Starting phenix.real_space_refine on Thu Feb 5 12:37:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ccg_45442/02_2026/9ccg_45442.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ccg_45442/02_2026/9ccg_45442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ccg_45442/02_2026/9ccg_45442.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ccg_45442/02_2026/9ccg_45442.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ccg_45442/02_2026/9ccg_45442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ccg_45442/02_2026/9ccg_45442.map" } resolution = 3.87 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 10752 2.51 5 N 2878 2.21 5 O 3312 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16978 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5150 Classifications: {'peptide': 659} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 18, 'TRANS': 640} Chain breaks: 1 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2, 'TYR:plan': 1, 'PHE:plan': 1, 'ARG:plan': 5, 'GLN:plan1': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 65 Chain: "B" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1684 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 12, 'TRANS': 214} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1614 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 201} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 5195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 666, 5195 Classifications: {'peptide': 666} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 18, 'TRANS': 647} Chain breaks: 1 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 86 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 5, 'GLU:plan': 2, 'PHE:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 59 Chain: "E" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1622 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 10, 'TRANS': 201} Chain: "F" Number of atoms: 1713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1713 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 12, 'TRANS': 214} Time building chain proxies: 3.57, per 1000 atoms: 0.21 Number of scatterers: 16978 At special positions: 0 Unit cell: (222.6, 98.7, 97.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 3312 8.00 N 2878 7.00 C 10752 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 213 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 195 " distance=2.04 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 195 " distance=2.04 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS F 99 " distance=2.03 Simple disulfide: pdb=" SG CYS F 157 " - pdb=" SG CYS F 213 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 708.3 milliseconds 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4004 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 40 sheets defined 12.7% alpha, 32.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 37 through 45 Processing helix chain 'A' and resid 54 through 69 removed outlier: 3.834A pdb=" N GLY A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.501A pdb=" N LEU A 101 " --> pdb=" O VAL A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 141 Processing helix chain 'A' and resid 151 through 164 Processing helix chain 'A' and resid 205 through 213 Processing helix chain 'A' and resid 222 through 240 Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 294 through 300 removed outlier: 3.834A pdb=" N ILE A 298 " --> pdb=" O LYS A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 326 removed outlier: 3.771A pdb=" N GLY A 326 " --> pdb=" O LEU A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 385 No H-bonds generated for 'chain 'A' and resid 383 through 385' Processing helix chain 'B' and resid 90 through 94 Processing helix chain 'C' and resid 80 through 84 removed outlier: 4.007A pdb=" N PHE C 84 " --> pdb=" O PRO C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 127 Processing helix chain 'C' and resid 184 through 190 Processing helix chain 'C' and resid 199 through 203 removed outlier: 3.580A pdb=" N SER C 203 " --> pdb=" O GLN C 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 45 Processing helix chain 'D' and resid 54 through 69 removed outlier: 3.834A pdb=" N GLY D 69 " --> pdb=" O LEU D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.500A pdb=" N LEU D 101 " --> pdb=" O VAL D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 141 Processing helix chain 'D' and resid 151 through 164 Processing helix chain 'D' and resid 205 through 213 Processing helix chain 'D' and resid 222 through 240 Processing helix chain 'D' and resid 285 through 290 Processing helix chain 'D' and resid 294 through 300 removed outlier: 3.833A pdb=" N ILE D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 326 removed outlier: 3.770A pdb=" N GLY D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 385 No H-bonds generated for 'chain 'D' and resid 383 through 385' Processing helix chain 'E' and resid 80 through 84 removed outlier: 4.007A pdb=" N PHE E 84 " --> pdb=" O PRO E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 127 Processing helix chain 'E' and resid 184 through 190 Processing helix chain 'E' and resid 199 through 203 removed outlier: 3.580A pdb=" N SER E 203 " --> pdb=" O GLN E 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 94 Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 81 Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 173 removed outlier: 6.161A pdb=" N VAL A 188 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N VAL A 170 " --> pdb=" O GLU A 186 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLU A 186 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N SER A 184 " --> pdb=" O PRO A 172 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 177 Processing sheet with id=AA4, first strand: chain 'A' and resid 195 through 199 removed outlier: 6.963A pdb=" N SER A 195 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE A 260 " --> pdb=" O SER A 195 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ILE A 197 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER A 251 " --> pdb=" O HIS A 259 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 266 through 267 removed outlier: 4.660A pdb=" N ILE A 338 " --> pdb=" O ASP A 341 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.825A pdb=" N GLU A 271 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ILE A 351 " --> pdb=" O GLU A 271 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LYS A 273 " --> pdb=" O ILE A 351 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N GLU A 353 " --> pdb=" O LYS A 273 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASN A 330 " --> pdb=" O ASP A 352 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 379 through 382 removed outlier: 3.883A pdb=" N ASN A 381 " --> pdb=" O GLN A 387 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N GLN A 387 " --> pdb=" O ASN A 381 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN A 360 " --> pdb=" O SER A 376 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN D 360 " --> pdb=" O SER D 376 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N GLN D 387 " --> pdb=" O ASN D 381 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN D 381 " --> pdb=" O GLN D 387 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 690 through 692 removed outlier: 3.558A pdb=" N ASP A 673 " --> pdb=" O TYR A 690 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN A 692 " --> pdb=" O ARG A 671 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N THR A 655 " --> pdb=" O VAL A 678 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY A 654 " --> pdb=" O GLY A 630 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU A 607 " --> pdb=" O ARG A 631 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY A 526 " --> pdb=" O TYR A 556 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 533 " --> pdb=" O PRO A 510 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE A 508 " --> pdb=" O ALA A 535 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A 465 " --> pdb=" O PHE A 445 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN A 360 " --> pdb=" O SER A 376 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN D 360 " --> pdb=" O SER D 376 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL D 465 " --> pdb=" O PHE D 445 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE D 508 " --> pdb=" O ALA D 535 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL D 533 " --> pdb=" O PRO D 510 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY D 526 " --> pdb=" O TYR D 556 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU D 607 " --> pdb=" O ARG D 631 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY D 654 " --> pdb=" O GLY D 630 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N THR D 655 " --> pdb=" O VAL D 678 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN D 692 " --> pdb=" O ARG D 671 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP D 673 " --> pdb=" O TYR D 690 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 478 through 479 removed outlier: 4.135A pdb=" N TRP A 485 " --> pdb=" O ILE A 496 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 585 through 587 Processing sheet with id=AB2, first strand: chain 'B' and resid 7 through 10 removed outlier: 3.519A pdb=" N VAL B 8 " --> pdb=" O ALA B 26 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 60 through 63 removed outlier: 4.084A pdb=" N TYR B 62 " --> pdb=" O SER B 53 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N SER B 53 " --> pdb=" O TYR B 62 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N TRP B 50 " --> pdb=" O ARG B 41 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ARG B 41 " --> pdb=" O TRP B 50 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR B 119 " --> pdb=" O ARG B 101 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 60 through 63 removed outlier: 4.084A pdb=" N TYR B 62 " --> pdb=" O SER B 53 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N SER B 53 " --> pdb=" O TYR B 62 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N TRP B 50 " --> pdb=" O ARG B 41 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ARG B 41 " --> pdb=" O TRP B 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 153 through 155 removed outlier: 3.739A pdb=" N ALA B 153 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 199 " --> pdb=" O LEU B 155 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 159 through 162 removed outlier: 3.500A pdb=" N ASP B 161 " --> pdb=" O TYR B 193 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N TYR B 193 " --> pdb=" O ASP B 161 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU B 192 " --> pdb=" O GLN B 188 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 169 through 171 removed outlier: 3.558A pdb=" N ASN B 214 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TYR B 211 " --> pdb=" O VAL B 228 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 24 through 25 Processing sheet with id=AB9, first strand: chain 'C' and resid 33 through 34 removed outlier: 4.252A pdb=" N ALA C 33 " --> pdb=" O PHE C 92 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR C 98 " --> pdb=" O GLN C 91 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER C 93 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU C 96 " --> pdb=" O SER C 93 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 38 through 39 Processing sheet with id=AC2, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AC3, first strand: chain 'C' and resid 134 through 136 Processing sheet with id=AC4, first strand: chain 'D' and resid 73 through 81 Processing sheet with id=AC5, first strand: chain 'D' and resid 167 through 173 removed outlier: 6.161A pdb=" N VAL D 188 " --> pdb=" O SER D 168 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N VAL D 170 " --> pdb=" O GLU D 186 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLU D 186 " --> pdb=" O VAL D 170 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N SER D 184 " --> pdb=" O PRO D 172 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 176 through 177 Processing sheet with id=AC7, first strand: chain 'D' and resid 195 through 199 removed outlier: 6.964A pdb=" N SER D 195 " --> pdb=" O LEU D 258 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ILE D 260 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE D 197 " --> pdb=" O ILE D 260 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER D 251 " --> pdb=" O HIS D 259 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 266 through 267 removed outlier: 4.660A pdb=" N ILE D 338 " --> pdb=" O ASP D 341 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 271 through 274 removed outlier: 6.825A pdb=" N GLU D 271 " --> pdb=" O LEU D 349 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ILE D 351 " --> pdb=" O GLU D 271 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LYS D 273 " --> pdb=" O ILE D 351 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N GLU D 353 " --> pdb=" O LYS D 273 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASN D 330 " --> pdb=" O ASP D 352 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 478 through 479 removed outlier: 4.135A pdb=" N TRP D 485 " --> pdb=" O ILE D 496 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 585 through 587 Processing sheet with id=AD3, first strand: chain 'E' and resid 24 through 25 Processing sheet with id=AD4, first strand: chain 'E' and resid 33 through 34 removed outlier: 4.252A pdb=" N ALA E 33 " --> pdb=" O PHE E 92 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR E 98 " --> pdb=" O GLN E 91 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER E 93 " --> pdb=" O LEU E 96 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU E 96 " --> pdb=" O SER E 93 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 38 through 39 Processing sheet with id=AD6, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AD7, first strand: chain 'E' and resid 134 through 136 Processing sheet with id=AD8, first strand: chain 'F' and resid 7 through 10 removed outlier: 3.519A pdb=" N VAL F 8 " --> pdb=" O ALA F 26 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 60 through 63 removed outlier: 4.084A pdb=" N TYR F 62 " --> pdb=" O SER F 53 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N SER F 53 " --> pdb=" O TYR F 62 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N TRP F 50 " --> pdb=" O ARG F 41 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ARG F 41 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR F 119 " --> pdb=" O ARG F 101 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 60 through 63 removed outlier: 4.084A pdb=" N TYR F 62 " --> pdb=" O SER F 53 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N SER F 53 " --> pdb=" O TYR F 62 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N TRP F 50 " --> pdb=" O ARG F 41 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ARG F 41 " --> pdb=" O TRP F 50 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 153 through 155 removed outlier: 3.740A pdb=" N ALA F 153 " --> pdb=" O VAL F 201 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL F 199 " --> pdb=" O LEU F 155 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 159 through 162 removed outlier: 3.500A pdb=" N ASP F 161 " --> pdb=" O TYR F 193 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N TYR F 193 " --> pdb=" O ASP F 161 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU F 192 " --> pdb=" O GLN F 188 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 169 through 171 removed outlier: 3.558A pdb=" N ASN F 214 " --> pdb=" O SER F 170 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TYR F 211 " --> pdb=" O VAL F 228 " (cutoff:3.500A) 638 hydrogen bonds defined for protein. 