Starting phenix.real_space_refine on Fri Apr 12 20:13:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xmi_38478/04_2024/8xmi_38478_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xmi_38478/04_2024/8xmi_38478.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xmi_38478/04_2024/8xmi_38478.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xmi_38478/04_2024/8xmi_38478.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xmi_38478/04_2024/8xmi_38478_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xmi_38478/04_2024/8xmi_38478_updated.pdb" } resolution = 3.0 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= 0.000 sd= 0.071 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: 7 Type Number sf(0) Gaussians K 4 8.98 5 P 24 5.49 5 S 115 5.16 5 Na 4 4.78 5 C 17302 2.51 5 N 4377 2.21 5 O 4892 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 26718 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 209} Chain: "B" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 209} Chain: "C" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 209} Chain: "D" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1582 Classifications: {'peptide': 202} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 196} Chain breaks: 3 Chain: "E" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1568 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 2, 'TRANS': 196} Chain breaks: 1 Chain: "F" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 209} Chain: "G" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 209} Chain: "H" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 209} Chain: "I" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3293 Classifications: {'peptide': 431} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 414} Chain: "J" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3293 Classifications: {'peptide': 431} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 414} Chain: "K" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3293 Classifications: {'peptide': 431} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 414} Chain: "L" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3293 Classifications: {'peptide': 431} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 414} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' NA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' NA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' NA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' NA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.97, per 1000 atoms: 0.52 Number of scatterers: 26718 At special positions: 0 Unit cell: (178.45, 172.64, 134.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 4 19.00 S 115 16.00 P 24 15.00 Na 4 11.00 O 4892 8.00 N 4377 7.00 C 17302 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 - 3.50 Amino acid : False - 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: 11.94 Conformation dependent library (CDL) restraints added in 5.5 seconds 6766 Ramachandran restraints generated. 3383 Oldfield, 0 Emsley, 3383 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6306 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 148 helices and 20 sheets defined 50.2% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.10 Creating SS restraints... Processing helix chain 'A' and resid 18 through 27 Processing helix chain 'A' and resid 39 through 45 Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 68 through 70 No H-bonds generated for 'chain 'A' and resid 68 through 70' Processing helix chain 'A' and resid 82 through 94 Processing helix chain 'A' and resid 107 through 115 Processing helix chain 'A' and resid 124 through 137 Processing helix chain 'A' and resid 211 through 220 removed outlier: 3.699A pdb=" N LYS A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 28 removed outlier: 3.668A pdb=" N SER B 20 " --> pdb=" O ARG B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 44 Processing helix chain 'B' and resid 60 through 66 removed outlier: 3.542A pdb=" N SER B 65 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU B 66 " --> pdb=" O GLU B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 70 No H-bonds generated for 'chain 'B' and resid 68 through 70' Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'B' and resid 107 through 115 Processing helix chain 'B' and resid 124 through 137 removed outlier: 3.517A pdb=" N SER B 135 " --> pdb=" O LYS B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 211 through 219 removed outlier: 3.895A pdb=" N LYS B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 27 removed outlier: 3.609A pdb=" N SER C 20 " --> pdb=" O ARG C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 44 Processing helix chain 'C' and resid 60 through 66 removed outlier: 3.681A pdb=" N LEU C 66 " --> pdb=" O GLU C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 70 No H-bonds generated for 'chain 'C' and resid 68 through 70' Processing helix chain 'C' and resid 82 through 94 Processing helix chain 'C' and resid 107 through 115 Processing helix chain 'C' and resid 124 through 137 Processing helix chain 'C' and resid 211 through 220 removed outlier: 3.618A pdb=" N LYS C 215 " --> pdb=" O LYS C 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 28 removed outlier: 3.587A pdb=" N SER D 20 " --> pdb=" O ARG D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 45 Processing helix chain 'D' and resid 60 through 65 Processing helix chain 'D' and resid 68 through 70 No H-bonds generated for 'chain 'D' and resid 68 through 70' Processing helix chain 'D' and resid 82 through 94 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 124 through 137 removed outlier: 3.550A pdb=" N SER D 135 " --> pdb=" O LYS D 131 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER D 137 " --> pdb=" O ALA D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 220 Processing helix chain 'E' and resid 18 through 27 Processing helix chain 'E' and resid 39 through 45 Processing helix chain 'E' and resid 60 through 65 Processing helix chain 'E' and resid 68 through 70 No H-bonds generated for 'chain 'E' and resid 68 through 70' Processing helix chain 'E' and resid 82 through 94 Processing helix chain 'E' and resid 107 through 115 Processing helix chain 'E' and resid 124 through 137 removed outlier: 3.573A pdb=" N SER E 135 " --> pdb=" O LYS E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 220 removed outlier: 3.642A pdb=" N LYS E 215 " --> pdb=" O LYS E 211 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG E 216 " --> pdb=" O LYS E 212 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE E 217 " --> pdb=" O ASP E 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 28 Processing helix chain 'F' and resid 39 through 44 Processing helix chain 'F' and resid 60 through 66 removed outlier: 3.855A pdb=" N LEU F 66 " --> pdb=" O GLU F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 70 No H-bonds generated for 'chain 'F' and resid 68 through 70' Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'F' and resid 107 through 115 Processing helix chain 'F' and resid 124 through 137 removed outlier: 3.587A pdb=" N SER F 135 " --> pdb=" O LYS F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 220 removed outlier: 3.558A pdb=" N ASN F 219 " --> pdb=" O LYS F 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 27 Processing helix chain 'G' and resid 39 through 44 Processing helix chain 'G' and resid 60 through 66 removed outlier: 3.729A pdb=" N LEU G 66 " --> pdb=" O GLU G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 70 No H-bonds generated for 'chain 'G' and resid 68 through 70' Processing helix chain 'G' and resid 82 through 94 Processing helix chain 'G' and resid 107 through 115 Processing helix chain 'G' and resid 124 through 137 Processing helix chain 'G' and resid 172 through 175 No H-bonds generated for 'chain 'G' and resid 172 through 175' Processing helix chain 'G' and resid 211 through 220 removed outlier: 3.909A pdb=" N LYS G 215 " --> pdb=" O LYS G 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 27 Processing helix chain 'H' and resid 39 through 44 Processing helix chain 'H' and resid 60 through 65 Processing helix chain 'H' and resid 68 through 70 No H-bonds generated for 'chain 'H' and resid 68 through 70' Processing helix chain 'H' and resid 82 through 94 Processing helix chain 'H' and resid 107 through 115 Processing helix chain 'H' and resid 124 through 137 removed outlier: 3.616A pdb=" N SER H 135 " --> pdb=" O LYS H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 220 removed outlier: 3.659A pdb=" N LYS H 215 " --> pdb=" O LYS H 211 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 36 removed outlier: 3.664A pdb=" N LEU I 20 " --> pdb=" O PRO I 16 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE I 28 " --> pdb=" O PHE I 24 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU I 35 " --> pdb=" O GLY I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 58 Processing helix chain 'I' and resid 68 through 71 No H-bonds generated for 'chain 'I' and resid 68 through 71' Processing helix chain 'I' and resid 74 through 89 Processing helix chain 'I' and resid 91 through 102 removed outlier: 3.660A pdb=" N LEU I 97 " --> pdb=" O