Starting phenix.real_space_refine on Mon Mar 18 19:33:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k23_22641/03_2024/7k23_22641.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k23_22641/03_2024/7k23_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k23_22641/03_2024/7k23_22641.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k23_22641/03_2024/7k23_22641.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k23_22641/03_2024/7k23_22641.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k23_22641/03_2024/7k23_22641.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Residue "L2 ARG 24": "NH1" <-> "NH2" Residue "L2 ARG 61": "NH1" <-> "NH2" Residue "L2 GLU 81": "OE1" <-> "OE2" Residue "H2 ARG 62": "NH1" <-> "NH2" Residue "H2 ARG 67": "NH1" <-> "NH2" Residue "H2 ARG 77": "NH1" <-> "NH2" Residue "H2 ARG 95": "NH1" <-> "NH2" Residue "A GLU 19": "OE1" <-> "OE2" Residue "A GLU 32": "OE1" <-> "OE2" Residue "A PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 52": "OE1" <-> "OE2" Residue "A GLU 71": "OE1" <-> "OE2" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A GLU 209": "OE1" <-> "OE2" Residue "A GLU 250": "OE1" <-> "OE2" Residue "A GLU 333": "OE1" <-> "OE2" Residue "A GLU 334": "OE1" <-> "OE2" Residue "B GLU 19": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 75": "OE1" <-> "OE2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B GLU 209": "OE1" <-> "OE2" Residue "B TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 250": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "B TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 19": "OE1" <-> "OE2" Residue "C GLU 48": "OE1" <-> "OE2" Residue "C GLU 71": "OE1" <-> "OE2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "C ASP 121": "OD1" <-> "OD2" Residue "C TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 250": "OE1" <-> "OE2" Residue "C GLU 328": "OE1" <-> "OE2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D GLU 71": "OE1" <-> "OE2" Residue "D ASP 121": "OD1" <-> "OD2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "D GLU 172": "OE1" <-> "OE2" Residue "D GLU 250": "OE1" <-> "OE2" Residue "D GLU 260": "OE1" <-> "OE2" Residue "D GLU 333": "OE1" <-> "OE2" Residue "D GLU 334": "OE1" <-> "OE2" Residue "E GLU 32": "OE1" <-> "OE2" Residue "E GLU 48": "OE1" <-> "OE2" Residue "E GLU 52": "OE1" <-> "OE2" Residue "E GLU 71": "OE1" <-> "OE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "E GLU 172": "OE1" <-> "OE2" Residue "E PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 250": "OE1" <-> "OE2" Residue "E GLU 260": "OE1" <-> "OE2" Residue "E GLU 328": "OE1" <-> "OE2" Residue "E GLU 334": "OE1" <-> "OE2" Residue "L3 ARG 24": "NH1" <-> "NH2" Residue "L3 ARG 61": "NH1" <-> "NH2" Residue "L3 GLU 81": "OE1" <-> "OE2" Residue "H3 ARG 62": "NH1" <-> "NH2" Residue "H3 ARG 67": "NH1" <-> "NH2" Residue "H3 ARG 77": "NH1" <-> "NH2" Residue "H3 ARG 95": "NH1" <-> "NH2" Residue "L4 ARG 24": "NH1" <-> "NH2" Residue "L4 ARG 61": "NH1" <-> "NH2" Residue "L4 GLU 81": "OE1" <-> "OE2" Residue "H4 ARG 62": "NH1" <-> "NH2" Residue "H4 ARG 67": "NH1" <-> "NH2" Residue "H4 ARG 77": "NH1" <-> "NH2" Residue "H4 ARG 95": "NH1" <-> "NH2" Residue "L5 ARG 24": "NH1" <-> "NH2" Residue "L5 ARG 61": "NH1" <-> "NH2" Residue "L5 GLU 81": "OE1" <-> "OE2" Residue "H5 ARG 62": "NH1" <-> "NH2" Residue "H5 ARG 67": "NH1" <-> "NH2" Residue "H5 ARG 77": "NH1" <-> "NH2" Residue "H5 ARG 95": "NH1" <-> "NH2" Residue "L6 ARG 24": "NH1" <-> "NH2" Residue "L6 ARG 61": "NH1" <-> "NH2" Residue "L6 GLU 81": "OE1" <-> "OE2" Residue "H6 ARG 62": "NH1" <-> "NH2" Residue "H6 ARG 67": "NH1" <-> "NH2" Residue "H6 ARG 77": "NH1" <-> "NH2" Residue "H6 ARG 95": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21923 Number of models: 1 Model: "" Number of chains: 15 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} Chain: "L3" 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: "H3" 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: "L4" 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: "H4" 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: "L5" 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: "H5" 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: "L6" 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: "H6" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 813 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 3, 'TRANS': 95} Time building chain proxies: 10.58, per 1000 atoms: 0.48 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 CYSH3 18 " - pdb=" SG CYSH3 91 " distance=2.02 Simple disulfide: pdb=" SG CYSL4 23 " - pdb=" SG CYSL4 88 " distance=2.03 Simple disulfide: pdb=" SG CYSH4 18 " - pdb=" SG CYSH4 91 " distance=2.02 Simple disulfide: pdb=" SG CYSL5 23 " - pdb=" SG CYSL5 88 " distance=2.03 Simple disulfide: pdb=" SG CYSH5 18 " - pdb=" SG CYSH5 91 " distance=2.02 Simple disulfide: pdb=" SG CYSL6 23 " - pdb=" SG CYSL6 88 " distance=2.03 Simple disulfide: pdb=" SG CYSH6 18 " - pdb=" SG CYSH6 91 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.75 Conformation dependent library (CDL) restraints added in 3.4 seconds 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: 2.23 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: 6.77 Time building geometry restraints manager: 7.56 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: 98.82 - 105.89: 684 105.89 - 112.95: 12001 112.95 - 120.02: 7437 120.02 - 127.09: 10182 127.09 - 134.15: 329 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: 39 2.28 - 2.93: 9782 2.93 - 3.59: 28657 3.59 - 4.24: 50456 4.24 - 4.90: 86024 Nonbonded interactions: 174958 Sorted by model distance: nonbonded pdb=" CD2 LEU E 50 " pdb=" CB GLN E 55 " model vdw 1.620 3.860 nonbonded pdb=" NE1 TRP E 272 " pdb=" CZ2 TRP E 283 " model vdw 1.766 3.420 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 ... (remaining 174953 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 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: 1.940 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: 0.010 Extract box with map and model: 7.150 Check model and map are aligned: 0.320 Set scattering table: 0.170 Process input model: 52.780 Find NCS groups from input model: 1.820 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.140 ------------------------------------------------------------------------------- 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 0.076 22489 Z= 0.436 Angle : 0.808 12.558 30633 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 : 19.51 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.018 0.002 TRPH5 104 HIS 0.007 0.002 HIS C 282 PHE 0.023 0.002 PHE D 149 TYR 0.015 0.002 TYR D 223 ARG 0.004 0.000 ARG C 273 *********************** 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 fitting. rotamer outliers: 132 poor density : 406 time to evaluate : 2.430 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: 0.3092 time to fit residues: 248.3622 Evaluate side-chains 426 residues out of total 2446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 346 time to evaluate : 2.276 ------------------------------------------------------------------------------- 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 225 optimal weight: 6.9990 chunk 202 optimal weight: 8.9990 chunk 112 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 209 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 242 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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** L2 37 GLN H2 69 ASN A 88 GLN A 126 ASN A 190 GLN A 212 HIS ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 147 HIS C 277 ASN C 282 HIS C 323 GLN C 331 GLN ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 HIS D 321 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 GLN ** E 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 L3 37 GLN H3 69 ASN ** L4 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L4 32 ASN L4 37 GLN L4 92 ASN H4 69 ASN L5 37 GLN ** H5 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L6 22 ASN L6 37 GLN L6 38 GLN H6 35 GLN H6 69 ASN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6019 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22489 Z= 0.246 Angle : 0.646 10.637 30633 Z= 0.332 Chirality : 0.046 0.196 3366 Planarity : 0.005 0.062 3948 Dihedral : 8.895 88.980 3171 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.65 % Favored : 91.24 % Rotamer: Outliers : 5.03 % Allowed : 23.59 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.14), residues: 2751 helix: -2.52 (0.38), residues: 142 sheet: -0.90 (0.18), residues: 761 loop : -2.74 (0.12), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 272 HIS 0.008 0.001 HIS E 281 PHE 0.022 0.002 PHE C 239 TYR 0.011 0.001 TYR A 223 ARG 0.006 0.000 ARGL2 24 *********************** 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 494 residues out of total 2446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 371 time to evaluate : 2.388 Fit side-chains revert: symmetry clash REVERT: A 11 LYS cc_start: 0.4710 (mmtt) cc_final: 0.3502 (ttpt) REVERT: A 125 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.8013 (t80) REVERT: A 130 ASP cc_start: 0.6840 (t0) cc_final: 0.6584 (t0) REVERT: A 159 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.7009 (tt0) REVERT: A 205 MET cc_start: 0.7785 (tpp) cc_final: 0.7530 (mmm) REVERT: A 226 ASN cc_start: 0.8468 (p0) cc_final: 0.8069 (p0) REVERT: B 11 LYS cc_start: 0.8171 (tttt) cc_final: 0.6455 (mptt) REVERT: B 86 LYS cc_start: 0.8718 (tttt) cc_final: 0.8480 (tttm) REVERT: B 300 LYS cc_start: 0.4524 (mtmt) cc_final: 0.3669 (tptm) REVERT: B 359 LYS cc_start: 0.3432 (tttt) cc_final: 0.3218 (tttt) REVERT: C 258 LYS cc_start: 0.7602 (ptpt) cc_final: 0.7110 (pttp) REVERT: C 295 ARG cc_start: 0.8177 (ptt180) cc_final: 0.7925 (ptt90) REVERT: D 250 GLU cc_start: 0.7670 (mp0) cc_final: 0.7352 (mp0) REVERT: D 273 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.7323 (ptt-90) REVERT: E 107 VAL cc_start: 0.9097 (t) cc_final: 0.8678 (m) REVERT: E 158 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7913 (pp) REVERT: E 203 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.7977 (t0) REVERT: E 205 MET cc_start: 0.8574 (tpp) cc_final: 0.8347 (mmm) REVERT: E 217 LYS cc_start: 0.3595 (OUTLIER) cc_final: 0.3078 (ptpt) REVERT: E 226 ASN cc_start: 0.8820 (p0) cc_final: 0.8598 (p0) REVERT: E 264 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.7932 (mt) REVERT: E 294 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8162 (pp) REVERT: E 326 GLU cc_start: 0.8278 (tt0) cc_final: 0.7117 (pm20) REVERT: E 333 GLU cc_start: 0.8291 (mt-10) cc_final: 0.8043 (mt-10) REVERT: H3 28 TYR cc_start: 0.8408 (m-80) cc_final: 0.8195 (m-80) REVERT: L6 11 MET cc_start: 0.3192 (OUTLIER) cc_final: 0.2986 (mtm) outliers start: 123 outliers final: 80 residues processed: 462 average time/residue: 0.3011 time to fit residues: 225.4875 Evaluate side-chains 433 residues out of total 2446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 344 time to evaluate : 2.407 ------------------------------------------------------------------------------- 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 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 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 55 GLN 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 125 PHE 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 168 LYS Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 221 THR 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 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 168 LYS Chi-restraints excluded: chain C residue 184 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 282 HIS Chi-restraints excluded: chain C residue 330 THR 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 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 233 THR 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 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 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 109 VAL Chi-restraints excluded: chain E residue 145 GLN Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 203 ASP 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 74 THR 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 L5 residue 58 VAL Chi-restraints excluded: chain H5 residue 26 SER Chi-restraints excluded: chain H5 residue 48 SER Chi-restraints excluded: chain L6 residue 11 MET Chi-restraints excluded: chain L6 residue 85 VAL Chi-restraints excluded: chain H6 residue 48 SER Chi-restraints excluded: chain H6 residue 64 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 134 optimal weight: 0.6980 chunk 75 optimal weight: 7.9990 chunk 201 optimal weight: 30.0000 chunk 165 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 242 optimal weight: 3.9990 chunk 262 optimal weight: 9.9990 chunk 216 optimal weight: 30.0000 chunk 240 optimal weight: 20.0000 chunk 82 optimal weight: 0.9990 chunk 194 optimal weight: 0.8980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L2 22 ASN L2 38 GLN H2 35 GLN ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 GLN B 277 ASN C 88 GLN C 281 HIS ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 HIS ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L4 22 ASN ** H4 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L5 38 GLN H5 35 GLN ** H5 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6053 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22489 Z= 0.277 Angle : 0.643 12.026 30633 Z= 0.327 Chirality : 0.046 0.195 3366 Planarity : 0.005 0.055 3948 Dihedral : 7.642 89.735 3089 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.01 % Favored : 90.84 % Rotamer: Outliers : 6.26 % Allowed : 23.51 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.14), residues: 2751 helix: -2.13 (0.42), residues: 135 sheet: -0.57 (0.18), residues: 761 loop : -2.48 (0.13), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRPH2 104 HIS 0.007 0.002 HIS C 282 PHE 0.021 0.002 PHE C 239 TYR 0.013 0.001 TYR D 223 ARG 0.007 0.000 ARGH3 77 *********************** 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 505 residues out of total 2446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 352 time to evaluate : 2.590 Fit side-chains REVERT: H2 19 SER cc_start: 0.7706 (t) cc_final: 0.7474 (m) REVERT: A 11 LYS cc_start: 0.4781 (mmtt) cc_final: 0.3550 (ttpt) REVERT: A 125 PHE cc_start: 0.8335 (OUTLIER) cc_final: 0.8082 (t80) REVERT: A 130 ASP cc_start: 0.6798 (t0) cc_final: 0.6433 (t0) REVERT: A 159 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7154 (tt0) REVERT: A 161 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7385 (tt) REVERT: A 172 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7576 (mt-10) REVERT: A 205 MET cc_start: 0.7718 (tpp) cc_final: 0.7491 (mmm) REVERT: A 214 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7413 (t0) REVERT: A 226 ASN cc_start: 0.8472 (p0) cc_final: 0.8084 (p0) REVERT: A 283 TRP cc_start: 0.7625 (OUTLIER) cc_final: 0.7291 (m100) REVERT: B 11 LYS cc_start: 0.8160 (tttt) cc_final: 0.6448 (mptt) REVERT: B 86 LYS cc_start: 0.8700 (tttt) cc_final: 0.8460 (tttm) REVERT: B 145 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8637 (pm20) REVERT: B 300 LYS cc_start: 0.4772 (mtmt) cc_final: 0.3958 (tptm) REVERT: B 326 GLU cc_start: 0.8597 (tm-30) cc_final: 0.8389 (tm-30) REVERT: B 334 GLU cc_start: 0.4694 (OUTLIER) cc_final: 0.4049 (pt0) REVERT: B 359 LYS cc_start: 0.3115 (tttt) cc_final: 0.2320 (ttpp) REVERT: C 154 GLU cc_start: 0.8655 (pt0) cc_final: 0.8270 (pt0) REVERT: C 258 LYS cc_start: 0.7657 (ptpt) cc_final: 0.7021 (pttp) REVERT: C 350 MET cc_start: 0.4836 (tpt) cc_final: 0.4626 (tpt) REVERT: D 273 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.7368 (ptt-90) REVERT: D 283 TRP cc_start: 0.7665 (OUTLIER) cc_final: 0.5863 (m-90) REVERT: D 334 GLU cc_start: 0.6541 (pt0) cc_final: 0.5564 (mt-10) REVERT: E 11 LYS cc_start: 0.7808 (ttmt) cc_final: 0.7507 (ttpp) REVERT: E 19 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7749 (mm-30) REVERT: E 107 VAL cc_start: 0.9082 (t) cc_final: 0.8678 (m) REVERT: E 157 ASP cc_start: 0.8294 (m-30) cc_final: 0.7346 (m-30) REVERT: E 158 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7936 (pp) REVERT: E 159 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.8042 (tt0) REVERT: E 203 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.8043 (t0) REVERT: E 205 MET cc_start: 0.8558 (tpp) cc_final: 0.8344 (mmm) REVERT: E 219 GLU cc_start: 