Starting phenix.real_space_refine on Sun Aug 24 16:19:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k23_22641/08_2025/7k23_22641.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k23_22641/08_2025/7k23_22641.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k23_22641/08_2025/7k23_22641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k23_22641/08_2025/7k23_22641.map" model { file = "/net/cci-nas-00/data/ceres_data/7k23_22641/08_2025/7k23_22641.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k23_22641/08_2025/7k23_22641.cif" } resolution = 3.3 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 ------------------------------------------------------------------------------- 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= 1.000 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 119 5.16 5 C 13914 2.51 5 N 3662 2.21 5 O 4228 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 89 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21923 Number of models: 1 Model: "" Number of chains: 7 Chain: "L2" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 770 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 93} Chain: "H2" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 813 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain: "A" Number of atoms: 2854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2854 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 31, 'TRANS': 334} Chain: "B" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 31, 'TRANS': 335} Chain: "C" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2789 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 30, 'TRANS': 326} Chain: "D" Number of atoms: 2650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2650 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 27, 'TRANS': 312} Chain: "E" Number of atoms: 2853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2853 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 31, 'TRANS': 334} Restraints were copied for chains: H3, H4, H5, H6, L3, L4, L5, L6 Time building chain proxies: 4.95, per 1000 atoms: 0.23 Number of scatterers: 21923 At special positions: 0 Unit cell: (167.2, 163.9, 132, 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 119 16.00 O 4228 8.00 N 3662 7.00 C 13914 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYSL2 23 " - pdb=" SG CYSL2 88 " distance=2.03 Simple disulfide: pdb=" SG CYSH2 18 " - pdb=" SG CYSH2 91 " distance=2.02 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS B 98 " distance=2.03 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS E 3 " distance=2.03 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS C 98 " distance=2.04 Simple disulfide: pdb=" SG CYS C 3 " - pdb=" SG CYS D 98 " distance=2.03 Simple disulfide: pdb=" SG CYS D 3 " - pdb=" SG CYS E 98 " distance=2.02 Simple disulfide: pdb=" SG CYSL3 23 " - pdb=" SG CYSL3 88 " distance=2.03 Simple disulfide: pdb=" SG CYSL4 23 " - pdb=" SG CYSL4 88 " distance=2.03 Simple disulfide: pdb=" SG CYSL5 23 " - pdb=" SG CYSL5 88 " distance=2.03 Simple disulfide: pdb=" SG CYSL6 23 " - pdb=" SG CYSL6 88 " distance=2.03 Simple disulfide: pdb=" SG CYSH3 18 " - pdb=" SG CYSH3 91 " distance=2.02 Simple disulfide: pdb=" SG CYSH4 18 " - pdb=" SG CYSH4 91 " distance=2.02 Simple disulfide: pdb=" SG CYSH5 18 " - pdb=" SG CYSH5 91 " distance=2.02 Simple disulfide: pdb=" SG CYSH6 18 " - pdb=" SG CYSH6 91 " distance=2.02 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.92 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5122 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 50 sheets defined 9.7% alpha, 34.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'L2' and resid 49 through 52 removed outlier: 3.658A pdb=" N SERL2 52 " --> pdb=" O TYRL2 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'L2' and resid 49 through 52' Processing helix chain 'L2' and resid 79 through 83 removed outlier: 3.542A pdb=" N LEUL2 83 " --> pdb=" O THRL2 80 " (cutoff:3.500A) Processing helix chain 'H2' and resid 24 through 28 removed outlier: 3.531A pdb=" N SERH2 27 " --> pdb=" O THRH2 24 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYRH2 28 " --> pdb=" O PHEH2 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'H2' and resid 24 through 28' Processing helix chain 'A' and resid 17 through 23 Processing helix chain 'A' and resid 75 through 79 Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 176 through 182 Processing helix chain 'A' and resid 186 through 190 Processing helix chain 'A' and resid 326 through 330 removed outlier: 4.085A pdb=" N ASN A 329 " --> pdb=" O GLU A 326 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR A 330 " --> pdb=" O GLY A 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 326 through 330' Processing helix chain 'B' and resid 17 through 23 Processing helix chain 'B' and resid 116 through 121 Processing helix chain 'B' and resid 176 through 181 Processing helix chain 'B' and resid 187 through 191 Processing helix chain 'B' and resid 304 through 315 Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 116 through 121 Processing helix chain 'C' and resid 176 through 182 Processing helix chain 'C' and resid 186 through 190 Processing helix chain 'C' and resid 304 through 315 removed outlier: 3.952A pdb=" N LEU C 308 " --> pdb=" O PRO C 304 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N PHE C 313 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 357 removed outlier: 3.611A pdb=" N ARG C 356 " --> pdb=" O TYR C 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 23 Processing helix chain 'D' and resid 75 through 79 Processing helix chain 'D' and resid 116 through 121 Processing helix chain 'D' and resid 176 through 181 Processing helix chain 'D' and resid 187 through 191 removed outlier: 3.552A pdb=" N VAL D 191 " --> pdb=" O LYS D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 317 Processing helix chain 'E' and resid 17 through 22 Processing helix chain 'E' and resid 75 through 79 Processing helix chain 'E' and resid 116 through 121 Processing helix chain 'E' and resid 176 through 181 Processing helix chain 'E' and resid 186 through 191 removed outlier: 3.720A pdb=" N VAL E 191 " --> pdb=" O LYS E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 317 Processing helix chain 'L3' and resid 49 through 52 removed outlier: 3.657A pdb=" N SERL3 52 " --> pdb=" O TYRL3 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'L3' and resid 49 through 52' Processing helix chain 'L3' and resid 79 through 83 removed outlier: 3.541A pdb=" N LEUL3 83 " --> pdb=" O THRL3 80 " (cutoff:3.500A) Processing helix chain 'H3' and resid 24 through 28 removed outlier: 3.531A pdb=" N SERH3 27 " --> pdb=" O THRH3 24 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYRH3 28 " --> pdb=" O PHEH3 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'H3' and resid 24 through 28' Processing helix chain 'L4' and resid 49 through 52 removed outlier: 3.657A pdb=" N SERL4 52 " --> pdb=" O TYRL4 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'L4' and resid 49 through 52' Processing helix chain 'L4' and resid 79 through 83 removed outlier: 3.541A pdb=" N LEUL4 83 " --> pdb=" O THRL4 80 " (cutoff:3.500A) Processing helix chain 'H4' and resid 24 through 28 removed outlier: 3.530A pdb=" N SERH4 27 " --> pdb=" O THRH4 24 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYRH4 28 " --> pdb=" O PHEH4 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'H4' and resid 24 through 28' Processing helix chain 'L5' and resid 49 through 52 removed outlier: 3.657A pdb=" N SERL5 52 " --> pdb=" O TYRL5 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'L5' and resid 49 through 52' Processing helix chain 'L5' and resid 79 through 83 removed outlier: 3.541A pdb=" N LEUL5 83 " --> pdb=" O THRL5 80 " (cutoff:3.500A) Processing helix chain 'H5' and resid 24 through 28 removed outlier: 3.530A pdb=" N SERH5 27 " --> pdb=" O THRH5 24 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYRH5 28 " --> pdb=" O PHEH5 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'H5' and resid 24 through 28' Processing helix chain 'L6' and resid 49 through 52 removed outlier: 3.658A pdb=" N SERL6 52 " --> pdb=" O TYRL6 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'L6' and resid 49 through 52' Processing helix chain 'L6' and resid 79 through 83 removed outlier: 3.542A pdb=" N LEUL6 83 " --> pdb=" O THRL6 80 " (cutoff:3.500A) Processing helix chain 'H6' and resid 24 through 28 removed outlier: 3.530A pdb=" N SERH6 27 " --> pdb=" O THRH6 24 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYRH6 28 " --> pdb=" O PHEH6 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'H6' and resid 24 through 28' Processing sheet with id=AA1, first strand: chain 'L2' and resid 4 through 6 removed outlier: 5.789A pdb=" N THRL2 69 " --> pdb=" O ALAL2 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L2' and resid 45 through 48 removed outlier: 6.470A pdb=" N TRPL2 35 " --> pdb=" O VALL2 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H2' and resid 18 through 19 removed outlier: 4.057A pdb=" N THRH2 73 " --> pdb=" O ASPH2 68 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H2' and resid 53 through 55 removed outlier: 3.681A pdb=" N GLYH2 40 " --> pdb=" O VALH2 36 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VALH2 36 " --> pdb=" O GLYH2 40 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TRPH2 32 " --> pdb=" O VALH2 44 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYRH2 46 " --> pdb=" O METH2 30 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N METH2 30 " --> pdb=" O TYRH2 46 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILEH2 33 " --> pdb=" O TYRH2 90 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYRH2 107 " --> pdb=" O ARGH2 93 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 30 through 37 removed outlier: 6.510A pdb=" N TYR A 289 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR A 111 " --> pdb=" O TYR A 289 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LYS A 291 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL A 109 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N THR A 293 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 83 through 88 removed outlier: 6.231A pdb=" N ARG A 284 " --> pdb=" O MET A 270 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TRP A 272 " --> pdb=" O HIS A 282 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N HIS A 282 " --> pdb=" O TRP A 272 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 83 through 88 Processing sheet with id=AA8, first strand: chain 'A' and resid 128 through 