Starting phenix.real_space_refine on Thu Feb 15 09:43:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnf_27565/02_2024/8dnf_27565_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnf_27565/02_2024/8dnf_27565.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnf_27565/02_2024/8dnf_27565.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnf_27565/02_2024/8dnf_27565.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnf_27565/02_2024/8dnf_27565_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnf_27565/02_2024/8dnf_27565_updated.pdb" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.095 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 8 5.49 5 Mg 4 5.21 5 S 88 5.16 5 C 7448 2.51 5 N 1980 2.21 5 O 2284 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 71": "OE1" <-> "OE2" Residue "A GLU 82": "OE1" <-> "OE2" Residue "A GLU 124": "OE1" <-> "OE2" Residue "A GLU 194": "OE1" <-> "OE2" Residue "A GLU 223": "OE1" <-> "OE2" Residue "A GLU 225": "OE1" <-> "OE2" Residue "A GLU 269": "OE1" <-> "OE2" Residue "A GLU 333": "OE1" <-> "OE2" Residue "A GLU 363": "OE1" <-> "OE2" Residue "B GLU 71": "OE1" <-> "OE2" Residue "B GLU 82": "OE1" <-> "OE2" Residue "B GLU 124": "OE1" <-> "OE2" Residue "B GLU 194": "OE1" <-> "OE2" Residue "B GLU 223": "OE1" <-> "OE2" Residue "B GLU 225": "OE1" <-> "OE2" Residue "B GLU 269": "OE1" <-> "OE2" Residue "B GLU 333": "OE1" <-> "OE2" Residue "B GLU 363": "OE1" <-> "OE2" Residue "C GLU 3": "OE1" <-> "OE2" Residue "C GLU 71": "OE1" <-> "OE2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "C GLU 124": "OE1" <-> "OE2" Residue "C GLU 223": "OE1" <-> "OE2" Residue "C GLU 225": "OE1" <-> "OE2" Residue "C GLU 269": "OE1" <-> "OE2" Residue "C GLU 333": "OE1" <-> "OE2" Residue "C GLU 363": "OE1" <-> "OE2" Residue "D GLU 2": "OE1" <-> "OE2" Residue "D GLU 71": "OE1" <-> "OE2" Residue "D GLU 82": "OE1" <-> "OE2" Residue "D GLU 124": "OE1" <-> "OE2" Residue "D GLU 194": "OE1" <-> "OE2" Residue "D GLU 223": "OE1" <-> "OE2" Residue "D GLU 225": "OE1" <-> "OE2" Residue "D GLU 269": "OE1" <-> "OE2" Residue "D GLU 333": "OE1" <-> "OE2" Residue "D GLU 363": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11812 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2925 Unusual residues: {'ACE': 1} Classifications: {'peptide': 374, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 19, 'TRANS': 354} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2925 Unusual residues: {'ACE': 1} Classifications: {'peptide': 374, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 19, 'TRANS': 354} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2925 Unusual residues: {'ACE': 1} Classifications: {'peptide': 374, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 19, 'TRANS': 354} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2925 Unusual residues: {'ACE': 1} Classifications: {'peptide': 374, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 19, 'TRANS': 354} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.64, per 1000 atoms: 0.56 Number of scatterers: 11812 At special positions: 0 Unit cell: (80.19, 125.631, 171.072, 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 88 16.00 P 8 15.00 Mg 4 11.99 O 2284 8.00 N 1980 7.00 C 7448 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.20 Conformation dependent library (CDL) restraints added in 2.4 seconds 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2768 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 17 sheets defined 42.5% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.39 Creating SS restraints... Processing helix chain 'A' and resid 54 through 59 Processing helix chain 'A' and resid 79 through 91 removed outlier: 3.684A pdb=" N LYS A 83 " --> pdb=" O ASP A 79 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TRP A 85 " --> pdb=" O MET A 81 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR A 90 " --> pdb=" O HIS A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 124 Processing helix chain 'A' and resid 136 through 144 removed outlier: 3.704A pdb=" N LEU A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR A 142 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 181 through 195 removed outlier: 3.699A pdb=" N THR A 193 " --> pdb=" O MET A 189 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N GLU A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ARG A 195 " --> pdb=" O ILE A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 215 removed outlier: 3.940A pdb=" N GLU A 206 " --> pdb=" O THR A 202 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU A 213 " --> pdb=" O ARG A 209 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS A 214 " --> pdb=" O ASP A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.568A pdb=" N MET A 226 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.705A pdb=" N PHE A 254 " --> pdb=" O ASN A 251 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG A 255 " --> pdb=" O GLU A 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 251 through 255' Processing helix chain 'A' and resid 257 through 260 Processing helix chain 'A' and resid 263 through 266 Processing helix chain 'A' and resid 273 through 283 removed outlier: 3.691A pdb=" N THR A 277 " --> pdb=" O ILE A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 294 removed outlier: 3.655A pdb=" N ALA A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 304 Processing helix chain 'A' and resid 308 through 319 removed outlier: 3.649A pdb=" N LEU A 319 " --> pdb=" O GLU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 347 removed outlier: 5.204A pdb=" N VAL A 338 " --> pdb=" O LYS A 335 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 340 " --> pdb=" O SER A 337 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA A 346 " --> pdb=" O SER A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 351 No H-bonds generated for 'chain 'A' and resid 349 through 351' Processing helix chain 'A' and resid 358 through 372 removed outlier: 3.678A pdb=" N ASP A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU A 363 " --> pdb=" O GLN A 359 