1656 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: 2.98 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5515 1.34 - 1.46: 4149 1.46 - 1.58: 7631 1.58 - 1.70: 0 1.70 - 1.81: 54 Bond restraints: 17349 Sorted by residual: bond pdb=" CA VAL D 276 " pdb=" CB VAL D 276 " ideal model delta sigma weight residual 1.527 1.544 -0.017 1.31e-02 5.83e+03 1.69e+00 bond pdb=" CA VAL A 276 " pdb=" CB VAL A 276 " ideal model delta sigma weight residual 1.527 1.544 -0.017 1.31e-02 5.83e+03 1.63e+00 bond pdb=" CA ASP E 152 " pdb=" CB ASP E 152 " ideal model delta sigma weight residual 1.530 1.548 -0.018 1.69e-02 3.50e+03 1.09e+00 bond pdb=" CA ASP C 152 " pdb=" CB ASP C 152 " ideal model delta sigma weight residual 1.530 1.548 -0.017 1.69e-02 3.50e+03 1.06e+00 bond pdb=" CB GLU E 188 " pdb=" CG GLU E 188 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.51e-01 ... (remaining 17344 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 22619 1.44 - 2.88: 740 2.88 - 4.32: 124 4.32 - 5.76: 35 5.76 - 7.20: 15 Bond angle restraints: 23533 Sorted by residual: angle pdb=" CA GLU E 188 " pdb=" CB GLU E 188 " pdb=" CG GLU E 188 " ideal model delta sigma weight residual 114.10 120.68 -6.58 2.00e+00 2.50e-01 1.08e+01 angle pdb=" CA GLU C 188 " pdb=" CB GLU C 188 " pdb=" CG GLU C 188 " ideal model delta sigma weight residual 114.10 120.66 -6.56 2.00e+00 2.50e-01 1.08e+01 angle pdb=" N SER C 51 " pdb=" CA SER C 51 " pdb=" C SER C 51 " ideal model delta sigma weight residual 113.18 108.96 4.22 1.33e+00 5.65e-01 1.01e+01 angle pdb=" N SER E 51 " pdb=" CA SER E 51 " pdb=" C SER E 51 " ideal model delta sigma weight residual 113.18 108.97 4.21 1.33e+00 5.65e-01 1.00e+01 angle pdb=" C TYR B 162 " pdb=" N PHE B 163 " pdb=" CA PHE B 163 " ideal model delta sigma weight residual 120.65 124.94 -4.29 1.36e+00 5.41e-01 9.95e+00 ... (remaining 23528 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 8669 17.95 - 35.91: 1239 35.91 - 53.86: 264 53.86 - 71.81: 47 71.81 - 89.76: 22 Dihedral angle restraints: 10241 sinusoidal: 3936 harmonic: 6305 Sorted by residual: dihedral pdb=" CB CYS C 135 " pdb=" SG CYS C 135 " pdb=" SG CYS C 195 " pdb=" CB CYS C 195 " ideal model delta sinusoidal sigma weight residual -86.00 -175.76 89.76 1 1.00e+01 1.00e-02 9.56e+01 dihedral pdb=" CB CYS E 135 " pdb=" SG CYS E 135 " pdb=" SG CYS E 195 " pdb=" CB CYS E 195 " ideal model delta sinusoidal sigma weight residual -86.00 -175.72 89.72 1 1.00e+01 1.00e-02 9.55e+01 dihedral pdb=" CA ILE D 108 " pdb=" C ILE D 108 " pdb=" N ASN D 109 " pdb=" CA ASN D 109 " ideal model delta harmonic sigma weight residual 180.00 156.31 23.69 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 10238 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1580 0.031 - 0.062: 640 0.062 - 0.093: 208 0.093 - 0.124: 159 0.124 - 0.155: 13 Chirality restraints: 2600 Sorted by residual: chirality pdb=" CA ASP C 152 " pdb=" N ASP C 152 " pdb=" C ASP C 152 " pdb=" CB ASP C 152 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.16 2.00e-01 2.50e+01 6.02e-01 chirality pdb=" CA ASP E 152 " pdb=" N ASP E 152 " pdb=" C ASP E 152 " pdb=" CB ASP E 152 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.81e-01 chirality pdb=" CA ILE C 118 " pdb=" N ILE C 118 " pdb=" C ILE C 118 " pdb=" CB ILE C 118 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.32e-01 ... (remaining 2597 not shown) Planarity restraints: 3031 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 151 " 0.011 2.00e-02 2.50e+03 2.19e-02 4.79e+00 pdb=" C ARG A 151 " -0.038 2.00e-02 2.50e+03 pdb=" O ARG A 151 " 0.014 2.00e-02 2.50e+03 pdb=" N SER A 152 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 151 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.67e+00 pdb=" C ARG D 151 " -0.037 2.00e-02 2.50e+03 pdb=" O ARG D 151 " 0.014 2.00e-02 2.50e+03 pdb=" N SER D 152 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 201 " 0.029 5.00e-02 4.00e+02 4.44e-02 3.16e+00 pdb=" N PRO B 202 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 202 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 202 " 0.025 5.00e-02 4.00e+02 ... (remaining 3028 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 549 2.68 - 3.23: 16875 3.23 - 3.79: 26510 3.79 - 4.34: 34275 4.34 - 4.90: 56387 Nonbonded interactions: 134596 Sorted by model distance: nonbonded pdb=" OG1 THR A 214 " pdb=" OD1 ASN A 225 " model vdw 2.125 3.040 nonbonded pdb=" OG1 THR D 214 " pdb=" OD1 ASN D 225 " model vdw 2.125 3.040 nonbonded pdb=" NH1 ARG E 95 " pdb=" OG SER F 60 " model vdw 2.200 3.120 nonbonded pdb=" O GLY F 174 " pdb=" OG1 THR F 177 " model vdw 2.207 3.040 nonbonded pdb=" O GLY B 174 " pdb=" OG1 THR B 177 " model vdw 2.208 3.040 ... (remaining 134591 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 or (resid 48 and (name N or name CA or nam \ e C or name O or name CB )) or resid 49 through 51 or (resid 52 and (name N or n \ ame CA or name C or name O or name CB )) or resid 53 through 69 or (resid 70 and \ (name N or name CA or name C or name O or name CB )) or resid 71 through 124 or \ (resid 125 and (name N or name CA or name C or name O or name CB )) or resid 12 \ 6 through 130 or (resid 131 and (name N or name CA or name C or name O or name C \ B )) or resid 132 through 135 or (resid 136 and (name N or name CA or name C or \ name O or name CB )) or resid 137 through 143 or (resid 144 through 145 and (nam \ e N or name CA or name C or name O or name CB )) or resid 146 through 281 or (re \ sid 282 through 284 and (name N or name CA or name C or name O or name CB )) or \ resid 285 through 693)) selection = (chain 'D' and (resid 23 through 107 or resid 120 or (resid 121 and (name N or n \ ame CA or name C or name O or name CB )) or resid 122 through 138 or (resid 139 \ and (name N or name CA or name C or name O or name CB )) or resid 140 through 14 \ 6 or (resid 147 through 149 and (name N or name CA or name C or name O or name C \ B )) or resid 150 through 170 or (resid 171 and (name N or name CA or name C or \ name O or name CB )) or resid 172 through 175 or (resid 176 through 178 and (nam \ e N or name CA or name C or name O or name CB )) or resid 179 through 286 or (re \ sid 287 through 288 and (name N or name CA or name C or name O or name CB )) or \ resid 289 through 693)) } ncs_group { reference = chain 'B' selection = (chain 'F' and (resid 4 through 145 or (resid 146 and (name N or name CA or name \ C or name O or name CB )) or resid 147 through 213 or (resid 214 and (name N or \ name CA or name C or name O or name CB )) or resid 215 through 217 or (resid 21 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 219 through \ 220 or (resid 221 and (name N or name CA or name C or name O or name CB )) or re \ sid 222 or (resid 223 and (name N or name CA or name C or name O or name CB )) o \ r resid 224 or (resid 225 and (name N or name CA or name C or name O or name CB \ )) or resid 226 or (resid 227 and (name N or name CA or name C or name O or name \ CB )) or resid 228 or (resid 229 and (name N or name CA or name C or name O or \ name CB )) or resid 230)) } ncs_group { reference = chain 'C' selection = (chain 'E' and (resid 4 through 42 or (resid 43 through 44 and (name N or name C \ A or name C or name O or name CB )) or resid 45 through 107 or (resid 108 and (n \ ame N or name CA or name C or name O or name CB )) or resid 109 through 215)) } 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 group one per residue 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: 5.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 14.720 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5286 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17357 Z= 0.167 Angle : 0.640 7.201 23549 Z= 0.355 Chirality : 0.044 0.155 2600 Planarity : 0.004 0.049 3031 Dihedral : 17.304 88.786 6213 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.65 % Favored : 90.12 % Rotamer: Outliers : 2.46 % Allowed : 28.78 % Favored : 68.