Starting phenix.real_space_refine on Fri Aug 7 02:15:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8twb_41665/08_2026/8twb_41665.cif Found real_map, /net/cci-nas-00/data/ceres_data/8twb_41665/08_2026/8twb_41665.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8twb_41665/08_2026/8twb_41665.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8twb_41665/08_2026/8twb_41665.map" model { file = "/net/cci-nas-00/data/ceres_data/8twb_41665/08_2026/8twb_41665.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8twb_41665/08_2026/8twb_41665.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.067 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 46 5.49 5 Mg 3 5.21 5 S 84 5.16 5 C 11991 2.51 5 N 3248 2.21 5 O 3795 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19167 Number of models: 1 Model: "" Number of chains: 14 Chain: "4" Number of atoms: 2457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2457 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 309} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "3" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2563 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 12, 'TRANS': 314} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "2" Number of atoms: 2677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2677 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 327} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "5" Number of atoms: 2639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2639 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 14, 'TRANS': 323} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "1" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2015 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 247} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 56 Chain: "A" Number of atoms: 2003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2003 Classifications: {'peptide': 258} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 249} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 2010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2010 Classifications: {'peptide': 258} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 249} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 1963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1963 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 245} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "T" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 372 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "P" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 345 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "4" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "3" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "2" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "5" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.42, per 1000 atoms: 0.18 Number of scatterers: 19167 At special positions: 0 Unit cell: (125.028, 123.372, 125.856, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 84 16.00 P 46 15.00 Mg 3 11.99 O 3795 8.00 N 3248 7.00 C 11991 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.58 Conformation dependent library (CDL) restraints added in 664.5 milliseconds 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4496 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 14 sheets defined 54.0% alpha, 16.0% beta 13 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain '4' and resid 10 through 15 Processing helix chain '4' and resid 19 through 23 removed outlier: 3.598A pdb=" N ILE 4 23 " --> pdb=" O LEU 4 20 " (cutoff:3.500A) Processing helix chain '4' and resid 26 through 40 Processing helix chain '4' and resid 55 through 68 Processing helix chain '4' and resid 70 through 74 Processing helix chain '4' and resid 85 through 99 removed outlier: 4.072A pdb=" N ILE 4 93 " --> pdb=" O VAL 4 89 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LYS 4 94 " --> pdb=" O ARG 4 90 " (cutoff:3.500A) Processing helix chain '4' and resid 116 through 119 Processing helix chain '4' and resid 120 through 134 removed outlier: 3.781A pdb=" N ARG 4 128 " --> pdb=" O GLN 4 124 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ARG 4 129 " --> pdb=" O GLN 4 125 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR 4 130 " --> pdb=" O ALA 4 126 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR 4 134 " --> pdb=" O THR 4 130 " (cutoff:3.500A) Processing helix chain '4' and resid 146 through 150 Processing helix chain '4' and resid 151 through 157 removed outlier: 3.677A pdb=" N ARG 4 157 " --> pdb=" O PRO 4 153 " (cutoff:3.500A) Processing helix chain '4' and resid 167 through 183 Processing helix chain '4' and resid 187 through 199 Processing helix chain '4' and resid 201 through 217 Processing helix chain '4' and resid 220 through 228 Processing helix chain '4' and resid 231 through 241 removed outlier: 3.878A pdb=" N ILE 4 235 " --> pdb=" O PRO 4 231 " (cutoff:3.500A) Processing helix chain '4' and resid 244 through 255 Processing helix chain '4' and resid 262 through 276 Processing helix chain '4' and resid 281 through 301 Processing helix chain '4' and resid 305 through 321 removed outlier: 3.725A pdb=" N LEU 4 309 " --> pdb=" O THR 4 305 " (cutoff:3.500A) Processing helix chain '3' and resid 9 through 13 Processing helix chain '3' and resid 14 through 19 Processing helix chain '3' and resid 23 through 27 removed outlier: 3.734A pdb=" N VAL 3 27 " --> pdb=" O LEU 3 24 " (cutoff:3.500A) Processing helix chain '3' and resid 31 through 44 removed outlier: 3.518A pdb=" N THR 3 36 " --> pdb=" O GLU 3 32 " (cutoff:3.500A) Processing helix chain '3' and resid 58 through 72 Processing helix chain '3' and resid 74 through 78 removed outlier: 3.514A pdb=" N MET 3 78 " --> pdb=" O ASN 3 74 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 74 through 78' Processing helix chain '3' and resid 89 through 103 removed outlier: 4.013A pdb=" N LYS 3 98 " --> pdb=" O ARG 3 94 " (cutoff:3.500A) Processing helix chain '3' and resid 118 through 122 removed outlier: 3.548A pdb=" N ALA 3 121 " --> pdb=" O GLU 3 118 " (cutoff:3.500A) Processing helix chain '3' and resid 123 through 137 removed outlier: 4.380A pdb=" N ARG 3 132 " --> pdb=" O ASN 3 128 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL 3 133 " --> pdb=" O ALA 3 129 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU 3 135 " --> pdb=" O ARG 3 131 " (cutoff:3.500A) Processing helix chain '3' and resid 154 through 160 removed outlier: 3.551A pdb=" N ARG 3 160 " --> pdb=" O ALA 3 156 " (cutoff:3.500A) Processing helix chain '3' and resid 170 through 185 Processing helix chain '3' and resid 190 through 200 Processing helix chain '3' and resid 204 through 219 Processing helix chain '3' and resid 228 through 237 Processing helix chain '3' and resid 240 through 253 Processing helix chain '3' and resid 255 through 270 removed outlier: 3.801A pdb=" N LYS 3 270 " --> pdb=" O VAL 3 266 " (cutoff:3.500A) Processing helix chain '3' and resid 273 through 286 Processing helix chain '3' and resid 293 through 311 Processing helix chain '3' and resid 315 through 332 Processing helix chain '2' and resid 15 through 24 Processing helix chain '2' and resid 26 through 31 Processing helix chain '2' and resid 42 through 55 removed outlier: 3.619A pdb=" N VAL 2 46 " --> pdb=" O GLN 2 42 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL 2 48 " --> pdb=" O HIS 2 44 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS 2 54 " --> pdb=" O LYS 2 50 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER 2 55 " --> pdb=" O LYS 2 51 " (cutoff:3.500A) Processing helix chain '2' and resid 70 through 88 Proline residue: 2 85 - end of helix Processing helix chain '2' and resid 102 through 116 removed outlier: 