THR I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 117 removed outlier: 3.785A pdb=" N LEU I 113 " --> pdb=" O LYS I 109 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL I 114 " --> pdb=" O GLU I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 126 through 156 removed outlier: 3.566A pdb=" N VAL I 130 " --> pdb=" O VAL I 126 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE I 150 " --> pdb=" O LEU I 146 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ARG I 151 " --> pdb=" O ILE I 147 " (cutoff:3.500A) Proline residue: I 154 - end of helix Processing helix chain 'I' and resid 159 through 173 removed outlier: 3.893A pdb=" N PHE I 163 " --> pdb=" O SER I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 192 through 206 Processing helix chain 'I' and resid 209 through 217 Processing helix chain 'I' and resid 221 through 223 No H-bonds generated for 'chain 'I' and resid 221 through 223' Processing helix chain 'I' and resid 226 through 249 Processing helix chain 'I' and resid 262 through 274 removed outlier: 3.515A pdb=" N VAL I 274 " --> pdb=" O TYR I 270 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 288 No H-bonds generated for 'chain 'I' and resid 286 through 288' Processing helix chain 'I' and resid 291 through 302 removed outlier: 3.528A pdb=" N PHE I 296 " --> pdb=" O GLY I 292 " (cutoff:3.500A) Processing helix chain 'I' and resid 316 through 330 Processing helix chain 'I' and resid 345 through 372 Processing helix chain 'I' and resid 377 through 388 Processing helix chain 'I' and resid 398 through 400 No H-bonds generated for 'chain 'I' and resid 398 through 400' Processing helix chain 'I' and resid 403 through 418 removed outlier: 3.509A pdb=" N CYS I 407 " --> pdb=" O THR I 403 " (cutoff:3.500A) Processing helix chain 'I' and resid 420 through 427 removed outlier: 4.194A pdb=" N PHE I 427 " --> pdb=" O PHE I 423 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 36 removed outlier: 3.725A pdb=" N LEU J 20 " --> pdb=" O PRO J 16 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE J 28 " --> pdb=" O PHE J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 40 No H-bonds generated for 'chain 'J' and resid 38 through 40' Processing helix chain 'J' and resid 47 through 58 Processing helix chain 'J' and resid 68 through 71 No H-bonds generated for 'chain 'J' and resid 68 through 71' Processing helix chain 'J' and resid 74 through 89 Processing helix chain 'J' and resid 91 through 102 Processing helix chain 'J' and resid 108 through 117 removed outlier: 3.515A pdb=" N LEU J 113 " --> pdb=" O LYS J 109 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL J 114 " --> pdb=" O GLU J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 156 removed outlier: 4.148A pdb=" N ARG J 151 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Proline residue: J 154 - end of helix Processing helix chain 'J' and resid 161 through 173 Processing helix chain 'J' and resid 192 through 206 Processing helix chain 'J' and resid 209 through 217 Processing helix chain 'J' and resid 221 through 223 No H-bonds generated for 'chain 'J' and resid 221 through 223' Processing helix chain 'J' and resid 226 through 249 Processing helix chain 'J' and resid 262 through 274 Processing helix chain 'J' and resid 291 through 302 Processing helix chain 'J' and resid 316 through 330 Processing helix chain 'J' and resid 345 through 372 Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 398 through 400 No H-bonds generated for 'chain 'J' and resid 398 through 400' Processing helix chain 'J' and resid 403 through 418 removed outlier: 3.556A pdb=" N CYS J 407 " --> pdb=" O THR J 403 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE J 408 " --> pdb=" O ALA J 404 " (cutoff:3.500A) Processing helix chain 'J' and resid 420 through 427 removed outlier: 4.022A pdb=" N PHE J 427 " --> pdb=" O PHE J 423 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 35 removed outlier: 3.624A pdb=" N LEU K 20 " --> pdb=" O PRO K 16 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE K 28 " --> pdb=" O PHE K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 58 Processing helix chain 'K' and resid 68 through 71 No H-bonds generated for 'chain 'K' and resid 68 through 71' Processing helix chain 'K' and resid 74 through 89 Processing helix chain 'K' and resid 91 through 102 Processing helix chain 'K' and resid 108 through 117 removed outlier: 3.844A pdb=" N VAL K 114 " --> pdb=" O GLU K 110 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 173 removed outlier: 4.212A pdb=" N ARG K 151 " --> pdb=" O ILE K 147 " (cutoff:3.500A) Proline residue: K 154 - end of helix removed outlier: 7.589A pdb=" N TRP K 158 " --> pdb=" O PRO K 154 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N SER K 159 " --> pdb=" O GLN K 155 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER K 160 " --> pdb=" O TYR K 156 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU K 162 " --> pdb=" O TRP K 158 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE K 163 " --> pdb=" O SER K 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 192 through 204 Processing helix chain 'K' and resid 209 through 217 Processing helix chain 'K' and resid 221 through 223 No H-bonds generated for 'chain 'K' and resid 221 through 223' Processing helix chain 'K' and resid 226 through 249 Processing helix chain 'K' and resid 262 through 274 removed outlier: 3.536A pdb=" N VAL K 274 " --> pdb=" O TYR K 270 " (cutoff:3.500A) Processing helix chain 'K' and resid 286 through 288 No H-bonds generated for 'chain 'K' and resid 286 through 288' Processing helix chain 'K' and resid 291 through 302 Processing helix chain 'K' and resid 316 through 330 Processing helix chain 'K' and resid 345 through 372 removed outlier: 3.561A pdb=" N ILE K 371 " --> pdb=" O PHE K 367 " (cutoff:3.500A) Processing helix chain 'K' and resid 377 through 388 Processing helix chain 'K' and resid 398 through 400 No H-bonds generated for 'chain 'K' and resid 398 through 400' Processing helix chain 'K' and resid 403 through 418 Processing helix chain 'K' and resid 420 through 427 removed outlier: 4.165A pdb=" N PHE K 427 " --> pdb=" O PHE K 423 " (cutoff:3.500A) Processing helix chain 'L' and resid 16 through 36 removed outlier: 3.859A pdb=" N ILE L 28 " --> pdb=" O PHE L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 58 Processing helix chain 'L' and resid 68 through 71 No H-bonds generated for 'chain 'L' and resid 68 through 71' Processing helix chain 'L' and resid 74 through 89 Processing helix chain 'L' and resid 91 through 102 removed outlier: 3.517A pdb=" N ALA L 95 " --> pdb=" O PHE L 91 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU L 97 " --> pdb=" O THR L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 108 through 117 removed outlier: 3.705A pdb=" N LEU L 113 " --> pdb=" O LYS L 109 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL L 114 " --> pdb=" O GLU L 110 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 173 removed outlier: 3.574A pdb=" N VAL L 130 " --> pdb=" O VAL L 126 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE L 150 " --> pdb=" O LEU L 146 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ARG L 151 " --> pdb=" O ILE L 147 " (cutoff:3.500A) Proline residue: L 154 - end of helix removed outlier: 7.977A pdb=" N TRP L 158 " --> pdb=" O PRO L 154 " (cutoff:3.500A) removed outlier: 9.125A pdb=" N SER L 159 " --> pdb=" O GLN L 155 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER L 160 " --> pdb=" O TYR L 156 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU L 162 " --> pdb=" O TRP L 158 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE L 163 " --> pdb=" O SER L 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 192 through 206 Processing helix chain 'L' and resid 209 through 217 removed outlier: 3.614A pdb=" N LYS L 217 " --> pdb=" O PHE L 213 " (cutoff:3.500A) Processing helix chain 'L' and resid 221 through 223 No H-bonds generated for 'chain 'L' and resid 221 through 223' Processing helix chain 'L' and resid 226 through 249 removed outlier: 3.502A pdb=" N LEU L 236 " --> pdb=" O LEU L 232 " (cutoff:3.500A) Processing helix chain 'L' and resid 262 through 274 removed outlier: 3.513A pdb=" N VAL L 274 " --> pdb=" O TYR L 270 " (cutoff:3.500A) Processing helix chain 'L' and resid 286 through 288 No H-bonds generated for 'chain 'L' and resid 286 through 288' Processing helix chain 'L' and resid 291 through 302 Processing helix chain 'L' and resid 316 through 330 Processing helix chain 'L' and resid 345 through 372 Processing helix chain 'L' and resid 377 through 388 Processing helix chain 'L' and resid 398 through 400 No H-bonds generated for 'chain 'L' and resid 398 through 400' Processing helix chain 'L' and resid 403 through 418 Processing helix chain 'L' and resid 420 through 427 removed outlier: 3.556A pdb=" N SER L 426 " --> pdb=" O THR L 422 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE L 427 " --> pdb=" O PHE L 423 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 120 through 122 removed outlier: 3.684A pdb=" N TYR A 73 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLU A 31 " --> pdb=" O PHE A 9 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL A 11 " --> pdb=" O GLU A 31 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU A 33 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N HIS A 51 " --> pdb=" O ALA A 34 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ASP A 36 " --> pdb=" O HIS A 51 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL A 53 " --> pdb=" O ASP A 36 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 141 through 146 removed outlier: 6.929A pdb=" N GLU A 155 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR A 144 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE A 153 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ASP A 146 " --> pdb=" O TYR A 151 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N TYR A 151 " --> pdb=" O ASP A 146 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY A 209 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 156 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N CYS A 204 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS A 184 " --> pdb=" O CYS A 204 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA A 182 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N MET A 208 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ILE A 180 " --> pdb=" O MET A 208 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 120 through 122 removed outlier: 3.528A pdb=" N TYR B 73 " --> pdb=" O GLN B 8 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLU B 31 " --> pdb=" O PHE B 9 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N VAL B 11 " --> pdb=" O GLU B 31 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU B 33 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N HIS B 51 " --> pdb=" O ALA B 34 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ASP B 36 " --> pdb=" O HIS B 51 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N VAL B 53 " --> pdb=" O ASP B 36 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 141 through 146 removed outlier: 6.914A pdb=" N GLU B 155 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N TYR B 144 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE B 153 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ASP B 146 " --> pdb=" O TYR B 151 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N TYR B 151 " --> pdb=" O ASP B 146 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY B 209 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N CYS B 204 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N MET B 208 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ILE B 180 " --> pdb=" O MET B 208 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 120 through 122 removed outlier: 3.621A pdb=" N TYR C 73 " --> pdb=" O GLN C 8 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N GLU C 31 " --> pdb=" O PHE C 9 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N VAL C 11 " --> pdb=" O GLU C 31 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU C 33 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N HIS C 51 " --> pdb=" O ALA C 34 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N ASP C 36 " --> pdb=" O HIS C 51 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL C 53 " --> pdb=" O ASP C 36 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 141 through 146 removed outlier: 6.953A pdb=" N GLU C 155 " --> pdb=" O LEU C 142 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N TYR C 144 " --> pdb=" O ILE C 153 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ASP C 146 " --> pdb=" O TYR C 151 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N TYR C 151 " --> pdb=" O ASP C 146 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N CYS C 204 " --> pdb=" O LYS C 184 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA C 182 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N MET C 208 " --> pdb=" O ILE C 180 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ILE C 180 " --> pdb=" O MET C 208 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 120 through 122 removed outlier: 3.618A pdb=" N TYR D 73 " --> pdb=" O GLN D 8 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLU D 31 " --> pdb=" O PHE D 9 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N VAL D 11 " --> pdb=" O GLU D 31 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU D 33 " --> pdb=" O VAL D 11 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N HIS D 51 " --> pdb=" O ALA D 34 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ASP D 36 " --> pdb=" O HIS D 51 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL D 53 " --> pdb=" O ASP D 36 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 141 through 145 removed outlier: 6.940A pdb=" N GLU D 155 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR D 144 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE D 153 " --> pdb=" O TYR D 144 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY D 209 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA D 182 " --> pdb=" O VAL D 206 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N MET D 208 " --> pdb=" O ILE D 180 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ILE D 180 " --> pdb=" O MET D 208 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 120 through 122 removed outlier: 3.732A pdb=" N TYR E 73 " --> pdb=" O GLN E 8 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLU E 31 " --> pdb=" O PHE E 9 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL E 11 " --> pdb=" O GLU E 31 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU E 33 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N HIS E 51 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N ASP E 36 " --> pdb=" O HIS E 51 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL E 53 " --> pdb=" O ASP E 36 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 141 through 146 removed outlier: 6.870A pdb=" N GLU E 155 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR E 144 " --> pdb=" O ILE E 153 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE E 153 " --> pdb=" O TYR E 144 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ASP E 146 " --> pdb=" O TYR E 151 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N TYR E 151 " --> pdb=" O ASP E 146 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA E 182 " --> pdb=" O VAL E 206 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N MET E 208 " --> pdb=" O ILE E 180 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ILE E 180 " --> pdb=" O MET E 208 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 120 through 122 removed outlier: 3.574A pdb=" N TYR F 73 " --> pdb=" O GLN F 8 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLU F 31 " --> pdb=" O PHE F 9 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N VAL F 11 " --> pdb=" O GLU F 31 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU F 33 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N HIS F 51 " --> pdb=" O ALA F 34 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N ASP F 36 " --> pdb=" O HIS F 51 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL F 53 " --> pdb=" O ASP F 36 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 141 through 146 removed outlier: 6.896A pdb=" N GLU F 155 " --> pdb=" O LEU F 142 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TYR F 144 " --> pdb=" O ILE F 153 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE F 153 " --> pdb=" O TYR F 144 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ASP F 146 " --> pdb=" O TYR F 151 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N TYR F 151 " --> pdb=" O ASP F 146 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N CYS F 204 " --> pdb=" O LYS F 184 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA F 182 " --> pdb=" O VAL F 206 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N MET F 208 " --> pdb=" O ILE F 180 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ILE F 180 " --> pdb=" O MET F 208 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 120 through 122 removed outlier: 6.317A pdb=" N GLU G 31 " --> pdb=" O PHE G 9 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N VAL G 11 " --> pdb=" O GLU G 31 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU G 33 " --> pdb=" O VAL G 11 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N HIS G 51 " --> pdb=" O ALA G 34 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ASP G 36 " --> pdb=" O HIS G 51 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL G 53 " --> pdb=" O ASP G 36 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 143 through 146 removed outlier: 4.002A pdb=" N ASN G 143 " --> pdb=" O GLU G 155 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N MET G 208 " --> pdb=" O ILE G 180 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ILE G 180 " --> pdb=" O MET G 208 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 120 through 122 removed outlier: 3.766A pdb=" N TYR H 73 " --> pdb=" O GLN H 8 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLU H 31 " --> pdb=" O PHE H 9 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N VAL H 11 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU H 33 " --> pdb=" O VAL H 11 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N HIS H 51 " --> pdb=" O ALA H 34 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ASP H 36 " --> pdb=" O HIS H 51 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL H 53 " --> pdb=" O ASP H 36 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 143 through 146 removed outlier: 3.800A pdb=" N ASN H 143 " --> pdb=" O GLU H 155 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS H 204 " --> pdb=" O LYS H 184 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N MET H 208 " --> pdb=" O ILE H 180 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ILE H 180 " --> pdb=" O MET H 208 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 336 through 338 removed outlier: 4.668A pdb=" N THR I 336 " --> pdb=" O ILE I 343 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'J' and resid 336 through 338 removed outlier: 4.685A pdb=" N THR J 336 " --> pdb=" O ILE J 343 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'K' and resid 336 through 338 removed outlier: 4.697A pdb=" N THR K 336 " --> pdb=" O ILE K 343 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'L' and resid 336 through 338 removed outlier: 4.568A pdb=" N THR L 336 " --> pdb=" O ILE L 343 " (cutoff:3.500A) 1240 hydrogen bonds defined for protein. 