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.19), residues: 2187 helix: -0.16 (0.34), residues: 246 sheet: -0.44 (0.20), residues: 762 loop : -1.66 (0.19), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 90 TYR 0.011 0.001 TYR D 509 PHE 0.024 0.002 PHE F 183 TRP 0.020 0.001 TRP C 36 HIS 0.005 0.001 HIS E 199 Details of bonding type rmsd covalent geometry : bond 0.00347 (17349) covalent geometry : angle 0.63960 (23533) SS BOND : bond 0.00360 ( 8) SS BOND : angle 0.47512 ( 16) hydrogen bonds : bond 0.23408 ( 600) hydrogen bonds : angle 10.06731 ( 1656) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 425 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.5410 (mt) cc_final: 0.5027 (mp) REVERT: A 74 VAL cc_start: 0.4427 (m) cc_final: 0.3371 (p) REVERT: A 237 TYR cc_start: 0.6498 (m-80) cc_final: 0.6240 (t80) REVERT: A 418 VAL cc_start: 0.5877 (OUTLIER) cc_final: 0.4645 (t) REVERT: B 133 THR cc_start: 0.6548 (m) cc_final: 0.5789 (p) REVERT: C 121 PRO cc_start: 0.1488 (Cg_exo) cc_final: 0.1277 (Cg_endo) REVERT: C 149 TRP cc_start: 0.1101 (m100) cc_final: 0.0512 (m100) REVERT: D 166 LYS cc_start: 0.6209 (ptpp) cc_final: 0.5795 (mmtm) REVERT: D 172 PRO cc_start: 0.2902 (Cg_endo) cc_final: 0.2050 (Cg_exo) REVERT: D 210 MET cc_start: 0.7908 (tmm) cc_final: 0.7486 (tmm) REVERT: D 348 ILE cc_start: 0.6511 (OUTLIER) cc_final: 0.5911 (mm) REVERT: D 411 TRP cc_start: 0.6332 (t60) cc_final: 0.5711 (t60) REVERT: D 414 ASP cc_start: 0.6394 (t0) cc_final: 0.6178 (t0) REVERT: D 664 ASN cc_start: 0.7419 (t0) cc_final: 0.7158 (m-40) outliers start: 45 outliers final: 26 residues processed: 462 average time/residue: 0.1294 time to fit residues: 88.6769 Evaluate side-chains 270 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 242 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 582 SER Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain F residue 48 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 GLN ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 GLN C 91 GLN C 125 GLN C 153 ASN C 200 GLN D 158 GLN D 221 GLN D 381 ASN D 386 ASN D 564 ASN E 91 GLN E 161 GLN F 31 ASN F 214 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.142129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.113726 restraints weight = 35785.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.111438 restraints weight = 41208.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.112947 restraints weight = 34708.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.113441 restraints weight = 23201.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.113589 restraints weight = 22347.450| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.6130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 17357 Z= 0.258 Angle : 0.824 8.439 23549 Z= 0.444 Chirality : 0.051 0.269 2600 Planarity : 0.006 0.096 3031 Dihedral : 6.918 69.166 2423 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.74 % Favored : 90.03 % Rotamer: Outliers : 7.76 % Allowed : 25.40 % Favored : 66.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.18), residues: 2187 helix: -0.70 (0.31), residues: 256 sheet: -0.60 (0.19), residues: 777 loop : -1.79 (0.19), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 517 TYR 0.031 0.003 TYR C 88 PHE 0.023 0.003 PHE A 531 TRP 0.032 0.003 TRP B 171 HIS 0.012 0.002 HIS A 651 Details of bonding type rmsd covalent geometry : bond 0.00552 (17349) covalent geometry : angle 0.82367 (23533) SS BOND : bond 0.01747 ( 8) SS BOND : angle 1.11552 ( 16) hydrogen bonds : bond 0.04397 ( 600) hydrogen bonds : angle 7.05211 ( 1656) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 254 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ILE cc_start: 0.5811 (mt) cc_final: 0.5533 (tp) REVERT: A 244 LEU cc_start: 0.9198 (tt) cc_final: 0.8968 (tp) REVERT: A 250 MET cc_start: 0.7330 (mmt) cc_final: 0.7077 (mmp) REVERT: A 275 MET cc_start: 0.8208 (ttp) cc_final: 0.7992 (ttt) REVERT: A 418 VAL cc_start: 0.8382 (OUTLIER) cc_final: 0.7661 (t) REVERT: A 560 LEU cc_start: 0.7528 (mt) cc_final: 0.7064 (tp) REVERT: B 113 TRP cc_start: 0.8273 (OUTLIER) cc_final: 0.7934 (m100) REVERT: B 122 GLN cc_start: 0.7671 (tt0) cc_final: 0.7403 (mt0) REVERT: B 133 THR cc_start: 0.7585 (OUTLIER) cc_final: 0.7238 (p) REVERT: B 158 LEU cc_start: 0.8331 (tt) cc_final: 0.8026 (mt) REVERT: B 162 TYR cc_start: 0.4959 (p90) cc_final: 0.4508 (p90) REVERT: C 162 GLU cc_start: 0.8180 (pm20) cc_final: 0.7445 (pp20) REVERT: C 166 GLU cc_start: 0.7471 (pm20) cc_final: 0.7099 (pp20) REVERT: D 53 PHE cc_start: 0.5846 (OUTLIER) cc_final: 0.5569 (t80) REVERT: D 244 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9151 (mt) REVERT: D 275 MET cc_start: 0.5861 (ppp) cc_final: 0.5105 (ppp) REVERT: D 377 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7927 (mp) REVERT: D 414 ASP cc_start: 0.6769 (t0) cc_final: 0.6429 (t0) REVERT: D 695 GLN cc_start: 0.7115 (mm110) cc_final: 0.6781 (mm-40) REVERT: E 39 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7956 (tm-30) REVERT: F 6 GLN cc_start: 0.7570 (pm20) cc_final: 0.6869 (pm20) REVERT: F 119 TYR cc_start: 0.7711 (m-80) cc_final: 0.7449 (m-80) REVERT: F 183 PHE cc_start: 0.6986 (OUTLIER) cc_final: 0.6638 (m-80) outliers start: 142 outliers final: 69 residues processed: 377 average time/residue: 0.1149 time to fit residues: 67.4359 Evaluate side-chains 251 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 174 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 487 TYR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 113 TRP Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain D residue 53 PHE Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 255 ASN Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 304 ILE Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 446 ARG Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 533 VAL Chi-restraints excluded: chain D residue 564 ASN Chi-restraints excluded: chain D residue 604 SER Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 183 PHE Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 228 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 176 optimal weight: 0.4980 chunk 165 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 136 optimal weight: 0.8980 chunk 157 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 95 optimal weight: 0.6980 chunk 116 optimal weight: 20.0000 chunk 175 optimal weight: 0.9980 chunk 14 optimal weight: 50.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 ASN B 31 ASN B 38 HIS B 112 GLN C 125 GLN ** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 GLN D 158 GLN ** D 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 646 ASN D 664 ASN F 87 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.139939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.112935 restraints weight = 35224.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.113714 restraints weight = 49213.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.114926 restraints weight = 39396.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.115148 restraints weight = 25521.