3.893A pdb=" N VAL 2 110 " --> pdb=" O VAL 2 106 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS 2 111 " --> pdb=" O ARG 2 107 " (cutoff:3.500A) Processing helix chain '2' and resid 122 through 129 removed outlier: 3.634A pdb=" N LEU 2 126 " --> pdb=" O SER 2 122 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU 2 127 " --> pdb=" O LYS 2 123 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN 2 128 " --> pdb=" O HIS 2 124 " (cutoff:3.500A) Processing helix chain '2' and resid 141 through 145 removed outlier: 3.634A pdb=" N SER 2 144 " --> pdb=" O GLU 2 141 " (cutoff:3.500A) Processing helix chain '2' and resid 146 through 160 removed outlier: 3.557A pdb=" N LEU 2 153 " --> pdb=" O ALA 2 149 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG 2 154 " --> pdb=" O GLN 2 150 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ARG 2 155 " --> pdb=" O SER 2 151 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N THR 2 156 " --> pdb=" O ALA 2 152 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR 2 160 " --> pdb=" O THR 2 156 " (cutoff:3.500A) Processing helix chain '2' and resid 172 through 176 Processing helix chain '2' and resid 177 through 184 Processing helix chain '2' and resid 193 through 208 removed outlier: 5.160A pdb=" N ASP 2 199 " --> pdb=" O SER 2 195 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ARG 2 200 " --> pdb=" O ASN 2 196 " (cutoff:3.500A) Processing helix chain '2' and resid 216 through 225 Processing helix chain '2' and resid 227 through 246 removed outlier: 3.639A pdb=" N LEU 2 245 " --> pdb=" O GLY 2 241 " (cutoff:3.500A) Processing helix chain '2' and resid 252 through 260 removed outlier: 3.579A pdb=" N LEU 2 259 " --> pdb=" O GLN 2 255 " (cutoff:3.500A) Processing helix chain '2' and resid 264 through 277 Processing helix chain '2' and resid 279 through 291 Processing helix chain '2' and resid 296 through 311 Processing helix chain '2' and resid 315 through 334 removed outlier: 3.504A pdb=" N GLN 2 321 " --> pdb=" O ASN 2 317 " (cutoff:3.500A) Processing helix chain '2' and resid 338 through 352 Processing helix chain '5' and resid 19 through 32 removed outlier: 4.416A pdb=" N GLN 5 32 " --> pdb=" O SER 5 28 " (cutoff:3.500A) Processing helix chain '5' and resid 48 through 61 Processing helix chain '5' and resid 62 through 66 removed outlier: 3.517A pdb=" N VAL 5 65 " --> pdb=" O GLY 5 62 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR 5 66 " --> pdb=" O PRO 5 63 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 62 through 66' Processing helix chain '5' and resid 97 through 101 removed outlier: 3.963A pdb=" N MET 5 101 " --> pdb=" O PRO 5 98 " (cutoff:3.500A) Processing helix chain '5' and resid 104 through 120 removed outlier: 3.692A pdb=" N VAL 5 108 " --> pdb=" O ASN 5 104 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU 5 120 " --> pdb=" O VAL 5 116 " (cutoff:3.500A) Processing helix chain '5' and resid 143 through 146 Processing helix chain '5' and resid 147 through 161 removed outlier: 4.059A pdb=" N ARG 5 156 " --> pdb=" O ALA 5 152 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR 5 157 " --> pdb=" O ALA 5 153 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU 5 159 " --> pdb=" O ARG 5 155 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR 5 161 " --> pdb=" O THR 5 157 " (cutoff:3.500A) Processing helix chain '5' and resid 178 through 185 Processing helix chain '5' and resid 194 through 209 Processing helix chain '5' and resid 216 through 227 removed outlier: 4.022A pdb=" N LYS 5 220 " --> pdb=" O LYS 5 216 " (cutoff:3.500A) Processing helix chain '5' and resid 229 through 244 removed outlier: 3.530A pdb=" N ASN 5 243 " --> pdb=" O SER 5 239 " (cutoff:3.500A) Processing helix chain '5' and resid 257 through 273 Processing helix chain '5' and resid 275 through 291 removed outlier: 3.654A pdb=" N GLU 5 281 " --> pdb=" O ASN 5 277 " (cutoff:3.500A) Processing helix chain '5' and resid 295 through 309 Processing helix chain '5' and resid 314 through 335 Processing helix chain '5' and resid 337 through 353 removed outlier: 3.737A pdb=" N HIS 5 341 " --> pdb=" O LYS 5 337 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY 5 344 " --> pdb=" O PHE 5 340 " (cutoff:3.500A) Processing helix chain '1' and resid 388 through 395 Processing helix chain '1' and resid 398 through 407 Processing helix chain '1' and resid 414 through 430 removed outlier: 3.636A pdb=" N GLY 1 430 " --> pdb=" O VAL 1 426 " (cutoff:3.500A) Processing helix chain '1' and resid 431 through 443 Processing helix chain '1' and resid 453 through 476 removed outlier: 4.088A pdb=" N ALA 1 457 " --> pdb=" O ILE 1 453 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP 1 461 " --> pdb=" O ALA 1 457 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR 1 474 " --> pdb=" O TYR 1 470 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA 1 475 " --> pdb=" O GLN 1 471 " (cutoff:3.500A) Processing helix chain '1' and resid 477 through 479 No H-bonds generated for 'chain '1' and resid 477 through 479' Processing helix chain '1' and resid 480 through 485 removed outlier: 3.860A pdb=" N SER 1 484 " --> pdb=" O LEU 1 480 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA 1 485 " --> pdb=" O LEU 1 481 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 480 through 485' Processing helix chain '1' and resid 485 through 496 removed outlier: 3.872A pdb=" N LEU 1 489 " --> pdb=" O ALA 1 485 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE 1 491 " --> pdb=" O VAL 1 487 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE 1 492 " --> pdb=" O PRO 1 488 " (cutoff:3.500A) Processing helix chain '1' and resid 508 through 534 removed outlier: 3.656A pdb=" N GLU 1 512 " --> pdb=" O ASN 1 508 " (cutoff:3.500A) Processing helix chain '1' and resid 537 through 542 removed outlier: 3.766A pdb=" N PHE 1 541 " --> pdb=" O LEU 1 537 " (cutoff:3.500A) Processing helix chain '1' and resid 543 through 550 Processing helix chain '1' and resid 550 through 561 removed outlier: 3.558A pdb=" N TYR 1 554 " --> pdb=" O GLU 1 550 " (cutoff:3.500A) Processing helix chain '1' and resid 562 through 566 Processing helix chain '1' and resid 568 through 586 Processing helix chain '1' and resid 610 through 615 Processing helix chain '1' and resid 617 through 643 removed outlier: 3.676A pdb=" N ASN 1 622 " --> pdb=" O PRO 1 618 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU 1 623 " --> pdb=" O LYS 1 619 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASN 1 630 " --> pdb=" O HIS 1 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 20 removed outlier: 4.309A pdb=" N PHE A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE A 19 " --> pdb=" O ILE A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 57 No H-bonds generated for 'chain 'A' and resid 55 through 57' Processing helix chain 'A' and resid 72 through 79 Processing helix chain 'A' and resid 141 through 153 removed outlier: 4.110A pdb=" N GLN A 153 " --> pdb=" O ARG A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 194 Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 217 through 221 Processing helix chain 'B' and resid 8 through 20 removed outlier: 4.309A pdb=" N PHE B 12 " --> pdb=" O GLU B 8 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE B 19 " --> pdb=" O ILE B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 57 No H-bonds generated for 'chain 'B' and resid 55 through 57' Processing helix chain 'B' and resid 72 through 79 Processing helix chain 'B' and resid 141 through 153 removed outlier: 4.108A pdb=" N GLN B 153 " --> pdb=" O ARG B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 194 Processing helix chain 'B' and resid 209 through 216 Processing helix chain 'B' and resid 217 through 221 Processing helix chain 'C' and resid 8 