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER A 364 " --> pdb=" O GLU A 360 " (cutoff:3.500A) Proline residue: A 366 - end of helix removed outlier: 4.374A pdb=" N VAL A 369 " --> pdb=" O GLY A 365 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N HIS A 370 " --> pdb=" O PRO A 366 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG A 371 " --> pdb=" O SER A 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 59 Processing helix chain 'B' and resid 79 through 91 removed outlier: 3.685A pdb=" N LYS B 83 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP B 85 " --> pdb=" O MET B 81 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR B 90 " --> pdb=" O HIS B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 124 Processing helix chain 'B' and resid 136 through 144 removed outlier: 3.704A pdb=" N LEU B 141 " --> pdb=" O ALA B 137 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR B 142 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 181 through 195 removed outlier: 3.699A pdb=" N THR B 193 " --> pdb=" O MET B 189 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N GLU B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ARG B 195 " --> pdb=" O ILE B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 215 removed outlier: 3.939A pdb=" N GLU B 206 " --> pdb=" O THR B 202 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU B 213 " --> pdb=" O ARG B 209 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS B 214 " --> pdb=" O ASP B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.569A pdb=" N MET B 226 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA B 227 " --> pdb=" O GLU B 223 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER B 231 " --> pdb=" O ALA B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 255 removed outlier: 3.705A pdb=" N PHE B 254 " --> pdb=" O ASN B 251 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG B 255 " --> pdb=" O GLU B 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 251 through 255' Processing helix chain 'B' and resid 257 through 260 Processing helix chain 'B' and resid 263 through 266 Processing helix chain 'B' and resid 273 through 283 removed outlier: 3.691A pdb=" N THR B 277 " --> pdb=" O ILE B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 294 removed outlier: 3.655A pdb=" N ALA B 294 " --> pdb=" O LYS B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 304 Processing helix chain 'B' and resid 308 through 319 removed outlier: 3.649A pdb=" N LEU B 319 " --> pdb=" O GLU B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 347 removed outlier: 5.204A pdb=" N VAL B 338 " --> pdb=" O LYS B 335 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE B 340 " --> pdb=" O SER B 337 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA B 346 " --> pdb=" O SER B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 351 No H-bonds generated for 'chain 'B' and resid 349 through 351' Processing helix chain 'B' and resid 358 through 372 removed outlier: 3.679A pdb=" N ASP B 362 " --> pdb=" O LYS B 358 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU B 363 " --> pdb=" O GLN B 359 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER B 364 " --> pdb=" O GLU B 360 " (cutoff:3.500A) Proline residue: B 366 - end of helix removed outlier: 4.374A pdb=" N VAL B 369 " --> pdb=" O GLY B 365 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N HIS B 370 " --> pdb=" O PRO B 366 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG B 371 " --> pdb=" O SER B 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 59 Processing helix chain 'C' and resid 79 through 91 removed outlier: 3.684A pdb=" N LYS C 83 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP C 85 " --> pdb=" O MET C 81 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR C 90 " --> pdb=" O HIS C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 124 Processing helix chain 'C' and resid 136 through 144 removed outlier: 3.704A pdb=" N LEU C 141 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR C 142 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA C 143 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 173 No H-bonds generated for 'chain 'C' and resid 171 through 173' Processing helix chain 'C' and resid 181 through 195 removed outlier: 3.699A pdb=" N THR C 193 " --> pdb=" O MET C 189 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N GLU C 194 " --> pdb=" O LYS C 190 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ARG C 195 " --> pdb=" O ILE C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 215 removed outlier: 3.940A pdb=" N GLU C 206 " --> pdb=" O THR C 202 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU C 213 " --> pdb=" O ARG C 209 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS C 214 " --> pdb=" O ASP C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 231 removed outlier: 3.569A pdb=" N MET C 226 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA C 227 " --> pdb=" O GLU C 223 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER C 231 " --> pdb=" O ALA C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 255 removed outlier: 3.705A pdb=" N PHE C 254 " --> pdb=" O ASN C 251 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG C 255 " --> pdb=" O GLU C 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 251 through 255' Processing helix chain 'C' and resid 257 through 260 Processing helix chain 'C' and resid 263 through 266 Processing helix chain 'C' and resid 273 through 283 removed outlier: 3.690A pdb=" N THR C 277 " --> pdb=" O ILE C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 294 removed outlier: 3.655A pdb=" N ALA C 294 " --> pdb=" O LYS C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 304 Processing helix chain 'C' and resid 308 through 319 removed outlier: 3.649A pdb=" N LEU C 319 " --> pdb=" O GLU C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 347 removed outlier: 5.205A pdb=" N VAL C 338 " --> pdb=" O LYS C 335 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE C 340 " --> pdb=" O SER C 337 