0.5944 (OUTLIER) cc_final: 0.4108 (tp30) REVERT: E 226 ASN cc_start: 0.8782 (p0) cc_final: 0.8558 (p0) REVERT: E 264 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.7961 (mt) REVERT: E 294 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8139 (pp) REVERT: E 326 GLU cc_start: 0.8235 (tt0) cc_final: 0.7091 (pm20) REVERT: E 333 GLU cc_start: 0.8273 (mt-10) cc_final: 0.8025 (mt-10) REVERT: H3 28 TYR cc_start: 0.8436 (m-80) cc_final: 0.8183 (m-80) REVERT: L4 4 MET cc_start: 0.7022 (mmt) cc_final: 0.6291 (mmt) outliers start: 153 outliers final: 101 residues processed: 460 average time/residue: 0.2927 time to fit residues: 217.5954 Evaluate side-chains 456 residues out of total 2446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 340 time to evaluate : 2.397 ------------------------------------------------------------------------------- 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 H2 residue 24 THR Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 55 GLN 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 154 GLU Chi-restraints excluded: chain A residue 157 ASP 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 253 VAL Chi-restraints excluded: chain A residue 283 TRP 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 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 145 GLN 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 184 ASP 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 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 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 100 THR 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 168 LYS 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 C residue 282 HIS 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 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 144 SER 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 174 VAL Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 233 THR 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 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 159 GLN Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 219 GLU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 268 ASP 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 1 ASP Chi-restraints excluded: chain L5 residue 3 VAL Chi-restraints excluded: chain L5 residue 58 VAL Chi-restraints excluded: chain L5 residue 88 CYS Chi-restraints excluded: chain H5 residue 26 SER Chi-restraints excluded: chain H5 residue 48 SER Chi-restraints excluded: chain H5 residue 94 THR Chi-restraints excluded: chain L6 residue 5 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 239 optimal weight: 20.0000 chunk 182 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 163 optimal weight: 0.0770 chunk 243 optimal weight: 9.9990 chunk 258 optimal weight: 20.0000 chunk 127 optimal weight: 1.9990 chunk 231 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L4 53 ASN L4 92 ASN ** H4 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L5 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H5 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L6 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6051 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22489 Z= 0.236 Angle : 0.609 12.514 30633 Z= 0.310 Chirality : 0.045 0.211 3366 Planarity : 0.004 0.052 3948 Dihedral : 7.055 89.329 3083 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.94 % Favored : 90.91 % Rotamer: Outliers : 6.17 % Allowed : 24.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.15), residues: 2751 helix: -1.63 (0.46), residues: 128 sheet: -0.32 (0.19), residues: 762 loop : -2.22 (0.13), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRPH2 104 HIS 0.006 0.001 HIS E 281 PHE 0.020 0.002 PHE D 149 TYR 0.012 0.001 TYR E 289 ARG 0.004 0.000 ARGH3 77 *********************** 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 511 residues out of total 2446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 360 time to evaluate : 2.407 Fit side-chains REVERT: H2 90 TYR cc_start: 0.7301 (m-10) cc_final: 0.6924 (m-10) REVERT: A 11 LYS cc_start: 0.4754 (mmtt) cc_final: 0.3563 (ttpt) REVERT: A 130 ASP cc_start: 0.6729 (t0) cc_final: 0.6376 (t0) REVERT: A 159 GLN cc_start: 0.7695 (OUTLIER) cc_final: 0.7229 (tt0) REVERT: A 161 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7321 (tt) REVERT: A 172 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7521 (mt-10) REVERT: A 205 MET cc_start: 0.7661 (tpp) cc_final: 0.7454 (mmm) REVERT: A 226 ASN cc_start: 0.8463 (p0) cc_final: 0.8073 (p0) REVERT: A 283 TRP cc_start: 0.7602 (OUTLIER) cc_final: 0.7252 (m100) REVERT: B 11 LYS cc_start: 0.8155 (tttt) cc_final: 0.6443 (mptt) REVERT: B 86 LYS cc_start: 0.8684 (tttt) cc_final: 0.8432 (tttm) REVERT: B 294 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8511 (mt) REVERT: B 300 LYS cc_start: 0.4762 (mtmt) cc_final: 0.4046 (tptp) REVERT: B 334 GLU cc_start: 0.4595 (OUTLIER) cc_final: 0.3853 (pt0) REVERT: B 359 LYS cc_start: 0.3318 (tttt) cc_final: 0.2495 (ttpp) REVERT: C 101 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.7026 (tt) REVERT: C 233 THR cc_start: 0.8276 (OUTLIER) cc_final: 0.7822 (p) REVERT: C 248 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8697 (mp) REVERT: C 258 LYS cc_start: 0.7676 (ptpt) cc_final: 0.7091 (pttp) REVERT: C 282 HIS cc_start: 0.8341 (OUTLIER) cc_final: 0.7884 (m-70) REVERT: C 292 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8766 (mp) REVERT: C 350 MET cc_start: 0.4847 (tpt) cc_final: 0.4583 (tpt) REVERT: D 75 GLU cc_start: 0.6914 (mm-30) cc_final: 0.6582 (tp30) REVERT: D 209 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7876 (tt0) REVERT: D 283 TRP cc_start: 0.7601 (OUTLIER) cc_final: 0.5872 (m-90) REVERT: E 19 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7734 (mm-30) REVERT: E 107 VAL cc_start: 0.9089 (t) cc_final: 0.8727 (m) REVERT: E 157 ASP cc_start: 0.8273 (m-30) cc_final: 0.7469 (m-30) REVERT: E 158 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7907 (pp) REVERT: E 159 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.8049 (tt0) REVERT: E 205 MET cc_start: 0.8507 (tpp) cc_final: 0.8280 (mmm) REVERT: E 219 GLU cc_start: 0.5941 (OUTLIER) cc_final: 0.3621 (mm-30) REVERT: E 264 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.7967 (mt) REVERT: E 294 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8151 (pp) REVERT: E 326 GLU cc_start: 0.8243 (tt0) cc_final: 0.7096 (pm20) REVERT: E 333 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7970 (mt-10) REVERT: E 361 LYS cc_start: 0.3507 (ttmt) cc_final: 0.3028 (mptt) REVERT: H3 28 TYR cc_start: 0.8421 (m-80) cc_final: 0.8151 (m-80) REVERT: L6 1 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7568 (m-30) outliers start: 151 outliers final: 97 residues processed: 466 average time/residue: 0.2815 time to fit residues: 212.7278 Evaluate side-chains 462 residues out of total 2446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 347 time to evaluate : 2.452 ------------------------------------------------------------------------------- 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 H2 residue 24 THR Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 157 ASP 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 283 TRP Chi-restraints excluded: chain A residue 320 VAL 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 50 LEU Chi-restraints excluded: chain B residue 60 SER 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 145 GLN 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 184 ASP Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 221 THR 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 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 137 ILE Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 248 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 C residue 292 ILE Chi-restraints excluded: chain C residue 330 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 91 MET Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 144 SER 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 209 GLU Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 239 PHE Chi-restraints excluded: chain D residue 253 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 D residue 326 GLU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 25 THR 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 109 VAL 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 191 VAL Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 219 GLU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 268 ASP 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 21 MET Chi-restraints excluded: chain H4 residue 19 SER Chi-restraints excluded: chain H4 residue 49 SER 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 48 SER Chi-restraints excluded: chain L6 residue 1 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 214 optimal weight: 30.0000 chunk 146 optimal weight: 0.4980 chunk 3 optimal weight: 20.0000 chunk 192 optimal weight: 6.9990 chunk 106 optimal weight: 0.0980 chunk 220 optimal weight: 6.9990 chunk 178 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 131 optimal weight: 9.9990 chunk 231 optimal weight: 20.0000 chunk 65 optimal weight: 6.9990 overall best weight: 4.