3663 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.31 Time building geometry restraints manager: 12.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4633 1.32 - 1.44: 6622 1.44 - 1.57: 15723 1.57 - 1.69: 40 1.69 - 1.81: 195 Bond restraints: 27213 Sorted by residual: bond pdb=" N LEU J 352 " pdb=" CA LEU J 352 " ideal model delta sigma weight residual 1.459 1.403 0.056 1.21e-02 6.83e+03 2.15e+01 bond pdb=" CA THR I 41 " pdb=" C THR I 41 " ideal model delta sigma weight residual 1.522 1.469 0.053 1.20e-02 6.94e+03 1.99e+01 bond pdb=" CA ALA J 351 " pdb=" C ALA J 351 " ideal model delta sigma weight residual 1.523 1.468 0.055 1.30e-02 5.92e+03 1.81e+01 bond pdb=" CA GLY G 67 " pdb=" C GLY G 67 " ideal model delta sigma weight residual 1.514 1.455 0.059 1.41e-02 5.03e+03 1.77e+01 bond pdb=" N VAL J 354 " pdb=" CA VAL J 354 " ideal model delta sigma weight residual 1.461 1.414 0.047 1.19e-02 7.06e+03 1.54e+01 ... (remaining 27208 not shown) Histogram of bond angle deviations from ideal: 99.87 - 107.92: 989 107.92 - 115.97: 17343 115.97 - 124.02: 18103 124.02 - 132.07: 441 132.07 - 140.12: 54 Bond angle restraints: 36930 Sorted by residual: angle pdb=" N SER J 283 " pdb=" CA SER J 283 " pdb=" C SER J 283 " ideal model delta sigma weight residual 114.31 107.90 6.41 1.29e+00 6.01e-01 2.47e+01 angle pdb=" N GLY G 67 " pdb=" CA GLY G 67 " pdb=" C GLY G 67 " ideal model delta sigma weight residual 113.18 101.57 11.61 2.37e+00 1.78e-01 2.40e+01 angle pdb=" N LEU J 298 " pdb=" CA LEU J 298 " pdb=" C LEU J 298 " ideal model delta sigma weight residual 111.14 106.00 5.14 1.08e+00 8.57e-01 2.26e+01 angle pdb=" N ASN J 282 " pdb=" CA ASN J 282 " pdb=" C ASN J 282 " ideal model delta sigma weight residual 108.79 115.93 -7.14 1.53e+00 4.27e-01 2.18e+01 angle pdb=" C VAL I 66 " pdb=" CA VAL I 66 " pdb=" CB VAL I 66 " ideal model delta sigma weight residual 110.82 103.89 6.93 1.54e+00 4.22e-01 2.03e+01 ... (remaining 36925 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 15241 17.70 - 35.39: 839 35.39 - 53.09: 121 53.09 - 70.78: 48 70.78 - 88.48: 17 Dihedral angle restraints: 16266 sinusoidal: 6469 harmonic: 9797 Sorted by residual: dihedral pdb=" CA MET K 301 " pdb=" C MET K 301 " pdb=" N PHE K 302 " pdb=" CA PHE K 302 " ideal model delta harmonic sigma weight residual 180.00 160.64 19.36 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA MET I 301 " pdb=" C MET I 301 " pdb=" N PHE I 302 " pdb=" CA PHE I 302 " ideal model delta harmonic sigma weight residual 180.00 161.71 18.29 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA MET J 301 " pdb=" C MET J 301 " pdb=" N PHE J 302 " pdb=" CA PHE J 302 " ideal model delta harmonic sigma weight residual 180.00 162.98 17.02 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 16263 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 3168 0.043 - 0.085: 974 0.085 - 0.128: 272 0.128 - 0.170: 31 0.170 - 0.213: 6 Chirality restraints: 4451 Sorted by residual: chirality pdb=" CA VAL I 66 " pdb=" N VAL I 66 " pdb=" C VAL I 66 " pdb=" CB VAL I 66 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA THR J 275 " pdb=" N THR J 275 " pdb=" C THR J 275 " pdb=" CB THR J 275 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA THR K 275 " pdb=" N THR K 275 " pdb=" C THR K 275 " pdb=" CB THR K 275 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 4448 not shown) Planarity restraints: 4527 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR J 15 " 0.034 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO J 16 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO J 16 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO J 16 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR I 15 " -0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO I 16 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO I 16 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO I 16 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE J 202 " 0.016 2.00e-02 2.50e+03 1.38e-02 3.32e+00 pdb=" CG PHE J 202 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE J 202 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE J 202 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE J 202 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE J 202 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE J 202 " 0.002 2.00e-02 2.50e+03 ... (remaining 4524 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.84: 8630 2.84 - 3.41: 28237 3.41 - 3.99: 50701 3.99 - 4.56: 73056 4.56 - 5.14: 107426 Nonbonded interactions: 268050 Sorted by model distance: nonbonded pdb=" O ASN K 195 " pdb=" OG1 THR K 199 " model vdw 2.262 2.440 nonbonded pdb=" OE2 GLU I 383 " pdb=" OG1 THR I 398 " model vdw 2.266 2.440 nonbonded pdb=" O ALA L 55 " pdb=" OG1 THR L 59 " model vdw 2.280 2.440 nonbonded pdb=" O LEU I 34 " pdb=" OG SER I 40 " model vdw 2.281 2.440 nonbonded pdb=" OD1 ASN A 56 " pdb=" OG1 THR A 58 " model vdw 2.287 2.440 ... (remaining 268045 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 161 or resid 166 through 184 or resid 204 throug \ h 221)) selection = (chain 'B' and (resid 7 through 161 or resid 166 through 184 or resid 204 throug \ h 221)) selection = (chain 'C' and (resid 7 through 161 or resid 166 through 184 or resid 204 throug \ h 221)) selection = (chain 'D' and (resid 7 through 184 or resid 204 through 221)) selection = (chain 'E' and (resid 7 through 161 or resid 166 through 184 or resid 204 throug \ h 221)) selection = (chain 'F' and (resid 7 through 161 or resid 166 through 184 or resid 204 throug \ h 221)) selection = (chain 'G' and (resid 7 through 161 or resid 166 through 184 or resid 204 throug \ h 221)) selection = (chain 'H' and (resid 7 through 161 or resid 166 through 184 or resid 204 throug \ h 221)) } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.700 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: 0.000 Extract box with map and model: 14.280 Check model and map are aligned: 0.370 Set scattering table: 0.260 Process input model: 78.320 Find NCS groups from input model: 2.390 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 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 : 0.004 0.059 27213 Z= 0.291 Angle : 0.599 11.605 36930 Z= 0.341 Chirality : 0.044 0.213 4451 Planarity : 0.004 0.050 4527 Dihedral : 11.901 88.481 9960 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.56 % Allowed : 5.16 % Favored : 93.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.12), residues: 3383 helix: -1.81 (0.09), residues: 1827 sheet: 0.23 (0.26), residues: 434 loop : -1.14 (0.16), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 181 HIS 0.005 0.001 HIS G 185 PHE 0.032 0.001 PHE J 202 TYR 0.010 0.001 TYR H 108 ARG 0.002 0.000 ARG K 111 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6766 Ramachandran restraints generated. 3383 Oldfield, 0 Emsley, 3383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6766 Ramachandran restraints generated. 3383 Oldfield, 0 Emsley, 3383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 723 time to evaluate : 3.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 20 SER cc_start: 0.8722 (t) cc_final: 0.8468 (m) REVERT: E 62 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6729 (mt-10) REVERT: E 85 SER cc_start: 0.8527 (t) cc_final: 0.8327 (m) REVERT: F 24 GLU cc_start: 0.7218 (tp30) cc_final: 0.6953 (tp30) REVERT: F 38 ASN cc_start: 0.8485 (t0) cc_final: 0.8127 (t0) REVERT: F 155 GLU cc_start: 0.7136 (tt0) cc_final: 0.6841 (tm-30) REVERT: J 188 TYR cc_start: 0.8752 (m-80) cc_final: 0.8550 (m-80) REVERT: K 158 TRP cc_start: 0.8135 (m100) cc_final: 0.7886 (m-90) REVERT: K 222 LYS cc_start: 0.7542 (pttm) cc_final: 0.7341 (mmmt) REVERT: K 299 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8643 (tp) REVERT: K 402 THR cc_start: 0.8803 (p) cc_final: 0.8543 (p) REVERT: L 24 PHE cc_start: 0.7820 (t80) cc_final: 0.7524 (t80) REVERT: L 127 ILE cc_start: 0.8151 (mm) cc_final: 0.7333 (pt) outliers start: 45 outliers final: 12 residues processed: 758 average time/residue: 1.3077 time to fit residues: 1160.7939 Evaluate side-chains 485 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 472 time to evaluate : 3.