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA C 346 " --> pdb=" O SER C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 351 No H-bonds generated for 'chain 'C' and resid 349 through 351' Processing helix chain 'C' and resid 358 through 372 removed outlier: 3.678A pdb=" N ASP C 362 " --> pdb=" O LYS C 358 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU C 363 " --> pdb=" O GLN C 359 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER C 364 " --> pdb=" O GLU C 360 " (cutoff:3.500A) Proline residue: C 366 - end of helix removed outlier: 4.374A pdb=" N VAL C 369 " --> pdb=" O GLY C 365 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N HIS C 370 " --> pdb=" O PRO C 366 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG C 371 " --> pdb=" O SER C 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 59 Processing helix chain 'D' and resid 79 through 91 removed outlier: 3.684A pdb=" N LYS D 83 " --> pdb=" O ASP D 79 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP D 85 " --> pdb=" O MET D 81 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR D 90 " --> pdb=" O HIS D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 124 Processing helix chain 'D' and resid 136 through 144 removed outlier: 3.704A pdb=" N LEU D 141 " --> pdb=" O ALA D 137 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR D 142 " --> pdb=" O VAL D 138 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA D 143 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 173 No H-bonds generated for 'chain 'D' and resid 171 through 173' Processing helix chain 'D' and resid 181 through 195 removed outlier: 3.699A pdb=" N THR D 193 " --> pdb=" O MET D 189 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N GLU D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ARG D 195 " --> pdb=" O ILE D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 215 removed outlier: 3.940A pdb=" N GLU D 206 " --> pdb=" O THR D 202 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE D 207 " --> pdb=" O ALA D 203 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU D 213 " --> pdb=" O ARG D 209 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS D 214 " --> pdb=" O ASP D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 231 removed outlier: 3.570A pdb=" N MET D 226 " --> pdb=" O PHE D 222 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA D 227 " --> pdb=" O GLU D 223 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER D 231 " --> pdb=" O ALA D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 255 removed outlier: 3.705A pdb=" N PHE D 254 " --> pdb=" O ASN D 251 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG D 255 " --> pdb=" O GLU D 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 251 through 255' Processing helix chain 'D' and resid 257 through 260 Processing helix chain 'D' and resid 263 through 266 Processing helix chain 'D' and resid 273 through 283 removed outlier: 3.691A pdb=" N THR D 277 " --> pdb=" O ILE D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 294 removed outlier: 3.656A pdb=" N ALA D 294 " --> pdb=" O LYS D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 304 Processing helix chain 'D' and resid 308 through 319 removed outlier: 3.650A pdb=" N LEU D 319 " --> pdb=" O GLU D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 347 removed outlier: 5.205A pdb=" N VAL D 338 " --> pdb=" O LYS D 335 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE D 340 " --> pdb=" O SER D 337 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA D 346 " --> pdb=" O SER D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 351 No H-bonds generated for 'chain 'D' and resid 349 through 351' Processing helix chain 'D' and resid 358 through 372 removed outlier: 3.678A pdb=" N ASP D 362 " --> pdb=" O LYS D 358 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU D 363 " --> pdb=" O GLN D 359 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER D 364 " --> pdb=" O GLU D 360 " (cutoff:3.500A) Proline residue: D 366 - end of helix removed outlier: 4.374A pdb=" N VAL D 369 " --> pdb=" O GLY D 365 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N HIS D 370 " --> pdb=" O PRO D 366 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG D 371 " --> pdb=" O SER D 367 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 28 through 31 removed outlier: 7.880A pdb=" N ILE A 9 " --> pdb=" O PRO A 101 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU A 103 " --> pdb=" O ILE A 9 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 51 through 53 removed outlier: 3.584A pdb=" N ARG A 36 " --> pdb=" O THR A 65 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 296 through 299 removed outlier: 6.425A pdb=" N ILE A 150 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N SER A 299 " --> pdb=" O ILE A 150 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N MET A 152 " --> pdb=" O SER A 299 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE A 164 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 151 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 162 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR A 161 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 175 " --> pdb=" O THR A 161 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 237 through 240 removed outlier: 3.639A pdb=" N LYS A 237 " --> pdb=" O ILE A 249 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 28 through 31 removed outlier: 7.881A pdb=" N ILE B 9 " --> pdb=" O PRO B 101 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU B 103 " --> pdb=" O ILE B 9 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 51 through 53 removed outlier: 3.585A pdb=" N ARG B 36 " --> pdb=" O THR B 65 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 296 through 299 removed outlier: 6.426A pdb=" N ILE B 150 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N SER B 299 " --> pdb=" O ILE B 150 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N MET B 152 " --> pdb=" O SER B 299 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B 164 " --> pdb=" O GLY B 149 