Starting phenix.real_space_refine on Thu May 29 01:44:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j7s_36047/05_2025/8j7s_36047.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j7s_36047/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8j7s_36047/05_2025/8j7s_36047.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j7s_36047/05_2025/8j7s_36047.map" model { file = "/net/cci-nas-00/data/ceres_data/8j7s_36047/05_2025/8j7s_36047.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j7s_36047/05_2025/8j7s_36047.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} 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: {'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} 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: {'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 2} 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: {'TYR:plan': 1, 'ASN:plan1': 1, 'ARG: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, 'GLN:plan1': 1, 'ARG:plan': 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: {'ASN:plan1': 1, 'ASP:plan': 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: 18.65, per 1000 atoms: 0.59 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: 8.04 Conformation dependent library (CDL) restraints added in 3.7 seconds 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: 11.33 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: 11.25 Time building geometry restraints manager: 9.31 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: 2.610 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: 1.250 Check model and map are aligned: 0.180 Set scattering table: 0.290 Process input model: 74.720 Find NCS groups from input model: 1.810 Set up NCS constraints: 0.150 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:10.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.190 ------------------------------------------------------------------------------- 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 : 12.29 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (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 TRP 0.039 0.001 TRP F 219 HIS 0.007 0.001 HIS N 340 PHE 0.023 0.001 PHE N 17 TYR 0.020 0.001 TYR A 411 ARG 0.018 0.000 ARG B 257 Details of bonding type rmsd hydrogen bonds : bond 0.14421 ( 1136) hydrogen bonds : angle 6.03803 ( 3076) covalent geometry : bond 0.00322 (32928) covalent geometry : angle 0.65875 (45228) *********************** 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 : 3.300 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: 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: 0.5466 (mmm) REVERT: M 399 THR cc_start: 0.7072 (OUTLIER) cc_final: 0.6651 (p) REVERT: N 223 PHE cc_start: 0.4722 (m-80) cc_final: 0.4418 (m-10) outliers start: 143 outliers final: 74 residues processed: 424 average time/residue: 1.1801 time to fit residues: 608.8478 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 : 3.375 ------------------------------------------------------------------------------- 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 300 optimal weight: 0.6980 chunk 269 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 182 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 279 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 169 optimal weight: 20.0000 chunk 207 optimal weight: 0.8980 chunk 323 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 HIS 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 E 217 HIS F 226 HIS F 364 GLN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.086817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.068261 restraints weight = 141090.413| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 4.05 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3738 r_free = 0.3738 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 355 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3661 r_free = 0.3661 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1130 | |-----------------------------------------------------------------------------| r_final: 0.3661 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32928 Z= 0.139 Angle : 0.646 10.387 45228 Z= 0.338 Chirality : 0.042 0.311 4980 Planarity : 0.004 0.063 5118 Dihedral : 18.642 169.991 6021 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.55 % Favored : 93.36 % Rotamer: Outliers : 5.86 % Allowed : 26.55 % Favored : 67.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.14), residues: 3464 helix: 1.14 (0.16), residues: 1148 sheet: -0.79 (0.21), residues: 620 loop : -1.66 (0.14), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 219 HIS 0.016 0.001 HIS J 188 PHE 0.023 0.001 PHE A 304 TYR 0.015 0.001 TYR J 233 ARG 0.009 0.001 ARG B 257 Details of bonding type rmsd hydrogen bonds : bond 0.04181 ( 1136) hydrogen bonds : angle 4.84146 ( 3076) covalent geometry : bond 0.00304 (32928) covalent geometry : angle 0.64554 (45228) *********************** 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 388 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 208 time to evaluate : 3.867 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: A 25 ASP cc_start: 0.9197 (m-30) cc_final: 0.8899 (m-30) REVERT: B 86 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8788 (mtmm) REVERT: B 138 GLN cc_start: 0.6255 (OUTLIER) cc_final: 0.5827 (mp10) REVERT: B 183 GLU cc_start: 0.9399 (pm20) cc_final: 0.9180 (tp30) REVERT: B 205 PHE cc_start: 0.8479 (OUTLIER) cc_final: 0.8217 (t80) REVERT: B 295 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7369 (mt) REVERT: B 301 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8176 (pp20) REVERT: B 309 MET cc_start: 0.7437 (tmm) cc_final: 0.7185 (tmm) REVERT: B 395 MET cc_start: 0.9257 (mmm) cc_final: 0.9003 (tpt) REVERT: E 118 VAL cc_start: 0.9283 (t) cc_final: 0.8951 (p) REVERT: E 207 HIS cc_start: 0.8566 (OUTLIER) cc_final: 0.8260 (t-170) REVERT: E 304 PHE cc_start: 0.7953 (t80) cc_final: 0.7692 (t80) REVERT: E 403 TYR cc_start: 0.6894 (m-10) cc_final: 0.6574 (m-80) REVERT: E 435 MET cc_start: 0.8688 (mmm) cc_final: 0.8444 (mtt) REVERT: F 119 ASP cc_start: 0.7640 (t0) cc_final: 0.7440 (t0) REVERT: F 132 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9179 (mp) REVERT: F 133 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8736 (mm-30) REVERT: F 193 MET cc_start: 0.7418 (tpp) cc_final: 0.7184 (mmm) REVERT: F 226 HIS cc_start: 0.8938 (t70) cc_final: 0.8591 (t-170) REVERT: I 85 LYS cc_start: 0.9037 (mmtp) cc_final: 0.8629 (mmmm) REVERT: I 422 THR cc_start: 0.9055 (p) cc_final: 0.8739 (m) REVERT: J 4 LYS cc_start: 0.9260 (OUTLIER) cc_final: 0.9035 (mptt) REVERT: J 55 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8354 (tp30) REVERT: J 313 LYS cc_start: 0.8182 (tptp) cc_final: 0.7829 (mmmt) REVERT: J 384 LEU cc_start: 0.8822 (pt) cc_final: 0.8186 (tp) REVERT: M 98 ASN cc_start: 0.7391 (p0) cc_final: 0.7087 (p0) REVERT: N 26 ILE cc_start: 0.9413 (OUTLIER) cc_final: 0.9208 (tp) REVERT: N 335 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8545 (tm) outliers start: 180 outliers final: 55 residues processed: 372 average time/residue: 1.0739 time to fit residues: 494.8501 Evaluate side-chains 