through 20 removed outlier: 4.308A pdb=" N PHE C 12 " --> pdb=" O GLU C 8 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE C 19 " --> pdb=" O ILE C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 57 No H-bonds generated for 'chain 'C' and resid 55 through 57' Processing helix chain 'C' and resid 72 through 79 Processing helix chain 'C' and resid 141 through 153 removed outlier: 4.106A pdb=" N GLN C 153 " --> pdb=" O ARG C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 194 Processing helix chain 'C' and resid 209 through 216 Processing helix chain 'C' and resid 217 through 221 Processing sheet with id=AA1, first strand: chain '4' and resid 75 through 78 removed outlier: 6.286A pdb=" N LYS 4 109 " --> pdb=" O ARG 4 139 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ALA 4 141 " --> pdb=" O LYS 4 109 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL 4 111 " --> pdb=" O ALA 4 141 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ALA 4 143 " --> pdb=" O VAL 4 111 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU 4 113 " --> pdb=" O ALA 4 143 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE 4 46 " --> pdb=" O LEU 4 161 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '4' and resid 185 through 186 removed outlier: 7.488A pdb=" N LYS 4 185 " --> pdb=" O VAL 4 219 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain '3' and resid 79 through 82 removed outlier: 6.605A pdb=" N LEU 3 49 " --> pdb=" O VAL 3 145 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ALA 3 147 " --> pdb=" O LEU 3 49 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N PHE 3 51 " --> pdb=" O ALA 3 147 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU 3 50 " --> pdb=" O PHE 3 164 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '2' and resid 92 through 95 removed outlier: 6.220A pdb=" N LEU 2 62 " --> pdb=" O PHE 2 187 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '5' and resid 69 through 74 removed outlier: 6.875A pdb=" N LEU 5 94 " --> pdb=" O ILE 5 139 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ASN 5 141 " --> pdb=" O LEU 5 94 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ILE 5 96 " --> pdb=" O ASN 5 141 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LYS 5 136 " --> pdb=" O ARG 5 166 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ILE 5 168 " --> pdb=" O LYS 5 136 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL 5 138 " --> pdb=" O ILE 5 168 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N VAL 5 170 " --> pdb=" O VAL 5 138 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE 5 140 " --> pdb=" O VAL 5 170 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU 5 40 " --> pdb=" O ILE 5 188 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '5' and resid 212 through 213 removed outlier: 5.834A pdb=" N GLN 5 212 " --> pdb=" O LEU 5 248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain '1' and resid 589 through 592 Processing sheet with id=AA8, first strand: chain 'A' and resid 59 through 60 removed outlier: 3.523A pdb=" N GLU A 59 " --> pdb=" O LYS A 5 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 66 through 71 removed outlier: 5.538A pdb=" N LEU A 25 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL A 40 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY A 244 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASP A 240 " --> pdb=" O ARG A 224 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ARG A 224 " --> pdb=" O ASP A 240 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 203 through 208 removed outlier: 6.289A pdb=" N SER A 157 " --> pdb=" O ASP A 172 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASP A 172 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 177 " --> pdb=" O SER C 115 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE A 181 " --> pdb=" O ILE C 111 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE C 111 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU C 59 " --> pdb=" O LYS C 5 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 59 through 60 removed outlier: 3.522A pdb=" N GLU B 59 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ASP C 172 " --> pdb=" O SER C 157 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N SER C 157 " --> pdb=" O ASP C 172 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 66 through 71 removed outlier: 5.538A pdb=" N LEU B 25 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL B 40 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY B 244 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ASP B 240 " --> pdb=" O ARG B 224 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ARG B 224 " --> pdb=" O ASP B 240 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 177 through 182 removed outlier: 4.661A pdb=" N ASP B 172 " --> pdb=" O SER B 157 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N SER B 157 " --> pdb=" O ASP B 172 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 66 through 71 removed outlier: 5.538A pdb=" N LEU C 25 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL C 40 " --> pdb=" O LEU C 25 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY C 244 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ASP C 240 " --> pdb=" O ARG C 224 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ARG C 224 " --> pdb=" O ASP C 240 " (cutoff:3.500A) 1065 hydrogen bonds defined for protein. 3015 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 31 hydrogen bonds 62 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 3.23 Time building geometry restraints manager: 2.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.26: 3191 1.26 - 1.43: 4875 1.43 - 1.61: 11334 1.61 - 1.78: 22 1.78 - 1.95: 121 Bond restraints: 19543 Sorted by residual: bond pdb=" C1' DC T 9 " pdb=" N1 DC T 9 " ideal model delta sigma weight residual 1.468 1.569 -0.101 1.40e-02 5.10e+03 5.18e+01 bond pdb=" C1' DC T 17 " pdb=" N1 DC T 17 " ideal model delta sigma weight residual 1.468 1.568 -0.100 1.40e-02 5.10e+03 5.10e+01 bond pdb=" C GLU A 258 " pdb=" OXT GLU A 258 " ideal model delta sigma weight residual 1.231 1.090 0.141 2.00e-02 2.50e+03 4.99e+01 bond pdb=" C GLU B 258 " pdb=" OXT GLU B 258 " ideal model delta sigma weight residual 1.231 1.091 0.140 2.00e-02 2.50e+03 4.92e+01 bond pdb=" C GLU B 258 " pdb=" O GLU B 258 " ideal model delta sigma weight residual 1.231 1.370 -0.139 2.00e-02 2.50e+03 4.83e+01 ... (remaining 19538 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.08: 25609 3.08 - 6.15: 857 6.15 - 9.23: 122 9.23 - 12.31: 12 12.31 - 15.39: 7 Bond angle restraints: 26607 Sorted by residual: angle pdb=" N GLU A 257 " pdb=" CA GLU A 257 " pdb=" C GLU A 257 " ideal model delta sigma weight residual 110.41 122.91 -12.50 1.18e+00 7.18e-01 1.12e+02 angle pdb=" N GLU B 257 " pdb=" CA GLU B 257 " pdb=" C GLU B 257 " ideal model delta sigma weight residual 110.41 122.85 -12.44 1.18e+00 7.18e-01 1.11e+02 angle pdb=" N ASP B 97 " pdb=" CA ASP B 97 " pdb=" C ASP B 97 " ideal model delta sigma weight residual 113.72 104.53 9.19 1.30e+00 5.92e-01 5.00e+01 angle pdb=" N ASP C 97 " pdb=" CA ASP C 97 " pdb=" C ASP C 97 " ideal model delta sigma weight residual 113.72 104.63 9.09 1.30e+00 5.92e-01 4.89e+01 angle pdb=" N ASP A 97 " pdb=" CA ASP A 97 " pdb=" C ASP A 97 " ideal model delta sigma weight residual 113.72 104.68 9.04 1.30e+00 5.92e-01 4.84e+01 ... (remaining 26602 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.96: 11524 33.96 - 67.93: 395 67.93 - 101.89: 46 101.89 - 135.86: 4 135.86 - 169.82: 4 Dihedral angle restraints: 11973 sinusoidal: 5078 harmonic: 6895 Sorted by residual: dihedral pdb=" O1B ADP 5 401 " pdb=" O3A ADP 5 401 " pdb=" PB ADP 5 401 " pdb=" PA ADP 5 401 " ideal model delta sinusoidal sigma weight residual 300.00 168.23 131.77 1 