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 GLN D 55 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L4 32 ASN L4 92 ASN H4 31 HIS H5 69 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6111 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 22489 Z= 0.380 Angle : 0.697 12.526 30633 Z= 0.353 Chirality : 0.048 0.256 3366 Planarity : 0.005 0.052 3948 Dihedral : 6.993 85.197 3071 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.60 % Favored : 90.22 % Rotamer: Outliers : 6.99 % Allowed : 23.30 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.15), residues: 2751 helix: -1.80 (0.45), residues: 130 sheet: -0.25 (0.19), residues: 766 loop : -2.20 (0.13), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 283 HIS 0.006 0.002 HIS E 281 PHE 0.026 0.002 PHE C 239 TYR 0.016 0.002 TYR D 223 ARG 0.005 0.001 ARGH3 77 *********************** 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 527 residues out of total 2446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 356 time to evaluate : 2.369 Fit side-chains revert: symmetry clash REVERT: H2 90 TYR cc_start: 0.7173 (m-10) cc_final: 0.6938 (m-80) REVERT: A 11 LYS cc_start: 0.4793 (mmtt) cc_final: 0.3481 (ttpt) REVERT: A 130 ASP cc_start: 0.6798 (t0) cc_final: 0.6453 (t0) REVERT: A 159 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.6867 (tm-30) REVERT: A 172 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7558 (mt-10) REVERT: A 209 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7299 (mp0) REVERT: A 214 ASP cc_start: 0.7799 (OUTLIER) cc_final: 0.7410 (t0) REVERT: A 226 ASN cc_start: 0.8655 (p0) cc_final: 0.8277 (p0) REVERT: A 283 TRP cc_start: 0.7627 (OUTLIER) cc_final: 0.7328 (m100) REVERT: B 11 LYS cc_start: 0.8177 (tttt) cc_final: 0.6460 (mptt) REVERT: B 86 LYS cc_start: 0.8645 (tttt) cc_final: 0.8400 (tttm) REVERT: B 268 ASP cc_start: 0.8504 (m-30) cc_final: 0.8272 (m-30) REVERT: B 300 LYS cc_start: 0.4832 (mtmt) cc_final: 0.3979 (tptp) REVERT: B 359 LYS cc_start: 0.3398 (tttt) cc_final: 0.3005 (tttt) REVERT: C 233 THR cc_start: 0.8215 (OUTLIER) cc_final: 0.7729 (p) REVERT: C 258 LYS cc_start: 0.7695 (ptpt) cc_final: 0.7134 (pttp) REVERT: C 291 LYS cc_start: 0.8741 (tttt) cc_final: 0.8499 (tttp) REVERT: C 292 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8773 (mp) REVERT: C 333 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7876 (mt-10) REVERT: D 48 GLU cc_start: 0.8248 (tp30) cc_final: 0.7881 (mm-30) REVERT: D 209 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7749 (tt0) REVERT: D 283 TRP cc_start: 0.7679 (OUTLIER) cc_final: 0.6054 (m-90) REVERT: D 305 MET cc_start: 0.7886 (tpt) cc_final: 0.7437 (mmm) REVERT: D 308 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.7011 (pt) REVERT: E 11 LYS cc_start: 0.7812 (ttmt) cc_final: 0.7506 (ttpp) REVERT: E 19 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7737 (mm-30) REVERT: E 107 VAL cc_start: 0.9053 (t) cc_final: 0.8587 (m) REVERT: E 158 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7991 (pp) REVERT: E 159 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8051 (tt0) REVERT: E 205 MET cc_start: 0.8545 (tpp) cc_final: 0.8282 (mmm) REVERT: E 219 GLU cc_start: 0.5809 (OUTLIER) cc_final: 0.4025 (tt0) REVERT: E 264 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8003 (mt) REVERT: E 294 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8211 (pp) REVERT: E 326 GLU cc_start: 0.8237 (tt0) cc_final: 0.7113 (pm20) REVERT: E 333 GLU cc_start: 0.8293 (mt-10) cc_final: 0.8045 (mt-10) REVERT: E 361 LYS cc_start: 0.3563 (ttmt) cc_final: 0.3051 (mptt) REVERT: H3 28 TYR cc_start: 0.8478 (m-80) cc_final: 0.8212 (m-80) REVERT: L4 4 MET cc_start: 0.7299 (mmt) cc_final: 0.7070 (mmt) REVERT: L6 1 ASP cc_start: 0.8028 (OUTLIER) cc_final: 0.7591 (m-30) outliers start: 171 outliers final: 121 residues processed: 473 average time/residue: 0.2778 time to fit residues: 214.8367 Evaluate side-chains 480 residues out of total 2446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 343 time to evaluate : 2.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L2 residue 5 THR 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 49 SER Chi-restraints excluded: chain A residue 55 GLN 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 157 ASP 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 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 283 TRP 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 341 THR 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 99 ASP Chi-restraints excluded: chain B residue 114 VAL 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 168 LYS Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 200 LEU 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 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 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 137 ILE Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 330 THR 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 133 ASN Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 167 THR 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 192 LEU Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 283 TRP Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 326 GLU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 25 THR 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 84 MET 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 159 GLN Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 219 GLU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 268 ASP 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 5 THR Chi-restraints excluded: chain L3 residue 74 THR Chi-restraints excluded: chain L3 residue 97 THR Chi-restraints excluded: chain H3 residue 64 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 H4 residue 19 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 L5 residue 69 THR Chi-restraints excluded: chain L5 residue 72 THR Chi-restraints excluded: chain L5 residue 88 CYS Chi-restraints excluded: chain H5 residue 94 THR Chi-restraints excluded: chain L6 residue 1 ASP Chi-restraints excluded: chain L6 residue 72 THR Chi-restraints excluded: chain L6 residue 85 VAL Chi-restraints excluded: chain H6 residue 48 SER Chi-restraints excluded: chain H6 residue 49 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 86 optimal weight: 8.9990 chunk 232 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 258 optimal weight: 20.0000 chunk 214 optimal weight: 40.0000 chunk 119 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L3 38 GLN H3 35 GLN L4 38 GLN L4 92 ASN H4 35 GLN L5 22 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6087 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22489 Z= 0.261 Angle : 0.624 12.943 30633 Z= 0.316 Chirality : 0.045 0.245 3366 Planarity : 0.005 0.050 3948 Dihedral : 6.625 87.129 3063 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.09 % Favored : 90.77 % Rotamer: Outliers : 6.62 % Allowed : 24.28 % Favored : 69.