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 349 ILE Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain L residue 85 GLN Chi-restraints excluded: chain L residue 352 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 284 optimal weight: 0.9980 chunk 255 optimal weight: 7.9990 chunk 141 optimal weight: 0.0270 chunk 87 optimal weight: 3.9990 chunk 172 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 264 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 160 optimal weight: 6.9990 chunk 196 optimal weight: 0.6980 chunk 306 optimal weight: 0.7980 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN B 8 GLN B 210 HIS D 8 GLN D 30 HIS D 143 ASN D 210 HIS E 134 GLN G 83 GLN ** H 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 70 ASN H 81 ASN I 85 GLN I 227 HIS K 85 GLN K 155 GLN K 195 ASN K 253 ASN L 282 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27213 Z= 0.190 Angle : 0.539 7.894 36930 Z= 0.284 Chirality : 0.043 0.168 4451 Planarity : 0.004 0.055 4527 Dihedral : 10.066 84.913 3891 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.60 % Allowed : 13.24 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.13), residues: 3383 helix: 0.42 (0.11), residues: 1843 sheet: 0.21 (0.26), residues: 417 loop : -1.05 (0.16), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 181 HIS 0.006 0.001 HIS G 185 PHE 0.035 0.001 PHE J 202 TYR 0.017 0.001 TYR L 156 ARG 0.010 0.001 ARG J 340 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6766 Ramachandran restraints generated. 3383 Oldfield, 0 Emsley, 3383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6766 Ramachandran restraints generated. 3383 Oldfield, 0 Emsley, 3383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 474 time to evaluate : 2.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.7445 (OUTLIER) cc_final: 0.7227 (m-30) REVERT: B 40 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7324 (pp20) REVERT: C 85 SER cc_start: 0.8572 (OUTLIER) cc_final: 0.8132 (m) REVERT: E 59 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7290 (mt-10) REVERT: F 31 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7201 (mt-10) REVERT: F 59 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7236 (mt-10) REVERT: F 155 GLU cc_start: 0.7166 (tt0) cc_final: 0.6954 (tm-30) REVERT: F 208 MET cc_start: 0.6515 (ttp) cc_final: 0.6089 (ptm) REVERT: G 134 GLN cc_start: 0.7700 (mp10) cc_final: 0.7320 (mp10) REVERT: H 151 TYR cc_start: 0.7634 (m-80) cc_final: 0.7414 (m-80) REVERT: K 97 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7739 (mm) REVERT: K 222 LYS cc_start: 0.7567 (pttm) cc_final: 0.7344 (mmmt) REVERT: K 383 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: K 402 THR cc_start: 0.8638 (p) cc_final: 0.8432 (p) REVERT: L 24 PHE cc_start: 0.7931 (t80) cc_final: 0.7510 (t80) outliers start: 104 outliers final: 35 residues processed: 546 average time/residue: 1.2719 time to fit residues: 816.5485 Evaluate side-chains 468 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 425 time to evaluate : 2.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain H residue 145 ILE Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 186 MET Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 371 ILE Chi-restraints excluded: chain I residue 439 ASP Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain K residue 248 ILE Chi-restraints excluded: chain K residue 383 GLU Chi-restraints excluded: chain K residue 398 THR Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain L residue 187 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 170 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 chunk 254 optimal weight: 0.6980 chunk 208 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 306 optimal weight: 1.9990 chunk 331 optimal weight: 2.9990 chunk 273 optimal weight: 0.9980 chunk 304 optimal weight: 0.6980 chunk 104 optimal weight: 0.0980 chunk 245 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN D 8 GLN E 134 GLN F 51 HIS ** H 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 GLN I 85 GLN L 77 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 27213 Z= 0.159 Angle : 0.491 7.648 36930 Z= 0.258 Chirality : 0.042 0.167 4451 Planarity : 0.004 0.050 4527 Dihedral : 9.268 89.669 3872 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.74 % Allowed : 14.66 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.14), residues: 3383 helix: 1.28 (0.12), residues: 1836 sheet: 0.09 (0.28), residues: 357 loop : -0.98 (0.16), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 181 HIS 0.006 0.001 HIS A 185 PHE 0.032 0.001 PHE J 202 TYR 0.015 0.001 TYR A 176 ARG 0.012 0.001 ARG J 340 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6766 Ramachandran restraints generated. 3383 Oldfield, 0 Emsley, 3383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6766 Ramachandran restraints generated. 3383 Oldfield, 0 Emsley, 3383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 438 time to evaluate : 3.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 THR cc_start: 0.8704 (t) cc_final: 0.8356 (m) REVERT: B 40 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7351 (pp20) REVERT: C 59 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6472 (mt-10) REVERT: C 85 SER cc_start: 0.8581 (OUTLIER) cc_final: 0.8079 (m) REVERT: C 146 ASP cc_start: 0.6377 (m-30) cc_final: 0.6122 (m-30) REVERT: F 31 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7211 (mt-10) REVERT: F 59 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7267 (mm-30) REVERT: F 155 GLU cc_start: 0.7124 (tt0) cc_final: 0.6913 (tm-30) REVERT: F 208 MET cc_start: 0.6488 (ttp) cc_final: 0.6262 (ptm) REVERT: H 151 TYR cc_start: 0.7592 (m-80) cc_final: 0.7389 (m-80) REVERT: I 91 PHE cc_start: 0.6392 (OUTLIER) cc_final: 0.5805 (t80) REVERT: I 335 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.7111 (pt0) REVERT: J 237 MET cc_start: 0.7079 (OUTLIER) cc_final: 0.6733 (tmt) REVERT: K 222 LYS cc_start: 0.7574 (pttm) cc_final: 0.7343 (mmmt) REVERT: K 383 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7138 (mp0) REVERT: L 106 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.8294 (mm) outliers start: 108 outliers final: 47 residues processed: 511 average time/residue: 1.3023 time to fit residues: 789.3200 Evaluate side-chains 459 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 402 time to evaluate : 3.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 216 ARG Chi-restraints excluded: chain H residue 145 ILE Chi-restraints excluded: chain H residue 146 ASP Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 190 CYS Chi-restraints excluded: chain H residue 207 ILE Chi-restraints excluded: chain I residue 22 ILE Chi-restraints excluded: chain I residue 91 PHE Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 186 MET Chi-restraints excluded: chain I residue 335 GLU Chi-restraints excluded: chain I residue 421 LEU Chi-restraints excluded: chain I residue 422 THR Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 371 ILE Chi-restraints excluded: chain K residue 146 LEU Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain K residue 248 ILE Chi-restraints excluded: chain K residue 312 SER Chi-restraints excluded: chain K residue 383 GLU Chi-restraints excluded: chain K residue 398 THR Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain L residue 344 LYS Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 357 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 302 optimal weight: 0.9990 chunk 230 optimal weight: 3.9990 chunk 159 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 146 optimal weight: 0.0970 chunk 205 optimal weight: 5.9990 chunk 307 optimal weight: 9.9990 chunk 325 optimal weight: 0.6980 chunk 160 optimal weight: 7.9990 chunk 291 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 105 GLN C 134 GLN ** H 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN I 77 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27213 Z= 0.181 Angle : 0.492 7.046 36930 Z= 0.256 Chirality : 0.042 0.169 4451 Planarity : 0.003 0.058 4527 Dihedral : 8.906 84.625 3872 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.05 % Allowed : 15.66 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.14), residues: 3383 helix: 1.60 (0.12), residues: 1839 sheet: 0.03 (0.28), residues: 357 loop : -1.00 (0.16), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 181 HIS 0.005 0.001 HIS A 185 PHE 0.032 0.001 PHE J 202 TYR 0.016 0.001 TYR B 151 ARG 0.011 0.001 ARG J 340 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6766 Ramachandran restraints generated. 3383 Oldfield, 0 Emsley, 3383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6766 Ramachandran restraints generated. 3383 Oldfield, 0 Emsley, 3383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 417 time to evaluate : 2.