2.00e+01 2.50e-03 4.00e+01 dihedral pdb=" O2A ADP 5 401 " pdb=" O3A ADP 5 401 " pdb=" PA ADP 5 401 " pdb=" PB ADP 5 401 " ideal model delta sinusoidal sigma weight residual -60.00 60.76 -120.76 1 2.00e+01 2.50e-03 3.63e+01 dihedral pdb=" N GLU A 257 " pdb=" C GLU A 257 " pdb=" CA GLU A 257 " pdb=" CB GLU A 257 " ideal model delta harmonic sigma weight residual 122.80 134.85 -12.05 0 2.50e+00 1.60e-01 2.32e+01 ... (remaining 11970 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 2756 0.127 - 0.253: 278 0.253 - 0.380: 56 0.380 - 0.506: 13 0.506 - 0.633: 7 Chirality restraints: 3110 Sorted by residual: chirality pdb=" P DA T 1 " pdb=" OP1 DA T 1 " pdb=" OP2 DA T 1 " pdb=" O5' DA T 1 " both_signs ideal model delta sigma weight residual True 2.34 -2.97 -0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" CA GLU A 257 " pdb=" N GLU A 257 " pdb=" C GLU A 257 " pdb=" CB GLU A 257 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.95e+00 chirality pdb=" CA GLU B 257 " pdb=" N GLU B 257 " pdb=" C GLU B 257 " pdb=" CB GLU B 257 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.71e+00 ... (remaining 3107 not shown) Planarity restraints: 3280 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 258 " -0.037 2.00e-02 2.50e+03 8.20e-02 6.72e+01 pdb=" C GLU A 258 " 0.141 2.00e-02 2.50e+03 pdb=" O GLU A 258 " -0.042 2.00e-02 2.50e+03 pdb=" OXT GLU A 258 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 258 " -0.037 2.00e-02 2.50e+03 8.17e-02 6.68e+01 pdb=" C GLU B 258 " 0.141 2.00e-02 2.50e+03 pdb=" O GLU B 258 " -0.042 2.00e-02 2.50e+03 pdb=" OXT GLU B 258 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE 1 563 " -0.087 2.00e-02 2.50e+03 5.82e-02 5.92e+01 pdb=" CG PHE 1 563 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE 1 563 " 0.064 2.00e-02 2.50e+03 pdb=" CD2 PHE 1 563 " 0.064 2.00e-02 2.50e+03 pdb=" CE1 PHE 1 563 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE 1 563 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE 1 563 " -0.081 2.00e-02 2.50e+03 ... (remaining 3277 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 229 2.62 - 3.19: 16555 3.19 - 3.76: 29600 3.76 - 4.33: 41973 4.33 - 4.90: 68060 Nonbonded interactions: 156417 Sorted by model distance: nonbonded pdb=" OD2 ASP 4 265 " pdb=" OH TYR 3 52 " model vdw 2.048 3.040 nonbonded pdb=" O3G AGS 3 401 " pdb="MG MG 3 402 " model vdw 2.104 2.170 nonbonded pdb=" OG1 THR 4 56 " pdb="MG MG 4 402 " model vdw 2.122 2.170 nonbonded pdb=" O3G AGS 4 401 " pdb="MG MG 4 402 " model vdw 2.124 2.170 nonbonded pdb=" OG1 THR 3 60 " pdb="MG MG 3 402 " model vdw 2.124 2.170 ... (remaining 156412 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 43 or (resid 44 and (name N or name CA or name C \ or name O or name CB )) or resid 45 through 69 or (resid 70 and (name N or name \ CA or name C or name O or name CB )) or resid 71 through 83 or (resid 84 and (n \ ame N or name CA or name C or name O or name CB )) or resid 85 or (resid 86 and \ (name N or name CA or name C or name O or name CB )) or resid 87 through 96 or ( \ resid 97 and (name N or name CA or name C or name O or name CB )) or resid 98 th \ rough 116 or (resid 117 and (name N or name CA or name C or name O or name CB )) \ or resid 118 or (resid 119 and (name N or name CA or name C or name O or name C \ B )) or resid 120 through 125 or (resid 126 and (name N or name CA or name C or \ name O or name CB )) or resid 127 through 173 or (resid 174 and (name N or name \ CA or name C or name O or name CB )) or resid 175 through 235 or (resid 236 and \ (name N or name CA or name C or name O or name CB )) or resid 237 through 254)) selection = (chain 'B' and (resid 1 through 19 or (resid 20 and (name N or name CA or name C \ or name O or name CB )) or resid 21 through 43 or (resid 44 and (name N or name \ CA or name C or name O or name CB )) or resid 45 through 67 or (resid 68 and (n \ ame N or name CA or name C or name O or name CB )) or resid 69 through 78 or (re \ sid 79 and (name N or name CA or name C or name O or name CB )) or resid 80 thro \ ugh 85 or (resid 86 and (name N or name CA or name C or name O or name CB )) or \ resid 87 through 96 or (resid 97 and (name N or name CA or name C or name O or n \ ame CB )) or resid 98 through 109 or (resid 110 and (name N or name CA or name C \ or name O or name CB )) or resid 111 through 125 or (resid 126 and (name N or n \ ame CA or name C or name O or name CB )) or resid 127 through 173 or (resid 174 \ and (name N or name CA or name C or name O or name CB )) or resid 175 through 23 \ 5 or (resid 236 and (name N or name CA or name C or name O or name CB )) or resi \ d 237 through 254)) selection = (chain 'C' and (resid 1 through 67 or (resid 68 and (name N or name CA or name C \ or name O or name CB )) or resid 69 or (resid 70 and (name N or name CA or name \ C or name O or name CB )) or resid 71 or (resid 72 and (name N or name CA or na \ me C or name O or name CB )) or resid 73 through 78 or (resid 79 and (name N or \ name CA or name C or name O or name CB )) or resid 80 through 109 or (resid 110 \ and (name N or name CA or name C or name O or name CB )) or resid 111 through 11 \ 8 or (resid 119 and (name N or name CA or name C or name O or name CB )) or resi \ d 120 through 252 or (resid 253 and (name N or name CA or name C or name O or na \ me CB )) or resid 254)) } 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: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 16.320 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:0.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 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 : 0.009 0.141 19543 Z= 0.569 Angle : 1.266 15.385 26607 Z= 0.813 Chirality : 0.090 0.633 3110 Planarity : 0.009 0.185 3280 Dihedral : 16.973 169.819 7477 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.86 % Allowed : 3.26 % Favored : 95.89 % Rotamer: Outliers : 0.64 % Allowed : 6.75 % Favored : 92.61 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.16), residues: 2334 helix: -0.50 (0.14), residues: 1105 sheet: 0.10 (0.22), residues: 505 loop : -1.81 (0.21), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.002 ARG B 224 TYR 0.078 0.006 TYR A 133 PHE 0.087 0.010 PHE 1 563 TRP 0.038 0.003 TRP 1 399 HIS 0.008 0.001 HIS 4 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00933 / 0.57 (19543) covalent geometry : angle 1.26563 / 0.81 (26607) hydrogen bonds : bond 0.15462 / 10.31 ( 1096) hydrogen bonds : angle 6.28535 / 4.47 ( 3077) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 371 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 4 19 VAL cc_start: 0.8661 (t) cc_final: 0.8417 (p) REVERT: 2 88 MET cc_start: 0.6990 (tpt) cc_final: 0.6769 (tpp) REVERT: 5 101 MET cc_start: 0.8037 (ptt) cc_final: 0.7434 (ptm) REVERT: 5 105 ASP cc_start: 0.6109 (m-30) cc_final: 0.5832 (m-30) REVERT: 5 107 ILE cc_start: 0.7952 (mm) cc_final: 0.7599 (pt) REVERT: 5 224 GLN cc_start: 0.8194 (tm-30) cc_final: 0.7961 (tm-30) REVERT: 5 240 MET cc_start: 0.7461 (ptp) cc_final: 0.7162 (ptm) REVERT: 1 421 GLU cc_start: 0.8073 (tt0) cc_final: 0.7600 (tt0) REVERT: 1 462 TRP cc_start: 0.7514 (m100) cc_final: 0.7200 (m100) REVERT: 1 469 MET cc_start: 0.6710 (mmm) cc_final: 0.6497 (mmt) REVERT: 1 515 GLU cc_start: 0.5165 (mm-30) cc_final: 0.4581 (tp30) outliers start: 13 outliers final: 2 residues processed: 380 average time/residue: 0.1373 time to fit residues: 76.2542 Evaluate side-chains 193 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 191 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 198 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 8.