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.15), residues: 2751 helix: -1.44 (0.48), residues: 122 sheet: -0.18 (0.19), residues: 760 loop : -2.07 (0.13), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPH2 104 HIS 0.005 0.001 HISH2 31 PHE 0.022 0.002 PHE C 239 TYR 0.012 0.001 TYR B 223 ARG 0.003 0.000 ARGH3 77 *********************** 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 515 residues out of total 2446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 353 time to evaluate : 2.397 Fit side-chains revert: symmetry clash REVERT: A 11 LYS cc_start: 0.4913 (mmtt) cc_final: 0.3655 (ttpt) REVERT: A 34 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8236 (mt-10) REVERT: A 96 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7694 (pp) REVERT: A 130 ASP cc_start: 0.6889 (t0) cc_final: 0.6508 (t0) REVERT: A 159 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.7261 (tt0) REVERT: A 172 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7512 (mt-10) REVERT: A 209 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7164 (mp0) REVERT: A 214 ASP cc_start: 0.7680 (OUTLIER) cc_final: 0.7346 (t0) REVERT: A 226 ASN cc_start: 0.8665 (p0) cc_final: 0.8303 (p0) REVERT: A 283 TRP cc_start: 0.7565 (OUTLIER) cc_final: 0.7277 (m100) REVERT: B 11 LYS cc_start: 0.8203 (tttt) cc_final: 0.6535 (mptt) REVERT: B 86 LYS cc_start: 0.8640 (tttt) cc_final: 0.8391 (tttm) REVERT: B 184 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.8198 (t0) REVERT: B 300 LYS cc_start: 0.4693 (mtmt) cc_final: 0.3979 (tptp) REVERT: C 154 GLU cc_start: 0.8684 (pt0) cc_final: 0.8267 (pt0) REVERT: C 217 LYS cc_start: 0.3243 (OUTLIER) cc_final: 0.2866 (ptpt) REVERT: C 233 THR cc_start: 0.8274 (OUTLIER) cc_final: 0.7820 (p) REVERT: C 248 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8725 (mp) REVERT: C 258 LYS cc_start: 0.7715 (ptpt) cc_final: 0.7013 (pttp) REVERT: C 292 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8783 (mp) REVERT: C 333 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7877 (mt-10) REVERT: D 48 GLU cc_start: 0.8124 (tp30) cc_final: 0.7703 (mp0) REVERT: D 205 MET cc_start: 0.8140 (mtp) cc_final: 0.7493 (mmm) REVERT: D 209 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7838 (tt0) REVERT: D 219 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.4059 (tp30) REVERT: D 283 TRP cc_start: 0.7651 (OUTLIER) cc_final: 0.5957 (m-90) REVERT: E 19 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7769 (mm-30) REVERT: E 107 VAL cc_start: 0.9088 (t) cc_final: 0.8684 (m) REVERT: E 157 ASP cc_start: 0.8394 (m-30) cc_final: 0.7694 (m-30) REVERT: E 158 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7921 (pp) REVERT: E 159 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.8035 (tt0) REVERT: E 205 MET cc_start: 0.8463 (tpp) cc_final: 0.8237 (mmm) REVERT: E 219 GLU cc_start: 0.5806 (OUTLIER) cc_final: 0.3731 (tp30) REVERT: E 264 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.7968 (mt) REVERT: E 294 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8169 (pp) REVERT: E 326 GLU cc_start: 0.8239 (tt0) cc_final: 0.7121 (pm20) REVERT: E 333 GLU cc_start: 0.8247 (mt-10) cc_final: 0.8008 (mt-10) REVERT: E 361 LYS cc_start: 0.3484 (ttmt) cc_final: 0.3048 (mptt) REVERT: H3 28 TYR cc_start: 0.8472 (m-80) cc_final: 0.8162 (m-80) REVERT: L4 4 MET cc_start: 0.7352 (mmt) cc_final: 0.7123 (mmt) REVERT: L6 1 ASP cc_start: 0.7998 (OUTLIER) cc_final: 0.7553 (m-30) REVERT: L6 11 MET cc_start: 0.4858 (pmm) cc_final: 0.3380 (ttp) REVERT: H6 108 TRP cc_start: 0.8495 (m100) cc_final: 0.8288 (m100) outliers start: 162 outliers final: 121 residues processed: 469 average time/residue: 0.2865 time to fit residues: 219.1651 Evaluate side-chains 486 residues out of total 2446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 344 time to evaluate : 2.477 ------------------------------------------------------------------------------- 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 34 GLU Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 55 GLN 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 96 LEU Chi-restraints excluded: chain A residue 114 VAL 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 209 GLU 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 253 VAL Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 283 TRP 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 341 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 60 SER 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 145 GLN Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 168 LYS Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 200 LEU 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 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 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 184 ASP Chi-restraints excluded: chain C residue 217 LYS Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 266 CYS Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 333 GLU 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 91 MET 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 133 ASN Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 167 THR 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 209 GLU Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 219 GLU Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 274 VAL 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 D residue 326 GLU Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 25 THR 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 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 219 GLU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 268 ASP 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 5 THR Chi-restraints excluded: chain H3 residue 31 HIS Chi-restraints excluded: chain H3 residue 49 SER Chi-restraints excluded: chain H3 residue 64 THR Chi-restraints excluded: chain L4 residue 3 VAL Chi-restraints excluded: chain L4 residue 5 THR 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 58 VAL Chi-restraints excluded: chain L5 residue 88 CYS Chi-restraints excluded: chain H5 residue 94 THR Chi-restraints excluded: chain L6 residue 1 ASP Chi-restraints excluded: chain L6 residue 85 VAL Chi-restraints excluded: chain L6 residue 89 LEU Chi-restraints excluded: chain H6 residue 48 SER Chi-restraints excluded: chain H6 residue 49 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 249 optimal weight: 20.0000 chunk 29 optimal weight: 3.9990 chunk 147 optimal weight: 9.9990 chunk 188 optimal weight: 7.9990 chunk 146 optimal weight: 0.0570 chunk 217 optimal weight: 20.0000 chunk 144 optimal weight: 4.9990 chunk 257 optimal weight: 30.0000 chunk 161 optimal weight: 9.9990 chunk 156 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 overall best weight: 2.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L5 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6072 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22489 Z= 0.219 Angle : 0.594 12.641 30633 Z= 0.301 Chirality : 0.044 0.219 3366 Planarity : 0.004 0.050 3948 Dihedral : 6.340 87.563 3062 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.72 % Favored : 91.13 % Rotamer: Outliers : 5.97 % Allowed : 25.10 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.15), residues: 2751 helix: -1.15 (0.51), residues: 119 sheet: -0.07 (0.19), residues: 750 loop : -1.95 (0.13), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPH2 104 HIS 0.005 0.001 HISH2 31 PHE 0.020 0.001 PHE D 149 TYR 0.012 0.001 TYR B 223 ARG 0.003 0.000 ARGH3 77 *********************** 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 492 residues out of total 2446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 346 time to evaluate : 2.368 Fit side-chains revert: symmetry clash REVERT: A 11 LYS cc_start: 0.4937 (mmtt) cc_final: 0.3701 (ttpt) REVERT: A 34 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8209 (mt-10) REVERT: A 96 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7705 (pp) REVERT: A 130 ASP cc_start: 0.7040 (t0) cc_final: 0.6579 (t0) REVERT: A 159 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.7233 (tt0) REVERT: A 172 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7480 (mt-10) REVERT: A 214 ASP cc_start: 0.7670 (OUTLIER) cc_final: 0.7350 (t0) REVERT: A 226 ASN cc_start: 0.8420 (p0) cc_final: 0.8030 (p0) REVERT: A 258 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7483 (ptpt) REVERT: A 283 TRP cc_start: 0.7590 (OUTLIER) cc_final: 0.6682 (m-90) REVERT: B 11 LYS