0.9051 (pm20) REVERT: B 193 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7385 (tpt) REVERT: B 198 PHE cc_start: 0.7928 (OUTLIER) cc_final: 0.7331 (t80) REVERT: B 205 PHE cc_start: 0.8975 (OUTLIER) cc_final: 0.8555 (t80) REVERT: B 215 CYS cc_start: 0.8482 (m) cc_final: 0.7130 (m) REVERT: B 295 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7619 (mt) REVERT: B 309 MET cc_start: 0.7010 (OUTLIER) cc_final: 0.6798 (tmm) REVERT: B 335 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8786 (tm) REVERT: B 395 MET cc_start: 0.8955 (tpt) cc_final: 0.8664 (OUTLIER) REVERT: E 435 MET cc_start: 0.8711 (mmm) cc_final: 0.8406 (mtt) REVERT: E 471 ILE cc_start: 0.7217 (OUTLIER) cc_final: 0.6756 (pp) REVERT: F 129 LYS cc_start: 0.8660 (tppt) cc_final: 0.8375 (tppt) REVERT: F 193 MET cc_start: 0.7295 (mmm) cc_final: 0.6876 (tpt) REVERT: F 277 MET cc_start: 0.8966 (mmp) cc_final: 0.8700 (mmp) REVERT: F 309 MET cc_start: 0.5803 (tmm) cc_final: 0.5566 (tmm) REVERT: I 85 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8567 (mmmm) REVERT: I 278 VAL cc_start: 0.9271 (OUTLIER) cc_final: 0.8828 (p) REVERT: I 370 TRP cc_start: 0.8710 (OUTLIER) cc_final: 0.7904 (t60) REVERT: I 457 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8863 (ttmm) REVERT: J 234 HIS cc_start: 0.8578 (p90) cc_final: 0.8268 (p90) REVERT: J 297 LYS cc_start: 0.6138 (OUTLIER) cc_final: 0.5704 (mptm) REVERT: J 309 MET cc_start: 0.7424 (tpt) cc_final: 0.6941 (tmm) REVERT: J 384 LEU cc_start: 0.9198 (pt) cc_final: 0.8681 (tp) REVERT: J 394 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7221 (pm20) REVERT: J 395 MET cc_start: 0.7484 (pmm) cc_final: 0.2852 (tmt) REVERT: M 41 SER cc_start: 0.8708 (OUTLIER) cc_final: 0.8337 (p) REVERT: N 167 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8414 (tmmm) REVERT: N 176 LEU cc_start: 0.7653 (mm) cc_final: 0.7220 (mm) REVERT: N 193 MET cc_start: 0.7409 (tpt) cc_final: 0.7202 (tpt) REVERT: N 223 PHE cc_start: 0.5959 (m-10) cc_final: 0.5278 (m-10) outliers start: 84 outliers final: 59 residues processed: 228 average time/residue: 0.5283 time to fit residues: 151.5744 Evaluate side-chains 227 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 151 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 205 PHE Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 471 ILE Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 234 HIS Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain I residue 150 TYR Chi-restraints excluded: chain I residue 208 ASP Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 278 VAL Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 370 TRP Chi-restraints excluded: chain I residue 437 VAL Chi-restraints excluded: chain I residue 457 LYS Chi-restraints excluded: chain I residue 463 THR Chi-restraints excluded: chain I residue 489 ILE Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 198 PHE Chi-restraints excluded: chain J residue 204 THR Chi-restraints excluded: chain J residue 297 LYS Chi-restraints excluded: chain J residue 394 GLU Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 403 VAL Chi-restraints excluded: chain M residue 41 SER Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 350 ILE Chi-restraints excluded: chain M residue 365 PHE Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 405 ILE Chi-restraints excluded: chain M residue 423 VAL Chi-restraints excluded: chain M residue 460 LEU Chi-restraints excluded: chain M residue 463 THR Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 160 HIS Chi-restraints excluded: chain N residue 167 LYS Chi-restraints excluded: chain N residue 239 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 281 optimal weight: 0.8980 chunk 182 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 214 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 347 optimal weight: 9.9990 chunk 350 optimal weight: 7.9990 chunk 344 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 ASN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 GLN ** I 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 160 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.069902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.051641 restraints weight = 145777.234| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 3.75 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3496 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1395 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3494 r_free = 0.3494 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1416 | |-----------------------------------------------------------------------------| r_final: 0.3494 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 32928 Z= 0.221 Angle : 0.749 13.976 45228 Z= 0.374 Chirality : 0.045 0.404 4980 Planarity : 0.004 0.052 5118 Dihedral : 18.843 179.724 5923 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.45 % Favored : 92.47 % Rotamer: Outliers : 3.12 % Allowed : 31.92 % Favored : 64.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.14), residues: 3464 helix: 0.72 (0.15), residues: 1194 sheet: -1.50 (0.22), residues: 610 loop : -1.67 (0.14), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 19 TYR 0.011 0.001 TYR N 233 PHE 0.019 0.002 PHE I 442 TRP 0.027 0.001 TRP B 219 HIS 0.021 0.001 HIS N 160 Details of bonding type rmsd covalent geometry : bond 0.00493 (32928) covalent geometry : angle 0.74949 (45228) hydrogen bonds : bond 0.04231 ( 1136) hydrogen bonds : angle 4.83426 ( 3076) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12284.85 seconds wall clock time: 210 minutes 16.83 seconds (12616.83 seconds total)