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.116302 restraints weight = 22061.382| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.7349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17357 Z= 0.155 Angle : 0.653 9.458 23549 Z= 0.348 Chirality : 0.046 0.245 2600 Planarity : 0.005 0.061 3031 Dihedral : 5.863 67.747 2406 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.37 % Favored : 91.45 % Rotamer: Outliers : 6.39 % Allowed : 26.00 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.18), residues: 2187 helix: -0.36 (0.32), residues: 268 sheet: -0.55 (0.19), residues: 782 loop : -1.79 (0.19), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 19 TYR 0.022 0.002 TYR B 193 PHE 0.024 0.002 PHE A 561 TRP 0.023 0.002 TRP E 36 HIS 0.006 0.001 HIS D 438 Details of bonding type rmsd covalent geometry : bond 0.00330 (17349) covalent geometry : angle 0.65275 (23533) SS BOND : bond 0.00244 ( 8) SS BOND : angle 1.28329 ( 16) hydrogen bonds : bond 0.03783 ( 600) hydrogen bonds : angle 6.32048 ( 1656) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 183 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ILE cc_start: 0.6121 (mt) cc_final: 0.5895 (tp) REVERT: A 236 LEU cc_start: 0.6980 (OUTLIER) cc_final: 0.6497 (tp) REVERT: A 275 MET cc_start: 0.8146 (ttp) cc_final: 0.7935 (ttt) REVERT: A 500 ASP cc_start: 0.7402 (m-30) cc_final: 0.7158 (t0) REVERT: A 553 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8911 (mt) REVERT: B 23 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8117 (mt) REVERT: B 85 GLN cc_start: 0.6642 (OUTLIER) cc_final: 0.6388 (tp40) REVERT: B 103 TYR cc_start: 0.6486 (t80) cc_final: 0.6037 (t80) REVERT: C 50 TYR cc_start: 0.8024 (m-80) cc_final: 0.7284 (m-10) REVERT: C 166 GLU cc_start: 0.7741 (pm20) cc_final: 0.7290 (mt-10) REVERT: C 210 PHE cc_start: 0.4257 (OUTLIER) cc_final: 0.3383 (m-80) REVERT: D 334 GLU cc_start: 0.8361 (mp0) cc_final: 0.8110 (mt-10) REVERT: D 351 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8384 (mt) REVERT: D 386 ASN cc_start: 0.8077 (t0) cc_final: 0.7872 (t0) REVERT: E 90 GLN cc_start: 0.9220 (OUTLIER) cc_final: 0.8792 (pt0) REVERT: E 199 HIS cc_start: 0.1017 (p-80) cc_final: 0.0717 (p-80) REVERT: F 50 TRP cc_start: 0.7524 (t60) cc_final: 0.7312 (t60) outliers start: 117 outliers final: 61 residues processed: 285 average time/residue: 0.1221 time to fit residues: 53.0720 Evaluate side-chains 216 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 148 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 487 TYR Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 85 GLN Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 213 CYS Chi-restraints excluded: chain C residue 5 MET Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 202 ASN Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 446 ARG Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 533 VAL Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 604 SER Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 224 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 44 optimal weight: 0.2980 chunk 164 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 130 optimal weight: 0.0870 chunk 156 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 62 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 21 optimal weight: 0.1980 chunk 157 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.4360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 ASN F 42 GLN F 87 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.141409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.105960 restraints weight = 35055.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.106625 restraints weight = 24622.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.105964 restraints weight = 20011.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.106241 restraints weight = 21501.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.106458 restraints weight = 19452.314| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.7988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 17357 Z= 0.116 Angle : 0.622 11.532 23549 Z= 0.321 Chirality : 0.045 0.234 2600 Planarity : 0.004 0.062 3031 Dihedral : 5.595 64.832 2404 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.46 % Favored : 91.36 % Rotamer: Outliers : 4.26 % Allowed : 28.78 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.19), residues: 2187 helix: 0.12 (0.34), residues: 260 sheet: -0.57 (0.19), residues: 781 loop : -1.66 (0.19), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 159 TYR 0.022 0.001 TYR E 141 PHE 0.026 0.002 PHE B 163 TRP 0.024 0.001 TRP C 36 HIS 0.005 0.001 HIS C 199 Details of bonding type rmsd covalent geometry : bond 0.00250 (17349) covalent geometry : angle 0.62110 (23533) SS BOND : bond 0.00327 ( 8) SS BOND : angle 1.32940 ( 16) hydrogen bonds : bond 0.02846 ( 600) hydrogen bonds : angle 5.85729 ( 1656) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 162 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ILE cc_start: 0.6294 (mt) cc_final: 0.6027 (mm) REVERT: A 236 LEU cc_start: 0.6935 (OUTLIER) cc_final: 0.6650 (tp) REVERT: A 500 ASP cc_start: 0.7428 (m-30) cc_final: 0.7137 (t0) REVERT: A 553 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.9045 (mt) REVERT: B 133 THR cc_start: 0.7932 (OUTLIER) cc_final: 0.7565 (p) REVERT: B 141 LEU cc_start: 0.5240 (tt) cc_final: 0.4985 (tt) REVERT: C 50 TYR cc_start: 0.7939 (m-80) cc_final: 0.7188 (m-10) REVERT: C 166 GLU cc_start: 0.7852 (pm20) cc_final: 0.7334 (mt-10) REVERT: C 210 PHE cc_start: 0.4423 (OUTLIER) cc_final: 0.3504 (m-80) REVERT: D 86 ARG cc_start: 0.6340 (ttp-170) cc_final: 0.5748 (mtp180) REVERT: D 160 ARG cc_start: 0.7896 (mtt180) cc_final: 0.7592 (ptp-170) REVERT: D 334 GLU cc_start: 0.8336 (mp0) cc_final: 0.7965 (mt-10) REVERT: D 351 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8364 (mt) REVERT: D 426 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.7014 (ttt-90) REVERT: E 90 GLN cc_start: 0.9296 (OUTLIER) cc_final: 0.8771 (pt0) REVERT: E 166 GLU cc_start: 0.8540 (tp30) cc_final: 0.8323 (tp30) REVERT: F 124 THR cc_start: 0.8810 (OUTLIER) cc_final: 0.8505 (p) outliers start: 78 outliers final: 45 residues processed: 230 average time/residue: 0.1151 time to fit residues: 41.6112 Evaluate side-chains 191 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 138 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 487 TYR Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 213 CYS Chi-restraints excluded: chain B residue 217 HIS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 426 ARG Chi-restraints excluded: chain D residue 446 ARG Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 604 SER Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain F residue 87 ASN Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 224 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 33 optimal weight: 6.9990 chunk 169 optimal weight: 0.9980 chunk 109 optimal weight: 8.9990 chunk 87 optimal weight: 0.0070 chunk 20 optimal weight: 0.3980 chunk 172 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 174 optimal weight: 0.8980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN C 38 GLN ** D 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 85 GLN F 87 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.139749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.101883 restraints weight = 35043.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.102638 restraints weight = 27946.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.102859 restraints weight = 22231.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.102861 restraints weight = 21096.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.102978 restraints weight = 21315.051| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.8761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17357 Z= 0.134 Angle : 0.615 8.193 23549 Z= 0.319 Chirality : 0.044 0.156 2600 Planarity : 0.004 0.045 3031 Dihedral : 5.382 63.578 2397 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.96 % Favored : 91.91 % Rotamer: Outliers : 5.68 % Allowed : 29.16 % Favored : 65.