234 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 168 time to evaluate : 3.334 ------------------------------------------------------------------------------- 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 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 138 GLN 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 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 274 VAL Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 317 VAL 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 55 GLU 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 214 LEU 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 215 LEU 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 26 ILE 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 26 optimal weight: 4.9990 chunk 220 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 231 optimal weight: 0.6980 chunk 170 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 139 optimal weight: 0.9980 chunk 229 optimal weight: 4.9990 chunk 169 optimal weight: 0.9990 chunk 318 optimal weight: 0.4980 chunk 328 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 HIS ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 HIS ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 251 HIS ** I 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 155 GLN J 174 ASN ** J 340 HIS ** 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 = 0.4179 r_free = 0.4179 target = 0.075256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.057311 restraints weight = 142842.085| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 4.19 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3617 r_free = 0.3617 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1130 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3612 r_free = 0.3612 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1117 | |-----------------------------------------------------------------------------| r_final: 0.3612 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1840 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= 0.136 Angle : 0.623 16.753 45228 Z= 0.322 Chirality : 0.042 0.301 4980 Planarity : 0.003 0.057 5118 Dihedral : 18.556 172.997 5945 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.12 % Favored : 93.79 % Rotamer: Outliers : 5.14 % Allowed : 27.56 % Favored : 67.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.14), residues: 3464 helix: 1.21 (0.16), residues: 1176 sheet: -0.54 (0.22), residues: 580 loop : -1.65 (0.14), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 219 HIS 0.005 0.001 HIS E 207 PHE 0.021 0.001 PHE N 181 TYR 0.018 0.001 TYR N 293 ARG 0.013 0.000 ARG J 19 Details of bonding type rmsd hydrogen bonds : bond 0.03844 ( 1136) hydrogen bonds : angle 4.61219 ( 3076) covalent geometry : bond 0.00300 (32928) covalent geometry : angle 0.62253 (45228) *********************** 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 344 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 186 time to evaluate : 3.385 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: 0.9206 (m-30) cc_final: 0.8888 (m-30) REVERT: B 138 GLN cc_start: 0.5990 (OUTLIER) cc_final: 0.5557 (mp10) REVERT: B 183 GLU cc_start: 0.9419 (pm20) cc_final: 0.9196 (tp30) REVERT: B 185 LEU cc_start: 0.9563 (OUTLIER) cc_final: 0.9231 (tt) REVERT: B 193 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.6728 (tpt) REVERT: B 295 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7438 (mt) REVERT: B 309 MET cc_start: 0.7233 (tmm) cc_final: 0.6992 (tmm) REVERT: B 323 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8739 (mm) REVERT: E 118 VAL cc_start: 0.9246 (t) cc_final: 0.8876 (p) REVERT: E 207 HIS cc_start: 0.8528 (OUTLIER) cc_final: 0.8148 (t-170) REVERT: E 304 PHE cc_start: 0.7831 (t80) cc_final: 0.7544 (t80) REVERT: F 132 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9063 (mp) REVERT: F 133 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8756 (mm-30) REVERT: I 85 LYS cc_start: 0.9104 (mmtp) cc_final: 0.8575 (mmmm) REVERT: I 207 HIS cc_start: 0.8586 (OUTLIER) cc_final: 0.8178 (t-170) REVERT: I 267 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8216 (ptpp) REVERT: I 422 THR cc_start: 0.9020 (p) cc_final: 0.8722 (m) REVERT: I 485 LYS cc_start: 0.8272 (mmmt) cc_final: 0.7909 (mttt) REVERT: J 4 LYS cc_start: 0.9283 (OUTLIER) cc_final: 0.9019 (mptt) REVERT: J 55 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8371 (tp30) REVERT: J 217 PHE cc_start: 0.6837 (OUTLIER) cc_final: 0.6534 (m-80) REVERT: J 234 HIS cc_start: 0.8557 (p90) cc_final: 0.8253 (p90) REVERT: J 266 VAL cc_start: 0.9301 (t) cc_final: 0.9080 (p) REVERT: J 384 LEU cc_start: 0.8646 (pt) cc_final: 0.8076 (tp) REVERT: M 48 GLN cc_start: 0.8682 (mp10) cc_final: 0.8383 (pm20) REVERT: N 26 ILE cc_start: 0.9472 (OUTLIER) cc_final: 0.9261 (tp) REVERT: N 335 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8684 (tm) outliers start: 158 outliers final: 65 residues processed: 326 average time/residue: 1.0841 time to fit residues: 442.1063 Evaluate side-chains 243 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 164 time to evaluate : 3.752 ------------------------------------------------------------------------------- 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 278 VAL 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 484 ASP Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 158 PHE 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 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 152 ARG 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 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 103 LYS Chi-restraints excluded: chain I residue 150 TYR Chi-restraints excluded: chain I residue 207 HIS Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 251 HIS 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 55 GLU 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 217 PHE Chi-restraints excluded: chain J residue 274 GLU Chi-restraints excluded: chain J residue 297 LYS Chi-restraints excluded: chain J residue 391 PHE Chi-restraints excluded: chain J residue 403 VAL 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 460 LEU Chi-restraints excluded: chain M residue 463 THR Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 335 LEU Chi-restraints excluded: chain N residue 377 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 200 optimal weight: 6.9990 chunk 183 optimal weight: 7.9990 chunk 180 optimal weight: 6.9990 chunk 116 optimal weight: 0.0980 chunk 175 optimal weight: 7.9990 chunk 260 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 chunk 318 optimal weight: 4.9990 chunk 262 optimal weight: 20.0000 chunk 325 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 overall best weight: 3.6188 ------------------------------------------------------------------------------- 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 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 430 GLN F 138 GLN F 357 GLN I 209 GLN ** I 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 314 GLN J 364 GLN J 367 ASN M 468 ASN N 160 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.071126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.053167 restraints weight = 146808.163| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 3.75 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3520 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3520 r_free = 0.3520 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1117 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3516 r_free = 0.3516 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1160 | |-----------------------------------------------------------------------------| r_final: 0.3516 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 32928 Z= 0.293 Angle : 0.711 15.371 45228 Z= 0.370 Chirality : 0.045 0.307 4980 Planarity : 0.004 0.055 5118 Dihedral : 18.735 174.458 5933 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.36 % Favored : 92.52 % Rotamer: Outliers : 6.41 % Allowed : 27.