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 4 18 GLN 4 92 GLN 4 177 GLN 4 210 GLN 4 220 ASN 4 244 ASN 4 320 ASN 3 180 ASN 3 317 GLN 2 96 ASN 2 236 GLN 2 288 ASN 2 352 GLN 5 18 HIS 5 19 ASN 5 104 ASN 5 141 ASN 5 244 ASN 1 477 ASN 1 534 GLN A 64 HIS A 83 ASN A 159 ASN B 24 GLN B 64 HIS B 159 ASN C 27 ASN C 64 HIS C 159 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.111220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.093804 restraints weight = 47783.402| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.88 r_work: 0.3291 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 19543 Z= 0.235 Angle : 0.715 8.024 26607 Z= 0.371 Chirality : 0.047 0.198 3110 Planarity : 0.005 0.059 3280 Dihedral : 16.187 177.754 3017 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.62 % Allowed : 10.88 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.17), residues: 2334 helix: 0.57 (0.15), residues: 1098 sheet: 0.36 (0.22), residues: 506 loop : -1.33 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG 2 107 TYR 0.030 0.002 TYR 2 64 PHE 0.023 0.003 PHE B 19 TRP 0.020 0.002 TRP 1 399 HIS 0.007 0.002 HIS 4 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.24 (19543) covalent geometry : angle 0.71468 / 0.37 (26607) hydrogen bonds : bond 0.04678 / 3.18 ( 1096) hydrogen bonds : angle 5.01122 / 3.57 ( 3077) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 0.726 Fit side-chains revert: symmetry clash REVERT: 4 272 ARG cc_start: 0.8833 (tpt-90) cc_final: 0.8628 (mmm-85) REVERT: 5 101 MET cc_start: 0.8116 (ptt) cc_final: 0.7393 (ptm) REVERT: 5 105 ASP cc_start: 0.7497 (m-30) cc_final: 0.7191 (m-30) REVERT: 5 107 ILE cc_start: 0.8144 (mm) cc_final: 0.7824 (pt) REVERT: 5 224 GLN cc_start: 0.8663 (tm-30) cc_final: 0.8008 (tm-30) REVERT: 5 240 MET cc_start: 0.7437 (ptp) cc_final: 0.7187 (ptm) REVERT: 1 421 GLU cc_start: 0.7529 (tt0) cc_final: 0.7217 (tt0) REVERT: 1 515 GLU cc_start: 0.5049 (mm-30) cc_final: 0.4590 (tp30) REVERT: A 51 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7091 (tt0) REVERT: A 108 LYS cc_start: 0.8312 (tmtt) cc_final: 0.8001 (tmmt) REVERT: B 19 PHE cc_start: 0.7873 (m-80) cc_final: 0.7605 (m-80) REVERT: B 51 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.6810 (tt0) REVERT: C 13 LYS cc_start: 0.8689 (ttpp) cc_final: 0.8458 (mtpp) REVERT: C 60 TYR cc_start: 0.7658 (t80) cc_final: 0.7354 (t80) outliers start: 33 outliers final: 13 residues processed: 210 average time/residue: 0.1187 time to fit residues: 38.6080 Evaluate side-chains 170 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 67 LEU Chi-restraints excluded: chain 2 residue 103 ILE Chi-restraints excluded: chain 5 residue 85 LEU Chi-restraints excluded: chain 5 residue 149 ASP Chi-restraints excluded: chain 5 residue 248 LEU Chi-restraints excluded: chain 5 residue 321 ILE Chi-restraints excluded: chain 1 residue 526 LEU Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 198 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 95 optimal weight: 0.0970 chunk 10 optimal weight: 5.9990 chunk 120 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 194 optimal weight: 2.9990 chunk 205 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 128 ASN 5 341 HIS 1 620 HIS C 27 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.111605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.093546 restraints weight = 47866.589| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.94 r_work: 0.3294 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 19543 Z= 0.145 Angle : 0.572 7.074 26607 Z= 0.296 Chirality : 0.042 0.176 3110 Planarity : 0.004 0.059 3280 Dihedral : 16.064 179.457 3017 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.48 % Allowed : 12.26 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.17), residues: 2334 helix: 1.07 (0.15), residues: 1096 sheet: 0.36 (0.22), residues: 508 loop : -1.09 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 2 107 TYR 0.019 0.001 TYR 4 71 PHE 0.015 0.002 PHE 1 443 TRP 0.012 0.001 TRP 1 399 HIS 0.004 0.001 HIS C 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (19543) covalent geometry : angle 0.57157 / 0.30 (26607) hydrogen bonds : bond 0.03868 / 2.62 ( 1096) hydrogen bonds : angle 4.68760 / 3.35 ( 3077) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 172 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: 5 101 MET cc_start: 0.8183 (ptt) cc_final: 0.7509 (ptm) REVERT: 5 105 ASP cc_start: 0.7590 (m-30) cc_final: 0.7279 (m-30) REVERT: 5 107 ILE cc_start: 0.8077 (mm) cc_final: 0.7771 (pt) REVERT: 5 240 MET cc_start: 0.7348 (ptp) cc_final: 0.7091 (ptm) REVERT: 1 421 GLU cc_start: 0.7467 (tt0) cc_final: 0.7090 (tt0) REVERT: 1 515 GLU cc_start: 0.4892 (mm-30) cc_final: 0.4429 (tp30) REVERT: 1 607 ASP cc_start: 0.7520 (t0) cc_final: 0.7301 (t0) REVERT: B 1 MET cc_start: 0.7610 (mtm) cc_final: 0.7078 (mtp) REVERT: C 60 TYR cc_start: 0.7615 (t80) cc_final: 0.7316 (t80) outliers start: 30 outliers final: 16 residues processed: 193 average time/residue: 0.1264 time to fit residues: 38.2879 Evaluate side-chains 170 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 131 MET Chi-restraints excluded: chain 3 residue 275 ILE Chi-restraints excluded: chain 2 residue 103 ILE Chi-restraints excluded: chain 2 residue 305 HIS Chi-restraints excluded: chain 5 residue 85 LEU Chi-restraints excluded: chain 5 residue 248 LEU Chi-restraints excluded: chain 5 residue 299 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 198 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 82 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 206 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 140 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 54 optimal weight: 0.0060 chunk 198 optimal weight: 2.9990 chunk 195 optimal weight: 10.0000 overall best weight: 2.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 25 GLN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.110467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.092970 restraints weight = 47788.946| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.91 r_work: 0.3269 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 19543 Z= 0.166 Angle : 0.583 9.517 26607 Z= 0.300 Chirality : 0.042 0.219 3110 Planarity : 0.004 0.057 3280 Dihedral : 16.021 179.758 3017 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.92 % Allowed : 12.85 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.17), residues: 2334 helix: 1.12 (0.15), residues: 1100 sheet: 0.30 (0.22), residues: 509 loop : -1.08 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 2 107 TYR 0.019 0.001 TYR 4 71 PHE 0.016 0.002 PHE 1 443 TRP 0.010 0.001 TRP 1 399 HIS 0.006 0.001 HIS 2 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (19543) covalent geometry : angle 0.58338 / 0.30 (26607) hydrogen bonds : bond 0.03745 / 2.52 ( 1096) hydrogen bonds : angle 4.61482 / 3.30 ( 3077) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 167 time to evaluate : 0.759 Fit side-chains revert: symmetry clash REVERT: 5 105 ASP cc_start: 0.7726 (m-30) cc_final: 0.7424 (m-30) REVERT: 5 107 ILE cc_start: 0.8119 (mm) cc_final: 0.7813 (pt) REVERT: 5 240 MET cc_start: 0.7354 (ptp) cc_final: 0.7066 (ptm) REVERT: 1 421 GLU cc_start: 0.7508 (tt0) cc_final: 0.7111 (tt0) REVERT: 1 515 GLU cc_start: 0.4719 (mm-30) cc_final: 0.4265 (tp30) REVERT: A 1 MET cc_start: 0.6794 (mtp) cc_final: 0.6556 (tpp) REVERT: A 70 MET cc_start: 0.8433 (ptt) cc_final: 0.8057 (ptt) REVERT: A 80 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7965 (mtt180) REVERT: A 199 MET cc_start: 0.8143 (ttt) cc_final: 0.7866 (ttt) REVERT: B 51 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.6840 (tt0) REVERT: B 232 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8251 (tp30) outliers start: 39 outliers final: 23 residues processed: 196 average time/residue: 0.1400 time to fit residues: 43.0477 Evaluate side-chains 182 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 131 MET Chi-restraints excluded: chain 4 residue 236 VAL Chi-restraints excluded: chain 4 residue 264 ILE Chi-restraints excluded: chain 3 residue 295 THR Chi-restraints excluded: chain 2 residue 25 GLN Chi-restraints excluded: chain 2 residue 103 ILE Chi-restraints excluded: chain 2 residue 305 HIS Chi-restraints excluded: chain 5 residue 85 LEU Chi-restraints excluded: chain 5 residue 88 VAL Chi-restraints excluded: chain 5 residue 149 ASP Chi-restraints excluded: chain 5 residue 248 LEU Chi-restraints excluded: chain 5 residue 299 ILE Chi-restraints excluded: chain 5 residue 308 LEU Chi-restraints excluded: chain 5 residue 321 ILE Chi-restraints excluded: chain 5 residue 339 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 198 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 90 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 150 optimal weight: 9.9990 chunk 125 optimal weight: 0.6980 chunk 166 optimal weight: 2.9990 chunk 123 optimal weight: 0.5980 chunk 202 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 136 optimal weight: 1.