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.19), residues: 2187 helix: 0.25 (0.34), residues: 260 sheet: -0.57 (0.19), residues: 779 loop : -1.64 (0.19), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 19 TYR 0.018 0.001 TYR D 514 PHE 0.025 0.002 PHE B 71 TRP 0.030 0.001 TRP F 50 HIS 0.004 0.001 HIS E 190 Details of bonding type rmsd covalent geometry : bond 0.00290 (17349) covalent geometry : angle 0.61425 (23533) SS BOND : bond 0.00344 ( 8) SS BOND : angle 1.27539 ( 16) hydrogen bonds : bond 0.02932 ( 600) hydrogen bonds : angle 5.76766 ( 1656) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 151 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ILE cc_start: 0.6692 (mt) cc_final: 0.6423 (mm) REVERT: A 236 LEU cc_start: 0.7174 (OUTLIER) cc_final: 0.6791 (tp) REVERT: A 425 TYR cc_start: 0.7315 (p90) cc_final: 0.7071 (p90) REVERT: A 500 ASP cc_start: 0.7496 (m-30) cc_final: 0.7236 (t0) REVERT: A 682 MET cc_start: 0.5444 (ptp) cc_final: 0.4964 (mtt) REVERT: B 103 TYR cc_start: 0.6717 (t80) cc_final: 0.6227 (t80) REVERT: B 112 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.8113 (mm-40) REVERT: B 133 THR cc_start: 0.8112 (OUTLIER) cc_final: 0.7823 (p) REVERT: B 141 LEU cc_start: 0.5292 (tt) cc_final: 0.5019 (tp) REVERT: C 18 ASP cc_start: 0.7537 (t0) cc_final: 0.7155 (t0) REVERT: C 19 ARG cc_start: 0.8295 (mmm-85) cc_final: 0.8082 (tpt-90) REVERT: C 50 TYR cc_start: 0.8080 (m-80) cc_final: 0.7448 (m-10) REVERT: C 144 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.5661 (tm-30) REVERT: C 166 GLU cc_start: 0.7777 (pm20) cc_final: 0.7405 (mt-10) REVERT: C 210 PHE cc_start: 0.4377 (OUTLIER) cc_final: 0.3387 (m-80) REVERT: D 334 GLU cc_start: 0.8359 (mp0) cc_final: 0.8115 (mt-10) REVERT: D 351 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8412 (mt) REVERT: E 39 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8328 (tm-30) REVERT: E 90 GLN cc_start: 0.9300 (OUTLIER) cc_final: 0.8901 (pt0) REVERT: E 152 ASP cc_start: 0.6520 (OUTLIER) cc_final: 0.5983 (m-30) REVERT: F 124 THR cc_start: 0.8824 (OUTLIER) cc_final: 0.8486 (p) REVERT: F 166 PRO cc_start: 0.7005 (Cg_exo) cc_final: 0.6772 (Cg_endo) outliers start: 104 outliers final: 59 residues processed: 245 average time/residue: 0.1182 time to fit residues: 44.9235 Evaluate side-chains 198 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 129 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 487 TYR Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 217 HIS Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 446 ARG Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 604 SER Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 71 PHE Chi-restraints excluded: chain F residue 87 ASN Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 217 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 43 optimal weight: 0.8980 chunk 180 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 167 optimal weight: 5.9990 chunk 160 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 133 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 179 optimal weight: 0.6980 chunk 120 optimal weight: 9.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN C 38 GLN ** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 HIS D 202 ASN ** D 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 85 GLN F 87 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.136017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.099634 restraints weight = 35447.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.098347 restraints weight = 26214.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.098179 restraints weight = 25745.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.098766 restraints weight = 23906.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.098852 restraints weight = 21677.403| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.9945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17357 Z= 0.180 Angle : 0.656 8.439 23549 Z= 0.345 Chirality : 0.046 0.168 2600 Planarity : 0.005 0.068 3031 Dihedral : 5.603 65.578 2394 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.05 % Favored : 90.72 % Rotamer: Outliers : 5.52 % Allowed : 29.33 % Favored : 65.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.19), residues: 2187 helix: 0.26 (0.34), residues: 263 sheet: -0.65 (0.19), residues: 816 loop : -1.70 (0.19), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 95 TYR 0.019 0.002 TYR E 88 PHE 0.035 0.002 PHE B 71 TRP 0.032 0.002 TRP F 50 HIS 0.012 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00398 (17349) covalent geometry : angle 0.65517 (23533) SS BOND : bond 0.00450 ( 8) SS BOND : angle 1.38945 ( 16) hydrogen bonds : bond 0.03221 ( 600) hydrogen bonds : angle 5.84628 ( 1656) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 136 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7225 (tp) REVERT: A 500 ASP cc_start: 0.7611 (m-30) cc_final: 0.7262 (t0) REVERT: A 661 ILE cc_start: 0.9493 (OUTLIER) cc_final: 0.9258 (pt) REVERT: B 133 THR cc_start: 0.8329 (OUTLIER) cc_final: 0.8087 (p) REVERT: B 170 SER cc_start: 0.7614 (OUTLIER) cc_final: 0.7116 (p) REVERT: C 18 ASP cc_start: 0.7711 (t0) cc_final: 0.7267 (t0) REVERT: C 19 ARG cc_start: 0.8432 (mmm-85) cc_final: 0.8204 (tpt-90) REVERT: C 37 TYR cc_start: 0.9091 (m-80) cc_final: 0.8679 (m-80) REVERT: C 50 TYR cc_start: 0.8030 (m-80) cc_final: 0.7320 (m-10) REVERT: C 106 GLU cc_start: 0.6646 (pm20) cc_final: 0.6195 (pm20) REVERT: C 149 TRP cc_start: 0.1373 (m100) cc_final: 0.0596 (m100) REVERT: C 162 GLU cc_start: 0.8435 (pm20) cc_final: 0.7515 (pp20) REVERT: C 199 HIS cc_start: 0.5191 (OUTLIER) cc_final: 0.4739 (p-80) REVERT: C 210 PHE cc_start: 0.4713 (OUTLIER) cc_final: 0.3534 (m-80) REVERT: D 426 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.7088 (ttt180) REVERT: E 152 ASP cc_start: 0.6611 (OUTLIER) cc_final: 0.6048 (m-30) REVERT: F 50 TRP cc_start: 0.8344 (t60) cc_final: 0.8065 (t60) REVERT: F 124 THR cc_start: 0.9236 (OUTLIER) cc_final: 0.8973 (p) outliers start: 101 outliers final: 58 residues processed: 226 average time/residue: 0.1112 time to fit residues: 39.5664 Evaluate side-chains 182 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 115 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 487 TYR Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 213 CYS Chi-restraints excluded: chain B residue 217 HIS Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 202 ASN Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 426 ARG Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 217 HIS Chi-restraints excluded: chain F residue 224 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 53 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 124 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 74 optimal weight: 0.1980 chunk 162 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 87 optimal weight: 0.0030 chunk 198 optimal weight: 0.9990 chunk 120 optimal weight: 10.0000 chunk 175 optimal weight: 0.9980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 ASN B 112 GLN ** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 HIS ** D 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 85 GLN F 87 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.137989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.101133 restraints weight = 34928.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.101594 restraints weight = 27252.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.101074 restraints weight = 22827.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.101091 restraints weight = 24306.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.101232 restraints weight = 22047.251| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 1.0239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17357 Z= 0.122 Angle : 0.611 8.645 23549 Z= 0.315 Chirality : 0.044 0.141 2600 Planarity : 0.004 0.046 3031 Dihedral : 5.278 64.330 2394 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.86 % Favored : 91.95 % Rotamer: Outliers : 4.75 % Allowed : 29.55 % Favored : 65.