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.14), residues: 3464 helix: 0.76 (0.15), residues: 1192 sheet: -0.87 (0.22), residues: 588 loop : -1.73 (0.14), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP I 254 HIS 0.016 0.002 HIS I 251 PHE 0.018 0.002 PHE I 14 TYR 0.019 0.002 TYR J 67 ARG 0.008 0.001 ARG J 19 Details of bonding type rmsd hydrogen bonds : bond 0.04777 ( 1136) hydrogen bonds : angle 4.85260 ( 3076) covalent geometry : bond 0.00648 (32928) covalent geometry : angle 0.71137 (45228) *********************** 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 363 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 166 time to evaluate : 4.140 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: A 25 ASP cc_start: 0.9181 (m-30) cc_final: 0.8829 (m-30) REVERT: A 85 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8840 (mtmp) REVERT: B 183 GLU cc_start: 0.9474 (pm20) cc_final: 0.9220 (pm20) REVERT: B 185 LEU cc_start: 0.9595 (OUTLIER) cc_final: 0.9228 (tt) REVERT: B 193 MET cc_start: 0.7666 (OUTLIER) cc_final: 0.7062 (tpt) REVERT: B 205 PHE cc_start: 0.8462 (OUTLIER) cc_final: 0.8073 (t80) REVERT: B 295 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7619 (mt) REVERT: B 309 MET cc_start: 0.7306 (tmm) cc_final: 0.7069 (tmm) REVERT: B 323 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8854 (mm) REVERT: B 335 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8632 (tm) REVERT: E 118 VAL cc_start: 0.9233 (t) cc_final: 0.8858 (p) REVERT: E 207 HIS cc_start: 0.8647 (OUTLIER) cc_final: 0.8336 (t-170) REVERT: E 430 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.8284 (mm-40) REVERT: E 435 MET cc_start: 0.8649 (mmm) cc_final: 0.8297 (mtt) REVERT: E 453 LYS cc_start: 0.9348 (OUTLIER) cc_final: 0.9090 (mmmm) REVERT: F 91 ASP cc_start: 0.7819 (t0) cc_final: 0.7495 (t0) REVERT: F 126 ARG cc_start: 0.8743 (tpp-160) cc_final: 0.8496 (tpp-160) REVERT: F 133 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8775 (mm-30) REVERT: F 392 TYR cc_start: 0.9233 (OUTLIER) cc_final: 0.8882 (p90) REVERT: I 7 ILE cc_start: 0.7880 (OUTLIER) cc_final: 0.7549 (pt) REVERT: I 70 ILE cc_start: 0.8975 (mp) cc_final: 0.8536 (tt) REVERT: I 85 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8727 (mmmm) REVERT: I 207 HIS cc_start: 0.8714 (OUTLIER) cc_final: 0.8335 (t-170) REVERT: I 370 TRP cc_start: 0.8661 (OUTLIER) cc_final: 0.7847 (t60) REVERT: J 4 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.8999 (mptt) REVERT: J 55 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8310 (tp30) REVERT: J 234 HIS cc_start: 0.8740 (OUTLIER) cc_final: 0.8492 (p90) REVERT: J 297 LYS cc_start: 0.6241 (OUTLIER) cc_final: 0.5937 (mptm) REVERT: J 384 LEU cc_start: 0.8825 (pt) cc_final: 0.8271 (tp) REVERT: M 7 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8476 (mm) REVERT: M 48 GLN cc_start: 0.8830 (mp10) cc_final: 0.8610 (pm20) REVERT: M 57 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7509 (tm) REVERT: M 234 PHE cc_start: 0.8982 (OUTLIER) cc_final: 0.8579 (m-80) REVERT: M 444 GLU cc_start: 0.6762 (OUTLIER) cc_final: 0.6394 (pp20) REVERT: N 193 MET cc_start: 0.7401 (OUTLIER) cc_final: 0.7042 (tpt) outliers start: 197 outliers final: 75 residues processed: 346 average time/residue: 1.1077 time to fit residues: 476.3481 Evaluate side-chains 252 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 153 time to evaluate : 3.418 ------------------------------------------------------------------------------- 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 278 VAL 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 A residue 486 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 160 HIS 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 222 ASP 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 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 125 ILE Chi-restraints excluded: chain E residue 152 ARG 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 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 338 SER Chi-restraints excluded: chain F residue 391 PHE Chi-restraints excluded: chain F residue 392 TYR 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 55 GLU 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 214 LEU 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 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 444 GLU 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 34 CYS Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 239 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 75 optimal weight: 10.0000 chunk 318 optimal weight: 4.9990 chunk 190 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 157 optimal weight: 5.9990 chunk 278 optimal weight: 7.9990 chunk 231 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 GLN ** I 307 ASN ** 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 = 0.4125 r_free = 0.4125 target = 0.072140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.054116 restraints weight = 144077.880| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 3.78 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3559 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3559 r_free = 0.3559 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1160 | |-----------------------------------------------------------------------------| |-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: 1204 | |-----------------------------------------------------------------------------| r_final: 0.3556 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 32928 Z= 0.167 Angle : 0.654 12.455 45228 Z= 0.335 Chirality : 0.043 0.315 4980 Planarity : 0.004 0.053 5118 Dihedral : 18.731 177.531 5931 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.44 % Favored : 93.45 % Rotamer: Outliers : 5.30 % Allowed : 28.05 % Favored : 66.