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 25 GLN C 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.110890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.093220 restraints weight = 47453.877| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.91 r_work: 0.3280 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19543 Z= 0.132 Angle : 0.555 10.226 26607 Z= 0.284 Chirality : 0.041 0.183 3110 Planarity : 0.004 0.057 3280 Dihedral : 15.943 178.044 3017 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.92 % Allowed : 14.23 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.17), residues: 2334 helix: 1.31 (0.16), residues: 1091 sheet: 0.22 (0.22), residues: 522 loop : -0.94 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 2 107 TYR 0.016 0.001 TYR 4 71 PHE 0.020 0.001 PHE 2 280 TRP 0.011 0.001 TRP 2 27 HIS 0.003 0.001 HIS 5 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (19543) covalent geometry : angle 0.55538 / 0.28 (26607) hydrogen bonds : bond 0.03501 / 2.37 ( 1096) hydrogen bonds : angle 4.51338 / 3.24 ( 3077) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 168 time to evaluate : 0.626 Fit side-chains REVERT: 5 107 ILE cc_start: 0.8103 (mm) cc_final: 0.7782 (pt) REVERT: 5 240 MET cc_start: 0.7324 (ptp) cc_final: 0.7101 (ptm) REVERT: 1 421 GLU cc_start: 0.7457 (tt0) cc_final: 0.7052 (tt0) REVERT: 1 515 GLU cc_start: 0.4647 (mm-30) cc_final: 0.4203 (tp30) REVERT: A 1 MET cc_start: 0.6799 (mtp) cc_final: 0.6440 (tpp) REVERT: A 51 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7096 (tt0) REVERT: A 70 MET cc_start: 0.8438 (ptt) cc_final: 0.8073 (ptt) REVERT: A 80 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7958 (mtt180) REVERT: A 199 MET cc_start: 0.8077 (ttt) cc_final: 0.7833 (ttt) REVERT: B 51 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.6920 (tt0) REVERT: B 232 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8276 (tp30) REVERT: C 7 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7716 (tp30) REVERT: C 60 TYR cc_start: 0.7624 (t80) cc_final: 0.7406 (t80) REVERT: C 139 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8740 (pt) outliers start: 39 outliers final: 20 residues processed: 200 average time/residue: 0.1306 time to fit residues: 41.3140 Evaluate side-chains 178 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 67 LEU Chi-restraints excluded: chain 4 residue 131 MET Chi-restraints excluded: chain 4 residue 264 ILE Chi-restraints excluded: chain 2 residue 103 ILE Chi-restraints excluded: chain 2 residue 245 LEU Chi-restraints excluded: chain 2 residue 305 HIS Chi-restraints excluded: chain 5 residue 80 ASN Chi-restraints excluded: chain 5 residue 88 VAL Chi-restraints excluded: chain 5 residue 149 ASP Chi-restraints excluded: chain 5 residue 248 LEU Chi-restraints excluded: chain 5 residue 299 ILE Chi-restraints excluded: chain 5 residue 308 LEU Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 198 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 224 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 118 optimal weight: 7.9990 chunk 229 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 155 optimal weight: 9.9990 chunk 173 optimal weight: 0.4980 chunk 215 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 112 optimal weight: 7.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 171 ASN 2 288 ASN 2 340 HIS ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.108495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.090166 restraints weight = 47876.193| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.89 r_work: 0.3227 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 19543 Z= 0.231 Angle : 0.655 9.187 26607 Z= 0.333 Chirality : 0.045 0.238 3110 Planarity : 0.005 0.058 3280 Dihedral : 16.062 176.569 3017 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.46 % Allowed : 14.52 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.17), residues: 2334 helix: 1.05 (0.15), residues: 1096 sheet: 0.03 (0.22), residues: 519 loop : -1.11 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 2 107 TYR 0.018 0.002 TYR 2 64 PHE 0.019 0.002 PHE C 19 TRP 0.012 0.002 TRP 2 295 HIS 0.007 0.001 HIS 2 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.23 (19543) covalent geometry : angle 0.65543 / 0.33 (26607) hydrogen bonds : bond 0.04083 / 2.75 ( 1096) hydrogen bonds : angle 4.71158 / 3.36 ( 3077) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 156 time to evaluate : 0.774 Fit side-chains revert: symmetry clash REVERT: 2 137 ILE cc_start: 0.8088 (mt) cc_final: 0.7870 (mt) REVERT: 2 140 ASP cc_start: 0.8329 (OUTLIER) cc_final: 0.8042 (m-30) REVERT: 5 107 ILE cc_start: 0.8152 (mm) cc_final: 0.7836 (pt) REVERT: 5 240 MET cc_start: 0.7289 (ptp) cc_final: 0.7083 (ptm) REVERT: 1 421 GLU cc_start: 0.7530 (tt0) cc_final: 0.7069 (tt0) REVERT: 1 515 GLU cc_start: 0.4676 (mm-30) cc_final: 0.4233 (tp30) REVERT: 1 594 ARG cc_start: 0.7197 (mtt180) cc_final: 0.6815 (mtt180) REVERT: A 51 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7273 (tt0) REVERT: A 70 MET cc_start: 0.8496 (ptt) cc_final: 0.8229 (ptt) REVERT: A 80 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.7994 (mtt180) REVERT: B 51 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7147 (tt0) REVERT: B 232 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8245 (tp30) REVERT: C 119 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.6920 (mmm) REVERT: C 139 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8762 (pt) outliers start: 50 outliers final: 31 residues processed: 189 average time/residue: 0.1399 time to fit residues: 42.0375 Evaluate side-chains 185 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 148 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 67 LEU Chi-restraints excluded: chain 4 residue 131 MET Chi-restraints excluded: chain 4 residue 154 LEU Chi-restraints excluded: chain 4 residue 236 VAL Chi-restraints excluded: chain 4 residue 264 ILE Chi-restraints excluded: chain 3 residue 295 THR Chi-restraints excluded: chain 2 residue 22 LEU Chi-restraints excluded: chain 2 residue 103 ILE Chi-restraints excluded: chain 2 residue 140 ASP Chi-restraints excluded: chain 2 residue 245 LEU Chi-restraints excluded: chain 2 residue 305 HIS Chi-restraints excluded: chain 5 residue 51 THR Chi-restraints excluded: chain 5 residue 79 SER Chi-restraints excluded: chain 5 residue 85 LEU Chi-restraints excluded: chain 5 residue 88 VAL Chi-restraints excluded: chain 5 residue 109 ILE Chi-restraints excluded: chain 5 residue 149 ASP Chi-restraints excluded: chain 5 residue 237 LEU Chi-restraints excluded: chain 5 residue 248 LEU Chi-restraints excluded: chain 5 residue 299 ILE Chi-restraints excluded: chain 5 residue 308 LEU Chi-restraints excluded: chain 5 residue 349 VAL Chi-restraints excluded: chain 1 residue 526 LEU Chi-restraints excluded: chain 1 residue 559 ILE Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 198 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 88 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 91 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 160 optimal weight: 8.9990 chunk 180 optimal weight: 10.0000 chunk 1 optimal weight: 0.0030 chunk 12 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 203 optimal weight: 10.0000 overall best weight: 2.