Starting phenix.real_space_refine on Sun Aug 24 14:48:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vgh_43200/08_2025/8vgh_43200.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vgh_43200/08_2025/8vgh_43200.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vgh_43200/08_2025/8vgh_43200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vgh_43200/08_2025/8vgh_43200.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vgh_43200/08_2025/8vgh_43200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vgh_43200/08_2025/8vgh_43200.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.011 sd= 0.279 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 84 5.16 5 C 12988 2.51 5 N 3488 2.21 5 O 3912 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20472 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1919 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 220} Chain: "B" Number of atoms: 1919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1919 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 220} Chain: "C" Number of atoms: 1919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1919 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 220} Chain: "D" Number of atoms: 1919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1919 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 220} Chain: "G" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1626 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 202} Chain: "H" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1573 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 196} Chain breaks: 1 Chain: "F" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1573 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 196} Chain breaks: 1 Chain: "J" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1573 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 196} Chain breaks: 1 Chain: "K" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1573 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 196} Chain breaks: 1 Chain: "E" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1626 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 202} Chain: "I" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1626 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 202} Chain: "L" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1626 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 202} Time building chain proxies: 5.51, per 1000 atoms: 0.27 Number of scatterers: 20472 At special positions: 0 Unit cell: (97, 111, 181, 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 84 16.00 O 3912 8.00 N 3488 7.00 C 12988 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 58 " distance=2.02 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 168 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 191 " - pdb=" SG CYS A 221 " distance=2.03 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 58 " distance=2.02 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 168 " - pdb=" SG CYS B 182 " distance=2.02 Simple disulfide: pdb=" SG CYS B 191 " - pdb=" SG CYS B 220 " distance=2.03 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 58 " distance=2.02 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 201 " distance=2.03 Simple disulfide: pdb=" SG CYS C 168 " - pdb=" SG CYS C 182 " distance=2.02 Simple disulfide: pdb=" SG CYS C 191 " - pdb=" SG CYS C 220 " distance=2.03 Simple disulfide: pdb=" SG CYS D 42 " - pdb=" SG CYS D 58 " distance=2.02 Simple disulfide: pdb=" SG CYS D 136 " - pdb=" SG CYS D 201 " distance=2.03 Simple disulfide: pdb=" SG CYS D 168 " - pdb=" SG CYS D 182 " distance=2.02 Simple disulfide: pdb=" SG CYS D 191 " - pdb=" SG CYS D 220 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 134 " - pdb=" SG CYS G 194 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 144 " - pdb=" SG CYS H 200 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.04 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 200 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS J 144 " - pdb=" SG CYS J 200 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.04 Simple disulfide: pdb=" SG CYS K 144 " - pdb=" SG CYS K 200 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 134 " - pdb=" SG CYS I 194 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.90 Conformation dependent library (CDL) restraints added in 911.