cc_start: 0.8205 (tttt) cc_final: 0.6529 (mptt) REVERT: B 86 LYS cc_start: 0.8649 (tttt) cc_final: 0.8387 (tttm) REVERT: B 184 ASP cc_start: 0.8511 (OUTLIER) cc_final: 0.8188 (t0) REVERT: B 300 LYS cc_start: 0.4966 (mtmt) cc_final: 0.4269 (tptm) REVERT: C 217 LYS cc_start: 0.3143 (OUTLIER) cc_final: 0.2729 (ptpt) REVERT: C 219 GLU cc_start: 0.6707 (OUTLIER) cc_final: 0.4106 (tp30) REVERT: C 233 THR cc_start: 0.8300 (OUTLIER) cc_final: 0.7847 (p) REVERT: C 248 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8670 (mp) REVERT: C 258 LYS cc_start: 0.7699 (ptpt) cc_final: 0.7084 (pttp) REVERT: C 292 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8771 (mp) REVERT: D 48 GLU cc_start: 0.8138 (tp30) cc_final: 0.7649 (mp0) REVERT: D 219 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.4298 (mm-30) REVERT: D 258 LYS cc_start: 0.7736 (mttt) cc_final: 0.6735 (mptt) REVERT: D 283 TRP cc_start: 0.7646 (OUTLIER) cc_final: 0.5870 (m-90) REVERT: E 11 LYS cc_start: 0.7770 (ttmt) cc_final: 0.7497 (ttpp) REVERT: E 12 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.7997 (tp) REVERT: E 19 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7811 (mm-30) REVERT: E 107 VAL cc_start: 0.9085 (t) cc_final: 0.8755 (m) REVERT: E 157 ASP cc_start: 0.8385 (m-30) cc_final: 0.7723 (m-30) REVERT: E 158 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7869 (pp) REVERT: E 159 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.8056 (tt0) REVERT: E 219 GLU cc_start: 0.5947 (OUTLIER) cc_final: 0.4005 (tp30) REVERT: E 264 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.7964 (mt) REVERT: E 294 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8182 (pp) REVERT: E 326 GLU cc_start: 0.8171 (tt0) cc_final: 0.7099 (pm20) REVERT: E 333 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7994 (mt-10) REVERT: E 361 LYS cc_start: 0.3478 (ttmt) cc_final: 0.3098 (mptt) REVERT: L3 4 MET cc_start: 0.7270 (mmt) cc_final: 0.6873 (mmt) REVERT: H3 28 TYR cc_start: 0.8467 (m-80) cc_final: 0.8171 (m-80) REVERT: L4 4 MET cc_start: 0.7358 (mmt) cc_final: 0.7130 (mmt) REVERT: L6 1 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.7501 (m-30) REVERT: L6 11 MET cc_start: 0.4850 (pmm) cc_final: 0.3590 (ttp) outliers start: 146 outliers final: 111 residues processed: 454 average time/residue: 0.3036 time to fit residues: 223.1984 Evaluate side-chains 473 residues out of total 2446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 341 time to evaluate : 2.437 ------------------------------------------------------------------------------- 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 34 GLU Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 55 GLN 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 96 LEU Chi-restraints excluded: chain A residue 114 VAL 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 214 ASP Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain A residue 283 TRP 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 341 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 60 SER 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 145 GLN Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 168 LYS Chi-restraints excluded: chain B residue 184 ASP 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 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 60 SER Chi-restraints excluded: chain C residue 68 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 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 217 LYS Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 266 CYS Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 51 THR 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 144 SER Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 219 GLU Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 274 VAL 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 D residue 317 LEU Chi-restraints excluded: chain D residue 326 GLU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 25 THR 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 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 219 GLU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 268 ASP 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 5 THR Chi-restraints excluded: chain H3 residue 49 SER 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 58 VAL Chi-restraints excluded: chain L5 residue 69 THR Chi-restraints excluded: chain H5 residue 26 SER Chi-restraints excluded: chain L6 residue 1 ASP Chi-restraints excluded: chain L6 residue 89 LEU Chi-restraints excluded: chain H6 residue 49 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 159 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 153 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 49 optimal weight: 0.0470 chunk 163 optimal weight: 0.9980 chunk 175 optimal weight: 2.9990 chunk 127 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 202 optimal weight: 30.0000 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6036 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22489 Z= 0.159 Angle : 0.556 12.061 30633 Z= 0.282 Chirality : 0.043 0.194 3366 Planarity : 0.004 0.053 3948 Dihedral : 6.013 87.780 3061 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.82 % Favored : 92.11 % Rotamer: Outliers : 4.91 % Allowed : 26.12 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.15), residues: 2751 helix: -1.16 (0.49), residues: 125 sheet: 0.07 (0.19), residues: 746 loop : -1.81 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRPH2 104 HIS 0.004 0.001 HISH3 31 PHE 0.016 0.001 PHE D 149 TYR 0.012 0.001 TYR D 289 ARG 0.003 0.000 ARG A 61 *********************** 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 479 residues out of total 2446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 359 time to evaluate : 2.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 LYS cc_start: 0.4805 (mmtt) cc_final: 0.3652 (ttpt) REVERT: A 34 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8211 (mt-10) REVERT: A 96 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7644 (pp) REVERT: A 130 ASP cc_start: 0.6934 (t0) cc_final: 0.6467 (t0) REVERT: A 159 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.7278 (tt0) REVERT: A 161 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7225 (tt) REVERT: A 172 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7388 (mt-10) REVERT: A 214 ASP cc_start: 0.7604 (OUTLIER) cc_final: 0.7239 (t0) REVERT: A 226 ASN cc_start: 0.8496 (p0) cc_final: 0.8092 (p0) REVERT: A 240 THR cc_start: 0.9164 (t) cc_final: 0.8863 (m) REVERT: A 258 LYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7399 (ptpt) REVERT: A 283 TRP cc_start: 0.7581 (OUTLIER) cc_final: 0.6722 (m-90) REVERT: B 11 LYS cc_start: 0.8181 (tttt) cc_final: 0.6512 (mptt) REVERT: B 20 VAL cc_start: 0.8390 (t) cc_final: 0.8084 (m) REVERT: B 86 LYS cc_start: 0.8650 (tttt) cc_final: 0.8379 (tttm) REVERT: B 184 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.8198 (t0) REVERT: B 300 LYS cc_start: 0.5002 (mtmt) cc_final: 0.4314 (tptm) REVERT: B 334 GLU cc_start: 0.4657 (OUTLIER) cc_final: 0.3765 (pt0) REVERT: C 55 GLN cc_start: 0.4179 (mm-40) cc_final: 0.3970 (mm-40) REVERT: C 107 VAL cc_start: 0.9240 (t) cc_final: 0.8803 (m) REVERT: C 217 LYS cc_start: 0.3171 (OUTLIER) cc_final: 0.2300 (ptpp) REVERT: C 248 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8683 (mp) REVERT: C 258 LYS cc_start: 0.7751 (ptpt) cc_final: 0.7138 (pttp) REVERT: C 292 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8722 (mp) REVERT: D 205 MET cc_start: 0.7934 (mtp) cc_final: 0.7470 (mmm) REVERT: D 209 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7822 (tt0) REVERT: D 219 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.4178 (mm-30) REVERT: D 258 LYS cc_start: 0.7600 (mttt) cc_final: 0.6652 (mptt) REVERT: D 283 TRP cc_start: 0.7620 (OUTLIER) cc_final: 0.5868 (m-90) REVERT: E 11 LYS cc_start: 0.7783 (ttmt) cc_final: 0.7500 (ttpp) REVERT: E 12 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.7955 (tp) REVERT: E 19 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7795 (mm-30) REVERT: E 107 VAL cc_start: 0.9050 (t) cc_final: 0.8794 (m) REVERT: E 157 ASP cc_start: 0.8368 (m-30) cc_final: 0.7626 (m-30) REVERT: E 158 