130 removed outlier: 6.241A pdb=" N ILE A 137 " --> pdb=" O PRO A 128 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 197 through 199 Processing sheet with id=AB1, first strand: chain 'A' and resid 236 through 240 Processing sheet with id=AB2, first strand: chain 'A' and resid 236 through 240 removed outlier: 6.690A pdb=" N ARG B 284 " --> pdb=" O MET B 270 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TRP B 272 " --> pdb=" O HIS B 282 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N HIS B 282 " --> pdb=" O TRP B 272 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AB4, first strand: chain 'B' and resid 31 through 37 removed outlier: 6.519A pdb=" N TYR B 289 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N THR B 111 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LYS B 291 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL B 109 " --> pdb=" O LYS B 291 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N THR B 293 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 31 through 37 removed outlier: 6.519A pdb=" N TYR B 289 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N THR B 111 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LYS B 291 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL B 109 " --> pdb=" O LYS B 291 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N THR B 293 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 128 through 130 removed outlier: 6.207A pdb=" N ILE B 137 " --> pdb=" O PRO B 128 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 197 through 198 Processing sheet with id=AB8, first strand: chain 'B' and resid 236 through 240 Processing sheet with id=AB9, first strand: chain 'B' and resid 236 through 240 removed outlier: 6.335A pdb=" N ARG C 284 " --> pdb=" O MET C 270 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N TRP C 272 " --> pdb=" O HIS C 282 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N HIS C 282 " --> pdb=" O TRP C 272 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 352 through 355 Processing sheet with id=AC2, first strand: chain 'C' and resid 30 through 37 removed outlier: 6.493A pdb=" N TYR C 289 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N THR C 111 " --> pdb=" O TYR C 289 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LYS C 291 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL C 109 " --> pdb=" O LYS C 291 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR C 293 " --> pdb=" O VAL C 107 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 128 through 130 removed outlier: 5.983A pdb=" N ILE C 137 " --> pdb=" O PRO C 128 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 197 through 199 Processing sheet with id=AC5, first strand: chain 'C' and resid 236 through 240 Processing sheet with id=AC6, first strand: chain 'C' and resid 236 through 240 removed outlier: 6.452A pdb=" N ARG D 284 " --> pdb=" O MET D 270 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 30 through 37 removed outlier: 6.499A pdb=" N TYR D 289 " --> pdb=" O THR D 111 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N THR D 111 " --> pdb=" O TYR D 289 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LYS D 291 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL D 109 " --> pdb=" O LYS D 291 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N THR D 293 " --> pdb=" O VAL D 107 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 30 through 37 removed outlier: 6.499A pdb=" N TYR D 289 " --> pdb=" O THR D 111 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N THR D 111 " --> pdb=" O TYR D 289 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LYS D 291 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL D 109 " --> pdb=" O LYS D 291 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N THR D 293 " --> pdb=" O VAL D 107 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 128 through 130 removed outlier: 6.271A pdb=" N ILE D 137 " --> pdb=" O PRO D 128 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 197 through 199 Processing sheet with id=AD2, first strand: chain 'D' and resid 236 through 240 Processing sheet with id=AD3, first strand: chain 'D' and resid 236 through 240 removed outlier: 4.494A pdb=" N GLY E 271 " --> pdb=" O ARG E 284 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 31 through 37 removed outlier: 6.492A pdb=" N TYR E 289 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR E 111 " --> pdb=" O TYR E 289 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LYS E 291 " --> pdb=" O VAL E 109 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N VAL E 109 " --> pdb=" O LYS E 291 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR E 293 " --> pdb=" O VAL E 107 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 128 through 130 removed outlier: 5.939A pdb=" N ILE E 137 " --> pdb=" O PRO E 128 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 197 through 199 Processing sheet with id=AD7, first strand: chain 'E' and resid 351 through 354 removed outlier: 4.003A pdb=" N THR E 351 " --> pdb=" O THR E 362 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L3' and resid 4 through 6 removed outlier: 5.790A pdb=" N THRL3 69 " --> pdb=" O ALAL3 25 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L3' and resid 45 through 48 removed outlier: 6.471A pdb=" N TRPL3 35 " --> pdb=" O VALL3 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H3' and resid 18 through 19 removed outlier: 4.058A pdb=" N THRH3 73 " --> pdb=" O ASPH3 68 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H3' and resid 53 through 55 removed outlier: 3.681A pdb=" N GLYH3 40 " --> pdb=" O VALH3 36 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VALH3 36 " --> pdb=" O GLYH3 40 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TRPH3 32 " --> pdb=" O VALH3 44 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N TYRH3 46 " --> pdb=" O METH3 30 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N METH3 30 " --> pdb=" O TYRH3 46 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILEH3 33 " --> pdb=" O TYRH3 90 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYRH3 107 " --> pdb=" O ARGH3 93 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L4' and resid 4 through 6 removed outlier: 5.789A pdb=" N THRL4 69 " --> pdb=" O ALAL4 25 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L4' and resid 45 through 48 removed outlier: 6.471A pdb=" N TRPL4 35 " --> pdb=" O VALL4 47 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H4' and resid 18 through 19 removed outlier: 4.059A pdb=" N THRH4 73 " --> pdb=" O ASPH4 68 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H4' and resid 53 through 55 removed outlier: 3.681A pdb=" N GLYH4 40 " --> pdb=" O VALH4 36 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VALH4 36 " --> pdb=" O GLYH4 40 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TRPH4 32 " --> pdb=" O VALH4 44 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYRH4 46 " --> pdb=" O METH4 30 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N METH4 30 " --> pdb=" O TYRH4 46 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILEH4 33 " --> pdb=" O TYRH4 90 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYRH4 107 " --> pdb=" O ARGH4 93 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L5' and resid 4 through 6 removed outlier: 5.790A pdb=" N THRL5 69 " --> pdb=" O ALAL5 25 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L5' and resid 45 through 48 removed outlier: 6.471A pdb=" N TRPL5 35 " --> pdb=" O VALL5 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H5' and resid 18 through 19 removed outlier: 4.057A pdb=" N THRH5 73 " --> pdb=" O ASPH5 68 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H5' and resid 53 through 55 removed outlier: 3.681A pdb=" N GLYH5 40 " --> pdb=" O VALH5 36 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VALH5 36 " --> pdb=" O GLYH5 40 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TRPH5 32 " --> pdb=" O VALH5 44 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYRH5 46 " --> pdb=" O METH5 30 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N METH5 30 " --> pdb=" O TYRH5 46 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILEH5 33 " --> pdb=" O TYRH5 90 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYRH5 107 " --> pdb=" O ARGH5 93 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L6' and resid 4 through 6 removed outlier: 5.790A pdb=" N THRL6 69 " --> pdb=" O ALAL6 25 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L6' and resid 45 through 48 removed outlier: 6.471A pdb=" N TRPL6 35 " --> pdb=" O VALL6 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H6' and resid 18 through 19 removed outlier: 4.058A pdb=" N THRH6 73 " --> pdb=" O ASPH6 68 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H6' and resid 53 through 55 removed outlier: 3.681A pdb=" N GLYH6 40 " --> pdb=" O VALH6 36 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VALH6 36 " --> pdb=" O GLYH6 40 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TRPH6 32 " --> pdb=" O VALH6 44 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYRH6 46 " --> pdb=" O METH6 30 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N METH6 30 " --> pdb=" O TYRH6 46 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILEH6 33 " --> pdb=" O TYRH6 90 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYRH6 107 " --> pdb=" O ARGH6 93 " (cutoff:3.500A) 682 hydrogen bonds defined for protein. 