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4904 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 56 sheets defined 9.9% alpha, 41.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 60E through 62 No H-bonds generated for 'chain 'A' and resid 60E through 62' Processing helix chain 'A' and resid 164 through 173A Processing helix chain 'A' and resid 235 through 240 Processing helix chain 'B' and resid 55 through 59 Processing helix chain 'B' and resid 60E through 62 No H-bonds generated for 'chain 'B' and resid 60E through 62' Processing helix chain 'B' and resid 164 through 173A Processing helix chain 'B' and resid 234 through 239 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'C' and resid 60E through 62 No H-bonds generated for 'chain 'C' and resid 60E through 62' Processing helix chain 'C' and resid 164 through 173A Processing helix chain 'C' and resid 234 through 239 Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'D' and resid 60E through 62 No H-bonds generated for 'chain 'D' and resid 60E through 62' Processing helix chain 'D' and resid 164 through 173A Processing helix chain 'D' and resid 234 through 239 Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.927A pdb=" N PHE G 83 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 128 Processing helix chain 'G' and resid 183 through 187 Processing helix chain 'H' and resid 62 through 65 removed outlier: 4.079A pdb=" N SER H 65 " --> pdb=" O TRP H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 189 through 195 removed outlier: 3.546A pdb=" N GLY H 194 " --> pdb=" O SER H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 205 through 208 Processing helix chain 'F' and resid 62 through 65 removed outlier: 4.077A pdb=" N SER F 65 " --> pdb=" O TRP F 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 62 through 65' Processing helix chain 'F' and resid 73 through 75 No H-bonds generated for 'chain 'F' and resid 73 through 75' Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'F' and resid 189 through 195 removed outlier: 3.545A pdb=" N GLY F 194 " --> pdb=" O SER F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 208 Processing helix chain 'J' and resid 62 through 65 removed outlier: 4.078A pdb=" N SER J 65 " --> pdb=" O TRP J 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 62 through 65' Processing helix chain 'J' and resid 73 through 75 No H-bonds generated for 'chain 'J' and resid 73 through 75' Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'J' and resid 189 through 195 removed outlier: 3.545A pdb=" N GLY J 194 " --> pdb=" O SER J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 205 through 208 Processing helix chain 'K' and resid 62 through 65 removed outlier: 4.080A pdb=" N SER K 65 " --> pdb=" O TRP K 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 62 through 65' Processing helix chain 'K' and resid 73 through 75 No H-bonds generated for 'chain 'K' and resid 73 through 75' Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'K' and resid 189 through 195 removed outlier: 3.543A pdb=" N GLY K 194 " --> pdb=" O SER K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 205 through 208 Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.926A pdb=" N PHE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 128 Processing helix chain 'E' and resid 183 through 187 Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.926A pdb=" N PHE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 128 Processing helix chain 'I' and resid 183 through 187 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.926A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 128 Processing helix chain 'L' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 35 removed outlier: 3.755A pdb=" N CYS A 42 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N VAL A 35 " --> pdb=" O HIS A 40 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N HIS A 40 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TRP A 51 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N VAL A 85 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LEU A 64 " --> pdb=" O VAL A 85 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 156 through 160 removed outlier: 4.123A pdb=" N CYS A 136 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR A 139 " --> pdb=" O PRO A 198 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU A 199 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL A 213 " --> pdb=" O THR A 230 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N THR A 230 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N CYS A 182 " --> pdb=" O MET A 163 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 30 through 35 removed outlier: 3.751A pdb=" N CYS B 42 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N VAL B 35 " --> pdb=" O HIS B 40 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N HIS B 40 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TRP B 51 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N VAL B 85 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LEU B 64 " --> pdb=" O VAL B 85 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 156 through 160 removed outlier: 4.121A pdb=" N CYS B 136 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR B 139 " --> pdb=" O PRO B 198 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU B 199 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL B 213 " --> pdb=" O THR B 229 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N THR B 229 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N CYS B 182 " --> pdb=" O MET B 163 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 30 through 35 removed outlier: 3.760A pdb=" N CYS C 42 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N VAL C 35 " --> pdb=" O HIS C 40 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N HIS C 40 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TRP C 51 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL C 85 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N LEU C 64 " --> pdb=" O VAL C 85 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 156 through 160 removed outlier: 4.126A pdb=" N CYS C 136 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR C 139 " --> pdb=" O PRO C 198 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU C 199 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL C 213 " --> pdb=" O THR C 229 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N THR C 229 " --> pdb=" O VAL C 213 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N CYS C 182 " --> pdb=" O MET C 163 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 30 through 35 removed outlier: 3.754A pdb=" N CYS D 42 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N VAL D 35 " --> pdb=" O HIS D 40 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N HIS D 40 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TRP D 51 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N VAL D 85 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N LEU D 64 " --> pdb=" O VAL D 85 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 156 through 160 removed outlier: 4.122A pdb=" N CYS D 136 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N THR D 139 " --> pdb=" O PRO D 198 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU D 199 " --> pdb=" O ALA D 210 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N VAL D 213 " --> pdb=" O THR D 229 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N THR D 229 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N CYS D 182 " --> pdb=" O MET D 163 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'G' and resid 10 through 14 removed outlier: 6.687A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LYS G 107 " --> pdb=" O LEU G 11 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ALA G 13 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA G 84 " --> pdb=" O VAL G 104 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 10 through 14 removed outlier: 6.687A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LYS G 107 " --> pdb=" O LEU G 11 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ALA G 13 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA G 84 " --> pdb=" O VAL G 104 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 114 through 118 removed outlier: 5.077A pdb=" N TYR G 173 " --> pdb=" O ASN G 138 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 129 through 130 Processing sheet with id=AB5, first strand: chain 'G' and resid 153 through 155 removed outlier: 4.678A pdb=" N TRP G 148 " --> pdb=" O GLN G 155 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL G 196 " --> pdb=" O VAL G 205 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL G 205 " --> pdb=" O VAL G 196 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AB7, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.839A pdb=" N ALA H 33 " --> pdb=" O ASP H 95 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.910A pdb=" N LEU H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 124 through 128 removed outlier: 5.722A pdb=" N TYR H 180 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 124 through 128 removed outlier: 5.722A pdb=" N TYR H 180 " --> pdb=" O ASP H 148 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER H 181 " --> pdb=" O VAL H 173 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL H 173 " --> pdb=" O SER H 181 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 155 through 158 Processing sheet with id=AC3, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AC4, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.839A pdb=" N ALA F 33 " --> pdb=" O ASP F 95 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE F 34 " --> pdb=" O GLY F 50 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.910A pdb=" N LEU F 102 " --> pdb=" O ARG F 94 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 124 through 128 removed outlier: 5.722A pdb=" N TYR F 180 " --> pdb=" O ASP F 148 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 124 through 128 removed outlier: 5.722A pdb=" N TYR F 180 " --> pdb=" O ASP F 148 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER F 181 " --> pdb=" O VAL F 173 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL F 173 " --> pdb=" O SER F 181 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 155 through 158 Processing sheet with id=AC9, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AD1, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.838A pdb=" N ALA J 33 " --> pdb=" O ASP J 95 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE J 34 " --> pdb=" O GLY J 50 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.911A pdb=" N LEU J 102 " --> pdb=" O ARG J 94 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 124 through 128 removed outlier: 5.725A pdb=" N TYR J 180 " --> pdb=" O ASP J 148 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 124 through 128 removed outlier: 5.725A pdb=" N TYR J 180 " --> pdb=" O ASP J 148 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER J 181 " --> pdb=" O VAL J 173 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL J 173 " --> pdb=" O SER J 181 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 155 through 158 Processing sheet with id=AD6, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AD7, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.839A pdb=" N ALA K 33 " --> pdb=" O ASP K 95 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE K 34 " --> pdb=" O GLY K 50 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY K 50 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.912A pdb=" N LEU K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 124 through 128 removed outlier: 5.724A pdb=" N TYR K 180 " --> pdb=" O ASP K 148 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 124 through 128 removed outlier: 5.724A pdb=" N TYR K 180 " --> pdb=" O ASP K 148 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER K 181 " --> pdb=" O VAL K 173 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL K 173 " --> pdb=" O SER K 181 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 155 through 158 Processing sheet with id=AE3, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AE4, first strand: chain 'E' and resid 10 through 14 removed outlier: 6.688A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LYS E 107 " --> pdb=" O LEU E 11 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA E 13 " --> pdb=" O LYS E 107 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA E 84 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 10 through 14 removed outlier: 6.688A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LYS E 107 " --> pdb=" O LEU E 11 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA E 13 " --> pdb=" O LYS E 107 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA E 84 " --> pdb=" O VAL E 104 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 114 through 118 removed outlier: 5.078A pdb=" N TYR E 173 " --> pdb=" O ASN E 138 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 129 through 130 Processing