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL B 151 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 162 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR B 161 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU B 175 " --> pdb=" O THR B 161 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 237 through 240 removed outlier: 3.638A pdb=" N LYS B 237 " --> pdb=" O ILE B 249 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 28 through 31 removed outlier: 7.881A pdb=" N ILE C 9 " --> pdb=" O PRO C 101 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU C 103 " --> pdb=" O ILE C 9 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 51 through 53 removed outlier: 3.585A pdb=" N ARG C 36 " --> pdb=" O THR C 65 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 296 through 299 removed outlier: 6.426A pdb=" N ILE C 150 " --> pdb=" O VAL C 297 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N SER C 299 " --> pdb=" O ILE C 150 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N MET C 152 " --> pdb=" O SER C 299 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE C 164 " --> pdb=" O GLY C 149 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL C 151 " --> pdb=" O VAL C 162 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL C 162 " --> pdb=" O VAL C 151 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR C 161 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU C 175 " --> pdb=" O THR C 161 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 237 through 240 removed outlier: 3.639A pdb=" N LYS C 237 " --> pdb=" O ILE C 249 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 7 through 9 Processing sheet with id= N, first strand: chain 'D' and resid 51 through 53 removed outlier: 3.585A pdb=" N ARG D 36 " --> pdb=" O THR D 65 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 102 through 106 Processing sheet with id= P, first strand: chain 'D' and resid 296 through 299 removed outlier: 6.426A pdb=" N ILE D 150 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N SER D 299 " --> pdb=" O ILE D 150 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N MET D 152 " --> pdb=" O SER D 299 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE D 164 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL D 151 " --> pdb=" O VAL D 162 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL D 162 " --> pdb=" O VAL D 151 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR D 161 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU D 175 " --> pdb=" O THR D 161 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 237 through 240 removed outlier: 3.638A pdb=" N LYS D 237 " --> pdb=" O ILE D 249 " (cutoff:3.500A) 342 hydrogen bonds defined for protein. 810 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.24 Time building geometry restraints manager: 4.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1977 1.31 - 1.44: 3135 1.44 - 1.56: 6792 1.56 - 1.68: 12 1.68 - 1.81: 152 Bond restraints: 12068 Sorted by residual: bond pdb=" C HIC C 72 " pdb=" O HIC C 72 " ideal model delta sigma weight residual 1.231 1.359 -0.128 2.00e-02 2.50e+03 4.07e+01 bond pdb=" C HIC A 72 " pdb=" O HIC A 72 " ideal model delta sigma weight residual 1.231 1.358 -0.127 2.00e-02 2.50e+03 4.05e+01 bond pdb=" C HIC D 72 " pdb=" O HIC D 72 " ideal model delta sigma weight residual 1.231 1.358 -0.127 2.00e-02 2.50e+03 4.04e+01 bond pdb=" C HIC B 72 " pdb=" O HIC B 72 " ideal model delta sigma weight residual 1.231 1.358 -0.127 2.00e-02 2.50e+03 4.01e+01 bond pdb=" C4 ADP A 401 " pdb=" C5 ADP A 401 " ideal model delta sigma weight residual 1.490 1.377 0.113 2.00e-02 2.50e+03 3.17e+01 ... (remaining 12063 not shown) Histogram of bond angle deviations from ideal: 98.87 - 106.30: 440 106.30 - 113.72: 6569 113.72 - 121.15: 6121 121.15 - 128.58: 3162 128.58 - 136.00: 76 Bond angle restraints: 16368 Sorted by residual: angle pdb=" CA HIC C 72 " pdb=" C HIC C 72 " pdb=" O HIC C 72 " ideal model delta sigma weight residual 120.80 113.59 7.21 1.70e+00 3.46e-01 1.80e+01 angle pdb=" CA HIC D 72 " pdb=" C HIC D 72 " pdb=" O HIC D 72 " ideal model delta sigma weight residual 120.80 113.59 7.21 1.70e+00 3.46e-01 1.80e+01 angle pdb=" CA HIC B 72 " pdb=" C HIC B 72 " pdb=" O HIC B 72 " ideal model delta sigma weight residual 120.80 113.64 7.16 1.70e+00 3.46e-01 1.77e+01 angle pdb=" CA HIC A 72 " pdb=" C HIC A 72 " pdb=" O HIC A 72 " ideal model delta sigma weight residual 120.80 113.64 7.16 1.70e+00 3.46e-01 1.77e+01 angle pdb=" C GLU D 3 " pdb=" N ILE D 4 " pdb=" CA ILE D 4 " ideal model delta sigma weight residual 122.93 118.41 4.52 1.31e+00 5.83e-01 1.19e+01 ... (remaining 16363 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 7043 35.96 - 71.92: 215 71.92 - 107.89: 8 107.89 - 143.85: 1 143.85 - 179.81: 1 Dihedral angle restraints: 7268 sinusoidal: 2948 harmonic: 4320 Sorted by residual: dihedral pdb=" CH3 ACE A 0 " pdb=" C ACE A 0 " pdb=" N GLU A 1 " pdb=" CA GLU A 1 " ideal model delta sinusoidal sigma weight residual -180.00 -0.19 -179.81 1 5.00e+00 4.00e-02 7.68e+02 dihedral pdb=" CH3 ACE B 0 " pdb=" C ACE B 0 " pdb=" N GLU B 1 " pdb=" CA GLU B 1 " ideal model delta sinusoidal sigma weight residual 180.00 94.37 85.63 1 5.00e+00 4.00e-02 3.55e+02 dihedral pdb=" CH3 ACE D 0 " pdb=" C ACE D 0 " pdb=" N GLU D 1 " pdb=" CA GLU D 1 " ideal model delta sinusoidal sigma weight residual 180.00 139.62 40.38 1 5.00e+00 4.00e-02 9.15e+01 ... (remaining 7265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1397 0.048 - 0.095: 304 0.095 - 0.143: 102 0.143 - 0.190: 7 0.190 - 0.238: 2 Chirality restraints: 1812 Sorted by residual: chirality pdb=" CA GLU D 3 " pdb=" N GLU D 3 " pdb=" C GLU D 3 " pdb=" CB GLU D 3 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA ILE C 4 " pdb=" N ILE C 4 " pdb=" C ILE C 4 " pdb=" CB ILE C 4 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA VAL D 8 " pdb=" N VAL D 8 " pdb=" C VAL D 8 " pdb=" CB VAL D 8 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.00e-01 ... (remaining 1809 not shown) Planarity restraints: 