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.19), residues: 2187 helix: 0.40 (0.35), residues: 261 sheet: -0.51 (0.19), residues: 793 loop : -1.60 (0.19), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 355 TYR 0.025 0.001 TYR B 103 PHE 0.021 0.002 PHE A 62 TRP 0.026 0.001 TRP D 676 HIS 0.007 0.001 HIS E 199 Details of bonding type rmsd covalent geometry : bond 0.00268 (17349) covalent geometry : angle 0.61083 (23533) SS BOND : bond 0.00263 ( 8) SS BOND : angle 0.96197 ( 16) hydrogen bonds : bond 0.02797 ( 600) hydrogen bonds : angle 5.60046 ( 1656) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 131 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ILE cc_start: 0.7457 (mm) cc_final: 0.7207 (mm) REVERT: A 236 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.7184 (tp) REVERT: A 500 ASP cc_start: 0.7606 (m-30) cc_final: 0.7312 (t70) REVERT: A 661 ILE cc_start: 0.9453 (OUTLIER) cc_final: 0.9224 (pt) REVERT: A 683 ASP cc_start: 0.6488 (OUTLIER) cc_final: 0.6162 (t0) REVERT: B 85 GLN cc_start: 0.6679 (OUTLIER) cc_final: 0.5751 (tp40) REVERT: B 103 TYR cc_start: 0.6807 (t80) cc_final: 0.6579 (t80) REVERT: B 133 THR cc_start: 0.8287 (OUTLIER) cc_final: 0.7954 (p) REVERT: B 158 LEU cc_start: 0.8509 (tt) cc_final: 0.8148 (mt) REVERT: B 170 SER cc_start: 0.7872 (OUTLIER) cc_final: 0.7517 (p) REVERT: C 18 ASP cc_start: 0.7811 (t0) cc_final: 0.7392 (t0) REVERT: C 50 TYR cc_start: 0.8025 (m-80) cc_final: 0.7681 (m-80) REVERT: C 106 GLU cc_start: 0.6793 (pm20) cc_final: 0.6369 (pm20) REVERT: C 144 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.5585 (tm-30) REVERT: C 149 TRP cc_start: 0.1692 (m100) cc_final: 0.1016 (m100) REVERT: C 199 HIS cc_start: 0.4934 (OUTLIER) cc_final: 0.4340 (p-80) REVERT: C 210 PHE cc_start: 0.4797 (OUTLIER) cc_final: 0.3663 (m-80) REVERT: D 426 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.7103 (ttt180) REVERT: E 152 ASP cc_start: 0.6623 (OUTLIER) cc_final: 0.6048 (m-30) REVERT: F 124 THR cc_start: 0.9215 (OUTLIER) cc_final: 0.8949 (p) outliers start: 87 outliers final: 56 residues processed: 212 average time/residue: 0.1083 time to fit residues: 36.4922 Evaluate side-chains 185 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 117 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 487 TYR Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 683 ASP Chi-restraints excluded: chain B residue 85 GLN Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 217 HIS Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain D residue 426 ARG Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 604 SER Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 87 ASN Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 217 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 155 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 116 optimal weight: 0.1980 chunk 134 optimal weight: 3.9990 chunk 146 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 143 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 79 optimal weight: 0.0030 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 GLN B 188 GLN ** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 GLN ** E 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 85 GLN F 87 ASN F 112 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.138691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.100317 restraints weight = 35186.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.101590 restraints weight = 28117.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.101439 restraints weight = 23121.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.101438 restraints weight = 22789.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.101651 restraints weight = 21557.766| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 1.0464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17357 Z= 0.112 Angle : 0.599 11.465 23549 Z= 0.308 Chirality : 0.044 0.149 2600 Planarity : 0.004 0.048 3031 Dihedral : 5.089 62.555 2394 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.86 % Favored : 92.00 % Rotamer: Outliers : 4.59 % Allowed : 29.22 % Favored : 66.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.19), residues: 2187 helix: 0.40 (0.34), residues: 262 sheet: -0.36 (0.19), residues: 803 loop : -1.63 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 355 TYR 0.017 0.001 TYR B 103 PHE 0.023 0.001 PHE F 71 TRP 0.022 0.001 TRP D 676 HIS 0.016 0.001 HIS C 199 Details of bonding type rmsd covalent geometry : bond 0.00246 (17349) covalent geometry : angle 0.59875 (23533) SS BOND : bond 0.00281 ( 8) SS BOND : angle 0.90552 ( 16) hydrogen bonds : bond 0.02720 ( 600) hydrogen bonds : angle 5.44197 ( 1656) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 126 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LEU cc_start: 0.8355 (mt) cc_final: 0.8110 (mt) REVERT: A 204 ILE cc_start: 0.7472 (mm) cc_final: 0.7242 (mm) REVERT: A 236 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7132 (tp) REVERT: A 500 ASP cc_start: 0.7580 (m-30) cc_final: 0.7301 (t0) REVERT: A 683 ASP cc_start: 0.6471 (OUTLIER) cc_final: 0.6141 (t0) REVERT: B 85 GLN cc_start: 0.6524 (OUTLIER) cc_final: 0.5500 (tp40) REVERT: B 133 THR cc_start: 0.8336 (OUTLIER) cc_final: 0.7987 (p) REVERT: B 158 LEU cc_start: 0.8516 (tt) cc_final: 0.8135 (mt) REVERT: B 170 SER cc_start: 0.7984 (OUTLIER) cc_final: 0.7656 (p) REVERT: C 50 TYR cc_start: 0.8020 (m-80) cc_final: 0.7574 (m-80) REVERT: C 106 GLU cc_start: 0.6831 (pm20) cc_final: 0.6403 (pm20) REVERT: C 144 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.5750 (tm-30) REVERT: C 210 PHE cc_start: 0.4590 (OUTLIER) cc_final: 0.3475 (m-80) REVERT: D 426 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.7078 (ttt180) REVERT: D 621 ILE cc_start: 0.8871 (mm) cc_final: 0.8660 (mm) REVERT: E 90 GLN cc_start: 0.9218 (OUTLIER) cc_final: 0.9003 (pt0) REVERT: E 152 ASP cc_start: 0.6615 (OUTLIER) cc_final: 0.6033 (m-30) REVERT: F 85 GLN cc_start: 0.5661 (OUTLIER) cc_final: 0.5416 (pp30) REVERT: F 90 ARG cc_start: 0.7896 (ptm160) cc_final: 0.7442 (ttp-170) REVERT: F 124 THR cc_start: 0.9178 (OUTLIER) cc_final: 0.8887 (p) outliers start: 84 outliers final: 57 residues processed: 204 average time/residue: 0.1076 time to fit residues: 35.1402 Evaluate side-chains 176 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 107 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 487 TYR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 674 PHE Chi-restraints excluded: chain A residue 683 ASP Chi-restraints excluded: chain B residue 85 GLN Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 217 HIS Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 202 ASN Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain D residue 426 ARG Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 604 SER Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 85 GLN Chi-restraints excluded: chain F residue 86 MET Chi-restraints excluded: chain F residue 87 ASN Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 217 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 196 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 166 optimal weight: 6.9990 chunk 200 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 110 optimal weight: 9.9990 chunk 74 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 GLN ** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN ** D 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 583 GLN F 85 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.135114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.3543 r_free = 0.3543 target = 0.098458 restraints weight = 36863.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.098644 restraints weight = 31630.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.098384 restraints weight = 30020.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.098297 restraints weight = 30418.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.098346 restraints weight = 27267.076| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 1.