1674 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: 4.53 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3633 1.31 - 1.44: 6194 1.44 - 1.57: 12464 1.57 - 1.70: 0 1.70 - 1.83: 198 Bond restraints: 22489 Sorted by residual: bond pdb=" C VAL E 274 " pdb=" O VAL E 274 " ideal model delta sigma weight residual 1.237 1.185 0.053 1.08e-02 8.57e+03 2.38e+01 bond pdb=" CA VAL E 274 " pdb=" CB VAL E 274 " ideal model delta sigma weight residual 1.535 1.487 0.048 1.24e-02 6.50e+03 1.53e+01 bond pdb=" C LEU A 37 " pdb=" N ASN A 38 " ideal model delta sigma weight residual 1.331 1.255 0.076 2.83e-02 1.25e+03 7.25e+00 bond pdb=" C SER D 73 " pdb=" N PRO D 74 " ideal model delta sigma weight residual 1.337 1.317 0.020 9.80e-03 1.04e+04 3.99e+00 bond pdb=" C LEU D 50 " pdb=" N THR D 51 " ideal model delta sigma weight residual 1.332 1.307 0.025 1.40e-02 5.10e+03 3.25e+00 ... (remaining 22484 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 30075 2.51 - 5.02: 504 5.02 - 7.53: 45 7.53 - 10.05: 6 10.05 - 12.56: 3 Bond angle restraints: 30633 Sorted by residual: angle pdb=" N VAL D 320 " pdb=" CA VAL D 320 " pdb=" C VAL D 320 " ideal model delta sigma weight residual 109.29 119.84 -10.55 1.42e+00 4.96e-01 5.52e+01 angle pdb=" N VAL E 274 " pdb=" CA VAL E 274 " pdb=" C VAL E 274 " ideal model delta sigma weight residual 107.37 118.16 -10.79 1.48e+00 4.57e-01 5.32e+01 angle pdb=" N GLN C 321 " pdb=" CA GLN C 321 " pdb=" C GLN C 321 " ideal model delta sigma weight residual 111.36 118.80 -7.44 1.09e+00 8.42e-01 4.66e+01 angle pdb=" N GLY B 259 " pdb=" CA GLY B 259 " pdb=" C GLY B 259 " ideal model delta sigma weight residual 113.18 100.62 12.56 2.37e+00 1.78e-01 2.81e+01 angle pdb=" C ARG D 5 " pdb=" N PRO D 6 " pdb=" CA PRO D 6 " ideal model delta sigma weight residual 119.85 124.67 -4.82 1.01e+00 9.80e-01 2.28e+01 ... (remaining 30628 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 11522 17.98 - 35.96: 1423 35.96 - 53.94: 351 53.94 - 71.91: 72 71.91 - 89.89: 33 Dihedral angle restraints: 13401 sinusoidal: 5369 harmonic: 8032 Sorted by residual: dihedral pdb=" CB CYSH4 18 " pdb=" SG CYSH4 18 " pdb=" SG CYSH4 91 " pdb=" CB CYSH4 91 " ideal model delta sinusoidal sigma weight residual 93.00 140.55 -47.55 1 1.00e+01 1.00e-02 3.12e+01 dihedral pdb=" CB CYSH5 18 " pdb=" SG CYSH5 18 " pdb=" SG CYSH5 91 " pdb=" CB CYSH5 91 " ideal model delta sinusoidal sigma weight residual 93.00 140.52 -47.52 1 1.00e+01 1.00e-02 3.12e+01 dihedral pdb=" CB CYSH6 18 " pdb=" SG CYSH6 18 " pdb=" SG CYSH6 91 " pdb=" CB CYSH6 91 " ideal model delta sinusoidal sigma weight residual 93.00 140.52 -47.52 1 1.00e+01 1.00e-02 3.12e+01 ... (remaining 13398 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2574 0.053 - 0.105: 656 0.105 - 0.158: 121 0.158 - 0.210: 9 0.210 - 0.263: 6 Chirality restraints: 3366 Sorted by residual: chirality pdb=" CA GLN E 55 " pdb=" N GLN E 55 " pdb=" C GLN E 55 " pdb=" CB GLN E 55 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA GLN C 55 " pdb=" N GLN C 55 " pdb=" C GLN C 55 " pdb=" CB GLN C 55 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA GLN D 55 " pdb=" N GLN D 55 " pdb=" C GLN D 55 " pdb=" CB GLN D 55 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 3363 not shown) Planarity restraints: 3948 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 73 " 0.050 5.00e-02 4.00e+02 7.67e-02 9.41e+00 pdb=" N PRO E 74 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO E 74 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO E 74 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 73 " -0.049 5.00e-02 4.00e+02 7.41e-02 8.79e+00 pdb=" N PRO D 74 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO D 74 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 74 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 355 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.91e+00 pdb=" C ASP B 355 " -0.049 2.00e-02 2.50e+03 pdb=" O ASP B 355 " 0.018 2.00e-02 2.50e+03 pdb=" N ARG B 356 " 0.016 2.00e-02 2.50e+03 ... (remaining 3945 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.28: 36 2.28 - 2.93: 9781 2.93 - 3.59: 28656 3.59 - 4.24: 50456 4.24 - 4.90: 86024 Nonbonded interactions: 174953 Sorted by model distance: nonbonded pdb=" CD2 LEU E 50 " pdb=" CB GLN E 55 " model vdw 1.620 3.860 nonbonded pdb=" CD2 LEU E 50 " pdb=" CG GLN E 55 " model vdw 1.889 3.860 nonbonded pdb=" CG2 THRH2 98 " pdb=" ND2 ASN C 277 " model vdw 1.911 3.540 nonbonded pdb=" CE MET C 103 " pdb=" O CYS C 257 " model vdw 2.062 3.460 nonbonded pdb=" OD2 ASP D 268 " pdb=" NH1 ARG D 288 " model vdw 2.083 3.120 ... (remaining 174948 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 2 through 340) selection = (chain 'B' and resid 2 through 340) selection = (chain 'C' and resid 2 through 340) selection = (chain 'D' and resid 2 through 340) selection = (chain 'E' and resid 2 through 340) } ncs_group { reference = chain 'H2' selection = chain 'H3' selection = chain 'H4' selection = chain 'H5' selection = chain 'H6' } ncs_group { reference = chain 'L2' selection = chain 'L3' selection = chain 'L4' selection = chain 'L5' selection = chain 'L6' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 21.390 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5988 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 : 0.007 0.336 22505 Z= 0.367 Angle : 0.809 12.558 30663 Z= 0.457 Chirality : 0.049 0.263 3366 Planarity : 0.005 0.077 3948 Dihedral : 17.183 89.893 8234 Min Nonbonded Distance : 1.620 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.27 % Favored : 90.51 % Rotamer: Outliers : 5.40 % Allowed : 20.28 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 aren not related in a simple way. whole: -3.86 (0.13), residues: 2751 helix: -3.24 (0.32), residues: 141 sheet: -1.43 (0.18), residues: 729 loop : -3.22 (0.11), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 273 TYR 0.015 0.002 TYR D 223 PHE 0.023 0.002 PHE D 149 TRP 0.018 0.002 TRPH5 104 HIS 0.007 0.002 HIS C 282 Details of bonding type rmsd covalent geometry : bond 0.00672 (22489) covalent geometry : angle 0.80824 (30633) SS BOND : bond 0.00615 ( 15) SS BOND : angle 1.22685 ( 30) hydrogen bonds : bond 0.15539 ( 566) hydrogen bonds : angle 8.64893 ( 1674) Misc. bond : bond 0.33627 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 406 time to evaluate : 0.850 Fit side-chains revert: symmetry clash REVERT: H2 66 SER cc_start: 0.8676 (t) cc_final: 0.8333 (t) REVERT: A 11 LYS cc_start: 0.4773 (mmtt) cc_final: 0.3523 (ttpt) REVERT: A 130 ASP cc_start: 0.7109 (t0) cc_final: 0.6901 (t0) REVERT: A 154 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7679 (pm20) REVERT: A 205 MET cc_start: 0.7910 (tpp) cc_final: 0.7561 (mmm) REVERT: A 219 GLU cc_start: 0.6411 (OUTLIER) cc_final: 0.4170 (tp30) REVERT: A 226 ASN cc_start: 0.8660 (p0) cc_final: 0.8334 (p0) REVERT: B 11 LYS cc_start: 0.8204 (tttt) cc_final: 0.6469 (mptt) REVERT: B 214 ASP cc_start: 0.8448 (OUTLIER) cc_final: 0.7841 (t0) REVERT: B 264 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8106 (mt) REVERT: B 268 ASP cc_start: 0.8704 (m-30) cc_final: 0.8273 (m-30) REVERT: B 300 LYS cc_start: 0.4523 (mtmt) cc_final: 0.3691 (tptp) REVERT: B 334 GLU cc_start: 0.5285 (OUTLIER) cc_final: 0.4922 (pt0) REVERT: B 359 LYS cc_start: 0.3818 (tttt) cc_final: 0.2950 (ttpp) REVERT: C 248 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8609 (mp) REVERT: C 258 LYS cc_start: 0.7516 (ptpt) cc_final: 0.6966 (pttp) REVERT: C 295 ARG cc_start: 0.8284 (ptt180) cc_final: 0.8026 (ptt90) REVERT: D 250 GLU cc_start: 0.7598 (mp0) cc_final: 0.7252 (mt-10) REVERT: D 273 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7267 (ptt-90) REVERT: E 11 LYS cc_start: 0.7820 (ttmt) cc_final: 0.7559 (ttmm) REVERT: E 55 GLN cc_start: 0.5920 (OUTLIER) cc_final: 0.5413 (mm-40) REVERT: E 157 ASP cc_start: 0.8308 (OUTLIER) cc_final: 0.8071 (m-30) REVERT: E 205 MET cc_start: 0.8616 (tpp) cc_final: 0.8372 (mmt) REVERT: E 219 GLU cc_start: 0.5921 (OUTLIER) cc_final: 0.4186 (tp30) REVERT: E 326 GLU cc_start: 0.8201 (tt0) cc_final: 0.7070 (pm20) REVERT: E 333 GLU cc_start: 0.8322 (mt-10) cc_final: 0.8114 (mt-10) REVERT: H3 28 TYR cc_start: 0.8294 (m-80) cc_final: 0.8090 (m-80) REVERT: H3 99 ASP cc_start: 0.8356 (m-30) cc_final: 0.8026 (m-30) outliers start: 132 outliers final: 70 residues processed: 509 average time/residue: 0.1456 time to fit residues: 118.2321 Evaluate side-chains 426 residues out of total 2446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 346 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L2 residue 58 VAL Chi-restraints excluded: chain L2 residue 85 VAL Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 145 GLN Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 145 GLN Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 282 HIS Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 55 GLN Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 145 GLN Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 239 PHE Chi-restraints excluded: chain D residue 266 CYS Chi-restraints excluded: chain D residue 273 ARG Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain E residue 125 PHE Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 219 GLU Chi-restraints excluded: chain E residue 239 PHE Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 268 ASP Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain L6 residue 85 VAL Chi-restraints excluded: chain L6 residue 89 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 30.0000 chunk 20 optimal weight: 0.0870 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L2 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H2 69 ASN A 88 GLN A 126 ASN A 190 GLN A 212 HIS B 55 GLN B 102 GLN B 126 ASN B 190 GLN B 282 HIS B 314 ASN B 321 GLN B 323 GLN B 331 GLN C 38 ASN C 55 GLN C 277 ASN C 281 HIS C 282 HIS C 323 GLN C 331 GLN D 55 GLN D 147 HIS D 321 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 GLN E 93 ASN E 102 GLN E 126 ASN E 145 GLN E 147 HIS E 190 GLN E 282 HIS E 319 GLN E 323 GLN ** L3 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H3 69 ASN ** L4 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H4 69 ASN ** H5 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L6 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H6 69 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.173329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.138796 restraints weight = 23991.702| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.40 r_work: 0.3080 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 22505 Z= 0.170 Angle : 0.669 10.647 30663 Z= 0.346 Chirality : 0.047 0.445 3366 Planarity : 0.005 0.060 3948 Dihedral : 8.937 88.735 3171 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.00 % Favored : 91.97 % Rotamer: Outliers : 4.95 % Allowed : 22.61 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 aren not related in a simple way. whole: -3.05 (0.14), residues: 2751 helix: -2.37 (0.40), residues: 129 sheet: -0.85 (0.18), residues: 763 loop : -2.70 (0.12), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 276 TYR 0.013 0.001 TYR A 223 PHE 0.021 0.002 PHE C 239 TRP 0.068 0.002 TRP E 272 HIS 0.006 0.001 HIS E 281 Details of bonding type rmsd covalent geometry : bond 0.00405 (22489) covalent geometry : angle 0.66770 (30633) SS BOND : bond 0.00595 ( 15) SS BOND : angle 1.25796 ( 30) hydrogen bonds : bond 0.03194 ( 566) hydrogen bonds : angle 5.96852 ( 1674) Misc. bond : bond 0.00717 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 380 time to evaluate : 0.784 Fit side-chains revert: symmetry clash REVERT: L2 4 MET cc_start: 0.8420 (mmm) cc_final: 0.7800 (mmm) REVERT: A 11 LYS cc_start: 0.6527 (mmtt) cc_final: 0.4536 (ttpt) REVERT: A 125 PHE cc_start: 0.8984 (OUTLIER) cc_final: 0.8478 (t80) REVERT: A 159 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.7919 (tt0) REVERT: A 205 MET cc_start: 0.8503 (tpp) cc_final: 0.8291 (mmm) REVERT: A 226 ASN cc_start: 0.8740 (p0) cc_final: 0.8398 (p0) REVERT: A 241 ASN cc_start: 0.8686 (t0) cc_final: 0.8435 (t0) REVERT: B 11 LYS cc_start: 0.8722 (tttt) cc_final: 0.6957 (mptt) REVERT: B 18 MET cc_start: 0.8999 (tpt) cc_final: 0.8746 (mmt) REVERT: B 86 LYS cc_start: 0.9110 (tttt) cc_final: 0.8828 (tttm) REVERT: B 88 GLN cc_start: 0.9235 (tp40) cc_final: 0.9012 (tp40) REVERT: B 300 LYS cc_start: 0.6284 (mtmt) cc_final: 0.4762 (tptm) REVERT: B 359 LYS cc_start: 0.4586 (tttt) cc_final: 0.4037 (tttt) REVERT: C 50 LEU cc_start: 0.9336 (mp) cc_final: 0.8981 (mt) REVERT: C 154 GLU cc_start: 0.8876 (pt0) cc_final: 0.8641 (pt0) REVERT: C 258 LYS cc_start: 0.8166 (ptpt) cc_final: 0.7841 (pttp) REVERT: D 107 VAL cc_start: 0.9048 (t) cc_final: 0.8775 (m) REVERT: D 273 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8501 (ptt-90) REVERT: E 158 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8713 (pp) REVERT: E 217 LYS cc_start: 0.5922 (OUTLIER) cc_final: 0.5248 (ptpt) REVERT: E 226 ASN cc_start: 0.8924 (p0) cc_final: 0.8609 (p0) REVERT: E 264 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8513 (mt) REVERT: E 294 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8756 (pp) REVERT: E 326 GLU cc_start: 0.8241 (tt0) cc_final: 0.7671 (pm20) REVERT: E 333 GLU cc_start: 0.8294 (mt-10) cc_final: 0.8009 (mt-10) REVERT: E 361 LYS cc_start: 0.6088 (ttmt) cc_final: 0.3555 (ttmt) REVERT: L3 31 SER cc_start: 0.8532 (t) cc_final: 0.8208 (t) REVERT: H3 28 TYR cc_start: 0.8741 (m-80) cc_final: 0.8292 (m-80) REVERT: H4 15 LYS cc_start: 0.7582 (ttpt) cc_final: 0.6824 (tptt) REVERT: H4 17 SER cc_start: 0.7615 (t) cc_final: 0.7228 (m) REVERT: H4 27 SER cc_start: 0.8503 (m) cc_final: 0.7924 (t) REVERT: H4 57 ASP cc_start: 0.6775 (OUTLIER) cc_final: 0.6460 (m-30) REVERT: L6 11 MET cc_start: 0.4290 (OUTLIER) cc_final: 0.4020 (mtm) REVERT: L6 21 MET cc_start: 0.5556 (OUTLIER) cc_final: 0.4311 (ttt) REVERT: L6 58 VAL cc_start: 0.6496 (OUTLIER) cc_final: 0.6265 (p) outliers start: 121 outliers final: 74 residues processed: 466 average time/residue: 0.1431 time to fit residues: 107.3258 Evaluate side-chains 444 residues out of total 2446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 359 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L2 residue 3 VAL Chi-restraints excluded: chain L2 residue 33 VAL Chi-restraints excluded: chain L2 residue 69 THR Chi-restraints excluded: chain L2 residue 76 THR Chi-restraints excluded: chain H2 residue 48 SER Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 GLN Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 168 LYS Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 266 CYS Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 282 HIS Chi-restraints excluded: chain D residue 55 GLN Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 239 PHE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 273 ARG Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 217 LYS Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 272 TRP Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain L3 residue 74 THR Chi-restraints excluded: chain H3 residue 48 SER Chi-restraints excluded: chain L4 residue 3 VAL Chi-restraints excluded: chain L4 residue 58 VAL Chi-restraints excluded: chain H4 residue 49 SER Chi-restraints excluded: chain H4 residue 57 ASP Chi-restraints excluded: chain L5 residue 58 VAL Chi-restraints excluded: chain H5 residue 26 SER Chi-restraints excluded: chain L6 residue 11 MET Chi-restraints excluded: chain L6 residue 21 MET Chi-restraints excluded: chain L6 residue 58 VAL Chi-restraints excluded: chain L6 residue 72 THR Chi-restraints excluded: chain L6 residue 85 VAL Chi-restraints excluded: chain H6 residue 48 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 191 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 chunk 201 optimal weight: 30.0000 chunk 128 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 263 optimal weight: 20.0000 chunk 23 optimal weight: 0.3980 chunk 1 optimal weight: 40.0000 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L2 22 ASN H2 69 ASN B 277 ASN C 88 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L3 22 ASN L3 37 GLN L4 22 ASN L5 38 GLN H5 35 GLN ** H5 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L6 22 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.172471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.136050 restraints weight = 23964.617| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.39 r_work: 0.3072 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22505 Z= 0.161 Angle : 0.640 12.296 30663 Z= 0.328 Chirality : 0.046 0.211 3366 Planarity : 0.005 0.051 3948 Dihedral : 7.458 86.816 3086 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.22 % Favored : 91.75 % Rotamer: Outliers : 5.72 % Allowed : 22.32 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 aren not related in a simple way. whole: -2.55 (0.15), residues: 2751 helix: -1.83 (0.45), residues: 122 sheet: -0.52 (0.18), residues: 763 loop : -2.36 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGH3 77 TYR 0.011 0.001 TYR D 223 PHE 0.019 0.002 PHE D 149 TRP 0.066 0.002 TRP E 272 HIS 0.006 0.001 HIS C 282 Details of bonding type rmsd covalent geometry : bond 0.00387 (22489) covalent geometry : angle 0.63973 (30633) SS BOND : bond 0.00467 ( 15) SS BOND : angle 1.16658 ( 30) hydrogen bonds : bond 0.03001 ( 566) hydrogen bonds : angle 5.48866 ( 1674) Misc. bond : bond 0.00735 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 358 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: L2 4 MET cc_start: 0.8433 (mmm) cc_final: 0.7510 (mmm) REVERT: H2 19 SER cc_start: 0.8727 (t) cc_final: 0.8209 (m) REVERT: A 11 LYS cc_start: 0.6440 (mmtt) cc_final: 0.4511 (ttpt) REVERT: A 125 PHE cc_start: 0.8999 (OUTLIER) cc_final: 0.8574 (t80) REVERT: A 159 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.7978 (tt0) REVERT: A 161 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8123 (tt) REVERT: A 172 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7886 (mt-10) REVERT: A 214 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.7979 (t0) REVERT: A 226 ASN cc_start: 0.8924 (p0) cc_final: 0.8575 (p0) REVERT: B 11 LYS cc_start: 0.8679 (tttt) cc_final: 0.6902 (mptt) REVERT: B 18 MET cc_start: 0.8955 (tpt) cc_final: 0.8727 (mmt) REVERT: B 86 LYS cc_start: 0.9090 (tttt) cc_final: 0.8780 (tttm) REVERT: B 88 GLN cc_start: 0.9261 (tp40) cc_final: 0.9038 (tp40) REVERT: B 268 ASP cc_start: 0.8330 (m-30) cc_final: 0.8112 (m-30) REVERT: B 300 LYS cc_start: 0.6453 (mtmt) cc_final: 0.4971 (tptm) REVERT: B 326 GLU cc_start: 0.8373 (tm-30) cc_final: 0.8100 (tm-30) REVERT: B 334 GLU cc_start: 0.6024 (OUTLIER) cc_final: 0.4562 (pt0) REVERT: B 347 ASP cc_start: 0.7868 (t0) cc_final: 0.7577 (p0) REVERT: B 359 LYS cc_start: 0.4507 (tttt) cc_final: 0.4058 (tttt) REVERT: C 154 GLU cc_start: 0.8806 (pt0) cc_final: 0.8605 (pt0) REVERT: C 258 LYS cc_start: 0.8155 (ptpt) cc_final: 0.7786 (pttp) REVERT: C 350 MET cc_start: 0.6672 (tpt) cc_final: 0.6400 (tpt) REVERT: D 273 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.8519 (ptt-90) REVERT: D 283 TRP cc_start: 0.8471 (OUTLIER) cc_final: 0.7072 (m-90) REVERT: D 334 GLU cc_start: 0.6594 (pt0) cc_final: 0.5407 (mt-10) REVERT: E 19 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8096 (mm-30) REVERT: E 158 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8683 (pp) REVERT: E 217 LYS cc_start: 0.5776 (OUTLIER) cc_final: 0.5263 (ptpt) REVERT: E 226 ASN cc_start: 0.8854 (p0) cc_final: 0.8583 (p0) REVERT: E 264 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8482 (mt) REVERT: E 294 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8673 (pp) REVERT: E 326 GLU cc_start: 0.8193 (tt0) cc_final: 0.7658 (pm20) REVERT: E 333 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7918 (mt-10) REVERT: L3 31 SER cc_start: 0.8458 (t) cc_final: 0.8097 (t) REVERT: H3 28 TYR cc_start: 0.8686 (m-80) cc_final: 0.8315 (m-80) REVERT: L4 4 MET cc_start: 0.7576 (mmt) cc_final: 0.6226 (mmt) REVERT: H5 30 MET cc_start: 0.8407 (mtp) cc_final: 0.7868 (mtt) REVERT: L6 21 MET cc_start: 0.5373 (OUTLIER) cc_final: 0.4017 (ttt) outliers start: 140 outliers final: 83 residues processed: 455 average time/residue: 0.1355 time to fit residues: 101.2660 Evaluate side-chains 437 residues out of total 2446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 342 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L2 residue 33 VAL Chi-restraints excluded: chain L2 residue 69 THR Chi-restraints excluded: chain L2 residue 85 VAL Chi-restraints excluded: chain H2 residue 24 THR Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 GLN Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 168 LYS Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 266 CYS Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 282 HIS Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 55 GLN Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 239 PHE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 273 ARG Chi-restraints excluded: chain D residue 283 TRP Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 217 LYS Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain L3 residue 3 VAL Chi-restraints excluded: chain L4 residue 3 VAL Chi-restraints excluded: chain H4 residue 49 SER Chi-restraints excluded: chain L5 residue 3 VAL Chi-restraints excluded: chain L5 residue 21 MET Chi-restraints excluded: chain L5 residue 58 VAL Chi-restraints excluded: chain H5 residue 26 SER Chi-restraints excluded: chain L6 residue 5 THR Chi-restraints excluded: chain L6 residue 21 MET Chi-restraints excluded: chain L6 residue 72 THR Chi-restraints excluded: chain L6 residue 85 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 93 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 233 optimal weight: 30.0000 chunk 231 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 188 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 75 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 214 optimal weight: 0.0370 overall best weight: 1.