2096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ACE B 0 " 0.064 2.00e-02 2.50e+03 2.81e-01 9.85e+02 pdb=" O ACE B 0 " -0.139 2.00e-02 2.50e+03 pdb=" CH3 ACE B 0 " -0.105 2.00e-02 2.50e+03 pdb=" N GLU B 1 " 0.504 2.00e-02 2.50e+03 pdb=" CA GLU B 1 " -0.324 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ACE D 0 " 0.139 2.00e-02 2.50e+03 2.00e-01 4.98e+02 pdb=" O ACE D 0 " 0.019 2.00e-02 2.50e+03 pdb=" CH3 ACE D 0 " -0.197 2.00e-02 2.50e+03 pdb=" N GLU D 1 " 0.284 2.00e-02 2.50e+03 pdb=" CA GLU D 1 " -0.245 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ACE C 0 " -0.038 2.00e-02 2.50e+03 9.25e-02 1.07e+02 pdb=" O ACE C 0 " -0.024 2.00e-02 2.50e+03 pdb=" CH3 ACE C 0 " 0.088 2.00e-02 2.50e+03 pdb=" N GLU C 1 " -0.141 2.00e-02 2.50e+03 pdb=" CA GLU C 1 " 0.115 2.00e-02 2.50e+03 ... (remaining 2093 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2948 2.79 - 3.32: 9769 3.32 - 3.85: 16553 3.85 - 4.37: 19390 4.37 - 4.90: 35217 Nonbonded interactions: 83877 Sorted by model distance: nonbonded pdb="MG MG B 400 " pdb=" O1B ADP B 401 " model vdw 2.266 2.170 nonbonded pdb="MG MG A 400 " pdb=" O1B ADP A 401 " model vdw 2.293 2.170 nonbonded pdb=" N GLU C 363 " pdb=" OE1 GLU C 363 " model vdw 2.391 2.520 nonbonded pdb=" N GLU D 363 " pdb=" OE1 GLU D 363 " model vdw 2.391 2.520 nonbonded pdb=" N GLU B 363 " pdb=" OE1 GLU B 363 " model vdw 2.392 2.520 ... (remaining 83872 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.160 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 33.200 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 12068 Z= 0.284 Angle : 0.686 9.969 16368 Z= 0.359 Chirality : 0.044 0.238 1812 Planarity : 0.010 0.281 2096 Dihedral : 15.956 179.812 4500 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.79 % Allowed : 19.78 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.20), residues: 1476 helix: -0.63 (0.22), residues: 460 sheet: -0.25 (0.36), residues: 204 loop : -0.45 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 85 HIS 0.002 0.000 HIS D 100 PHE 0.004 0.001 PHE D 254 TYR 0.011 0.001 TYR D 305 ARG 0.006 0.001 ARG C 205 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 216 time to evaluate : 1.240 Fit side-chains REVERT: B 71 GLU cc_start: 0.7428 (mt-10) cc_final: 0.7162 (pt0) REVERT: C 71 GLU cc_start: 0.7501 (mt-10) cc_final: 0.6690 (pp20) REVERT: C 326 ILE cc_start: 0.8850 (mm) cc_final: 0.8592 (mm) REVERT: C 360 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7485 (mt-10) REVERT: D 67 LYS cc_start: 0.7951 (mtpt) cc_final: 0.7449 (mtpp) REVERT: D 79 ASP cc_start: 0.7607 (m-30) cc_final: 0.7057 (t0) REVERT: D 140 SER cc_start: 0.9266 (t) cc_final: 0.9058 (m) REVERT: D 189 MET cc_start: 0.7928 (mtp) cc_final: 0.7712 (mtp) REVERT: D 201 THR cc_start: 0.7078 (m) cc_final: 0.6785 (t) REVERT: D 282 MET cc_start: 0.8464 (mmt) cc_final: 0.7985 (mpp) outliers start: 10 outliers final: 0 residues processed: 222 average time/residue: 0.2308 time to fit residues: 72.9443 Evaluate side-chains 140 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 chunk 62 optimal weight: 0.2980 chunk 38 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 116 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 134 optimal weight: 0.6980 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 160 HIS A 353 GLN A 370 HIS B 160 HIS C 160 HIS D 86 HIS D 160 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12068 Z= 0.245 Angle : 0.615 7.563 16368 Z= 0.300 Chirality : 0.045 0.141 1812 Planarity : 0.004 0.030 2096 Dihedral : 7.727 179.670 1684 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.16 % Allowed : 17.64 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.21), residues: 1476 helix: -0.45 (0.23), residues: 504 sheet: -0.09 (0.30), residues: 280 loop : -0.38 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 355 HIS 0.006 0.001 HIS D 86 PHE 0.008 0.001 PHE B 254 TYR 0.011 0.001 TYR B 132 ARG 0.004 0.001 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 132 time to evaluate : 1.282 Fit side-chains revert: symmetry clash REVERT: A 112 LYS cc_start: 0.7933 (pttt) cc_final: 0.7627 (ptmt) REVERT: B 13 SER cc_start: 0.7458 (OUTLIER) cc_final: 0.7082 (p) REVERT: B 166 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7542 (tm-30) REVERT: B 204 GLU cc_start: 0.6778 (OUTLIER) cc_final: 0.6423 (mt-10) REVERT: B 221 ASP cc_start: 0.7880 (t0) cc_final: 0.7632 (t0) REVERT: C 71 GLU cc_start: 0.7500 (mt-10) cc_final: 0.7247 (mt-10) REVERT: C 282 MET cc_start: 0.8194 (mmt) cc_final: 0.7759 (tpp) REVERT: C 360 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7600 (mt-10) REVERT: D 86 HIS cc_start: 0.6846 (OUTLIER) cc_final: 0.6592 (t-90) REVERT: D 282 MET cc_start: 0.7988 (mmt) cc_final: 0.7073 (mpp) outliers start: 40 outliers final: 23 residues processed: 155 average time/residue: 0.1794 time to fit residues: 43.8070 Evaluate side-chains 150 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 124 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASN Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 86 HIS Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 194 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 134 optimal weight: 9.9990 chunk 145 optimal weight: 8.9990 chunk 119 optimal weight: 0.9980 chunk 133 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN B 370 HIS C 11 ASN D 86 HIS D 370 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 12068 Z= 0.508 Angle : 0.753 7.920 16368 Z= 0.380 Chirality : 0.052 0.178 1812 Planarity : 0.005 0.035 2096 Dihedral : 8.088 179.115 1684 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 4.11 % Allowed : 18.51 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.21), residues: 1476 helix: -0.47 (0.24), residues: 468 sheet: -0.34 (0.31), residues: 276 loop : -1.09 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 355 HIS 0.029 0.002 HIS D 86 PHE 0.013 0.002 PHE B 199 TYR 0.019 0.002 TYR B 132 ARG 0.005 0.001 ARG C 255 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 135 time to evaluate : 1.394 Fit side-chains REVERT: A 273 ILE cc_start: 0.8330 (tt) cc_final: 0.8052 (tt) REVERT: B 13 SER cc_start: 0.7696 (OUTLIER) cc_final: 0.7325 (p) REVERT: B 112 LYS cc_start: 0.8392 (pttt) cc_final: 0.8111 (ptpt) REVERT: B 166 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7568 (tm-30) REVERT: B 204 GLU cc_start: 0.6856 (OUTLIER) cc_final: 0.6510 (mt-10) REVERT: B 221 ASP cc_start: 0.8050 (t0) cc_final: 0.7787 (t0) REVERT: C 71 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7539 (mt-10) REVERT: C 282 MET cc_start: 0.8258 (mmt) cc_final: 0.7975 (tpp) REVERT: C 360 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7636 (mt-10) REVERT: D 24 ASP cc_start: 0.7213 (t0) cc_final: 0.7000 (t0) REVERT: D 201 THR cc_start: 0.7538 (OUTLIER) cc_final: 0.7321 (t) outliers start: 52 outliers final: 33 residues processed: 172 average time/residue: 0.2024 time to fit residues: 53.3654 Evaluate side-chains 155 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 119 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 367 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 8.9990 chunk 101 optimal weight: 0.9980 chunk 69 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 12068 Z= 0.151 Angle : 0.539 6.204 16368 Z= 0.260 Chirality : 0.043 0.131 1812 Planarity : 0.003 0.032 2096 Dihedral : 7.532 179.905 1684 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.90 % Allowed : 20.17 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.21), residues: 1476 helix: -0.41 (0.24), residues: 488 sheet: -0.12 (0.31), residues: 276 loop : -0.81 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 355 HIS 0.003 0.001 HIS B 100 PHE 0.007 0.001 PHE B 30 TYR 0.008 0.001 TYR B 239 ARG 0.003 0.000 ARG C 205 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 120 time to evaluate : 1.368 Fit side-chains REVERT: A 166 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7565 (tm-30) REVERT: A 224 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.7048 (mp10) REVERT: A 273 ILE cc_start: 0.8229 (tt) cc_final: 0.7906 (tt) REVERT: B 13 SER cc_start: 0.7627 (OUTLIER) cc_final: 0.7237 (p) REVERT: B 81 MET cc_start: 0.7570 (tpt) cc_final: 0.7302 (tpt) REVERT: B 166 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7316 (tm-30) REVERT: B 221 ASP cc_start: 0.7773 (t0) cc_final: 0.6049 (p0) REVERT: C 106 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.6954 (tm-30) REVERT: C 282 MET cc_start: 0.8128 (mmt) cc_final: 0.7829 (tpp) REVERT: C 360 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7674 (mt-10) REVERT: D 46 MET cc_start: 0.7328 (mmm) cc_final: 0.6745 (mmm) REVERT: D 279 ASN cc_start: 0.8622 (m-40) cc_final: 0.8363 (m-40) REVERT: D 282 MET cc_start: 0.7969 (tpp) cc_final: 0.7714 (tpp) outliers start: 24 outliers final: 17 residues processed: 134 average time/residue: 0.1988 time to fit residues: 41.5119 Evaluate side-chains 132 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain D residue 287 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 2 optimal weight: 9.9990 chunk 106 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 chunk 122 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 128 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12068 Z= 0.301 Angle : 0.593 6.879 16368 Z= 0.289 Chirality : 0.046 0.144 1812 Planarity : 0.004 0.035 2096 Dihedral : 7.529 179.628 1684 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.93 % Allowed : 19.70 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.21), residues: 1476 helix: -0.41 (0.24), residues: 480 sheet: -0.11 (0.32), residues: 268 loop : -0.92 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 355 HIS 0.004 0.001 HIS B 100 PHE 0.008 0.001 PHE B 199 TYR 0.012 0.001 TYR B 239 ARG 0.003 0.000 ARG C 255 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 112 time to evaluate : 1.429 Fit side-chains REVERT: A 166 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7624 (tm-30) REVERT: A 224 GLN cc_start: 0.7550 (OUTLIER) cc_final: 0.7008 (mp10) REVERT: A 273 ILE cc_start: 0.8419 (tt) cc_final: 0.8037 (tt) REVERT: A 282 MET cc_start: 0.8142 (tpp) cc_final: 0.7806 (tpp) REVERT: B 81 MET cc_start: 0.7560 (tpt) cc_final: 0.7253 (tpt) REVERT: B 122 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.7336 (tpp) REVERT: B 152 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.8082 (tpp) REVERT: B 166 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7367 (tm-30) REVERT: B 221 ASP cc_start: 0.7818 (t0) cc_final: 0.7566 (t0) REVERT: C 106 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7073 (tm-30) REVERT: C 282 MET cc_start: 0.8124 (mmt) cc_final: 0.7741 (tpp) REVERT: C 360 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7548 (mt-10) REVERT: D 46 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.6787 (mmm) REVERT: D 106 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.8006 (tt0) REVERT: D 282 MET cc_start: 0.8100 (tpp) cc_final: 0.7635 (mpp) outliers start: 37 outliers final: 27 residues processed: 137 average time/residue: 0.1871 time to fit residues: 40.1454 Evaluate side-chains 143 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 110 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 367 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 4.9990 chunk 128 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 143 optimal weight: 5.9990 chunk 118 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 12068 Z= 0.375 Angle : 0.636 7.318 16368 Z= 0.314 Chirality : 0.048 0.152 1812 Planarity : 0.004 0.043 2096 Dihedral : 7.711 179.754 1684 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.80 % Allowed : 18.67 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.21), residues: 1476 helix: -0.55 (0.24), residues: 480 sheet: -0.32 (0.31), residues: 268 loop : -1.13 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 355 HIS 0.005 0.001 HIS B 100 PHE 0.009 0.001 PHE B 199 TYR 0.014 0.002 TYR B 132 ARG 0.004 0.000 ARG C 255 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 112 time to evaluate : 1.575 Fit side-chains REVERT: A 166 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7667 (tm-30) REVERT: A 224 GLN