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.14), residues: 3464 helix: 1.01 (0.15), residues: 1192 sheet: -0.62 (0.22), residues: 608 loop : -1.71 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 370 HIS 0.007 0.001 HIS N 160 PHE 0.023 0.001 PHE N 181 TYR 0.013 0.001 TYR N 293 ARG 0.006 0.000 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.03910 ( 1136) hydrogen bonds : angle 4.61693 ( 3076) covalent geometry : bond 0.00369 (32928) covalent geometry : angle 0.65407 (45228) *********************** 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 337 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 174 time to evaluate : 3.841 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: A 25 ASP cc_start: 0.9198 (m-30) cc_final: 0.8789 (m-30) REVERT: B 137 LYS cc_start: 0.9164 (OUTLIER) cc_final: 0.8952 (pttm) REVERT: B 138 GLN cc_start: 0.6300 (OUTLIER) cc_final: 0.5633 (mp10) REVERT: B 183 GLU cc_start: 0.9483 (pm20) cc_final: 0.9203 (pm20) REVERT: B 185 LEU cc_start: 0.9576 (OUTLIER) cc_final: 0.9133 (tt) REVERT: B 193 MET cc_start: 0.7767 (OUTLIER) cc_final: 0.7401 (tpt) REVERT: B 198 PHE cc_start: 0.7496 (OUTLIER) cc_final: 0.7227 (t80) REVERT: B 205 PHE cc_start: 0.8642 (OUTLIER) cc_final: 0.8326 (t80) REVERT: B 295 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7560 (mt) REVERT: B 309 MET cc_start: 0.7252 (tmm) cc_final: 0.7011 (tmm) REVERT: B 323 ILE cc_start: 0.9160 (OUTLIER) cc_final: 0.8855 (mm) REVERT: B 335 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8681 (tm) REVERT: E 41 SER cc_start: 0.7735 (OUTLIER) cc_final: 0.7489 (p) REVERT: E 118 VAL cc_start: 0.9233 (t) cc_final: 0.8855 (p) REVERT: E 207 HIS cc_start: 0.8644 (OUTLIER) cc_final: 0.8400 (t-170) REVERT: E 453 LYS cc_start: 0.9322 (OUTLIER) cc_final: 0.9051 (mmmm) REVERT: F 91 ASP cc_start: 0.7752 (t0) cc_final: 0.7352 (t0) REVERT: F 193 MET cc_start: 0.7596 (tpp) cc_final: 0.6917 (tpp) REVERT: F 392 TYR cc_start: 0.9288 (OUTLIER) cc_final: 0.8972 (p90) REVERT: I 85 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8569 (mmmm) REVERT: I 207 HIS cc_start: 0.8676 (OUTLIER) cc_final: 0.8275 (t-170) REVERT: I 267 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8384 (ptpp) REVERT: I 370 TRP cc_start: 0.8609 (OUTLIER) cc_final: 0.7803 (t60) REVERT: I 457 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8816 (mtmm) REVERT: J 4 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.9017 (mptt) REVERT: J 162 LYS cc_start: 0.4547 (mptp) cc_final: 0.4302 (mmtt) REVERT: J 234 HIS cc_start: 0.8767 (OUTLIER) cc_final: 0.8508 (p90) REVERT: J 297 LYS cc_start: 0.6175 (OUTLIER) cc_final: 0.5857 (mptm) REVERT: J 384 LEU cc_start: 0.8850 (pt) cc_final: 0.8260 (tp) REVERT: J 395 MET cc_start: 0.7651 (pmm) cc_final: 0.3066 (tmt) REVERT: M 234 PHE cc_start: 0.8870 (OUTLIER) cc_final: 0.8494 (m-80) REVERT: M 430 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8396 (mp10) outliers start: 163 outliers final: 71 residues processed: 320 average time/residue: 1.0326 time to fit residues: 415.1137 Evaluate side-chains 256 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 162 time to evaluate : 3.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 305 LEU 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 486 ILE 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 160 HIS 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 198 PHE 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 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 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 36 ILE 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 311 VAL Chi-restraints excluded: chain F residue 391 PHE Chi-restraints excluded: chain F residue 392 TYR 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 207 HIS Chi-restraints excluded: chain I residue 208 ASP 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 305 LEU Chi-restraints excluded: chain I residue 370 TRP 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 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 214 LEU 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 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 430 GLN 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 136 GLU Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 377 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 321 optimal weight: 1.9990 chunk 228 optimal weight: 0.0020 chunk 77 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 130 optimal weight: 0.0060 chunk 12 optimal weight: 0.8980 chunk 281 optimal weight: 4.9990 chunk 118 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 overall best weight: 0.5404 ------------------------------------------------------------------------------- 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 160 HIS B 226 HIS ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 GLN ** I 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 61 GLN M 468 ASN N 160 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.073144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.055136 restraints weight = 142461.737| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 4.05 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3587 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3587 r_free = 0.3587 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1204 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3585 r_free = 0.3585 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1273 | |-----------------------------------------------------------------------------| r_final: 0.3585 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32928 Z= 0.123 Angle : 0.660 13.896 45228 Z= 0.331 Chirality : 0.043 0.314 4980 Planarity : 0.003 0.054 5118 Dihedral : 18.654 177.456 5929 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.29 % Favored : 93.62 % Rotamer: Outliers : 4.59 % Allowed : 28.73 % Favored : 66.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.15), residues: 3464 helix: 1.26 (0.16), residues: 1176 sheet: -0.58 (0.21), residues: 648 loop : -1.66 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 370 HIS 0.007 0.001 HIS J 188 PHE 0.034 0.001 PHE A 304 TYR 0.024 0.001 TYR F 225 ARG 0.005 0.000 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.03651 ( 1136) hydrogen bonds : angle 4.52472 ( 3076) covalent geometry : bond 0.00269 (32928) covalent geometry : angle 0.65988 (45228) *********************** 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 331 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 190 time to evaluate : 3.394 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: 0.9205 (m-30) cc_final: 0.8769 (m-30) REVERT: A 208 ASP cc_start: 0.8291 (OUTLIER) cc_final: 0.7903 (p0) REVERT: A 303 MET cc_start: 0.7641 (tmt) cc_final: 0.7419 (tmt) REVERT: B 138 GLN cc_start: 0.6100 (OUTLIER) cc_final: 0.5502 (mp10) REVERT: B 165 ILE cc_start: 0.7301 (mt) cc_final: 0.6940 (pp) REVERT: B 183 GLU cc_start: 0.9495 (pm20) cc_final: 0.9207 (pm20) REVERT: B 185 LEU cc_start: 0.9586 (OUTLIER) cc_final: 0.9131 (tt) REVERT: B 193 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7077 (tpt) REVERT: B 205 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.8216 (t80) REVERT: B 215 CYS cc_start: 0.7815 (m) cc_final: 0.6731 (m) REVERT: B 295 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7482 (mt) REVERT: B 309 MET cc_start: 0.7087 (tmm) cc_final: 0.6833 (tmm) REVERT: B 323 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8803 (mm) REVERT: B 335 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8626 (tm) REVERT: B 364 GLN cc_start: 0.9299 (OUTLIER) cc_final: 0.8939 (tp-100) REVERT: B 395 MET