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 THR cc_start: 0.8888 (t) cc_final: 0.8444 (m) REVERT: B 40 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7326 (pp20) REVERT: C 59 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6502 (mt-10) REVERT: C 85 SER cc_start: 0.8583 (OUTLIER) cc_final: 0.8035 (m) REVERT: E 86 THR cc_start: 0.8520 (t) cc_final: 0.8152 (m) REVERT: F 31 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7212 (mt-10) REVERT: F 59 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7267 (mm-30) REVERT: F 155 GLU cc_start: 0.7200 (tt0) cc_final: 0.6953 (tm-30) REVERT: H 28 MET cc_start: 0.8111 (mtt) cc_final: 0.7882 (mtt) REVERT: I 18 GLN cc_start: 0.7914 (mt0) cc_final: 0.7619 (mt0) REVERT: I 85 GLN cc_start: 0.7403 (mm110) cc_final: 0.7057 (mm110) REVERT: I 170 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8176 (mp) REVERT: J 237 MET cc_start: 0.7107 (OUTLIER) cc_final: 0.6745 (tmt) REVERT: K 97 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7802 (mm) REVERT: K 222 LYS cc_start: 0.7610 (pttm) cc_final: 0.7389 (mmmt) REVERT: K 383 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7173 (mp0) REVERT: L 92 MET cc_start: 0.6531 (OUTLIER) cc_final: 0.6286 (mmt) REVERT: L 106 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8343 (mm) REVERT: L 141 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7747 (mt-10) outliers start: 117 outliers final: 60 residues processed: 497 average time/residue: 1.2008 time to fit residues: 708.5304 Evaluate side-chains 463 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 392 time to evaluate : 2.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 216 ARG Chi-restraints excluded: chain H residue 145 ILE Chi-restraints excluded: chain H residue 146 ASP Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 190 CYS Chi-restraints excluded: chain H residue 207 ILE Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain I residue 186 MET Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 321 VAL Chi-restraints excluded: chain I residue 421 LEU Chi-restraints excluded: chain I residue 422 THR Chi-restraints excluded: chain I residue 439 ASP Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 303 ILE Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 357 THR Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain K residue 245 THR Chi-restraints excluded: chain K residue 312 SER Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 357 THR Chi-restraints excluded: chain K residue 383 GLU Chi-restraints excluded: chain K residue 398 THR Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain L residue 92 MET Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain L residue 344 LYS Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 357 THR Chi-restraints excluded: chain L residue 434 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 271 optimal weight: 0.9980 chunk 184 optimal weight: 0.6980 chunk 4 optimal weight: 6.9990 chunk 242 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 277 optimal weight: 3.9990 chunk 225 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 292 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN B 8 GLN D 143 ASN G 134 GLN ** H 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 27213 Z= 0.270 Angle : 0.532 8.365 36930 Z= 0.276 Chirality : 0.043 0.184 4451 Planarity : 0.003 0.061 4527 Dihedral : 8.890 85.178 3872 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.40 % Allowed : 16.35 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.14), residues: 3383 helix: 1.53 (0.12), residues: 1830 sheet: -0.07 (0.28), residues: 357 loop : -0.96 (0.16), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 181 HIS 0.005 0.001 HIS A 185 PHE 0.035 0.002 PHE J 202 TYR 0.017 0.001 TYR B 151 ARG 0.013 0.001 ARG J 340 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6766 Ramachandran restraints generated. 3383 Oldfield, 0 Emsley, 3383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6766 Ramachandran restraints generated. 3383 Oldfield, 0 Emsley, 3383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 392 time to evaluate : 3.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7336 (pp20) REVERT: C 22 CYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7979 (m) REVERT: C 59 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6537 (mm-30) REVERT: C 85 SER cc_start: 0.8642 (OUTLIER) cc_final: 0.8040 (m) REVERT: E 86 THR cc_start: 0.8610 (t) cc_final: 0.8160 (m) REVERT: F 31 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7242 (mt-10) REVERT: F 59 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7268 (mt-10) REVERT: F 145 ILE cc_start: 0.7515 (OUTLIER) cc_final: 0.7274 (pt) REVERT: F 155 GLU cc_start: 0.7297 (tt0) cc_final: 0.7014 (tm-30) REVERT: G 134 GLN cc_start: 0.7693 (mp-120) cc_final: 0.7466 (mp10) REVERT: I 335 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.7012 (pt0) REVERT: J 237 MET cc_start: 0.7121 (OUTLIER) cc_final: 0.6764 (tmt) REVERT: K 97 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7829 (mm) REVERT: K 222 LYS cc_start: 0.7628 (pttm) cc_final: 0.7393 (mmmt) REVERT: K 383 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7204 (mp0) REVERT: L 106 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8291 (mm) REVERT: L 110 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7101 (mp0) REVERT: L 141 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7762 (mt-10) outliers start: 127 outliers final: 64 residues processed: 481 average time/residue: 1.2693 time to fit residues: 725.3589 Evaluate side-chains 455 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 378 time to evaluate : 3.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 145 ILE Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 190 CYS Chi-restraints excluded: chain H residue 207 ILE Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 186 MET Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain I residue 217 LYS Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 321 VAL Chi-restraints excluded: chain I residue 335 GLU Chi-restraints excluded: chain I residue 421 LEU Chi-restraints excluded: chain I residue 422 THR Chi-restraints excluded: chain I residue 439 ASP Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 357 THR Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 146 LEU Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain K residue 245 THR Chi-restraints excluded: chain K residue 266 LEU Chi-restraints excluded: chain K residue 312 SER Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 357 THR Chi-restraints excluded: chain K residue 383 GLU Chi-restraints excluded: chain K residue 398 THR Chi-restraints excluded: chain K residue 402 THR Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain L residue 344 LYS Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 357 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 109 optimal weight: 6.9990 chunk 293 optimal weight: 0.3980 chunk 64 optimal weight: 2.9990 chunk 191 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 326 optimal weight: 3.9990 chunk 270 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 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 8 GLN B 8 GLN B 105 GLN D 143 ASN D 210 HIS E 134 GLN ** H 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27213 Z= 0.197 Angle : 0.502 9.967 36930 Z= 0.260 Chirality : 0.042 0.174 4451 Planarity : 0.003 0.063 4527 Dihedral : 8.659 83.626 3870 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.74 % Allowed : 17.53 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.14), residues: 3383 helix: 1.69 (0.12), residues: 1841 sheet: -0.05 (0.27), residues: 357 loop : -0.97 (0.16), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 181 HIS 0.005 0.001 HIS B 185 PHE 0.032 0.001 PHE J 202 TYR 0.018 0.001 TYR B 151 ARG 0.014 0.000 ARG J 340 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6766 Ramachandran restraints generated. 3383 Oldfield, 0 Emsley, 3383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6766 Ramachandran restraints generated. 3383 Oldfield, 0 Emsley, 3383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 387 time to evaluate : 3.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7352 (pp20) REVERT: C 59 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6564 (mm-30) REVERT: C 85 SER cc_start: 0.8610 (OUTLIER) cc_final: 0.8002 (m) REVERT: E 86 THR cc_start: 0.8568 (t) cc_final: 0.8148 (m) REVERT: F 31 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7213 (mt-10) REVERT: F 59 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7259 (mt-10) REVERT: F 155 GLU cc_start: 0.7245 (tt0) cc_final: 0.6966 (tm-30) REVERT: F 203 ASP cc_start: 0.6198 (OUTLIER) cc_final: 0.5610 (t0) REVERT: I 85 GLN cc_start: 0.7399 (mm110) cc_final: 0.7016 (mm110) REVERT: I 100 MET cc_start: 0.7070 (mtm) cc_final: 0.6844 (ttm) REVERT: I 418 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8476 (tp) REVERT: J 237 MET cc_start: 0.7084 (OUTLIER) cc_final: 0.6742 (tmt) REVERT: K 97 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7818 (mm) REVERT: K 142 LEU cc_start: 0.6843 (OUTLIER) cc_final: 0.6541 (mp) REVERT: K 222 LYS cc_start: 0.7622 (pttm) cc_final: 0.7389 (mmmt) REVERT: L 36 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7579 (mtm) REVERT: L 106 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8307 (mm) REVERT: L 110 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7088 (mp0) outliers start: 108 outliers final: 59 residues processed: 463 average time/residue: 1.2583 time to fit residues: 688.4270 Evaluate side-chains 451 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 379 time to evaluate : 3.