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7850 (pp) REVERT: E 159 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.8052 (tt0) REVERT: E 219 GLU cc_start: 0.5901 (OUTLIER) cc_final: 0.3696 (mm-30) REVERT: E 326 GLU cc_start: 0.8076 (tt0) cc_final: 0.7012 (pm20) REVERT: E 333 GLU cc_start: 0.8295 (mt-10) cc_final: 0.8064 (mt-10) REVERT: E 361 LYS cc_start: 0.3625 (ttmt) cc_final: 0.3297 (mptt) REVERT: L3 4 MET cc_start: 0.7224 (mmt) cc_final: 0.6961 (mmt) REVERT: H3 28 TYR cc_start: 0.8453 (m-80) cc_final: 0.8160 (m-80) REVERT: L6 1 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.7483 (m-30) REVERT: H6 108 TRP cc_start: 0.8403 (m100) cc_final: 0.8171 (m100) outliers start: 120 outliers final: 83 residues processed: 448 average time/residue: 0.2948 time to fit residues: 211.9184 Evaluate side-chains 446 residues out of total 2446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 343 time to evaluate : 2.477 ------------------------------------------------------------------------------- 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 34 GLU 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 214 ASP Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 283 TRP Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 145 GLN Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 203 ASP 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 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 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 217 LYS Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 266 CYS Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 354 VAL 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 144 SER Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 219 GLU Chi-restraints excluded: chain D residue 233 THR 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 D residue 317 LEU Chi-restraints excluded: chain D residue 326 GLU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 25 THR 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 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 219 GLU Chi-restraints excluded: chain E residue 268 ASP Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain L3 residue 3 VAL Chi-restraints excluded: chain L3 residue 5 THR Chi-restraints excluded: chain H3 residue 24 THR Chi-restraints excluded: chain L4 residue 3 VAL Chi-restraints excluded: chain L4 residue 21 MET 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 26 SER Chi-restraints excluded: chain L6 residue 1 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 234 optimal weight: 20.0000 chunk 246 optimal weight: 9.9990 chunk 224 optimal weight: 7.9990 chunk 239 optimal weight: 7.9990 chunk 144 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 188 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 chunk 216 optimal weight: 9.9990 chunk 226 optimal weight: 9.9990 chunk 238 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 GLN ** E 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L5 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6151 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 22489 Z= 0.541 Angle : 0.772 12.603 30633 Z= 0.391 Chirality : 0.052 0.328 3366 Planarity : 0.005 0.057 3948 Dihedral : 6.923 82.915 3057 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.51 % Favored : 89.31 % Rotamer: Outliers : 5.93 % Allowed : 25.35 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.15), residues: 2751 helix: -1.81 (0.45), residues: 129 sheet: -0.07 (0.19), residues: 753 loop : -2.03 (0.13), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 283 HIS 0.006 0.002 HIS D 147 PHE 0.036 0.003 PHE C 239 TYR 0.020 0.002 TYR D 223 ARG 0.005 0.001 ARG C 276 *********************** 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 484 residues out of total 2446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 339 time to evaluate : 2.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 LYS cc_start: 0.4854 (mmtt) cc_final: 0.3466 (ttpt) REVERT: A 34 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8310 (mt-10) REVERT: A 96 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7696 (pp) REVERT: A 130 ASP cc_start: 0.6917 (t0) cc_final: 0.6585 (t0) REVERT: A 159 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7122 (tm-30) REVERT: A 172 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7432 (mt-10) REVERT: A 209 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7378 (mp0) REVERT: A 214 ASP cc_start: 0.7786 (OUTLIER) cc_final: 0.7395 (t0) REVERT: A 226 ASN cc_start: 0.8686 (p0) cc_final: 0.8300 (p0) REVERT: A 283 TRP cc_start: 0.7694 (OUTLIER) cc_final: 0.7409 (m100) REVERT: B 11 LYS cc_start: 0.8201 (tttt) cc_final: 0.6494 (mptt) REVERT: B 86 LYS cc_start: 0.8648 (tttt) cc_final: 0.8401 (tttm) REVERT: B 184 ASP cc_start: 0.8564 (OUTLIER) cc_final: 0.8251 (t0) REVERT: B 300 LYS cc_start: 0.4791 (mtmt) cc_final: 0.4005 (tptm) REVERT: C 217 LYS cc_start: 0.3178 (OUTLIER) cc_final: 0.2355 (ptpp) REVERT: C 219 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.4818 (tp30) REVERT: C 248 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8728 (mp) REVERT: C 258 LYS cc_start: 0.7680 (ptpt) cc_final: 0.7065 (pttp) REVERT: C 292 ILE cc_start: 0.9161 (OUTLIER) cc_final: 0.8816 (mp) REVERT: C 333 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7945 (mt-10) REVERT: D 205 MET cc_start: 0.8293 (mtp) cc_final: 0.7953 (mmm) REVERT: D 209 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7775 (tt0) REVERT: D 283 TRP cc_start: 0.7730 (OUTLIER) cc_final: 0.6233 (m-90) REVERT: E 11 LYS cc_start: 0.7776 (ttmt) cc_final: 0.7499 (ttpp) REVERT: E 19 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7737 (mm-30) REVERT: E 107 VAL cc_start: 0.9094 (t) cc_final: 0.8599 (m) REVERT: E 157 ASP cc_start: 0.8573 (m-30) cc_final: 0.7926 (m-30) REVERT: E 158 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8014 (pp) REVERT: E 159 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.8056 (tt0) REVERT: E 185 MET cc_start: 0.7920 (mtt) cc_final: 0.7703 (mtt) REVERT: E 219 GLU cc_start: 0.5778 (OUTLIER) cc_final: 0.4139 (tp30) REVERT: E 264 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8043 (mt) REVERT: E 326 GLU cc_start: 0.8247 (tt0) cc_final: 0.7160 (pm20) REVERT: E 333 GLU cc_start: 0.8333 (mt-10) cc_final: 0.8073 (mt-10) REVERT: E 361 LYS cc_start: 0.3603 (ttmt) cc_final: 0.3149 (mptt) REVERT: L3 11 MET cc_start: 0.5459 (ptp) cc_final: 0.5152 (ptp) REVERT: L3 21 MET cc_start: 0.6739 (mtp) cc_final: 0.6497 (mtp) REVERT: H3 28 TYR cc_start: 0.8489 (m-80) cc_final: 0.8134 (m-80) REVERT: L6 1 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7688 (m-30) outliers start: 145 outliers final: 109 residues processed: 447 average time/residue: 0.3009 time to fit residues: 220.0926 Evaluate side-chains 460 residues out of total 2446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 332 time to evaluate : 2.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L2 residue 5 THR 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 34 GLU Chi-restraints excluded: chain A residue 49 SER 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 157 ASP 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 209 GLU Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 283 TRP Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 145 GLN Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 240 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 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 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 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 219 GLU 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 292 ILE Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 333 GLU Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 71 GLU 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 144 SER Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 167 THR 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 209 GLU Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 262 LEU 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 D residue 326 GLU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 41 MET 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 