cc_start: 0.8986 (tpt) cc_final: 0.8780 (tpp) REVERT: B 411 LYS cc_start: 0.9225 (tmmt) cc_final: 0.8987 (tmmm) REVERT: E 41 SER cc_start: 0.7687 (OUTLIER) cc_final: 0.7473 (p) REVERT: E 207 HIS cc_start: 0.8644 (OUTLIER) cc_final: 0.8347 (t-170) REVERT: E 435 MET cc_start: 0.8548 (mmm) cc_final: 0.8195 (mtt) REVERT: E 453 LYS cc_start: 0.9307 (OUTLIER) cc_final: 0.9021 (mmmm) REVERT: F 91 ASP cc_start: 0.7855 (t0) cc_final: 0.7408 (t0) REVERT: F 133 GLU cc_start: 0.9178 (mm-30) cc_final: 0.8829 (mm-30) REVERT: I 16 HIS cc_start: 0.8276 (OUTLIER) cc_final: 0.7881 (m90) REVERT: I 33 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.9050 (tp) REVERT: I 85 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8475 (mmmm) REVERT: I 207 HIS cc_start: 0.8680 (OUTLIER) cc_final: 0.8310 (t-170) REVERT: I 370 TRP cc_start: 0.8588 (OUTLIER) cc_final: 0.7756 (t60) REVERT: I 422 THR cc_start: 0.8936 (p) cc_final: 0.8677 (m) REVERT: J 55 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8421 (tp30) REVERT: J 162 LYS cc_start: 0.4550 (mptp) cc_final: 0.4330 (mmtt) REVERT: J 234 HIS cc_start: 0.8774 (OUTLIER) cc_final: 0.8525 (p90) REVERT: J 297 LYS cc_start: 0.6108 (OUTLIER) cc_final: 0.5854 (mptm) REVERT: J 384 LEU cc_start: 0.8865 (pt) cc_final: 0.8308 (tp) REVERT: J 395 MET cc_start: 0.7533 (pmm) cc_final: 0.2781 (tmt) REVERT: M 48 GLN cc_start: 0.8873 (mp10) cc_final: 0.8606 (pm20) REVERT: M 56 TYR cc_start: 0.8397 (t80) cc_final: 0.7956 (t80) REVERT: M 258 THR cc_start: 0.9291 (m) cc_final: 0.8924 (t) REVERT: N 137 LYS cc_start: 0.9079 (tmtt) cc_final: 0.8680 (tmmt) REVERT: N 193 MET cc_start: 0.7512 (tpt) cc_final: 0.7133 (tpt) REVERT: N 223 PHE cc_start: 0.6524 (m-10) cc_final: 0.5817 (m-10) outliers start: 141 outliers final: 60 residues processed: 316 average time/residue: 1.0714 time to fit residues: 433.5140 Evaluate side-chains 246 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 166 time to evaluate : 3.697 ------------------------------------------------------------------------------- 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 278 VAL 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 484 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 247 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 364 GLN 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 453 LYS Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain F residue 16 ASP 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 391 PHE Chi-restraints excluded: chain F residue 392 TYR 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 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 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 463 THR Chi-restraints excluded: chain I residue 489 ILE Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 55 GLU 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 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 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 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 36 ILE Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 377 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 286 optimal weight: 3.9990 chunk 263 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 273 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 252 optimal weight: 5.9990 chunk 262 optimal weight: 0.9990 chunk 143 optimal weight: 0.0570 chunk 29 optimal weight: 4.9990 chunk 216 optimal weight: 7.9990 overall best weight: 2.2106 ------------------------------------------------------------------------------- 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 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 207 HIS ** I 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 61 GLN N 160 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.071254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.053181 restraints weight = 144608.836| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 3.94 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3533 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3533 r_free = 0.3533 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1273 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1331 | |-----------------------------------------------------------------------------| r_final: 0.3531 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 32928 Z= 0.196 Angle : 0.691 14.084 45228 Z= 0.349 Chirality : 0.044 0.366 4980 Planarity : 0.004 0.054 5118 Dihedral : 18.682 177.302 5923 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.76 % Favored : 93.13 % Rotamer: Outliers : 4.65 % Allowed : 29.32 % Favored : 66.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.14), residues: 3464 helix: 1.10 (0.15), residues: 1192 sheet: -0.65 (0.21), residues: 636 loop : -1.69 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 86 HIS 0.006 0.001 HIS J 188 PHE 0.025 0.002 PHE I 442 TYR 0.012 0.001 TYR N 293 ARG 0.012 0.000 ARG M 232 Details of bonding type rmsd hydrogen bonds : bond 0.04091 ( 1136) hydrogen bonds : angle 4.65019 ( 3076) covalent geometry : bond 0.00438 (32928) covalent geometry : angle 0.69126 (45228) *********************** 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 308 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 165 time to evaluate : 3.860 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 25 ASP cc_start: 0.9208 (m-30) cc_final: 0.8746 (m-30) REVERT: A 327 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8386 (tm-30) REVERT: A 364 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7540 (mtm110) REVERT: B 138 GLN cc_start: 0.6163 (OUTLIER) cc_final: 0.5870 (mp10) REVERT: B 183 GLU cc_start: 0.9502 (pm20) cc_final: 0.9196 (pm20) REVERT: B 185 LEU cc_start: 0.9574 (OUTLIER) cc_final: 0.9153 (tt) REVERT: B 193 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7649 (tpt) REVERT: B 198 PHE cc_start: 0.7356 (OUTLIER) cc_final: 0.7141 (t80) REVERT: B 205 PHE cc_start: 0.8721 (OUTLIER) cc_final: 0.8335 (t80) REVERT: B 295 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7499 (mt) REVERT: B 323 ILE cc_start: 0.9170 (OUTLIER) cc_final: 0.8880 (mm) REVERT: B 335 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8720 (tm) REVERT: E 207 HIS cc_start: 0.8637 (OUTLIER) cc_final: 0.8356 (t-170) REVERT: E 435 MET cc_start: 0.8574 (mmm) cc_final: 0.8230 (mtt) REVERT: E 453 LYS cc_start: 0.9345 (OUTLIER) cc_final: 0.9073 (mmmm) REVERT: F 91 ASP cc_start: 0.7915 (t0) cc_final: 0.7508 (t0) REVERT: F 129 LYS cc_start: 0.8808 (tppt) cc_final: 0.8442 (tppt) REVERT: F 392 TYR cc_start: 0.9291 (OUTLIER) cc_final: 0.9017 (p90) REVERT: I 85 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8505 (mmmm) REVERT: I 370 TRP cc_start: 0.8625 (OUTLIER) cc_final: 0.7848 (t60) REVERT: J 4 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.9109 (mptt) REVERT: J 55 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8350 (OUTLIER) REVERT: J 193 MET cc_start: 0.6250 (pmm) cc_final: 0.5929 (pmm) REVERT: J 234 HIS cc_start: 0.8792 (OUTLIER) cc_final: 0.8541 (p90) REVERT: J 297 LYS cc_start: 0.6085 (OUTLIER) cc_final: 0.5708 (mptm) REVERT: J 394 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7104 (pm20) REVERT: J 395 MET cc_start: 0.7381 (pmm) cc_final: 0.2515 (tmt) REVERT: M 48 GLN cc_start: 0.8921 (mp10) cc_final: 0.8701 (pm20) REVERT: M 429 ILE cc_start: 0.9244 (pt) cc_final: 0.9040 (pp) REVERT: N 137 LYS cc_start: 0.9099 (tmtt) cc_final: 0.8704 (tmmt) REVERT: N 223 PHE cc_start: 0.6103 (m-10) cc_final: 0.5346 (m-10) outliers start: 143 outliers final: 70 residues processed: 292 average time/residue: 0.9846 time to fit residues: 365.0323 Evaluate side-chains 245 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 156 time to evaluate : 3.394 ------------------------------------------------------------------------------- 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 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 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 484 ASP 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 185 LEU 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 227 LEU 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 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 52 ILE 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 391 PHE Chi-restraints excluded: chain F residue 392 TYR 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 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 55 GLU 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 204 THR Chi-restraints excluded: chain J residue 234 HIS Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 297 LYS Chi-restraints excluded: chain J residue 318 ASN Chi-restraints excluded: chain J residue 341 ILE 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 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 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 459 ILE 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 65 SER Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain N residue 239 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 199 optimal weight: 4.9990 chunk 241 optimal weight: 5.9990 chunk 331 optimal weight: 20.0000 chunk 76 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 196 optimal weight: 0.0050 chunk 81 optimal weight: 1.9990 chunk 142 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 overall best weight: 1.5400 ------------------------------------------------------------------------------- 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 364 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 207 HIS ** I 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 367 ASN M 468 ASN N 160 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.071674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.053599 restraints weight = 143549.059| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 4.03 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3546 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3546 r_free = 0.3546 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1331 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | 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: 1412 | |-----------------------------------------------------------------------------| r_final: 0.3545 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 32928 Z= 0.158 Angle : 0.690 13.607 45228 Z= 0.345 Chirality : 0.044 0.376 4980 Planarity : 0.004 0.057 5118 Dihedral : 18.651 178.713 5920 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.70 % Favored : 93.22 % Rotamer: Outliers : 4.10 % Allowed : 30.00 % Favored : 65.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.14), residues: 3464 helix: 1.14 (0.15), residues: 1192 sheet: -0.63 (0.21), residues: 636 loop : -1.66 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 370 HIS 0.006 0.001 HIS E 207 PHE 0.016 0.001 PHE I 442 TYR 0.012 0.001 TYR F 225 ARG 0.017 0.000 ARG J 19 Details of bonding type rmsd hydrogen bonds : bond 0.03812 ( 1136) hydrogen bonds : angle 4.60771 ( 3076) covalent geometry : bond 0.00352 (32928) covalent geometry : angle 0.69047 (45228) *********************** 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 294 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 168 time to evaluate : 3.394 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: A 25 ASP cc_start: 0.9202 (m-30) cc_final: 0.8759 (m-30) REVERT: A 327 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8398 (tm-30) REVERT: A 364 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7655 (mpp80) REVERT: B 138 GLN cc_start: 0.6101 (OUTLIER) cc_final: 0.5856 (mp10) REVERT: B 183 GLU cc_start: 0.9529 (pm20) cc_final: 0.9203 (pm20) REVERT: B 185 LEU cc_start: 0.9588 (OUTLIER) cc_final: 0.9161 (tt) REVERT: B 193 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7695 (tpt) REVERT: B 198 PHE cc_start: 0.7648 (OUTLIER) cc_final: 0.7211 (t80) REVERT: B 205 PHE cc_start: 0.8683 (OUTLIER) cc_final: 0.8295 (t80) REVERT: B 295 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7378 (mt) REVERT: B 323 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8841 (mm) REVERT: B 335 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8761 (tm) REVERT: B 364 GLN cc_start: 0.9169 (OUTLIER) cc_final: 0.8950 (tp-100) REVERT: B 395 MET cc_start: 0.8918 (tpt) cc_final: 0.8690 (OUTLIER) REVERT: E 207 HIS cc_start: 0.8599 (OUTLIER) cc_final: 0.8354 (t-170) REVERT: E 453 LYS cc_start: 0.9350 (OUTLIER) cc_final: 0.9076 (mmmm) REVERT: E 471 ILE cc_start: 0.7210 (OUTLIER) cc_final: 0.6760 (pp) REVERT: F 91 ASP cc_start: 0.7922 (t0) cc_final: 0.7512 (t0) REVERT: F 129 LYS cc_start: 0.8871 (tppt) cc_final: 0.8515 (tppt) REVERT: F 392 TYR cc_start: 0.9301 (OUTLIER) cc_final: 0.9029 (p90) REVERT: I 85 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8498 (mmmm) REVERT: I 364 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7667 (mmt90) REVERT: I 370 TRP cc_start: 0.8604 (OUTLIER) cc_final: 0.7787 (t60) REVERT: J 4 LYS cc_start: 0.9303 (OUTLIER) cc_final: 0.9086 (mptt) REVERT: J 55 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8373 (tp30) REVERT: J 193 MET cc_start: 0.6626 (pmm) cc_final: 0.6234 (pmm) REVERT: J 234 HIS cc_start: 0.8751 (OUTLIER) cc_final: 0.8481 (p90) REVERT: J 384 LEU cc_start: 0.8954 (pt) cc_final: 0.8462 (tp) REVERT: J 394 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7139 (pm20) REVERT: J 395 MET cc_start: 0.7328 (pmm) cc_final: 0.2495 (tmt) REVERT: N 129 LYS cc_start: 0.9350 (tppt) cc_final: 0.9141 (tppt) REVERT: N 137 LYS cc_start: 0.9096 (tmtt) cc_final: 0.8734 (tmmt) REVERT: N 223 PHE cc_start: 0.6167 (m-10) cc_final: 0.5431 (m-10) outliers start: 126 outliers final: 71 residues processed: 279 average time/residue: 1.0338 time to fit residues: 363.6300 Evaluate side-chains 245 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 153 time to evaluate : 3.