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 145 ILE Chi-restraints excluded: chain H residue 146 ASP Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 190 CYS Chi-restraints excluded: chain H residue 207 ILE Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 186 MET Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 321 VAL Chi-restraints excluded: chain I residue 418 ILE Chi-restraints excluded: chain I residue 421 LEU Chi-restraints excluded: chain I residue 422 THR Chi-restraints excluded: chain I residue 439 ASP Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 303 ILE Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 357 THR Chi-restraints excluded: chain J residue 371 ILE Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 245 THR Chi-restraints excluded: chain K residue 312 SER Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 357 THR Chi-restraints excluded: chain K residue 398 THR Chi-restraints excluded: chain L residue 36 MET Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain L residue 344 LYS Chi-restraints excluded: chain L residue 352 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 314 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 185 optimal weight: 6.9990 chunk 238 optimal weight: 3.9990 chunk 184 optimal weight: 0.5980 chunk 274 optimal weight: 0.9980 chunk 182 optimal weight: 4.9990 chunk 324 optimal weight: 2.9990 chunk 203 optimal weight: 0.0070 chunk 198 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 overall best weight: 1.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN B 105 GLN D 143 ASN ** H 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 27213 Z= 0.206 Angle : 0.511 9.692 36930 Z= 0.264 Chirality : 0.042 0.174 4451 Planarity : 0.003 0.071 4527 Dihedral : 8.576 83.034 3870 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.36 % Allowed : 18.26 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.14), residues: 3383 helix: 1.71 (0.12), residues: 1841 sheet: -0.06 (0.27), residues: 357 loop : -0.95 (0.16), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 181 HIS 0.004 0.001 HIS B 185 PHE 0.032 0.001 PHE J 202 TYR 0.018 0.001 TYR B 151 ARG 0.015 0.000 ARG J 340 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6766 Ramachandran restraints generated. 3383 Oldfield, 0 Emsley, 3383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6766 Ramachandran restraints generated. 3383 Oldfield, 0 Emsley, 3383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 393 time to evaluate : 3.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7382 (pp20) REVERT: C 59 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6585 (mm-30) REVERT: C 85 SER cc_start: 0.8622 (OUTLIER) cc_final: 0.8248 (m) REVERT: E 86 THR cc_start: 0.8568 (t) cc_final: 0.8133 (m) REVERT: F 31 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7214 (mt-10) REVERT: F 59 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7258 (mt-10) REVERT: F 145 ILE cc_start: 0.7515 (OUTLIER) cc_final: 0.7295 (pt) REVERT: F 155 GLU cc_start: 0.7317 (tt0) cc_final: 0.7010 (tm-30) REVERT: I 91 PHE cc_start: 0.6325 (OUTLIER) cc_final: 0.5654 (t80) REVERT: I 170 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.8247 (mp) REVERT: I 418 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8485 (tp) REVERT: J 237 MET cc_start: 0.7086 (OUTLIER) cc_final: 0.6740 (tmt) REVERT: K 97 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7813 (mm) REVERT: K 142 LEU cc_start: 0.6888 (OUTLIER) cc_final: 0.6575 (mp) REVERT: K 222 LYS cc_start: 0.7611 (pttm) cc_final: 0.7386 (mmmt) REVERT: L 36 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7587 (mtm) REVERT: L 106 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8415 (mm) outliers start: 97 outliers final: 63 residues processed: 457 average time/residue: 1.2157 time to fit residues: 658.3109 Evaluate side-chains 449 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 372 time to evaluate : 3.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 145 ILE Chi-restraints excluded: chain H residue 146 ASP Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 190 CYS Chi-restraints excluded: chain H residue 207 ILE Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 91 PHE Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain I residue 186 MET Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 321 VAL Chi-restraints excluded: chain I residue 418 ILE Chi-restraints excluded: chain I residue 421 LEU Chi-restraints excluded: chain I residue 422 THR Chi-restraints excluded: chain I residue 439 ASP Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 303 ILE Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 357 THR Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 146 LEU Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 245 THR Chi-restraints excluded: chain K residue 249 LEU Chi-restraints excluded: chain K residue 312 SER Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 357 THR Chi-restraints excluded: chain K residue 398 THR Chi-restraints excluded: chain K residue 402 THR Chi-restraints excluded: chain L residue 36 MET Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain L residue 344 LYS Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 357 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 200 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 193 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 62 optimal weight: 9.9990 chunk 206 optimal weight: 1.9990 chunk 221 optimal weight: 6.9990 chunk 160 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 255 optimal weight: 6.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 105 GLN D 143 ASN G 134 GLN ** H 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 27213 Z= 0.279 Angle : 0.546 9.366 36930 Z= 0.282 Chirality : 0.043 0.185 4451 Planarity : 0.004 0.075 4527 Dihedral : 8.682 83.754 3869 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.60 % Allowed : 18.33 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.14), residues: 3383 helix: 1.57 (0.12), residues: 1842 sheet: -0.12 (0.28), residues: 357 loop : -0.96 (0.16), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP L 181 HIS 0.005 0.001 HIS L 168 PHE 0.034 0.002 PHE J 202 TYR 0.016 0.001 TYR D 73 ARG 0.016 0.001 ARG J 340 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6766 Ramachandran restraints generated. 3383 Oldfield, 0 Emsley, 3383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6766 Ramachandran restraints generated. 3383 Oldfield, 0 Emsley, 3383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 373 time to evaluate : 3.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 40 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7356 (pp20) REVERT: C 59 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6575 (mm-30) REVERT: E 86 THR cc_start: 0.8617 (t) cc_final: 0.8134 (m) REVERT: F 31 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7243 (mt-10) REVERT: F 59 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7232 (mt-10) REVERT: F 138 ASP cc_start: 0.7006 (t0) cc_final: 0.6806 (t70) REVERT: F 145 ILE cc_start: 0.7560 (OUTLIER) cc_final: 0.7309 (pt) REVERT: F 155 GLU cc_start: 0.7282 (tt0) cc_final: 0.6960 (tm-30) REVERT: F 203 ASP cc_start: 0.6382 (OUTLIER) cc_final: 0.5974 (t0) REVERT: G 216 ARG cc_start: 0.7884 (ttp-170) cc_final: 0.7653 (ttp-170) REVERT: I 85 GLN cc_start: 0.7436 (mm110) cc_final: 0.7004 (mm110) REVERT: I 170 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8189 (mp) REVERT: I 418 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8481 (tp) REVERT: J 237 MET cc_start: 0.7118 (OUTLIER) cc_final: 0.6765 (tmt) REVERT: K 97 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7776 (mm) REVERT: K 142 LEU cc_start: 0.6907 (OUTLIER) cc_final: 0.6573 (mp) REVERT: K 222 LYS cc_start: 0.7632 (pttm) cc_final: 0.7377 (mmmt) REVERT: K 383 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7276 (mp0) REVERT: L 36 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7566 (mtm) REVERT: L 106 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8359 (mm) REVERT: L 110 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7202 (mp0) outliers start: 104 outliers final: 63 residues processed: 453 average time/residue: 1.2069 time to fit residues: 649.3931 Evaluate side-chains 446 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 368 time to evaluate : 2.