cc_start: 0.7575 (OUTLIER) cc_final: 0.6952 (mp10) REVERT: A 273 ILE cc_start: 0.8544 (tt) cc_final: 0.8131 (tt) REVERT: B 81 MET cc_start: 0.7642 (tpt) cc_final: 0.7224 (tpt) REVERT: B 122 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7269 (tpp) REVERT: B 152 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.8104 (tpp) REVERT: B 166 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7360 (tm-30) REVERT: B 221 ASP cc_start: 0.7846 (t0) cc_final: 0.7646 (t0) REVERT: C 106 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7234 (tm-30) REVERT: C 191 ILE cc_start: 0.7506 (tt) cc_final: 0.7274 (tt) REVERT: C 282 MET cc_start: 0.8133 (mmt) cc_final: 0.7746 (tpp) REVERT: C 360 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7530 (mt-10) REVERT: D 24 ASP cc_start: 0.7122 (t0) cc_final: 0.6910 (t0) REVERT: D 46 MET cc_start: 0.7286 (OUTLIER) cc_final: 0.6712 (mmm) REVERT: D 106 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8092 (tt0) REVERT: D 282 MET cc_start: 0.8281 (tpp) cc_final: 0.7670 (mpp) REVERT: D 359 GLN cc_start: 0.8309 (mm110) cc_final: 0.7830 (tp40) outliers start: 48 outliers final: 37 residues processed: 147 average time/residue: 0.1814 time to fit residues: 41.8359 Evaluate side-chains 153 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 110 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 15 MET Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 367 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 142 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 86 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12068 Z= 0.299 Angle : 0.588 7.050 16368 Z= 0.286 Chirality : 0.046 0.138 1812 Planarity : 0.004 0.044 2096 Dihedral : 7.620 179.986 1684 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.03 % Allowed : 19.07 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.21), residues: 1476 helix: -0.53 (0.24), residues: 480 sheet: -0.35 (0.31), residues: 268 loop : -1.17 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 355 HIS 0.004 0.001 HIS B 100 PHE 0.008 0.001 PHE B 30 TYR 0.011 0.001 TYR B 239 ARG 0.003 0.000 ARG C 255 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 114 time to evaluate : 1.389 Fit side-chains REVERT: A 106 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8378 (tm-30) REVERT: A 166 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7579 (tm-30) REVERT: A 224 GLN cc_start: 0.7574 (OUTLIER) cc_final: 0.6965 (mp10) REVERT: A 273 ILE cc_start: 0.8558 (tt) cc_final: 0.8098 (tt) REVERT: B 81 MET cc_start: 0.7674 (tpt) cc_final: 0.7259 (tpt) REVERT: B 112 LYS cc_start: 0.7983 (pttt) cc_final: 0.7540 (ptpt) REVERT: B 122 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7283 (tpp) REVERT: B 152 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.8082 (tpp) REVERT: B 166 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7336 (tm-30) REVERT: C 24 ASP cc_start: 0.8139 (m-30) cc_final: 0.7935 (m-30) REVERT: C 106 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7222 (tm-30) REVERT: C 191 ILE cc_start: 0.7494 (tt) cc_final: 0.7251 (tt) REVERT: C 282 MET cc_start: 0.8118 (mmt) cc_final: 0.7718 (tpp) REVERT: C 360 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7529 (mt-10) REVERT: D 24 ASP cc_start: 0.7293 (t0) cc_final: 0.7056 (t0) REVERT: D 46 MET cc_start: 0.7257 (OUTLIER) cc_final: 0.7037 (mmm) REVERT: D 106 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.8047 (tt0) REVERT: D 147 THR cc_start: 0.7311 (p) cc_final: 0.6930 (t) REVERT: D 282 MET cc_start: 0.8286 (tpp) cc_final: 0.7643 (mpp) REVERT: D 359 GLN cc_start: 0.8304 (mm110) cc_final: 0.7838 (tp40) outliers start: 51 outliers final: 42 residues processed: 152 average time/residue: 0.1868 time to fit residues: 45.1875 Evaluate side-chains 161 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 112 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 367 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 7.9990 chunk 85 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 chunk 129 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12068 Z= 0.326 Angle : 0.606 7.208 16368 Z= 0.296 Chirality : 0.046 0.146 1812 Planarity : 0.004 0.047 2096 Dihedral : 7.668 179.937 1684 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.27 % Allowed : 19.07 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.21), residues: 1476 helix: -0.56 (0.24), residues: 480 sheet: -0.40 (0.31), residues: 268 loop : -1.25 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 355 HIS 0.004 0.001 HIS B 100 PHE 0.009 0.001 PHE A 126 TYR 0.012 0.001 TYR B 132 ARG 0.003 0.000 ARG C 255 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 113 time to evaluate : 1.353 Fit side-chains REVERT: A 106 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8381 (tm-30) REVERT: A 166 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7588 (tm-30) REVERT: A 224 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.6949 (mp10) REVERT: A 273 ILE cc_start: 0.8614 (tt) cc_final: 0.8219 (tt) REVERT: B 81 MET cc_start: 0.7751 (tpt) cc_final: 0.7296 (tpt) REVERT: B 112 LYS cc_start: 0.8042 (pttt) cc_final: 0.7577 (ptpt) REVERT: B 122 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.7241 (tpp) REVERT: B 152 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.8077 (tpp) REVERT: B 166 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7346 (tm-30) REVERT: C 106 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7228 (tm-30) REVERT: C 191 ILE cc_start: 0.7504 (tt) cc_final: 0.7260 (tt) REVERT: C 282 MET cc_start: 0.8119 (mmt) cc_final: 0.7718 (tpp) REVERT: C 360 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7652 (mt-10) REVERT: D 24 ASP cc_start: 0.7418 (t0) cc_final: 0.7176 (t0) REVERT: D 46 MET cc_start: 0.7173 (OUTLIER) cc_final: 0.6902 (mmm) REVERT: D 106 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.8052 (tt0) REVERT: D 147 THR cc_start: 0.7432 (p) cc_final: 0.7051 (t) REVERT: D 282 MET cc_start: 0.8294 (tpp) cc_final: 0.7597 (mpp) REVERT: D 359 GLN cc_start: 0.8407 (mm110) cc_final: 0.7934 (tp40) outliers start: 54 outliers final: 44 residues processed: 153 average time/residue: 0.1784 time to fit residues: 43.1269 Evaluate side-chains 163 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 112 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 15 MET Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 367 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 140 optimal weight: 6.