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 278 VAL 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 131 ILE 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 185 LEU 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 227 LEU 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 335 LEU Chi-restraints excluded: chain B residue 364 GLN 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 52 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 471 ILE 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 391 PHE Chi-restraints excluded: chain F residue 392 TYR 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 274 VAL Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 364 ARG Chi-restraints excluded: chain I residue 370 TRP Chi-restraints excluded: chain I residue 374 LEU Chi-restraints excluded: chain I residue 390 LYS 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 4 LYS Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 55 GLU 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 204 THR Chi-restraints excluded: chain J residue 234 HIS Chi-restraints excluded: chain J residue 297 LYS Chi-restraints excluded: chain J residue 341 ILE Chi-restraints excluded: chain J residue 391 PHE 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 384 VAL 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 459 ILE 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 65 SER Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 315 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 39 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 147 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 70 optimal weight: 0.0970 chunk 243 optimal weight: 0.0670 chunk 255 optimal weight: 20.0000 chunk 201 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 239 optimal weight: 5.9990 chunk 135 optimal weight: 0.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- 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 160 HIS B 226 HIS ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 ASN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 207 HIS I 251 HIS ** I 307 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.072906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.054904 restraints weight = 142541.947| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 4.13 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3587 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3587 r_free = 0.3587 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1412 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3586 r_free = 0.3586 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1428 | |-----------------------------------------------------------------------------| r_final: 0.3586 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 32928 Z= 0.123 Angle : 0.695 14.604 45228 Z= 0.342 Chirality : 0.043 0.368 4980 Planarity : 0.004 0.074 5118 Dihedral : 18.580 177.039 5918 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.15 % Favored : 93.76 % Rotamer: Outliers : 3.29 % Allowed : 31.04 % Favored : 65.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.15), residues: 3464 helix: 1.29 (0.16), residues: 1176 sheet: -0.56 (0.21), residues: 662 loop : -1.60 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 86 HIS 0.011 0.001 HIS I 207 PHE 0.031 0.001 PHE E 224 TYR 0.031 0.001 TYR F 225 ARG 0.017 0.001 ARG J 19 Details of bonding type rmsd hydrogen bonds : bond 0.03575 ( 1136) hydrogen bonds : angle 4.54415 ( 3076) covalent geometry : bond 0.00272 (32928) covalent geometry : angle 0.69474 (45228) *********************** 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 279 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 178 time to evaluate : 3.537 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: 0.9199 (m-30) cc_final: 0.8745 (m-30) REVERT: B 165 ILE cc_start: 0.7312 (mt) cc_final: 0.6980 (pp) REVERT: B 183 GLU cc_start: 0.9462 (pm20) cc_final: 0.9093 (pm20) REVERT: B 185 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9146 (tt) REVERT: B 193 MET cc_start: 0.8055 (tpt) cc_final: 0.7355 (tpt) REVERT: B 205 PHE cc_start: 0.8738 (OUTLIER) cc_final: 0.8403 (t80) REVERT: B 295 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7442 (mt) REVERT: B 323 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8823 (mm) REVERT: B 335 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8770 (tm) REVERT: E 435 MET cc_start: 0.8028 (tpt) cc_final: 0.7806 (mtt) REVERT: E 453 LYS cc_start: 0.9301 (OUTLIER) cc_final: 0.9008 (mmmm) REVERT: E 471 ILE cc_start: 0.7291 (OUTLIER) cc_final: 0.6825 (pp) REVERT: F 91 ASP cc_start: 0.7913 (t0) cc_final: 0.7463 (t0) REVERT: F 129 LYS cc_start: 0.8912 (tppt) cc_final: 0.8610 (tppt) REVERT: I 33 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.9063 (tp) REVERT: I 85 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8599 (mmmm) REVERT: I 370 TRP cc_start: 0.8585 (OUTLIER) cc_final: 0.7799 (t60) REVERT: I 422 THR cc_start: 0.8810 (p) cc_final: 0.8568 (m) REVERT: J 55 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8351 (tp30) REVERT: J 193 MET cc_start: 0.7042 (pmm) cc_final: 0.6590 (pmm) REVERT: J 234 HIS cc_start: 0.8768 (OUTLIER) cc_final: 0.8444 (p90) REVERT: J 297 LYS cc_start: 0.5993 (OUTLIER) cc_final: 0.5633 (mptm) REVERT: J 309 MET cc_start: 0.7389 (tpt) cc_final: 0.7162 (tpt) REVERT: J 313 LYS cc_start: 0.8372 (tptp) cc_final: 0.8102 (tptp) REVERT: J 394 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7174 (pm20) REVERT: J 395 MET cc_start: 0.7161 (pmm) cc_final: 0.2462 (tmt) REVERT: M 56 TYR cc_start: 0.8439 (t80) cc_final: 0.8040 (t80) REVERT: M 258 THR cc_start: 0.9319 (m) cc_final: 0.8952 (t) REVERT: N 83 LYS cc_start: 0.9336 (OUTLIER) cc_final: 0.9071 (mmtm) REVERT: N 137 LYS cc_start: 0.9104 (tmtt) cc_final: 0.8707 (tmmt) REVERT: N 193 MET cc_start: 0.7268 (tpt) cc_final: 0.7039 (tpt) REVERT: N 223 PHE cc_start: 0.6118 (m-10) cc_final: 0.5417 (m-10) outliers start: 101 outliers final: 60 residues processed: 265 average time/residue: 1.0393 time to fit residues: 345.5134 Evaluate side-chains 237 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 162 time to evaluate : 3.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 185 LEU 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 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 453 LYS Chi-restraints excluded: chain E residue 471 ILE 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 391 PHE Chi-restraints excluded: chain F residue 392 TYR 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 274 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 390 LYS 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 55 GLU 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 214 LEU Chi-restraints excluded: chain J residue 234 HIS Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 297 LYS Chi-restraints excluded: chain J residue 391 PHE 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 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 463 THR Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 83 LYS Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 315 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 247 optimal weight: 10.0000 chunk 163 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 133 optimal weight: 0.2980 chunk 140 optimal weight: 6.9990 chunk 253 optimal weight: 6.9990 chunk 212 optimal weight: 10.0000 chunk 224 optimal weight: 1.9990 chunk 182 optimal weight: 6.