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 219 GLU Chi-restraints excluded: chain E residue 264 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 L3 residue 3 VAL Chi-restraints excluded: chain L3 residue 5 THR Chi-restraints excluded: chain H3 residue 24 THR Chi-restraints excluded: chain H3 residue 49 SER Chi-restraints excluded: chain L4 residue 3 VAL Chi-restraints excluded: chain L4 residue 5 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 L5 residue 24 ARG Chi-restraints excluded: chain L5 residue 58 VAL Chi-restraints excluded: chain L5 residue 69 THR Chi-restraints excluded: chain H5 residue 24 THR Chi-restraints excluded: chain H5 residue 26 SER Chi-restraints excluded: chain H5 residue 94 THR Chi-restraints excluded: chain L6 residue 1 ASP Chi-restraints excluded: chain L6 residue 72 THR Chi-restraints excluded: chain L6 residue 89 LEU Chi-restraints excluded: chain H6 residue 49 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 157 optimal weight: 4.9990 chunk 253 optimal weight: 9.9990 chunk 154 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 176 optimal weight: 4.9990 chunk 266 optimal weight: 9.9990 chunk 244 optimal weight: 7.9990 chunk 211 optimal weight: 0.0670 chunk 21 optimal weight: 2.9990 chunk 163 optimal weight: 0.0870 chunk 129 optimal weight: 0.8980 overall best weight: 1.0100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 GLN ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 GLN L6 32 ASN L6 92 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6053 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22489 Z= 0.166 Angle : 0.577 14.172 30633 Z= 0.293 Chirality : 0.044 0.293 3366 Planarity : 0.004 0.058 3948 Dihedral : 5.868 56.583 3054 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.18 % Favored : 91.75 % Rotamer: Outliers : 3.80 % Allowed : 27.68 % Favored : 68.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.15), residues: 2751 helix: -1.39 (0.48), residues: 125 sheet: 0.03 (0.19), residues: 755 loop : -1.80 (0.14), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPH2 104 HIS 0.004 0.001 HISH2 31 PHE 0.016 0.001 PHE D 149 TYR 0.013 0.001 TYR B 223 ARG 0.003 0.000 ARGH3 77 ********************** 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 440 residues out of total 2446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 347 time to evaluate : 2.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 LYS cc_start: 0.4897 (mmtt) cc_final: 0.3641 (ttpt) REVERT: A 34 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8224 (mt-10) REVERT: A 96 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7621 (pp) REVERT: A 130 ASP cc_start: 0.6957 (t0) cc_final: 0.6545 (t0) REVERT: A 159 GLN cc_start: 0.7612 (OUTLIER) cc_final: 0.7343 (tt0) REVERT: A 161 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7278 (tt) REVERT: A 172 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7406 (mt-10) REVERT: A 214 ASP cc_start: 0.7581 (OUTLIER) cc_final: 0.7241 (t0) REVERT: A 226 ASN cc_start: 0.8482 (p0) cc_final: 0.8094 (p0) REVERT: A 283 TRP cc_start: 0.7523 (OUTLIER) cc_final: 0.7242 (m100) REVERT: A 336 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.8176 (ptp-170) REVERT: B 11 LYS cc_start: 0.8210 (tttt) cc_final: 0.6532 (mptt) REVERT: B 20 VAL cc_start: 0.8387 (t) cc_final: 0.8074 (m) REVERT: B 55 GLN cc_start: 0.5730 (OUTLIER) cc_final: 0.5357 (mm110) REVERT: B 86 LYS cc_start: 0.8728 (tttt) cc_final: 0.8468 (tttm) REVERT: B 184 ASP cc_start: 0.8496 (OUTLIER) cc_final: 0.8222 (t0) REVERT: B 300 LYS cc_start: 0.5010 (mtmt) cc_final: 0.4310 (tptm) REVERT: C 69 ASP cc_start: 0.7796 (OUTLIER) cc_final: 0.7277 (m-30) REVERT: C 107 VAL cc_start: 0.9240 (t) cc_final: 0.8878 (m) REVERT: C 201 ASP cc_start: 0.8225 (m-30) cc_final: 0.7984 (p0) REVERT: C 219 GLU cc_start: 0.6539 (OUTLIER) cc_final: 0.4145 (tp30) REVERT: C 237 LEU cc_start: 0.8188 (mt) cc_final: 0.7973 (mt) REVERT: C 258 LYS cc_start: 0.7729 (ptpt) cc_final: 0.7092 (pttp) REVERT: D 209 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7860 (tt0) REVERT: D 258 LYS cc_start: 0.7601 (mttt) cc_final: 0.6636 (mptt) REVERT: D 283 TRP cc_start: 0.7654 (OUTLIER) cc_final: 0.5878 (m-90) REVERT: E 11 LYS cc_start: 0.7779 (ttmt) cc_final: 0.7491 (ttpp) REVERT: E 19 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7846 (mm-30) REVERT: E 107 VAL cc_start: 0.9067 (t) cc_final: 0.8793 (m) REVERT: E 157 ASP cc_start: 0.8377 (m-30) cc_final: 0.7683 (m-30) REVERT: E 158 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7841 (pp) REVERT: E 159 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.8050 (tt0) REVERT: E 185 MET cc_start: 0.7631 (mtt) cc_final: 0.7194 (mtt) REVERT: E 219 GLU cc_start: 0.5975 (OUTLIER) cc_final: 0.3901 (mm-30) REVERT: E 326 GLU cc_start: 0.8185 (tt0) cc_final: 0.7098 (pm20) REVERT: E 333 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8061 (mt-10) REVERT: E 361 LYS cc_start: 0.3706 (ttmt) cc_final: 0.3350 (mptt) REVERT: H3 28 TYR cc_start: 0.8478 (m-80) cc_final: 0.8151 (m-80) REVERT: L6 1 ASP cc_start: 0.7994 (OUTLIER) cc_final: 0.7666 (m-30) REVERT: H6 108 TRP cc_start: 0.8385 (m100) cc_final: 0.8116 (m100) outliers start: 93 outliers final: 71 residues processed: 416 average time/residue: 0.2966 time to fit residues: 200.1275 Evaluate side-chains 429 residues out of total 2446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 341 time to evaluate : 2.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 9 VAL Chi-restraints excluded: chain A residue 34 GLU 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 214 ASP Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 283 TRP 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 14 ILE Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 145 GLN Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 203 ASP 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 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 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 219 GLU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 71 GLU 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 167 THR Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 262 LEU 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 D residue 326 GLU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 145 GLN 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 219 GLU Chi-restraints excluded: chain E residue 268 ASP Chi-restraints excluded: chain E residue 350 MET 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 L5 residue 24 ARG Chi-restraints excluded: chain L5 residue 69 THR Chi-restraints excluded: chain H5 residue 26 SER Chi-restraints excluded: chain L6 residue 1 ASP Chi-restraints excluded: chain H6 residue 49 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 168 optimal weight: 6.9990 chunk 225 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 195 optimal weight: 30.0000 chunk 31 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 212 optimal weight: 9.9990 chunk 88 optimal weight: 0.0040 chunk 217 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 overall best weight: 2.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** 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 = 0.3753 r_free = 0.3753 target = 0.170634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.135842 restraints weight = 23764.837| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.39 r_work: 0.3080 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22489 Z= 0.262 Angle : 0.625 13.319 30633 Z= 0.315 Chirality : 0.046 0.297 3366 Planarity : 0.005 0.059 3948 Dihedral : 6.037 61.535 3054 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.72 % Favored : 91.13 % Rotamer: Outliers : 4.17 % Allowed : 27.15 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.15), residues: 2751 helix: -1.33 (0.50), residues: 117 sheet: -0.03 (0.19), residues: 779 loop : -1.75 (0.14), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 283 HIS 0.005 0.001 HIS E 281 PHE 0.021 0.002 PHE D 149 TYR 0.013 0.001 TYR E 146 ARG 0.003 0.000 ARGL5 24 =============================================================================== Job complete usr+sys time: 5098.67 seconds wall clock time: 92 minutes 39.59 seconds (5559.59 seconds total)