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12068 Z= 0.195 Angle : 0.537 6.398 16368 Z= 0.257 Chirality : 0.044 0.132 1812 Planarity : 0.004 0.045 2096 Dihedral : 7.413 179.930 1684 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.40 % Allowed : 19.94 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.22), residues: 1476 helix: -0.45 (0.24), residues: 488 sheet: -0.22 (0.32), residues: 268 loop : -1.13 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 355 HIS 0.003 0.001 HIS B 100 PHE 0.007 0.001 PHE B 30 TYR 0.008 0.001 TYR B 239 ARG 0.002 0.000 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 117 time to evaluate : 1.330 Fit side-chains REVERT: A 106 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8374 (tm-30) REVERT: A 166 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7476 (tm-30) REVERT: A 224 GLN cc_start: 0.7562 (OUTLIER) cc_final: 0.6965 (mp10) REVERT: A 273 ILE cc_start: 0.8551 (tt) cc_final: 0.8049 (tt) REVERT: B 81 MET cc_start: 0.7577 (tpt) cc_final: 0.7322 (tpt) REVERT: B 112 LYS cc_start: 0.7864 (pttt) cc_final: 0.7365 (ptpt) REVERT: B 122 MET cc_start: 0.7712 (OUTLIER) cc_final: 0.7303 (tpp) REVERT: B 166 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7279 (tm-30) REVERT: C 106 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7145 (tm-30) REVERT: C 122 MET cc_start: 0.7996 (mmt) cc_final: 0.7562 (mmt) REVERT: C 191 ILE cc_start: 0.7447 (tt) cc_final: 0.7190 (tt) REVERT: C 251 ASN cc_start: 0.8638 (p0) cc_final: 0.8332 (p0) REVERT: C 360 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7653 (mt-10) REVERT: D 24 ASP cc_start: 0.7428 (t0) cc_final: 0.7213 (t0) REVERT: D 46 MET cc_start: 0.7190 (OUTLIER) cc_final: 0.6908 (mmm) REVERT: D 106 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7969 (tt0) REVERT: D 147 THR cc_start: 0.7470 (p) cc_final: 0.7122 (t) REVERT: D 282 MET cc_start: 0.8274 (tpp) cc_final: 0.7665 (mpp) REVERT: D 359 GLN cc_start: 0.8344 (mm110) cc_final: 0.7878 (tp40) outliers start: 43 outliers final: 32 residues processed: 149 average time/residue: 0.1944 time to fit residues: 45.1637 Evaluate side-chains 150 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 112 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 287 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 0.9990 chunk 66 optimal weight: 0.4980 chunk 97 optimal weight: 0.0370 chunk 147 optimal weight: 8.9990 chunk 135 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 90 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 chunk 125 optimal weight: 9.9990 overall best weight: 1.2862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12068 Z= 0.158 Angle : 0.523 6.254 16368 Z= 0.248 Chirality : 0.043 0.160 1812 Planarity : 0.003 0.041 2096 Dihedral : 7.210 179.999 1684 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.24 % Allowed : 19.94 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.22), residues: 1476 helix: -0.37 (0.24), residues: 492 sheet: -0.00 (0.32), residues: 260 loop : -1.03 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 355 HIS 0.003 0.001 HIS B 100 PHE 0.016 0.001 PHE A 278 TYR 0.009 0.001 TYR D 305 ARG 0.002 0.000 ARG A 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 117 time to evaluate : 1.418 Fit side-chains REVERT: A 106 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8362 (tm-30) REVERT: A 112 LYS cc_start: 0.8177 (ptmt) cc_final: 0.7885 (mtpt) REVERT: A 166 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7473 (tm-30) REVERT: A 224 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.7044 (mp10) REVERT: A 273 ILE cc_start: 0.8358 (tt) cc_final: 0.8005 (tt) REVERT: B 166 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7307 (tm-30) REVERT: C 106 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7002 (tm-30) REVERT: C 204 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.6363 (mt-10) REVERT: C 251 ASN cc_start: 0.8583 (p0) cc_final: 0.8281 (p0) REVERT: C 360 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7678 (mt-10) REVERT: D 24 ASP cc_start: 0.7398 (t0) cc_final: 0.7176 (t0) REVERT: D 46 MET cc_start: 0.7208 (OUTLIER) cc_final: 0.6916 (mmm) REVERT: D 106 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7937 (tt0) REVERT: D 147 THR cc_start: 0.7493 (p) cc_final: 0.7172 (t) REVERT: D 282 MET cc_start: 0.8253 (tpp) cc_final: 0.7671 (mpp) REVERT: D 359 GLN cc_start: 0.8362 (mm110) cc_final: 0.7916 (tp40) outliers start: 41 outliers final: 28 residues processed: 148 average time/residue: 0.1903 time to fit residues: 44.0746 Evaluate side-chains 148 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 114 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 287 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 6 optimal weight: 10.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.127691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.108023 restraints weight = 16763.910| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.46 r_work: 0.3142 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12068 Z= 0.224 Angle : 0.552 6.438 16368 Z= 0.264 Chirality : 0.044 0.133 1812 Planarity : 0.004 0.041 2096 Dihedral : 7.226 179.985 1684 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.01 % Allowed : 19.86 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.22), residues: 1476 helix: -0.32 (0.24), residues: 488 sheet: -0.15 (0.32), residues: 268 loop : -1.08 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 355 HIS 0.003 0.001 HIS A 100 PHE 0.009 0.001 PHE B 351 TYR 0.010 0.001 TYR B 239 ARG 0.002 0.000 ARG C 255 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2256.98 seconds wall clock time: 41 minutes 57.70 seconds (2517.70 seconds total)