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN E 55 GLN ** E 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L4 53 ASN ** H5 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L6 53 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.173452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.138388 restraints weight = 23856.093| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.38 r_work: 0.3091 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22505 Z= 0.138 Angle : 0.609 11.700 30663 Z= 0.311 Chirality : 0.045 0.178 3366 Planarity : 0.004 0.049 3948 Dihedral : 6.859 87.161 3076 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.07 % Favored : 91.89 % Rotamer: Outliers : 5.48 % Allowed : 23.10 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 aren not related in a simple way. whole: -2.20 (0.15), residues: 2751 helix: -1.35 (0.49), residues: 116 sheet: -0.27 (0.19), residues: 754 loop : -2.13 (0.13), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 288 TYR 0.011 0.001 TYR A 223 PHE 0.018 0.002 PHE D 149 TRP 0.031 0.002 TRP E 272 HIS 0.005 0.001 HIS E 281 Details of bonding type rmsd covalent geometry : bond 0.00329 (22489) covalent geometry : angle 0.60807 (30633) SS BOND : bond 0.00346 ( 15) SS BOND : angle 0.98106 ( 30) hydrogen bonds : bond 0.02804 ( 566) hydrogen bonds : angle 5.24000 ( 1674) Misc. bond : bond 0.00596 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 344 time to evaluate : 0.881 Fit side-chains revert: symmetry clash REVERT: H2 19 SER cc_start: 0.8764 (t) cc_final: 0.8179 (m) REVERT: A 11 LYS cc_start: 0.6495 (mmtt) cc_final: 0.4535 (ttpt) REVERT: A 161 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8062 (tt) REVERT: A 172 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7916 (mt-10) REVERT: A 226 ASN cc_start: 0.8818 (p0) cc_final: 0.8447 (p0) REVERT: B 11 LYS cc_start: 0.8669 (tttt) cc_final: 0.6899 (mptt) REVERT: B 18 MET cc_start: 0.8957 (tpt) cc_final: 0.8730 (mmt) REVERT: B 86 LYS cc_start: 0.9095 (tttt) cc_final: 0.8788 (tttm) REVERT: B 88 GLN cc_start: 0.9236 (tp40) cc_final: 0.9003 (tp40) REVERT: B 258 LYS cc_start: 0.7585 (OUTLIER) cc_final: 0.7368 (pttt) REVERT: B 294 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8895 (mt) REVERT: B 300 LYS cc_start: 0.6404 (mtmt) cc_final: 0.5061 (tptp) REVERT: B 334 GLU cc_start: 0.5918 (OUTLIER) cc_final: 0.4554 (pt0) REVERT: C 101 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7594 (tt) REVERT: C 248 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.8927 (mp) REVERT: C 258 LYS cc_start: 0.8164 (ptpt) cc_final: 0.7907 (pttp) REVERT: C 350 MET cc_start: 0.6550 (tpt) cc_final: 0.6276 (tpt) REVERT: D 98 CYS cc_start: 0.7786 (m) cc_final: 0.7547 (m) REVERT: D 283 TRP cc_start: 0.8413 (OUTLIER) cc_final: 0.6978 (m-90) REVERT: E 19 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8126 (mm-30) REVERT: E 158 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8679 (pp) REVERT: E 217 LYS cc_start: 0.5678 (OUTLIER) cc_final: 0.4164 (ptpt) REVERT: E 226 ASN cc_start: 0.8843 (p0) cc_final: 0.8610 (p0) REVERT: E 264 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8494 (mt) REVERT: E 326 GLU cc_start: 0.8208 (tt0) cc_final: 0.7624 (pm20) REVERT: E 333 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7890 (mt-10) REVERT: E 361 LYS cc_start: 0.5690 (ttmt) cc_final: 0.4164 (mptt) REVERT: L3 31 SER cc_start: 0.8414 (t) cc_final: 0.8101 (t) REVERT: H3 28 TYR cc_start: 0.8650 (m-80) cc_final: 0.8323 (m-80) REVERT: L4 4 MET cc_start: 0.7836 (mmt) cc_final: 0.6612 (mmt) REVERT: H4 57 ASP cc_start: 0.6598 (OUTLIER) cc_final: 0.6358 (m-30) REVERT: H5 30 MET cc_start: 0.8391 (mtp) cc_final: 0.7815 (mtt) REVERT: L6 21 MET cc_start: 0.5454 (OUTLIER) cc_final: 0.4193 (ttt) outliers start: 134 outliers final: 88 residues processed: 437 average time/residue: 0.1383 time to fit residues: 98.9319 Evaluate side-chains 434 residues out of total 2446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 334 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L2 residue 33 VAL Chi-restraints excluded: chain L2 residue 69 THR Chi-restraints excluded: chain H2 residue 24 THR Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 168 LYS Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 266 CYS Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 239 PHE Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 55 GLN Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 239 PHE Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 283 TRP Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 217 LYS Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain L3 residue 3 VAL Chi-restraints excluded: chain L4 residue 3 VAL Chi-restraints excluded: chain L4 residue 21 MET Chi-restraints excluded: chain H4 residue 19 SER Chi-restraints excluded: chain H4 residue 49 SER Chi-restraints excluded: chain H4 residue 57 ASP Chi-restraints excluded: chain L5 residue 3 VAL Chi-restraints excluded: chain L5 residue 21 MET Chi-restraints excluded: chain L5 residue 58 VAL Chi-restraints excluded: chain L5 residue 72 THR Chi-restraints excluded: chain L5 residue 88 CYS Chi-restraints excluded: chain H5 residue 26 SER Chi-restraints excluded: chain L6 residue 21 MET Chi-restraints excluded: chain L6 residue 72 THR Chi-restraints excluded: chain H6 residue 48 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 69 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 179 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 chunk 105 optimal weight: 8.9990 chunk 235 optimal weight: 20.0000 chunk 12 optimal weight: 9.9990 chunk 16 optimal weight: 20.0000 chunk 183 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B 102 GLN ** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H5 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.164808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.125382 restraints weight = 23875.625| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.45 r_work: 0.2952 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.072 22505 Z= 0.361 Angle : 0.819 12.189 30663 Z= 0.417 Chirality : 0.053 0.299 3366 Planarity : 0.006 0.075 3948 Dihedral : 7.541 83.406 3067 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.18 % Favored : 89.75 % Rotamer: Outliers : 6.58 % Allowed : 22.32 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 aren not related in a simple way. whole: -2.42 (0.15), residues: 2751 helix: -2.22 (0.41), residues: 135 sheet: -0.29 (0.19), residues: 748 loop : -2.29 (0.13), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 40 TYR 0.018 0.002 TYR A 289 PHE 0.032 0.003 PHE D 149 TRP 0.050 0.003 TRP E 283 HIS 0.008 0.002 HIS E 281 Details of bonding type rmsd covalent geometry : bond 0.00889 (22489) covalent geometry : angle 0.81816 (30633) SS BOND : bond 0.00471 ( 15) SS BOND : angle 1.46223 ( 30) hydrogen bonds : bond 0.03531 ( 566) hydrogen bonds : angle 5.79080 ( 1674) Misc. bond : bond 0.01289 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 359 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: L2 4 MET cc_start: 0.8427 (mmm) cc_final: 0.7644 (mtt) REVERT: A 11 LYS cc_start: 0.6678 (mmtt) cc_final: 0.4512 (ttpt) REVERT: A 34 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8073 (mt-10) REVERT: A 159 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.7784 (tt0) REVERT: A 172 GLU cc_start: 0.8424 (mm-30) cc_final: 0.7880 (mt-10) REVERT: A 209 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8011 (mp0) REVERT: A 214 ASP cc_start: 0.8352 (OUTLIER) cc_final: 0.8110 (t0) REVERT: A 226 ASN cc_start: 0.8954 (p0) cc_final: 0.8566 (p0) REVERT: B 11 LYS cc_start: 0.8743 (tttt) cc_final: 0.6952 (mptt) REVERT: B 86 LYS cc_start: 0.9101 (tttt) cc_final: 0.8817 (tttm) REVERT: B 184 ASP cc_start: 0.8475 (m-30) cc_final: 0.8159 (t0) REVERT: B 300 LYS cc_start: 0.6545 (mtmt) cc_final: 0.4883 (tptm) REVERT: B 359 LYS cc_start: 0.4754 (tttt) cc_final: 0.4542 (tttt) REVERT: C 48 GLU cc_start: 0.8129 (mp0) cc_final: 0.7916 (mm-30) REVERT: C 239 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.7845 (m-80) REVERT: C 248 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.8976 (mp) REVERT: C 258 LYS cc_start: 0.8324 (ptpt) cc_final: 0.7940 (pttp) REVERT: C 333 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8203 (mt-10) REVERT: D 48 GLU cc_start: 0.8240 (tp30) cc_final: 0.7956 (mm-30) REVERT: D 209 GLU cc_start: 0.9049 (OUTLIER) cc_final: 0.8733 (tt0) REVERT: D 283 TRP cc_start: 0.8462 (OUTLIER) cc_final: 0.7282 (m-90) REVERT: D 314 ASN cc_start: 0.8666 (m-40) cc_final: 0.8165 (m110) REVERT: E 11 LYS cc_start: 0.8433 (ttmt) cc_final: 0.8093 (ttpp) REVERT: E 19 GLU cc_start: 0.8313 (mm-30) cc_final: 0.8032 (mm-30) REVERT: E 52 GLU cc_start: 0.6950 (pm20) cc_final: 0.6674 (pm20) REVERT: E 158 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8786 (pp) REVERT: E 159 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8479 (tt0) REVERT: E 217 LYS cc_start: 0.5618 (OUTLIER) cc_final: 0.4719 (ptpt) REVERT: E 219 GLU cc_start: 0.6568 (OUTLIER) cc_final: 0.5017 (tp30) REVERT: E 264 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8543 (mt) REVERT: E 294 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8759 (pp) REVERT: E 326 GLU cc_start: 0.8267 (tt0) cc_final: 0.7708 (pm20) REVERT: E 333 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7935 (mt-10) REVERT: H3 28 TYR cc_start: 0.8678 (m-80) cc_final: 0.8382 (m-80) REVERT: L4 4 MET cc_start: 0.8274 (mmt) cc_final: 0.7044 (mmt) REVERT: L4 89 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7424 (tp) REVERT: H4 57 ASP cc_start: 0.6717 (OUTLIER) cc_final: 0.6496 (m-30) REVERT: L6 21 MET cc_start: 0.5458 (ptt) cc_final: 0.4158 (ttt) outliers start: 161 outliers final: 113 residues processed: 471 average time/residue: 0.1372 time to fit residues: 106.6178 Evaluate side-chains 480 residues out of total 2446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 350 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L2 residue 33 VAL Chi-restraints excluded: chain L2 residue 69 THR Chi-restraints excluded: chain L2 residue 76 THR Chi-restraints excluded: chain L2 residue 85 VAL Chi-restraints excluded: chain H2 residue 24 THR Chi-restraints excluded: chain H2 residue 48 SER Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 GLN Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 168 LYS Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 266 CYS Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 239 PHE Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 333 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 272 TRP Chi-restraints excluded: chain D residue 283 TRP Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 159 GLN Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 217 LYS Chi-restraints excluded: chain E residue 219 GLU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain L3 residue 3 VAL Chi-restraints excluded: chain L3 residue 74 THR Chi-restraints excluded: chain L4 residue 3 VAL Chi-restraints excluded: chain L4 residue 9 THR Chi-restraints excluded: chain L4 residue 21 MET Chi-restraints excluded: chain L4 residue 63 THR Chi-restraints excluded: chain L4 residue 89 LEU Chi-restraints excluded: chain H4 residue 19 SER Chi-restraints excluded: chain H4 residue 49 SER Chi-restraints excluded: chain H4 residue 57 ASP Chi-restraints excluded: chain L5 residue 3 VAL Chi-restraints excluded: chain L5 residue 21 MET Chi-restraints excluded: chain L5 residue 58 VAL Chi-restraints excluded: chain L5 residue 67 SER Chi-restraints excluded: chain L5 residue 69 THR Chi-restraints excluded: chain L5 residue 72 THR Chi-restraints excluded: chain H5 residue 48 SER Chi-restraints excluded: chain L6 residue 72 THR Chi-restraints excluded: chain L6 residue 85 VAL Chi-restraints excluded: chain L6 residue 89 LEU Chi-restraints excluded: chain H6 residue 47 ILE Chi-restraints excluded: chain H6 residue 48 SER Chi-restraints excluded: chain H6 residue 64 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 74 optimal weight: 0.1980 chunk 119 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 chunk 148 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 141 optimal weight: 0.1980 chunk 173 optimal weight: 0.9980 chunk 26 optimal weight: 0.0070 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L2 38 GLN H2 35 GLN A 76 ASN B 88 GLN B 102 GLN C 277 ASN D 88 GLN D 281 HIS ** E 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L4 38 GLN H4 35 GLN H5 69 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.175623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.145153 restraints weight = 23926.182| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.28 r_work: 0.3163 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22505 Z= 0.104 Angle : 0.571 12.988 30663 Z= 0.294 Chirality : 0.043 0.220 3366 Planarity : 0.004 0.048 3948 Dihedral : 5.907 70.350 3057 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.34 % Favored : 92.62 % Rotamer: Outliers : 3.80 % Allowed : 25.67 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 aren not related in a simple way. whole: -1.93 (0.15), residues: 2751 helix: -1.41 (0.48), residues: 123 sheet: -0.12 (0.19), residues: 748 loop : -1.90 (0.13), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGH3 77 TYR 0.012 0.001 TYR D 289 PHE 0.015 0.001 PHE D 149 TRP 0.019 0.001 TRP E 283 HIS 0.005 0.001 HISH3 31 Details of bonding type rmsd covalent geometry : bond 0.00226 (22489) covalent geometry : angle 0.57057 (30633) SS BOND : bond 0.00321 ( 15) SS BOND : angle 0.63985 ( 30) hydrogen bonds : bond 0.02699 ( 566) hydrogen bonds : angle 5.09586 ( 1674) Misc. bond : bond 0.00392 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 361 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 LYS cc_start: 0.6430 (mmtt) cc_final: 0.4609 (ttpt) REVERT: A 96 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8071 (pp) REVERT: A 161 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.7951 (tt) REVERT: A 172 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7802 (mt-10) REVERT: A 226 ASN cc_start: 0.8823 (p0) cc_final: 0.8448 (p0) REVERT: A 241 ASN cc_start: 0.8399 (t0) cc_final: 0.8138 (t0) REVERT: A 336 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8423 (ptp-170) REVERT: B 11 LYS cc_start: 0.8692 (tttt) cc_final: 0.6932 (mptt) REVERT: B 86 LYS cc_start: 0.9063 (tttt) cc_final: 0.8742 (tttm) REVERT: B 300 LYS cc_start: 0.6325 (mtmt) cc_final: 0.5047 (tptp) REVERT: C 105 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8554 (tm-30) REVERT: C 239 PHE cc_start: 0.8032 (OUTLIER) cc_final: 0.7275 (m-80) REVERT: C 258 LYS cc_start: 0.8054 (ptpt) cc_final: 0.7773 (pttp) REVERT: C 350 MET cc_start: 0.6293 (tpt) cc_final: 0.6066 (tpt) REVERT: D 60 SER cc_start: 0.9176 (p) cc_final: 0.8743 (p) REVERT: D 258 LYS cc_start: 0.8310 (mttt) cc_final: 0.7538 (mptt) REVERT: D 283 TRP cc_start: 0.8337 (OUTLIER) cc_final: 0.6734 (m-90) REVERT: D 314 ASN cc_start: 0.8609 (m-40) cc_final: 0.8005 (m110) REVERT: E 11 LYS cc_start: 0.8423 (ttmt) cc_final: 0.8109 (ttpp) REVERT: E 19 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8179 (mm-30) REVERT: E 158 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8636 (pp) REVERT: E 226 ASN cc_start: 0.8806 (p0) cc_final: 0.8579 (p0) REVERT: E 268 ASP cc_start: 0.8070 (m-30) cc_final: 0.7678 (m-30) REVERT: E 326 GLU cc_start: 0.8198 (tt0) cc_final: 0.7681 (pm20) REVERT: E 333 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7971 (mt-10) REVERT: E 361 LYS cc_start: 0.5480 (ttmt) cc_final: 0.4232 (mptt) REVERT: H3 28 TYR cc_start: 0.8634 (m-80) cc_final: 0.8320 (m-80) REVERT: L4 4 MET cc_start: 0.8145 (mmt) cc_final: 0.7179 (mmt) REVERT: L6 21 MET cc_start: 0.5662 (OUTLIER) cc_final: 0.4379 (ttt) REVERT: H6 30 MET cc_start: 0.8150 (mmt) cc_final: 0.7944 (mmm) REVERT: H6 108 TRP cc_start: 0.8357 (m100) cc_final: 0.8065 (m100) outliers start: 93 outliers final: 61 residues processed: 426 average time/residue: 0.1391 time to fit residues: 96.9562 Evaluate side-chains 412 residues out of total 2446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 343 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L2 residue 11 MET Chi-restraints excluded: chain L2 residue 33 VAL Chi-restraints excluded: chain L2 residue 69 THR Chi-restraints excluded: chain L2 residue 85 VAL Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 239 PHE Chi-restraints excluded: chain C residue 266 CYS Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 283 TRP Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain L3 residue 3 VAL Chi-restraints excluded: chain H3 residue 31 HIS Chi-restraints excluded: chain L4 residue 3 VAL Chi-restraints excluded: chain L4 residue 9 THR Chi-restraints excluded: chain L4 residue 21 MET Chi-restraints excluded: chain H4 residue 49 SER Chi-restraints excluded: chain L5 residue 3 VAL Chi-restraints excluded: chain L5 residue 21 MET Chi-restraints excluded: chain L6 residue 21 MET Chi-restraints excluded: chain L6 residue 85 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 238 optimal weight: 10.0000 chunk 226 optimal weight: 10.0000 chunk 244 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 199 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 233 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 chunk 257 optimal weight: 30.0000 chunk 2 optimal weight: 40.0000 chunk 184 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 GLN ** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 GLN ** E 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L4 92 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.167484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.131235 restraints weight = 23886.352| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.39 r_work: 0.3007 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 22505 Z= 0.263 Angle : 0.721 12.005 30663 Z= 0.366 Chirality : 0.049 0.253 3366 Planarity : 0.005 0.054 3948 Dihedral : 6.218 62.028 3046 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.34 % Favored : 90.59 % Rotamer: Outliers : 4.58 % Allowed : 25.63 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 aren not related in a simple way. whole: -2.04 (0.15), residues: 2751 helix: -1.56 (0.48), residues: 121 sheet: -0.34 (0.18), residues: 794 loop : -1.93 (0.13), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 40 TYR 0.017 0.002 TYR D 223 PHE 0.025 0.002 PHE D 149 TRP 0.041 0.002 TRP E 283 HIS 0.006 0.002 HISH3 31 Details of bonding type rmsd covalent geometry : bond 0.00647 (22489) covalent geometry : angle 0.72020 (30633) SS BOND : bond 0.00380 ( 15) SS BOND : angle 1.10382 ( 30) hydrogen bonds : bond 0.03127 ( 566) hydrogen bonds : angle 5.44610 ( 1674) Misc. bond : bond 0.01069 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 354 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L2 4 MET cc_start: 0.8406 (mmm) cc_final: 0.7671 (mtt) REVERT: A 11 LYS cc_start: 0.6594 (mmtt) cc_final: 0.4466 (ttpt) REVERT: A 96 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8270 (pp) REVERT: A 159 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7848 (tt0) REVERT: A 172 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7835 (mt-10) REVERT: A 203 ASP cc_start: 0.8136 (t0) cc_final: 0.7580 (t70) REVERT: A 214 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7928 (t0) REVERT: A 226 ASN cc_start: 0.8930 (p0) cc_final: 0.8569 (p0) REVERT: B 11 LYS cc_start: 0.8753 (tttt) cc_final: 0.6977 (mptt) REVERT: B 86 LYS cc_start: 0.9045 (tttt) cc_final: 0.8712 (tttm) REVERT: B 300 LYS cc_start: 0.6614 (mtmt) cc_final: 0.5114 (tptm) REVERT: B 359 LYS cc_start: 0.4595 (tttt) cc_final: 0.4079 (tttt) REVERT: C 239 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.7751 (m-80) REVERT: C 258 LYS cc_start: 0.8198 (ptpt) cc_final: 0.7885 (pttp) REVERT: D 75 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8404 (tp30) REVERT: D 283 TRP cc_start: 0.8448 (OUTLIER) cc_final: 0.7248 (m-90) REVERT: D 314 ASN cc_start: 0.8679 (m-40) cc_final: 0.8107 (m110) REVERT: E 19 GLU cc_start: 0.8309 (mm-30) cc_final: 0.8064 (mm-30) REVERT: E 65 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8470 (mp) REVERT: E 158 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8698 (pp) REVERT: E 185 MET cc_start: 0.8534 (mtt) cc_final: 0.8255 (mtt) REVERT: E 217 LYS cc_start: 0.5007 (OUTLIER) cc_final: 0.4242 (ptpt) REVERT: E 226 ASN cc_start: 0.8854 (p0) cc_final: 0.8581 (p0) REVERT: E 326 GLU cc_start: 0.8165 (tt0) cc_final: 0.7694 (pm20) REVERT: E 333 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7906 (mt-10) REVERT: E 361 LYS cc_start: 0.5671 (ttmt) cc_final: 0.4250 (mptt) REVERT: H3 28 TYR cc_start: 0.8656 (m-80) cc_final: 0.8392 (m-80) REVERT: L4 4 MET cc_start: 0.8264 (mmt) cc_final: 0.7292 (mmt) REVERT: L6 11 MET cc_start: 0.5446 (pmm) cc_final: 0.3967 (ttp) REVERT: L6 21 MET cc_start: 0.5170 (OUTLIER) cc_final: 0.3993 (ttt) REVERT: H6 108 TRP cc_start: 0.8587 (m100) cc_final: 0.8348 (m100) outliers start: 112 outliers final: 91 residues processed: 434 average time/residue: 0.1425 time to fit residues: 100.6511 Evaluate side-chains 446 residues out of total 2446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 346 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L2 residue 33 VAL Chi-restraints excluded: chain L2 residue 69 THR Chi-restraints excluded: chain L2 residue 76 THR Chi-restraints excluded: chain L2 residue 85 VAL Chi-restraints excluded: chain H2 residue 24 THR Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 GLN Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 266 CYS Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 