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 3 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 171 ASN ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.109539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.091791 restraints weight = 47755.957| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.92 r_work: 0.3246 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19543 Z= 0.151 Angle : 0.572 9.380 26607 Z= 0.292 Chirality : 0.042 0.192 3110 Planarity : 0.004 0.058 3280 Dihedral : 15.943 175.959 3017 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.02 % Allowed : 15.21 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.17), residues: 2334 helix: 1.26 (0.16), residues: 1089 sheet: 0.02 (0.21), residues: 522 loop : -0.99 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG 2 107 TYR 0.020 0.001 TYR 4 71 PHE 0.020 0.001 PHE 2 280 TRP 0.010 0.001 TRP 2 324 HIS 0.003 0.001 HIS 5 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (19543) covalent geometry : angle 0.57236 / 0.29 (26607) hydrogen bonds : bond 0.03617 / 2.44 ( 1096) hydrogen bonds : angle 4.57796 / 3.28 ( 3077) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 163 time to evaluate : 0.722 Fit side-chains revert: symmetry clash REVERT: 5 107 ILE cc_start: 0.8098 (mm) cc_final: 0.7799 (pt) REVERT: 5 240 MET cc_start: 0.7263 (ptp) cc_final: 0.7045 (ptm) REVERT: 1 421 GLU cc_start: 0.7541 (tt0) cc_final: 0.7068 (tt0) REVERT: 1 594 ARG cc_start: 0.7215 (mtt180) cc_final: 0.6841 (mtt180) REVERT: A 51 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7238 (tt0) REVERT: A 70 MET cc_start: 0.8489 (ptt) cc_final: 0.8200 (ptt) REVERT: A 80 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8033 (mtt180) REVERT: B 51 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7064 (tt0) REVERT: B 232 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8265 (tp30) REVERT: C 7 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7818 (tp30) REVERT: C 139 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8731 (pt) outliers start: 41 outliers final: 25 residues processed: 192 average time/residue: 0.1376 time to fit residues: 41.7956 Evaluate side-chains 187 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 157 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 67 LEU Chi-restraints excluded: chain 4 residue 131 MET Chi-restraints excluded: chain 4 residue 236 VAL Chi-restraints excluded: chain 4 residue 264 ILE Chi-restraints excluded: chain 3 residue 295 THR Chi-restraints excluded: chain 2 residue 103 ILE Chi-restraints excluded: chain 2 residue 245 LEU Chi-restraints excluded: chain 2 residue 305 HIS Chi-restraints excluded: chain 5 residue 80 ASN Chi-restraints excluded: chain 5 residue 88 VAL Chi-restraints excluded: chain 5 residue 149 ASP Chi-restraints excluded: chain 5 residue 248 LEU Chi-restraints excluded: chain 5 residue 299 ILE Chi-restraints excluded: chain 5 residue 308 LEU Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 198 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 196 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 191 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 131 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 chunk 44 optimal weight: 0.9980 chunk 173 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 3 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 171 ASN ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.109243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.090952 restraints weight = 47504.565| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.88 r_work: 0.3244 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 19543 Z= 0.169 Angle : 0.587 9.252 26607 Z= 0.298 Chirality : 0.042 0.187 3110 Planarity : 0.004 0.057 3280 Dihedral : 15.902 175.253 3017 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.12 % Allowed : 15.26 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.17), residues: 2334 helix: 1.29 (0.16), residues: 1090 sheet: -0.02 (0.22), residues: 522 loop : -1.00 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 2 107 TYR 0.021 0.001 TYR 4 71 PHE 0.020 0.002 PHE A 254 TRP 0.010 0.001 TRP 2 324 HIS 0.003 0.001 HIS 2 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (19543) covalent geometry : angle 0.58728 / 0.30 (26607) hydrogen bonds : bond 0.03675 / 2.48 ( 1096) hydrogen bonds : angle 4.57139 / 3.27 ( 3077) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 162 time to evaluate : 0.762 Fit side-chains revert: symmetry clash REVERT: 3 99 ASP cc_start: 0.8187 (m-30) cc_final: 0.7986 (m-30) REVERT: 2 140 ASP cc_start: 0.8308 (OUTLIER) cc_final: 0.8031 (m-30) REVERT: 5 107 ILE cc_start: 0.8123 (mm) cc_final: 0.7825 (pt) REVERT: 5 240 MET cc_start: 0.7231 (ptp) cc_final: 0.6995 (ptm) REVERT: 1 421 GLU cc_start: 0.7578 (tt0) cc_final: 0.7111 (tt0) REVERT: 1 594 ARG cc_start: 0.7194 (mtt180) cc_final: 0.6823 (mtt180) REVERT: A 51 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7350 (tt0) REVERT: A 80 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8002 (mtt180) REVERT: B 51 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7099 (tt0) REVERT: B 232 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8301 (tp30) REVERT: C 139 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8773 (pt) outliers start: 43 outliers final: 34 residues processed: 192 average time/residue: 0.1261 time to fit residues: 38.4413 Evaluate side-chains 197 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 158 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 67 LEU Chi-restraints excluded: chain 4 residue 131 MET Chi-restraints excluded: chain 4 residue 236 VAL Chi-restraints excluded: chain 4 residue 264 ILE Chi-restraints excluded: chain 3 residue 90 ILE Chi-restraints excluded: chain 3 residue 202 ASN Chi-restraints excluded: chain 3 residue 295 THR Chi-restraints excluded: chain 2 residue 103 ILE Chi-restraints excluded: chain 2 residue 140 ASP Chi-restraints excluded: chain 2 residue 245 LEU Chi-restraints excluded: chain 2 residue 305 HIS Chi-restraints excluded: chain 5 residue 79 SER Chi-restraints excluded: chain 5 residue 88 VAL Chi-restraints excluded: chain 5 residue 96 ILE Chi-restraints excluded: chain 5 residue 105 ASP Chi-restraints excluded: chain 5 residue 149 ASP Chi-restraints excluded: chain 5 residue 237 LEU Chi-restraints excluded: chain 5 residue 248 LEU Chi-restraints excluded: chain 5 residue 299 ILE Chi-restraints excluded: chain 5 residue 308 LEU Chi-restraints excluded: chain 5 residue 321 ILE Chi-restraints excluded: chain 5 residue 349 VAL Chi-restraints excluded: chain 1 residue 526 LEU Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 241 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 28 optimal weight: 9.9990 chunk 223 optimal weight: 9.9990 chunk 205 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 123 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 219 optimal weight: 2.9990 chunk 175 optimal weight: 5.9990 chunk 182 optimal weight: 3.