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 145 ILE Chi-restraints excluded: chain H residue 146 ASP Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 190 CYS Chi-restraints excluded: chain H residue 207 ILE Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain I residue 186 MET Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 321 VAL Chi-restraints excluded: chain I residue 418 ILE Chi-restraints excluded: chain I residue 421 LEU Chi-restraints excluded: chain I residue 422 THR Chi-restraints excluded: chain I residue 439 ASP Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 357 THR Chi-restraints excluded: chain J residue 371 ILE Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 146 LEU Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 245 THR Chi-restraints excluded: chain K residue 249 LEU Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 343 ILE Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 357 THR Chi-restraints excluded: chain K residue 383 GLU Chi-restraints excluded: chain K residue 398 THR Chi-restraints excluded: chain K residue 402 THR Chi-restraints excluded: chain L residue 36 MET Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain L residue 344 LYS Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 357 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 295 optimal weight: 0.9980 chunk 311 optimal weight: 4.9990 chunk 283 optimal weight: 0.0370 chunk 302 optimal weight: 0.4980 chunk 182 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 237 optimal weight: 10.0000 chunk 92 optimal weight: 0.9990 chunk 273 optimal weight: 5.9990 chunk 286 optimal weight: 0.8980 chunk 301 optimal weight: 3.9990 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 143 ASN G 134 GLN ** H 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 155 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 27213 Z= 0.162 Angle : 0.499 9.401 36930 Z= 0.258 Chirality : 0.042 0.166 4451 Planarity : 0.003 0.079 4527 Dihedral : 8.432 83.727 3869 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.60 % Allowed : 19.58 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.14), residues: 3383 helix: 1.77 (0.12), residues: 1857 sheet: -0.13 (0.28), residues: 351 loop : -0.92 (0.16), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 181 HIS 0.005 0.001 HIS K 168 PHE 0.030 0.001 PHE L 202 TYR 0.014 0.001 TYR G 151 ARG 0.019 0.000 ARG J 340 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6766 Ramachandran restraints generated. 3383 Oldfield, 0 Emsley, 3383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6766 Ramachandran restraints generated. 3383 Oldfield, 0 Emsley, 3383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 400 time to evaluate : 2.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7379 (pp20) REVERT: C 59 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6597 (mm-30) REVERT: C 85 SER cc_start: 0.8585 (OUTLIER) cc_final: 0.7989 (m) REVERT: E 86 THR cc_start: 0.8527 (t) cc_final: 0.8114 (m) REVERT: F 31 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7170 (mt-10) REVERT: F 59 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7273 (mt-10) REVERT: F 155 GLU cc_start: 0.7291 (tt0) cc_final: 0.6966 (tm-30) REVERT: F 203 ASP cc_start: 0.6402 (OUTLIER) cc_final: 0.6196 (t0) REVERT: G 216 ARG cc_start: 0.7771 (ttp-170) cc_final: 0.7555 (ttp-170) REVERT: I 85 GLN cc_start: 0.7360 (mm110) cc_final: 0.7055 (mm110) REVERT: I 170 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8156 (mp) REVERT: K 97 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7762 (mm) REVERT: K 142 LEU cc_start: 0.6888 (mm) cc_final: 0.6587 (mp) REVERT: K 222 LYS cc_start: 0.7640 (pttm) cc_final: 0.7395 (mmmt) REVERT: L 36 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.7539 (mtm) REVERT: L 110 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7230 (mp0) outliers start: 75 outliers final: 47 residues processed: 455 average time/residue: 1.2242 time to fit residues: 660.4391 Evaluate side-chains 431 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 374 time to evaluate : 3.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain H residue 145 ILE Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 190 CYS Chi-restraints excluded: chain H residue 207 ILE Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain I residue 186 MET Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 421 LEU Chi-restraints excluded: chain I residue 422 THR Chi-restraints excluded: chain I residue 439 ASP Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 150 ILE Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 303 ILE Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 371 ILE Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 146 LEU Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 245 THR Chi-restraints excluded: chain K residue 249 LEU Chi-restraints excluded: chain K residue 266 LEU Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 398 THR Chi-restraints excluded: chain L residue 36 MET Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain L residue 344 LYS Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 357 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 198 optimal weight: 2.9990 chunk 320 optimal weight: 0.3980 chunk 195 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 222 optimal weight: 5.9990 chunk 335 optimal weight: 4.9990 chunk 309 optimal weight: 6.9990 chunk 267 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 206 optimal weight: 0.8980 chunk 163 optimal weight: 7.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN D 143 ASN ** F 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN I 85 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 27213 Z= 0.322 Angle : 0.582 11.440 36930 Z= 0.299 Chirality : 0.044 0.186 4451 Planarity : 0.004 0.077 4527 Dihedral : 8.701 84.954 3869 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.67 % Allowed : 19.99 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.14), residues: 3383 helix: 1.48 (0.12), residues: 1848 sheet: -0.25 (0.28), residues: 351 loop : -0.97 (0.16), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP K 181 HIS 0.006 0.001 HIS K 168 PHE 0.034 0.002 PHE J 202 TYR 0.021 0.001 TYR B 107 ARG 0.017 0.001 ARG J 340 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6766 Ramachandran restraints generated. 3383 Oldfield, 0 Emsley, 3383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6766 Ramachandran restraints generated. 3383 Oldfield, 0 Emsley, 3383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 372 time to evaluate : 2.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7351 (pp20) REVERT: C 59 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6574 (mm-30) REVERT: F 31 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7238 (mt-10) REVERT: F 59 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7231 (mt-10) REVERT: F 155 GLU cc_start: 0.7412 (tt0) cc_final: 0.7058 (tm-30) REVERT: I 170 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8247 (mp) REVERT: K 97 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7778 (mm) REVERT: K 142 LEU cc_start: 0.6956 (mm) cc_final: 0.6622 (mp) REVERT: K 222 LYS cc_start: 0.7708 (pttm) cc_final: 0.7434 (mmmt) REVERT: L 110 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7255 (mp0) outliers start: 77 outliers final: 50 residues processed: 429 average time/residue: 1.2398 time to fit residues: 629.2507 Evaluate side-chains 418 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 361 time to evaluate : 2.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 146 ASP Chi-restraints excluded: chain H residue 145 ILE Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 190 CYS Chi-restraints excluded: chain H residue 207 ILE Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain I residue 186 MET Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 421 LEU Chi-restraints excluded: chain I residue 422 THR Chi-restraints excluded: chain I residue 439 ASP Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 371 ILE Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 146 LEU Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 245 THR Chi-restraints excluded: chain K residue 249 LEU Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 357 THR Chi-restraints excluded: chain K residue 398 THR Chi-restraints excluded: chain K residue 402 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain L residue 344 LYS Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 357 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 212 optimal weight: 0.9980 chunk 284 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 246 optimal weight: 0.4980 chunk 39 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 267 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 274 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN D 143 ASN E 83 GLN F 143 ASN F 185 HIS ** H 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 432 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.163065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.126563 restraints weight = 32452.905| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.04 r_work: 0.3228 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27213 Z= 0.210 Angle : 0.536 11.599 36930 Z= 0.276 Chirality : 0.043 0.177 4451 Planarity : 0.004 0.084 4527 Dihedral : 8.595 84.518 3869 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.36 % Allowed : 20.76 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.14), residues: 3383 helix: 1.59 (0.12), residues: 1848 sheet: -0.22 (0.28), residues: 351 loop : -0.95 (0.16), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP K 181 HIS 0.006 0.001 HIS K 168 PHE 0.031 0.001 PHE J 202 TYR 0.016 0.001 TYR D 73 ARG 0.019 0.001 ARG J 340 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10684.92 seconds wall clock time: 193 minutes 3.30 seconds (11583.30 seconds total)