239 PHE Chi-restraints excluded: chain C residue 266 CYS Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 55 GLN Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 283 TRP Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 217 LYS Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain L3 residue 3 VAL Chi-restraints excluded: chain H3 residue 31 HIS Chi-restraints excluded: chain L4 residue 3 VAL Chi-restraints excluded: chain L4 residue 9 THR Chi-restraints excluded: chain L4 residue 21 MET Chi-restraints excluded: chain H4 residue 19 SER Chi-restraints excluded: chain H4 residue 49 SER Chi-restraints excluded: chain L5 residue 3 VAL Chi-restraints excluded: chain L5 residue 21 MET Chi-restraints excluded: chain L5 residue 24 ARG Chi-restraints excluded: chain L5 residue 69 THR Chi-restraints excluded: chain H5 residue 24 THR Chi-restraints excluded: chain L6 residue 21 MET Chi-restraints excluded: chain L6 residue 85 VAL Chi-restraints excluded: chain L6 residue 89 LEU Chi-restraints excluded: chain H6 residue 47 ILE Chi-restraints excluded: chain H6 residue 48 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 9 optimal weight: 20.0000 chunk 166 optimal weight: 0.3980 chunk 80 optimal weight: 3.9990 chunk 202 optimal weight: 8.9990 chunk 151 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 215 optimal weight: 30.0000 chunk 234 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 248 optimal weight: 10.0000 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 GLN ** E 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.171996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.137261 restraints weight = 23779.386| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.43 r_work: 0.3071 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22505 Z= 0.127 Angle : 0.605 13.012 30663 Z= 0.309 Chirality : 0.045 0.246 3366 Planarity : 0.005 0.058 3948 Dihedral : 5.734 60.072 3046 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.74 % Favored : 92.22 % Rotamer: Outliers : 4.05 % Allowed : 26.37 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 aren not related in a simple way. whole: -1.84 (0.15), residues: 2751 helix: -1.30 (0.49), residues: 122 sheet: -0.18 (0.19), residues: 764 loop : -1.78 (0.14), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 288 TYR 0.012 0.001 TYR D 289 PHE 0.018 0.001 PHE D 149 TRP 0.025 0.001 TRP E 283 HIS 0.005 0.001 HISH3 31 Details of bonding type rmsd covalent geometry : bond 0.00300 (22489) covalent geometry : angle 0.60479 (30633) SS BOND : bond 0.00297 ( 15) SS BOND : angle 0.73195 ( 30) hydrogen bonds : bond 0.02761 ( 566) hydrogen bonds : angle 5.17375 ( 1674) Misc. bond : bond 0.00660 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 348 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L2 4 MET cc_start: 0.8422 (mmm) cc_final: 0.7243 (mtt) REVERT: A 11 LYS cc_start: 0.6501 (mmtt) cc_final: 0.4496 (ttpt) REVERT: A 96 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8247 (pp) REVERT: A 161 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8023 (tt) REVERT: A 172 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7864 (mt-10) REVERT: A 226 ASN cc_start: 0.8941 (p0) cc_final: 0.8605 (p0) REVERT: B 11 LYS cc_start: 0.8713 (tttt) cc_final: 0.6971 (mptt) REVERT: B 55 GLN cc_start: 0.6447 (OUTLIER) cc_final: 0.5685 (tp40) REVERT: B 86 LYS cc_start: 0.9093 (tttt) cc_final: 0.8773 (tttm) REVERT: B 300 LYS cc_start: 0.6323 (mtmt) cc_final: 0.5031 (tptp) REVERT: B 334 GLU cc_start: 0.6113 (OUTLIER) cc_final: 0.4025 (pt0) REVERT: C 69 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.7646 (m-30) REVERT: C 101 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7615 (tt) REVERT: C 107 VAL cc_start: 0.9183 (t) cc_final: 0.8853 (m) REVERT: C 239 PHE cc_start: 0.8306 (OUTLIER) cc_final: 0.7616 (m-80) REVERT: C 258 LYS cc_start: 0.8064 (ptpt) cc_final: 0.7753 (pttp) REVERT: D 75 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8477 (mm-30) REVERT: D 258 LYS cc_start: 0.8367 (mttt) cc_final: 0.7502 (mptt) REVERT: D 283 TRP cc_start: 0.8374 (OUTLIER) cc_final: 0.6925 (m-90) REVERT: D 314 ASN cc_start: 0.8616 (m-40) cc_final: 0.8014 (m110) REVERT: E 12 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8274 (tp) REVERT: E 19 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8112 (mm-30) REVERT: E 65 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8378 (mp) REVERT: E 72 ASP cc_start: 0.7726 (m-30) cc_final: 0.7218 (t0) REVERT: E 158 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8648 (pp) REVERT: E 185 MET cc_start: 0.8533 (mtt) cc_final: 0.8309 (mtt) REVERT: E 226 ASN cc_start: 0.8865 (p0) cc_final: 0.8634 (p0) REVERT: E 326 GLU cc_start: 0.8154 (tt0) cc_final: 0.7682 (pm20) REVERT: E 333 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7869 (mt-10) REVERT: E 361 LYS cc_start: 0.5659 (ttmt) cc_final: 0.4308 (mptt) REVERT: L3 4 MET cc_start: 0.7448 (mmt) cc_final: 0.7154 (mmt) REVERT: H3 28 TYR cc_start: 0.8612 (m-80) cc_final: 0.8182 (m-80) REVERT: L4 4 MET cc_start: 0.8245 (mmt) cc_final: 0.7312 (mmt) REVERT: L4 32 ASN cc_start: 0.7982 (p0) cc_final: 0.7769 (p0) REVERT: L6 11 MET cc_start: 0.5396 (pmm) cc_final: 0.3712 (ttp) REVERT: L6 21 MET cc_start: 0.5591 (OUTLIER) cc_final: 0.4306 (ttt) REVERT: H6 30 MET cc_start: 0.8220 (mmt) cc_final: 0.7983 (mtt) outliers start: 99 outliers final: 81 residues processed: 419 average time/residue: 0.1412 time to fit residues: 96.2118 Evaluate side-chains 433 residues out of total 2446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 340 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L2 residue 33 VAL Chi-restraints excluded: chain L2 residue 69 THR Chi-restraints excluded: chain L2 residue 85 VAL Chi-restraints excluded: chain H2 residue 48 SER Chi-restraints excluded: chain H2 residue 73 THR Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 266 CYS Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 239 PHE Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 266 CYS Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 283 TRP Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain L3 residue 3 VAL Chi-restraints excluded: chain H3 residue 31 HIS Chi-restraints excluded: chain L4 residue 3 VAL Chi-restraints excluded: chain L4 residue 21 MET Chi-restraints excluded: chain H4 residue 49 SER Chi-restraints excluded: chain L5 residue 3 VAL Chi-restraints excluded: chain L5 residue 21 MET Chi-restraints excluded: chain L5 residue 24 ARG Chi-restraints excluded: chain H5 residue 48 SER Chi-restraints excluded: chain L6 residue 21 MET Chi-restraints excluded: chain L6 residue 72 THR Chi-restraints excluded: chain L6 residue 85 VAL Chi-restraints excluded: chain L6 residue 89 LEU Chi-restraints excluded: chain H6 residue 47 ILE Chi-restraints excluded: chain H6 residue 48 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 20 optimal weight: 0.0770 chunk 250 optimal weight: 1.9990 chunk 159 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 209 optimal weight: 20.0000 chunk 204 optimal weight: 0.6980 chunk 264 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 99 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 258 optimal weight: 9.9990 overall best weight: 2.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.171013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.135498 restraints weight = 23800.711| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.36 r_work: 0.3067 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22505 Z= 0.155 Angle : 0.626 12.511 30663 Z= 0.319 Chirality : 0.045 0.267 3366 Planarity : 0.005 0.063 3948 Dihedral : 5.747 62.534 3045 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.32 % Favored : 91.64 % Rotamer: Outliers : 4.46 % Allowed : 26.12 % Favored : 69.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 aren not related in a simple way. whole: -1.77 (0.15), residues: 2751 helix: -1.46 (0.46), residues: 130 sheet: -0.16 (0.19), residues: 785 loop : -1.72 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 40 TYR 0.012 0.001 TYR B 223 PHE 0.020 0.002 PHE D 149 TRP 0.029 0.002 TRP E 283 HIS 0.005 0.001 HISH2 31 Details of bonding type rmsd covalent geometry : bond 0.00374 (22489) covalent geometry : angle 0.62563 (30633) SS BOND : bond 0.00295 ( 15) SS BOND : angle 0.81463 ( 30) hydrogen bonds : bond 0.02792 ( 566) hydrogen bonds : angle 5.16538 ( 1674) Misc. bond : bond 0.00763 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 342 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L2 4 MET cc_start: 0.8435 (mmm) cc_final: 0.7282 (mtt) REVERT: A 11 LYS cc_start: 0.6521 (mmtt) cc_final: 0.4517 (ttpt) REVERT: A 96 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8195 (pp) REVERT: A 172 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7851 (mt-10) REVERT: A 226 ASN cc_start: 0.8908 (p0) cc_final: 0.8561 (p0) REVERT: B 11 LYS cc_start: 0.8721 (tttt) cc_final: 0.6966 (mptt) REVERT: B 55 GLN cc_start: 0.6608 (OUTLIER) cc_final: 0.5725 (tp40) REVERT: B 86 LYS cc_start: 0.9056 (tttt) cc_final: 0.8715 (tttm) REVERT: B 300 LYS cc_start: 0.6527 (mtmt) cc_final: 0.5214 (tptm) REVERT: B 334 GLU cc_start: 0.5998 (OUTLIER) cc_final: 0.3856 (pt0) REVERT: C 69 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.7674 (m-30) REVERT: C 101 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7636 (tt) REVERT: C 154 GLU cc_start: 0.8880 (pt0) cc_final: 0.8639 (pt0) REVERT: C 217 LYS cc_start: 0.4945 (OUTLIER) cc_final: 0.4051 (ptpt) REVERT: C 239 PHE cc_start: 0.8347 (OUTLIER) cc_final: 0.7700 (m-80) REVERT: C 258 LYS cc_start: 0.8074 (ptpt) cc_final: 0.7743 (pttp) REVERT: D 205 MET cc_start: 0.8737 (mmm) cc_final: 0.8424 (mmm) REVERT: D 209 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8665 (tt0) REVERT: D 258 LYS cc_start: 0.8373 (mttt) cc_final: 0.7492 (mptt) REVERT: D 283 TRP cc_start: 0.8391 (OUTLIER) cc_final: 0.7025 (m-90) REVERT: D 314 ASN cc_start: 0.8655 (m-40) cc_final: 0.8047 (m110) REVERT: E 19 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8104 (mm-30) REVERT: E 72 ASP cc_start: 0.7779 (m-30) cc_final: 0.7274 (t0) REVERT: E 158 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8675 (pp) REVERT: E 159 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8435 (tt0) REVERT: E 185 MET cc_start: 0.8338 (mtt) cc_final: 0.8132 (mtt) REVERT: E 217 LYS cc_start: 0.5352 (OUTLIER) cc_final: 0.4627 (ptpt) REVERT: E 226 ASN cc_start: 0.8854 (p0) cc_final: 0.8620 (p0) REVERT: E 326 GLU cc_start: 0.8137 (tt0) cc_final: 0.7687 (pm20) REVERT: E 333 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7907 (mt-10) REVERT: E 361 LYS cc_start: 0.5741 (ttmt) cc_final: 0.4487 (mptt) REVERT: H3 28 TYR cc_start: 0.8596 (m-80) cc_final: 0.8185 (m-80) REVERT: L4 4 MET cc_start: 0.8211 (mmt) cc_final: 0.7311 (mmt) REVERT: L4 32 ASN cc_start: 0.8086 (p0) cc_final: 0.7876 (p0) REVERT: L6 11 MET cc_start: 0.5467 (pmm) cc_final: 0.3753 (ttp) REVERT: L6 21 MET cc_start: 0.5606 (OUTLIER) cc_final: 0.4286 (ttt) REVERT: H6 30 MET cc_start: 0.8230 (mmt) cc_final: 0.7961 (mtt) outliers start: 109 outliers final: 86 residues processed: 421 average time/residue: 0.1473 time to fit residues: 101.2805 Evaluate side-chains 439 residues out of total 2446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 340 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L2 residue 33 VAL Chi-restraints excluded: chain L2 residue 69 THR Chi-restraints excluded: chain L2 residue 85 VAL Chi-restraints excluded: chain H2 residue 24 THR Chi-restraints excluded: chain H2 residue 48 SER Chi-restraints excluded: chain H2 residue 73 THR Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 168 LYS Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 266 CYS Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 55 GLN Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 217 LYS Chi-restraints excluded: chain C residue 239 PHE Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 266 CYS Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 283 TRP Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 159 GLN Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 217 LYS Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain L3 residue 3 VAL Chi-restraints excluded: chain H3 residue 31 HIS Chi-restraints excluded: chain L4 residue 3 VAL Chi-restraints excluded: chain L4 residue 21 MET Chi-restraints excluded: chain H4 residue 49 SER Chi-restraints excluded: chain L5 residue 3 VAL Chi-restraints excluded: chain L5 residue 21 MET Chi-restraints excluded: chain L5 residue 24 ARG Chi-restraints excluded: chain H5 residue 48 SER Chi-restraints excluded: chain L6 residue 21 MET Chi-restraints excluded: chain L6 residue 72 THR Chi-restraints excluded: chain L6 residue 85 VAL Chi-restraints excluded: chain L6 residue 89 LEU Chi-restraints excluded: chain H6 residue 47 ILE Chi-restraints excluded: chain H6 residue 48 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 216 optimal weight: 7.9990 chunk 259 optimal weight: 10.0000 chunk 178 optimal weight: 5.9990 chunk 146 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 204 optimal weight: 7.9990 chunk 209 optimal weight: 5.9990 chunk 264 optimal weight: 10.0000 chunk 54 optimal weight: 0.5980 chunk 9 optimal weight: 20.0000 chunk 203 optimal weight: 20.0000 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 GLN D 282 HIS ** E 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.167889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.132572 restraints weight = 23858.974| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.35 r_work: 0.3020 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 22505 Z= 0.232 Angle : 0.700 12.902 30663 Z= 0.356 Chirality : 0.048 0.279 3366 Planarity : 0.005 0.067 3948 Dihedral : 6.159 65.300 3045 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.12 % Favored : 90.80 % Rotamer: Outliers : 4.54 % Allowed : 25.96 % Favored : 69.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 aren not related in a simple way. whole: -1.89 (0.15), residues: 2751 helix: -1.53 (0.47), residues: 125 sheet: -0.21 (0.19), residues: 784 loop : -1.81 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 40 TYR 0.015 0.002 TYR E 289 PHE 0.024 0.002 PHE D 149 TRP 0.038 0.002 TRP E 283 HIS 0.005 0.002 HISH3 31 Details of bonding type rmsd covalent geometry : bond 0.00567 (22489) covalent geometry : angle 0.69989 (30633) SS BOND : bond 0.00351 ( 15) SS BOND : angle 1.04568 ( 30) hydrogen bonds : bond 0.03065 ( 566) hydrogen bonds : angle 5.40782 ( 1674) Misc. bond : bond 0.01007 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 342 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L2 4 MET cc_start: 0.8413 (mmm) cc_final: 0.7859 (mtt) REVERT: A 11 LYS cc_start: 0.6548 (mmtt) cc_final: 0.4456 (ttpt) REVERT: A 96 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8196 (pp) REVERT: A 159 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.7991 (tt0) REVERT: A 172 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7927 (mt-10) REVERT: A 209 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7972 (mp0) REVERT: A 226 ASN cc_start: 0.8930 (p0) cc_final: 0.8571 (p0) REVERT: B 11 LYS cc_start: 0.8722 (tttt) cc_final: 0.6922 (mptt) REVERT: B 86 LYS cc_start: 0.9028 (tttt) cc_final: 0.8696 (tttm) REVERT: B 300 LYS cc_start: 0.6341 (mtmt) cc_final: 0.4935 (tptp) REVERT: C 69 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.7718 (m-30) REVERT: C 121 ASP cc_start: 0.8017 (t70) cc_final: 0.7599 (t70) REVERT: C 154 GLU cc_start: 0.8882 (pt0) cc_final: 0.8618 (pt0) REVERT: C 217 LYS cc_start: 0.5105 (OUTLIER) cc_final: 0.3684 (ptpp) REVERT: C 239 PHE cc_start: 0.8517 (OUTLIER) cc_final: 0.7820 (m-80) REVERT: C 258 LYS cc_start: 0.8139 (ptpt) cc_final: 0.7767 (pttp) REVERT: D 209 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8674 (tt0) REVERT: D 283 TRP cc_start: 0.8455 (OUTLIER) cc_final: 0.7231 (m-90) REVERT: D 314 ASN cc_start: 0.8603 (m-40) cc_final: 0.8030 (m110) REVERT: E 19 GLU cc_start: 0.8309 (mm-30) cc_final: 0.8061 (mm-30) REVERT: E 52 GLU cc_start: 0.6950 (pm20) cc_final: 0.6409 (pt0) REVERT: E 72 ASP cc_start: 0.7706 (m-30) cc_final: 0.7438 (t0) REVERT: E 158 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8707 (pp) REVERT: E 159 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8429 (tt0) REVERT: E 217 LYS cc_start: 0.5311 (OUTLIER) cc_final: 0.4653 (ptpt) REVERT: E 226 ASN cc_start: 0.8847 (p0) cc_final: 0.8579 (p0) REVERT: E 264 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8540 (mt) REVERT: E 326 GLU cc_start: 0.8183 (tt0) cc_final: 0.7725 (pm20) REVERT: E 333 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7972 (mt-10) REVERT: E 361 LYS cc_start: 0.5610 (ttmt) cc_final: 0.4374 (mptt) REVERT: H3 28 TYR cc_start: 0.8671 (m-80) cc_final: 0.8405 (m-80) REVERT: L4 4 MET cc_start: 0.8254 (mmt) cc_final: 0.7931 (mmm) REVERT: L6 11 MET cc_start: 0.5572 (pmm) cc_final: 0.3621 (ttp) REVERT: L6 21 MET cc_start: 0.5130 (OUTLIER) cc_final: 0.4014 (ttt) outliers start: 111 outliers final: 91 residues processed: 422 average time/residue: 0.1465 time to fit residues: 101.2745 Evaluate side-chains 444 residues out of total 2446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 340 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L2 residue 33 VAL Chi-restraints excluded: chain L2 residue 69 THR Chi-restraints excluded: chain L2 residue 76 THR Chi-restraints excluded: chain L2 residue 85 VAL Chi-restraints excluded: chain H2 residue 24 THR Chi-restraints excluded: chain H2 residue 48 SER Chi-restraints excluded: chain H2 residue 73 THR Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 GLN Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 266 CYS Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 55 GLN Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 217 LYS Chi-restraints excluded: chain C residue 239 PHE Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 283 TRP Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 159 GLN Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 217 LYS Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain L3 residue 3 VAL Chi-restraints excluded: chain H3 residue 24 THR Chi-restraints excluded: chain H3 residue 31 HIS Chi-restraints excluded: chain L4 residue 21 MET Chi-restraints excluded: chain H4 residue 49 SER Chi-restraints excluded: chain L5 residue 3 VAL Chi-restraints excluded: chain L5 residue 21 MET Chi-restraints excluded: chain L5 residue 24 ARG Chi-restraints excluded: chain L5 residue 67 SER Chi-restraints excluded: chain H5 residue 24 THR Chi-restraints excluded: chain H5 residue 48 SER Chi-restraints excluded: chain L6 residue 21 MET Chi-restraints excluded: chain L6 residue 72 THR Chi-restraints excluded: chain L6 residue 85 VAL Chi-restraints excluded: chain L6 residue 89 LEU Chi-restraints excluded: chain H6 residue 47 ILE Chi-restraints excluded: chain H6 residue 48 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.7198 > 50: distance: 8 - 12: 11.628 distance: 12 - 13: 29.054 distance: 13 - 14: 42.699 distance: 13 - 16: 10.996 distance: 14 - 15: 16.278 distance: 14 - 19: 31.007 distance: 16 - 17: 11.534 distance: 16 - 18: 41.334 distance: 19 - 20: 15.347 distance: 19 - 211: 20.486 distance: 20 - 21: 14.392 distance: 20 - 23: 23.184 distance: 21 - 22: 9.947 distance: 21 - 26: 12.861 distance: 22 - 208: 21.301 distance: 23 - 24: 16.371 distance: 23 - 25: 11.369 distance: 26 - 27: 16.014 distance: 27 - 28: 22.239 distance: 27 - 30: 31.359 distance: 28 - 29: 15.915 distance: 28 - 35: 31.644 distance: 30 - 31: 15.393 distance: 31 - 32: 10.672 distance: 32 - 34: 18.954 distance: 35 - 36: 12.698 distance: 35 - 197: 12.133 distance: 36 - 37: 19.034 distance: 36 - 39: 7.819 distance: 37 - 38: 12.424 distance: 37 - 43: 11.026 distance: 38 - 194: 13.021 distance: 39 - 40: 14.350 distance: 39 - 41: 23.388 distance: 40 - 42: 20.200 distance: 43 - 44: 3.818 distance: 44 - 45: 4.677 distance: 44 - 47: 9.833 distance: 45 - 46: 12.500 distance: 45 - 52: 11.446 distance: 47 - 48: 9.211 distance: 48 - 49: 17.523 distance: 49 - 50: 14.117 distance: 49 - 51: 11.924 distance: 52 - 53: 11.875 distance: 52 - 179: 9.885 distance: 53 - 56: 17.456 distance: 54 - 55: 14.605 distance: 54 - 57: 11.696 distance: 55 - 176: 20.366 distance: 57 - 58: 12.052 distance: 58 - 59: 4.014 distance: 58 - 61: 17.010 distance: 59 - 60: 29.824 distance: 59 - 68: 19.341 distance: 61 - 62: 5.923 distance: 62 - 63: 8.856 distance: 62 - 64: 18.167 distance: 64 - 66: 9.206 distance: 65 - 67: 17.617 distance: 66 - 67: 8.845 distance: 68 - 69: 9.901 distance: 68 - 164: 25.795 distance: 69 - 70: 7.881 distance: 69 - 72: 17.033 distance: 70 - 71: 16.220 distance: 70 - 76: 31.439 distance: 71 - 161: 28.787 distance: 72 - 73: 37.303 distance: 73 - 74: 31.880 distance: 73 - 75: 18.496 distance: 76 - 77: 13.943 distance: 77 - 78: 16.376 distance: 77 - 80: 18.811 distance: 78 - 79: 43.745 distance: 78 - 84: 22.375 distance: 81 - 82: 5.334 distance: 81 - 83: 34.081 distance: 84 - 85: 14.253 distance: 84 - 90: 11.684 distance: 85 - 86: 9.545 distance: 85 - 88: 15.401 distance: 86 - 87: 7.871 distance: 86 - 91: 7.734 distance: 88 - 89: 21.400 distance: 89 - 90: 18.754