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 3 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 171 ASN ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.109337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.091366 restraints weight = 47213.507| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.92 r_work: 0.3251 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 19543 Z= 0.158 Angle : 0.573 8.600 26607 Z= 0.291 Chirality : 0.042 0.191 3110 Planarity : 0.004 0.059 3280 Dihedral : 15.868 175.041 3017 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.12 % Allowed : 15.61 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.17), residues: 2334 helix: 1.33 (0.16), residues: 1090 sheet: -0.00 (0.22), residues: 522 loop : -0.94 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 2 107 TYR 0.022 0.001 TYR 4 71 PHE 0.016 0.002 PHE 1 443 TRP 0.010 0.001 TRP 2 324 HIS 0.003 0.001 HIS 5 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (19543) covalent geometry : angle 0.57350 / 0.29 (26607) hydrogen bonds : bond 0.03617 / 2.44 ( 1096) hydrogen bonds : angle 4.54042 / 3.25 ( 3077) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 157 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: 2 140 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.7998 (m-30) REVERT: 5 107 ILE cc_start: 0.8131 (mm) cc_final: 0.7840 (pt) REVERT: 5 240 MET cc_start: 0.7206 (ptp) cc_final: 0.6966 (ptm) REVERT: 1 421 GLU cc_start: 0.7557 (tt0) cc_final: 0.7096 (tt0) REVERT: 1 594 ARG cc_start: 0.7172 (mtt180) cc_final: 0.6806 (mtt180) REVERT: A 51 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7392 (tt0) REVERT: A 80 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8004 (mtt180) REVERT: B 51 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7100 (tt0) REVERT: B 232 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8319 (tp30) REVERT: C 7 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7853 (tp30) REVERT: C 110 ARG cc_start: 0.7669 (ttp80) cc_final: 0.7116 (mtp-110) REVERT: C 139 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8761 (pt) outliers start: 43 outliers final: 32 residues processed: 189 average time/residue: 0.1291 time to fit residues: 38.5128 Evaluate side-chains 194 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 156 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 67 LEU Chi-restraints excluded: chain 4 residue 131 MET Chi-restraints excluded: chain 4 residue 154 LEU Chi-restraints excluded: chain 4 residue 236 VAL Chi-restraints excluded: chain 4 residue 264 ILE Chi-restraints excluded: chain 3 residue 295 THR Chi-restraints excluded: chain 2 residue 103 ILE Chi-restraints excluded: chain 2 residue 140 ASP Chi-restraints excluded: chain 2 residue 245 LEU Chi-restraints excluded: chain 2 residue 305 HIS Chi-restraints excluded: chain 5 residue 51 THR Chi-restraints excluded: chain 5 residue 88 VAL Chi-restraints excluded: chain 5 residue 96 ILE Chi-restraints excluded: chain 5 residue 109 ILE Chi-restraints excluded: chain 5 residue 149 ASP Chi-restraints excluded: chain 5 residue 248 LEU Chi-restraints excluded: chain 5 residue 299 ILE Chi-restraints excluded: chain 5 residue 308 LEU Chi-restraints excluded: chain 5 residue 349 VAL Chi-restraints excluded: chain 1 residue 526 LEU Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 241 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 51 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 101 optimal weight: 0.1980 chunk 178 optimal weight: 0.6980 chunk 99 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 162 optimal weight: 7.9990 chunk 210 optimal weight: 0.0370 overall best weight: 1.1862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 4 125 GLN ** 3 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.110362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.092074 restraints weight = 47417.716| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.89 r_work: 0.3267 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 19543 Z= 0.113 Angle : 0.540 9.156 26607 Z= 0.274 Chirality : 0.040 0.198 3110 Planarity : 0.004 0.057 3280 Dihedral : 15.768 175.439 3017 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.67 % Allowed : 15.95 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.18), residues: 2334 helix: 1.47 (0.16), residues: 1093 sheet: 0.07 (0.22), residues: 526 loop : -0.84 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 2 107 TYR 0.022 0.001 TYR 4 71 PHE 0.021 0.001 PHE C 28 TRP 0.011 0.001 TRP 2 324 HIS 0.003 0.001 HIS 5 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (19543) covalent geometry : angle 0.54042 / 0.27 (26607) hydrogen bonds : bond 0.03389 / 2.30 ( 1096) hydrogen bonds : angle 4.42735 / 3.18 ( 3077) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 166 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: 2 140 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.7998 (m-30) REVERT: 5 107 ILE cc_start: 0.8097 (mm) cc_final: 0.7799 (pt) REVERT: 5 240 MET cc_start: 0.7179 (ptp) cc_final: 0.6924 (ptm) REVERT: 1 421 GLU cc_start: 0.7570 (tt0) cc_final: 0.7078 (tt0) REVERT: 1 594 ARG cc_start: 0.7209 (mtt180) cc_final: 0.6845 (mtt180) REVERT: A 80 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.7959 (mtt180) REVERT: B 51 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7057 (tt0) REVERT: B 232 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8283 (tp30) REVERT: C 7 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7792 (tp30) REVERT: C 110 ARG cc_start: 0.7627 (ttp80) cc_final: 0.7067 (mtp-110) outliers start: 34 outliers final: 24 residues processed: 189 average time/residue: 0.1225 time to fit residues: 36.6896 Evaluate side-chains 184 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 67 LEU Chi-restraints excluded: chain 4 residue 131 MET Chi-restraints excluded: chain 4 residue 154 LEU Chi-restraints excluded: chain 4 residue 236 VAL Chi-restraints excluded: chain 2 residue 103 ILE Chi-restraints excluded: chain 2 residue 140 ASP Chi-restraints excluded: chain 2 residue 245 LEU Chi-restraints excluded: chain 2 residue 305 HIS Chi-restraints excluded: chain 5 residue 88 VAL Chi-restraints excluded: chain 5 residue 149 ASP Chi-restraints excluded: chain 5 residue 248 LEU Chi-restraints excluded: chain 5 residue 299 ILE Chi-restraints excluded: chain 5 residue 308 LEU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 198 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 177 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 175 optimal weight: 0.9990 chunk 200 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 189 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 chunk 109 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 4 208 ASN ** 3 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 148 ASN 2 24 GLN 2 171 ASN ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.108428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.090956 restraints weight = 47638.085| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.82 r_work: 0.3219 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 19543 Z= 0.235 Angle : 0.639 8.369 26607 Z= 0.323 Chirality : 0.044 0.267 3110 Planarity : 0.005 0.060 3280 Dihedral : 15.881 174.316 3017 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.17 % Allowed : 15.71 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.17), residues: 2334 helix: 1.22 (0.15), residues: 1095 sheet: -0.03 (0.22), residues: 522 loop : -1.00 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 2 107 TYR 0.022 0.002 TYR 4 71 PHE 0.018 0.002 PHE 2 189 TRP 0.011 0.002 TRP 1 399 HIS 0.005 0.001 HIS 3 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.23 (19543) covalent geometry : angle 0.63882 / 0.32 (26607) hydrogen bonds : bond 0.03960 / 2.67 ( 1096) hydrogen bonds : angle 4.63461 / 3.32 ( 3077) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5099.86 seconds wall clock time: 87 minutes 59.33 seconds (5279.33 seconds total)