sheet with id=AE8, first strand: chain 'E' and resid 153 through 155 removed outlier: 4.678A pdb=" N TRP E 148 " --> pdb=" O GLN E 155 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL E 196 " --> pdb=" O VAL E 205 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL E 205 " --> pdb=" O VAL E 196 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AF1, first strand: chain 'I' and resid 10 through 14 removed outlier: 6.687A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LYS I 107 " --> pdb=" O LEU I 11 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA I 13 " --> pdb=" O LYS I 107 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA I 84 " --> pdb=" O VAL I 104 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 10 through 14 removed outlier: 6.687A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LYS I 107 " --> pdb=" O LEU I 11 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA I 13 " --> pdb=" O LYS I 107 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA I 84 " --> pdb=" O VAL I 104 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 114 through 118 removed outlier: 5.076A pdb=" N TYR I 173 " --> pdb=" O ASN I 138 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 129 through 130 Processing sheet with id=AF5, first strand: chain 'I' and resid 153 through 155 removed outlier: 4.677A pdb=" N TRP I 148 " --> pdb=" O GLN I 155 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL I 196 " --> pdb=" O VAL I 205 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL I 205 " --> pdb=" O VAL I 196 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AF7, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.686A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LYS L 107 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.686A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LYS L 107 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.078A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 129 through 130 Processing sheet with id=AG2, first strand: chain 'L' and resid 153 through 155 removed outlier: 4.678A pdb=" N TRP L 148 " --> pdb=" O GLN L 155 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL L 196 " --> pdb=" O VAL L 205 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL L 205 " --> pdb=" O VAL L 196 " (cutoff:3.500A) 808 hydrogen bonds defined for protein. 1980 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.49 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6575 1.34 - 1.46: 5142 1.46 - 1.58: 9195 1.58 - 1.70: 0 1.70 - 1.82: 104 Bond restraints: 21016 Sorted by residual: bond pdb=" CB TRP D 29 " pdb=" CG TRP D 29 " ideal model delta sigma weight residual 1.498 1.432 0.066 3.10e-02 1.04e+03 4.51e+00 bond pdb=" CB TRP B 29 " pdb=" CG TRP B 29 " ideal model delta sigma weight residual 1.498 1.433 0.065 3.10e-02 1.04e+03 4.46e+00 bond pdb=" CB TRP A 29 " pdb=" CG TRP A 29 " ideal model delta sigma weight residual 1.498 1.433 0.065 3.10e-02 1.04e+03 4.43e+00 bond pdb=" CB TRP C 29 " pdb=" CG TRP C 29 " ideal model delta sigma weight residual 1.498 1.433 0.065 3.10e-02 1.04e+03 4.40e+00 bond pdb=" CA TRP A 51 " pdb=" CB TRP A 51 " ideal model delta sigma weight residual 1.534 1.485 0.049 2.47e-02 1.64e+03 3.99e+00 ... (remaining 21011 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 26342 1.60 - 3.21: 2002 3.21 - 4.81: 253 4.81 - 6.41: 75 6.41 - 8.01: 16 Bond angle restraints: 28688 Sorted by residual: angle pdb=" N PRO B 152A" pdb=" CA PRO B 152A" pdb=" C PRO B 152A" ideal model delta sigma weight residual 110.70 116.33 -5.63 1.22e+00 6.72e-01 2.13e+01 angle pdb=" N PRO C 152A" pdb=" CA PRO C 152A" pdb=" C PRO C 152A" ideal model delta sigma weight residual 110.70 116.32 -5.62 1.22e+00 6.72e-01 2.12e+01 angle pdb=" N PRO D 152A" pdb=" CA PRO D 152A" pdb=" C PRO D 152A" ideal model delta sigma weight residual 110.70 116.28 -5.58 1.22e+00 6.72e-01 2.09e+01 angle pdb=" N PRO A 152A" pdb=" CA PRO A 152A" pdb=" C PRO A 152A" ideal model delta sigma weight residual 110.70 116.07 -5.37 1.22e+00 6.72e-01 1.94e+01 angle pdb=" CA PRO C 152A" pdb=" C PRO C 152A" pdb=" N PRO C 152B" ideal model delta sigma weight residual 117.93 122.03 -4.10 1.20e+00 6.94e-01 1.17e+01 ... (remaining 28683 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 11499 17.14 - 34.27: 855 34.27 - 51.41: 106 51.41 - 68.54: 26 68.54 - 85.68: 30 Dihedral