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 364 GLN ** 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 329 HIS ** 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 = 0.4125 r_free = 0.4125 target = 0.071523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.053343 restraints weight = 143304.556| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 4.03 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3541 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1428 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1454 | |-----------------------------------------------------------------------------| r_final: 0.3540 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 32928 Z= 0.176 Angle : 0.716 14.036 45228 Z= 0.355 Chirality : 0.044 0.386 4980 Planarity : 0.004 0.062 5118 Dihedral : 18.605 177.294 5918 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.76 % Favored : 93.16 % Rotamer: Outliers : 3.12 % Allowed : 31.47 % Favored : 65.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.15), residues: 3464 helix: 1.22 (0.16), residues: 1176 sheet: -0.72 (0.21), residues: 676 loop : -1.61 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 86 HIS 0.006 0.001 HIS J 160 PHE 0.016 0.001 PHE B 187 TYR 0.024 0.001 TYR J 293 ARG 0.015 0.000 ARG J 19 Details of bonding type rmsd hydrogen bonds : bond 0.03893 ( 1136) hydrogen bonds : angle 4.62527 ( 3076) covalent geometry : bond 0.00394 (32928) covalent geometry : angle 0.71600 (45228) ********************** 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 261 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 165 time to evaluate : 3.590 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 25 ASP cc_start: 0.9227 (m-30) cc_final: 0.8734 (m-30) REVERT: B 183 GLU cc_start: 0.9469 (pm20) cc_final: 0.9071 (pm20) REVERT: B 185 LEU cc_start: 0.9565 (OUTLIER) cc_final: 0.9145 (tt) REVERT: B 193 MET cc_start: 0.8126 (tpt) cc_final: 0.7699 (tpt) REVERT: B 198 PHE cc_start: 0.7896 (OUTLIER) cc_final: 0.7355 (t80) REVERT: B 205 PHE cc_start: 0.8789 (OUTLIER) cc_final: 0.8360 (t80) REVERT: B 323 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8891 (mm) REVERT: B 335 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8775 (tm) REVERT: B 364 GLN cc_start: 0.9305 (OUTLIER) cc_final: 0.8992 (tp-100) REVERT: E 435 MET cc_start: 0.8110 (tpt) cc_final: 0.7865 (mtt) REVERT: E 453 LYS cc_start: 0.9330 (OUTLIER) cc_final: 0.9045 (mmmm) REVERT: E 471 ILE cc_start: 0.7265 (OUTLIER) cc_final: 0.6812 (pp) REVERT: F 91 ASP cc_start: 0.7910 (t0) cc_final: 0.7477 (t0) REVERT: F 129 LYS cc_start: 0.8930 (tppt) cc_final: 0.8232 (tppt) REVERT: F 133 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8334 (mm-30) REVERT: I 85 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8522 (mmmm) REVERT: I 370 TRP cc_start: 0.8630 (OUTLIER) cc_final: 0.7837 (t60) REVERT: J 4 LYS cc_start: 0.9338 (OUTLIER) cc_final: 0.9133 (mptt) REVERT: J 55 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8339 (tp30) REVERT: J 142 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8210 (tmtt) REVERT: J 193 MET cc_start: 0.7012 (pmm) cc_final: 0.6592 (pmm) REVERT: J 234 HIS cc_start: 0.8742 (OUTLIER) cc_final: 0.8415 (p90) REVERT: J 297 LYS cc_start: 0.6087 (OUTLIER) cc_final: 0.5650 (mptm) REVERT: J 309 MET cc_start: 0.7387 (tpt) cc_final: 0.7163 (tpt) REVERT: J 394 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7133 (pm20) REVERT: J 395 MET cc_start: 0.7269 (pmm) cc_final: 0.2544 (tmt) REVERT: N 83 LYS cc_start: 0.9316 (OUTLIER) cc_final: 0.9068 (mmtm) REVERT: N 137 LYS cc_start: 0.9091 (tmtt) cc_final: 0.8689 (tmmt) REVERT: N 223 PHE cc_start: 0.6137 (m-10) cc_final: 0.5566 (m-10) REVERT: N 287 MET cc_start: 0.6605 (mmm) cc_final: 0.6359 (mmp) outliers start: 96 outliers final: 60 residues processed: 249 average time/residue: 1.1039 time to fit residues: 346.9638 Evaluate side-chains 238 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 161 time to evaluate : 3.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 460 LEU 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 185 LEU Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 205 PHE Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 364 GLN 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 453 LYS Chi-restraints excluded: chain E residue 471 ILE 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 391 PHE Chi-restraints excluded: chain F residue 392 TYR 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 274 VAL Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 370 TRP Chi-restraints excluded: chain I residue 390 LYS 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 4 LYS Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 55 GLU 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 142 LYS Chi-restraints excluded: chain J residue 191 ASN Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 234 HIS Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 297 LYS Chi-restraints excluded: chain J residue 391 PHE 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 459 ILE Chi-restraints excluded: chain M residue 463 THR Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 83 LYS Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 315 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 206 optimal weight: 6.9990 chunk 273 optimal weight: 4.9990 chunk 263 optimal weight: 0.0770 chunk 162 optimal weight: 7.9990 chunk 248 optimal weight: 5.9990 chunk 228 optimal weight: 2.9990 chunk 197 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 240 optimal weight: 0.9990 chunk 266 optimal weight: 6.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 207 HIS ** 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 = 0.4125 r_free = 0.4125 target = 0.071497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.053162 restraints weight = 143714.446| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 3.79 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3546 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3546 r_free = 0.3546 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1454 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | 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: 1486 | |-----------------------------------------------------------------------------| r_final: 0.3545 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.149 32928 Z= 0.187 Angle : 0.807 59.114 45228 Z= 0.421 Chirality : 0.044 0.388 4980 Planarity : 0.004 0.063 5118 Dihedral : 18.605 177.265 5918 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.73 % Favored : 93.19 % Rotamer: Outliers : 2.90 % Allowed : 31.83 % Favored : 65.28 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.15), residues: 3464 helix: 1.22 (0.16), residues: 1176 sheet: -0.65 (0.21), residues: 662 loop : -1.62 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 86 HIS 0.054 0.002 HIS M 207 PHE 0.015 0.001 PHE J 273 TYR 0.021 0.001 TYR J 293 ARG 0.015 0.000 ARG J 19 Details of bonding type rmsd hydrogen bonds : bond 0.03902 ( 1136) hydrogen bonds : angle 4.63900 ( 3076) covalent geometry : bond 0.00413 (32928) covalent geometry : angle 0.80735 (45228) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25685.85 seconds wall clock time: 443 minutes 2.31 seconds (26582.31 seconds total)