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.100 17357 Z= 0.405 Angle : 0.890 13.011 23549 Z= 0.469 Chirality : 0.052 0.199 2600 Planarity : 0.006 0.063 3031 Dihedral : 6.601 67.202 2392 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.48 % Favored : 88.34 % Rotamer: Outliers : 4.70 % Allowed : 29.22 % Favored : 66.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.18), residues: 2187 helix: 0.27 (0.34), residues: 250 sheet: -0.83 (0.19), residues: 797 loop : -1.91 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 268 TYR 0.032 0.003 TYR D 511 PHE 0.030 0.003 PHE A 403 TRP 0.061 0.004 TRP E 36 HIS 0.011 0.002 HIS E 199 Details of bonding type rmsd covalent geometry : bond 0.00907 (17349) covalent geometry : angle 0.88891 (23533) SS BOND : bond 0.00688 ( 8) SS BOND : angle 1.84127 ( 16) hydrogen bonds : bond 0.04439 ( 600) hydrogen bonds : angle 6.71001 ( 1656) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 112 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 VAL cc_start: 0.9425 (t) cc_final: 0.9143 (p) REVERT: A 682 MET cc_start: 0.7823 (mtt) cc_final: 0.7525 (mtt) REVERT: A 683 ASP cc_start: 0.7324 (OUTLIER) cc_final: 0.6778 (t70) REVERT: B 85 GLN cc_start: 0.6617 (OUTLIER) cc_final: 0.6018 (tp40) REVERT: B 170 SER cc_start: 0.8052 (OUTLIER) cc_final: 0.7683 (p) REVERT: C 23 THR cc_start: 0.8615 (OUTLIER) cc_final: 0.8402 (t) REVERT: C 37 TYR cc_start: 0.9181 (m-80) cc_final: 0.8485 (m-10) REVERT: C 50 TYR cc_start: 0.8095 (m-80) cc_final: 0.7586 (m-10) REVERT: C 152 ASP cc_start: 0.7723 (t0) cc_final: 0.7409 (m-30) REVERT: D 86 ARG cc_start: 0.6883 (mtp180) cc_final: 0.6569 (mmm-85) REVERT: D 621 ILE cc_start: 0.9214 (mm) cc_final: 0.8962 (mm) REVERT: E 90 GLN cc_start: 0.9449 (OUTLIER) cc_final: 0.8953 (pt0) REVERT: E 152 ASP cc_start: 0.6775 (OUTLIER) cc_final: 0.6177 (m-30) REVERT: F 4 GLU cc_start: 0.7752 (pm20) cc_final: 0.7533 (pm20) outliers start: 86 outliers final: 57 residues processed: 192 average time/residue: 0.1108 time to fit residues: 34.3581 Evaluate side-chains 159 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 96 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 487 TYR Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 683 ASP Chi-restraints excluded: chain B residue 85 GLN Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 217 HIS Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 202 ASN Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 481 ASN Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 604 SER Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 217 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 102 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 122 optimal weight: 20.0000 chunk 92 optimal weight: 0.4980 chunk 216 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 163 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 GLN ** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 85 GLN F 87 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.141436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.104395 restraints weight = 36382.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.104022 restraints weight = 30304.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.104662 restraints weight = 27502.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.104504 restraints weight = 26027.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.104797 restraints weight = 24002.968| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 1.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17357 Z= 0.149 Angle : 0.668 8.510 23549 Z= 0.349 Chirality : 0.046 0.174 2600 Planarity : 0.004 0.052 3031 Dihedral : 5.675 63.694 2392 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.28 % Favored : 91.59 % Rotamer: Outliers : 3.17 % Allowed : 30.64 % Favored : 66.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.18), residues: 2187 helix: 0.23 (0.34), residues: 262 sheet: -0.66 (0.19), residues: 769 loop : -1.78 (0.19), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 25 TYR 0.019 0.002 TYR B 103 PHE 0.019 0.002 PHE D 310 TRP 0.036 0.002 TRP C 36 HIS 0.010 0.001 HIS E 199 Details of bonding type rmsd covalent geometry : bond 0.00331 (17349) covalent geometry : angle 0.66797 (23533) SS BOND : bond 0.00294 ( 8) SS BOND : angle 1.05810 ( 16) hydrogen bonds : bond 0.03034 ( 600) hydrogen bonds : angle 5.82992 ( 1656) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 122 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 500 ASP cc_start: 0.7382 (m-30) cc_final: 0.7165 (t70) REVERT: A 682 MET cc_start: 0.7746 (mtt) cc_final: 0.7484 (mtt) REVERT: C 37 TYR cc_start: 0.9006 (m-80) cc_final: 0.8418 (m-10) REVERT: C 50 TYR cc_start: 0.8046 (m-80) cc_final: 0.7617 (m-80) REVERT: C 149 TRP cc_start: 0.1885 (m100) cc_final: 0.0895 (m100) REVERT: D 86 ARG cc_start: 0.6645 (mtp180) cc_final: 0.6410 (mmm-85) REVERT: D 446 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7641 (mtm180) REVERT: D 621 ILE cc_start: 0.9071 (mm) cc_final: 0.8808 (mm) outliers start: 58 outliers final: 51 residues processed: 177 average time/residue: 0.1011 time to fit residues: 28.6506 Evaluate side-chains 160 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 108 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 487 TYR Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 217 HIS Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain D residue 446 ARG Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 487 TYR Chi-restraints excluded: chain D residue 533 VAL Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 604 SER Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 115 TYR Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 217 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 206 optimal weight: 0.5980 chunk 192 optimal weight: 2.9990 chunk 191 optimal weight: 0.9990 chunk 212 optimal weight: 0.8980 chunk 165 optimal weight: 1.9990 chunk 85 optimal weight: 0.0030 chunk 62 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 69 optimal weight: 0.4980 chunk 121 optimal weight: 10.0000 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 GLN ** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 HIS ** D 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 85 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.142415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.103856 restraints weight = 36914.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.105591 restraints weight = 26589.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.105484 restraints weight = 20498.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.105556 restraints weight = 20807.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.105718 restraints weight = 19772.279| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 1.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17357 Z= 0.132 Angle : 0.644 9.244 23549 Z= 0.334 Chirality : 0.045 0.200 2600 Planarity : 0.004 0.051 3031 Dihedral : 5.402 60.489 2392 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.92 % Favored : 90.95 % Rotamer: Outliers : 3.22 % Allowed : 31.13 % Favored : 65.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.19), residues: 2187 helix: 0.31 (0.34), residues: 262 sheet: -0.59 (0.19), residues: 799 loop : -1.75 (0.19), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 25 TYR 0.025 0.001 TYR B 103 PHE 0.015 0.002 PHE E 63 TRP 0.026 0.001 TRP C 36 HIS 0.017 0.002 HIS A 651 Details of bonding type rmsd covalent geometry : bond 0.00297 (17349) covalent geometry : angle 0.64373 (23533) SS BOND : bond 0.00242 ( 8) SS BOND : angle 0.97339 ( 16) hydrogen bonds : bond 0.02893 ( 600) hydrogen bonds : angle 5.60035 ( 1656) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2600.40 seconds wall clock time: 45 minutes 58.66 seconds (2758.66 seconds total)