angle restraints: 12516 sinusoidal: 4852 harmonic: 7664 Sorted by residual: dihedral pdb=" CA SER A 25 " pdb=" C SER A 25 " pdb=" N LYS A 26 " pdb=" CA LYS A 26 " ideal model delta harmonic sigma weight residual -180.00 -149.70 -30.30 0 5.00e+00 4.00e-02 3.67e+01 dihedral pdb=" CA SER B 25 " pdb=" C SER B 25 " pdb=" N LYS B 26 " pdb=" CA LYS B 26 " ideal model delta harmonic sigma weight residual -180.00 -151.13 -28.87 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA SER D 25 " pdb=" C SER D 25 " pdb=" N LYS D 26 " pdb=" CA LYS D 26 " ideal model delta harmonic sigma weight residual -180.00 -151.14 -28.86 0 5.00e+00 4.00e-02 3.33e+01 ... (remaining 12513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1866 0.042 - 0.083: 901 0.083 - 0.125: 401 0.125 - 0.166: 42 0.166 - 0.208: 14 Chirality restraints: 3224 Sorted by residual: chirality pdb=" CA LYS B 26 " pdb=" N LYS B 26 " pdb=" C LYS B 26 " pdb=" CB LYS B 26 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA LYS C 26 " pdb=" N LYS C 26 " pdb=" C LYS C 26 " pdb=" CB LYS C 26 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.89e-01 chirality pdb=" CA LYS D 26 " pdb=" N LYS D 26 " pdb=" C LYS D 26 " pdb=" CB LYS D 26 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.45e-01 ... (remaining 3221 not shown) Planarity restraints: 3668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 97 " -0.161 9.50e-02 1.11e+02 7.30e-02 4.45e+00 pdb=" NE ARG F 97 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG F 97 " -0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG F 97 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG F 97 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 97 " 0.162 9.50e-02 1.11e+02 7.34e-02 4.45e+00 pdb=" NE ARG J 97 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG J 97 " 0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG J 97 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG J 97 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 97 " -0.162 9.50e-02 1.11e+02 7.32e-02 4.43e+00 pdb=" NE ARG K 97 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG K 97 " -0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG K 97 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG K 97 " 0.000 2.00e-02 2.50e+03 ... (remaining 3665 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4660 2.77 - 3.30: 20426 3.30 - 3.84: 33979 3.84 - 4.37: 40483 4.37 - 4.90: 68767 Nonbonded interactions: 168315 Sorted by model distance: nonbonded pdb=" OD1 ASN K 208 " pdb=" NZ LYS K 210 " model vdw 2.239 3.120 nonbonded pdb=" OD1 ASN H 208 " pdb=" NZ LYS H 210 " model vdw 2.239 3.120 nonbonded pdb=" OD1 ASN F 208 " pdb=" NZ LYS F 210 " model vdw 2.240 3.120 nonbonded pdb=" OD1 ASN J 208 " pdb=" NZ LYS J 210 " model vdw 2.241 3.120 nonbonded pdb=" O SER I 77 " pdb=" NE2 GLN I 79 " model vdw 2.273 3.120 ... (remaining 168310 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'K' } 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: 7.200 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: 0.030 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.090 Process input model: 21.590 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 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 : 0.011 0.066 21048 Z= 0.501 Angle : 0.942 8.013 28752 Z= 0.498 Chirality : 0.055 0.208 3224 Planarity : 0.007 0.073 3668 Dihedral : 12.792 85.677 7516 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.13 % Favored : 92.41 % Rotamer: Outliers : 0.13 % Allowed : 2.09 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.15), residues: 2636 helix: -3.23 (0.28), residues: 164 sheet: -0.23 (0.16), residues: 931 loop : -1.01 (0.15), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.003 ARG F 97 TYR 0.029 0.004 TYR B 75 PHE 0.024 0.003 PHE C 153 TRP 0.022 0.003 TRP D 27 HIS 0.008 0.003 HIS A 91 Details of bonding type rmsd covalent geometry : bond 0.01112 (21016) covalent geometry : angle 0.94076 (28688) SS BOND : bond 0.00673 ( 32) SS BOND : angle 1.42154 ( 64) hydrogen bonds : bond 0.21246 ( 724) hydrogen bonds : angle 9.35744 ( 1980) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 618 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.9403 (tp30) cc_final: 0.9157 (tp30) REVERT: A 146 ASN cc_start: 0.9122 (OUTLIER) cc_final: 0.8631 (m-40) REVERT: A 149 GLU cc_start: 0.9135 (mp0) cc_final: 0.8866 (mp0) REVERT: A 180 MET cc_start: 0.9535 (mtt) cc_final: 0.9289 (mtp) REVERT: A 209 GLN cc_start: 0.9440 (tt0) cc_final: 0.9199 (tt0) REVERT: B 128 GLU cc_start: 0.9399 (tp30) cc_final: 0.9147 (tp30) REVERT: B 146 ASN cc_start: 0.9197 (OUTLIER) cc_final: 0.8623 (m-40) REVERT: B 149 GLU cc_start: 0.9208 (mp0) cc_final: 0.8728 (mp0) REVERT: B 209 GLN cc_start: 0.9426 (tt0) cc_final: 0.9193 (tt0) REVERT: C 128 GLU cc_start: 0.9399 (tp30) cc_final: 0.9149 (tp30) REVERT: C 146 ASN cc_start: 0.9138 (OUTLIER) cc_final: 0.8620 (m-40) REVERT: C 149 GLU cc_start: 0.9144 (mp0) cc_final: 0.8877 (mp0) REVERT: C 180 MET cc_start: 0.9538 (mtt) cc_final: 0.9293 (mtp) REVERT: C 209 GLN cc_start: 0.9430 (tt0) cc_final: 0.9193 (tt0) REVERT: D 21 GLU cc_start: 0.8990 (tt0) cc_final: 0.8790 (pp20) REVERT: D 128 GLU cc_start: 0.9392 (tp30) cc_final: 0.9140 (tp30) REVERT: D 149 GLU cc_start: 0.9082 (mp0) cc_final: 0.8638 (mp0) REVERT: D 180 MET cc_start: 0.9529 (mtt) cc_final: 0.9288 (mtp) REVERT: D 209 GLN cc_start: 0.9426 (tt0) cc_final: 0.9197 (tt0) REVERT: G 31 ASN cc_start: 0.9197 (m110) cc_final: 0.8997 (m-40) REVERT: G 36 TYR cc_start: 0.8830 (m-80) cc_final: 0.8124 (m-80) REVERT: G 50 GLU cc_start: 0.9216 (mt-10) cc_final: 0.8822 (tp30) REVERT: G 67 SER cc_start: 0.9158 (m) cc_final: 0.8889 (p) REVERT: G 92 PHE cc_start: 0.9255 (m-80) cc_final: 0.8886 (m-80) REVERT: G 93 ASP cc_start: 0.9332 (t0) cc_final: 0.8911 (t0) REVERT: G 103 LYS cc_start: 0.9145 (mttt) cc_final: 0.8627 (mtpp) REVERT: G 106 ILE cc_start: 0.8702 (mt) cc_final: 0.8054 (pp) REVERT: G 117 ILE cc_start: 0.7180 (tt) cc_final: 0.6897 (tt) REVERT: G 148 TRP cc_start: 0.6944 (m100) cc_final: 0.6448 (m100) REVERT: H 3 GLN cc_start: 0.8852 (pm20) cc_final: 0.8451 (pm20) REVERT: H 46 GLU cc_start: 0.8916 (tt0) cc_final: 0.8189 (pt0) REVERT: H 72 ASP cc_start: 0.8737 (t0) cc_final: 0.8522 (t0) REVERT: H 100 LEU cc_start: 0.9656 (mt) cc_final: 0.9195 (mp) REVERT: H 105 GLN cc_start: 0.9406 (mt0) cc_final: 0.9099 (mm110) REVERT: F 3 GLN cc_start: 0.8855 (pm20) cc_final: 0.8453 (pm20) REVERT: F 46 GLU cc_start: 0.8919 (tt0) cc_final: 0.8194 (pt0) REVERT: F 72 ASP cc_start: 0.8746 (t0) cc_final: 0.8526 (t0) REVERT: F 100 LEU cc_start: 0.9654 (mt) cc_final: 0.9190 (mp) REVERT: F 105 GLN cc_start: 0.9395 (mt0) cc_final: 0.9088 (mm110) REVERT: J 3 GLN cc_start: 0.8847 (pm20) cc_final: 0.8452 (pm20) REVERT: J 46 GLU cc_start: 0.8904 (tt0) cc_final: 0.8176 (pt0) REVERT: J 72 ASP cc_start: 0.8722 (t0) cc_final: 0.8497 (t0) REVERT: J 100 LEU cc_start: 0.9654 (mt) cc_final: 0.9192 (mp) REVERT: J 105 GLN cc_start: 0.9395 (mt0) cc_final: 0.9087 (mm110) REVERT: K 3 GLN cc_start: 0.8856 (pm20) cc_final: 0.8460 (pm20) REVERT: K 46 GLU cc_start: 0.8906 (tt0) cc_final: 0.8176 (pt0) REVERT: K 72 ASP cc_start: 0.8724 (t0) cc_final: 0.8500 (t0) REVERT: K 100 LEU cc_start: 0.9655 (mt) cc_final: 0.9195 (mp) REVERT: K 105 GLN cc_start: 0.9399 (mt0) cc_final: 0.9092 (mm110) REVERT: E 36 TYR cc_start: 0.8823 (m-80) cc_final: 0.8138 (m-80) REVERT: E 50 GLU cc_start: 0.9216 (mt-10) cc_final: 0.8822 (tp30) REVERT: E 67 SER cc_start: 0.9150 (m) cc_final: 0.8876 (p) REVERT: E 92 PHE cc_start: 0.9256 (m-80) cc_final: 0.8883 (m-80) REVERT: E 93 ASP cc_start: 0.9338 (t0) cc_final: 0.8920 (t0) REVERT: E 103 LYS cc_start: 0.9149 (mttt) cc_final: 0.8636 (mtpp) REVERT: E 106 ILE cc_start: 0.8689 (mt) cc_final: 0.8025 (pp) REVERT: E 117 ILE cc_start: 0.7209 (tt) cc_final: 0.6925 (tt) REVERT: E 148 TRP cc_start: 0.6939 (m100) cc_final: 0.6436 (m100) REVERT: I 31 ASN cc_start: 0.9182 (m110) cc_final: 0.8981 (m-40) REVERT: I 36 TYR cc_start: 0.8825 (m-80) cc_final: 0.8119 (m-80) REVERT: I 50 GLU cc_start: 0.9213 (mt-10) cc_final: 0.8813 (tp30) REVERT: I 67 SER cc_start: 0.9158 (m) cc_final: 0.8906 (p) REVERT: I 92 PHE cc_start: 0.9256 (m-80) cc_final: 0.8882 (m-80) REVERT: I 93 ASP cc_start: 0.9342 (t0) cc_final: 0.8912 (t0) REVERT: I 103 LYS cc_start: 0.9149 (mttt) cc_final: 0.8637 (mtpp) REVERT: I 106 ILE cc_start: 0.8721 (mt) cc_final: 0.8070 (pp) REVERT: I 117 ILE cc_start: 0.7202 (tt) cc_final: 0.6917 (tt) REVERT: I 148 TRP cc_start: 0.6956 (m100) cc_final: 0.6452 (m100) REVERT: L 36 TYR cc_start: 0.8837 (m-80) cc_final: 0.8154 (m-80) REVERT: L 50 GLU cc_start: 0.9224 (mt-10) cc_final: 0.8819 (tp30) REVERT: L 67 SER cc_start: 0.9148 (m) cc_final: 0.8893 (p) REVERT: L 92 PHE cc_start: 0.9262 (m-80) cc_final: 0.8885 (m-80) REVERT: L 93 ASP cc_start: 0.9341 (t0) cc_final: 0.8923 (t0) REVERT: L 103 LYS cc_start: 0.9152 (mttt) cc_final: 0.8642 (mtpp) REVERT: L 106 ILE cc_start: 0.8704 (mt) cc_final: 0.8054 (pp) REVERT: L 117 ILE cc_start: 0.7179 (tt) cc_final: 0.6898 (tt) REVERT: L 148 TRP cc_start: 0.6932 (m100) cc_final: 0.6422 (m100) outliers start: 3 outliers final: 0 residues processed: 621 average time/residue: 0.6307 time to fit residues: 441.7476 Evaluate side-chains 371 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 368 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain C residue 146 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.3980 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 240 HIS B 165 ASN B 239 HIS C 165 ASN C 239 HIS D 146 ASN D 165 ASN D 239 HIS H 76 ASN H 208 ASN F 76 ASN F 208 ASN J 76 ASN J 208 ASN K 76 ASN K 208 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.090789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.061112 restraints weight = 50867.772| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 4.01 r_work: 0.2754 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 21048 Z= 0.164 Angle : 0.762 7.586 28752 Z= 0.401 Chirality : 0.048 0.169 3224 Planarity : 0.006 0.062 3668 Dihedral : 6.413 46.036 2866 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.23 % Allowed : 12.70 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.16), residues: 2636 helix: -2.39 (0.34), residues: 144 sheet: 0.35 (0.17), residues: 850 loop : -0.36 (0.16), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 142 TYR 0.016 0.002 TYR F 180 PHE 0.031 0.002 PHE L 209 TRP 0.014 0.002 TRP A 51 HIS 0.005 0.001 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00365 (21016) covalent geometry : angle 0.76016 (28688) SS BOND : bond 0.00500 ( 32) SS BOND : angle 1.41110 ( 64) hydrogen bonds : bond 0.03716 ( 724) hydrogen bonds : angle 6.69326 ( 1980) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 485 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 GLU cc_start: 0.8819 (tp30) cc_final: 0.8242 (tp30) REVERT: A 128 GLU cc_start: 0.9518 (tp30) cc_final: 0.9185 (tp30) REVERT: A 164 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7655 (tm-30) REVERT: A 230 THR cc_start: 0.9663 (m) cc_final: 0.9295 (p) REVERT: B 128 GLU cc_start: 0.9503 (tp30) cc_final: 0.9160 (tp30) REVERT: B 164 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7616 (tm-30) REVERT: C 128 GLU cc_start: 0.9501 (tp30) cc_final: 0.9161 (tp30) REVERT: C 164 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7665 (tm-30) REVERT: C 229 THR cc_start: 0.9649 (m) cc_final: 0.9274 (p) REVERT: D 128 GLU cc_start: 0.9500 (tp30) cc_final: 0.9156 (tp30) REVERT: D 149 GLU cc_start: 0.9210 (mp0) cc_final: 0.8979 (mp0) REVERT: D 164 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7634 (tm-30) REVERT: D 229 THR cc_start: 0.9657 (m) cc_final: 0.9281 (p) REVERT: G 36 TYR cc_start: 0.8966 (m-80) cc_final: 0.8740 (m-80) REVERT: G 45 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8968 (ttpt) REVERT: G 67 SER cc_start: 0.9080 (m) cc_final: 0.8854 (p) REVERT: G 93 ASP cc_start: 0.9398 (t0) cc_final: 0.9004 (t70) REVERT: G 103 LYS cc_start: 0.9290 (mttt) cc_final: 0.8779 (mtpp) REVERT: G 106 ILE cc_start: 0.8889 (mt) cc_final: 0.8058 (pp) REVERT: H 3 GLN cc_start: 0.8880 (pm20) cc_final: 0.8501 (pm20) REVERT: H 46 GLU cc_start: 0.8903 (tt0) cc_final: 0.8457 (tt0) REVERT: H 72 ASP cc_start: 0.9021 (t0) cc_final: 0.8572 (OUTLIER) REVERT: H 77 GLN cc_start: 0.9097 (mt0) cc_final: 0.8419 (mm110) REVERT: H 86 ASP cc_start: 0.9091 (m-30) cc_final: 0.8656 (m-30) REVERT: H 95 ASP cc_start: 0.9502 (t0) cc_final: 0.8971 (t0) REVERT: H 100 LEU cc_start: 0.9714 (mt) cc_final: 0.9473 (mm) REVERT: H 105 GLN cc_start: 0.9369 (mt0) cc_final: 0.9141 (mm110) REVERT: H 149 TYR cc_start: 0.8058 (p90) cc_final: 0.7813 (p90) REVERT: H 199 ILE cc_start: 0.8468 (mm) cc_final: 0.8171 (tp) REVERT: F 3 GLN cc_start: 0.8876 (pm20) cc_final: 0.8493 (pm20) REVERT: F 46 GLU cc_start: 0.8904 (tt0) cc_final: 0.8458 (pt0) REVERT: F 72 ASP cc_start: 0.9038 (t0) cc_final: 0.8590 (OUTLIER) REVERT: F 77 GLN cc_start: 0.9100 (mt0) cc_final: 0.8424 (mm110) REVERT: F 86 ASP cc_start: 0.9064 (m-30) cc_final: 0.8620 (m-30) REVERT: F 95 ASP cc_start: 0.9501 (t0) cc_final: 0.8990 (t0) REVERT: F 100 LEU cc_start: 0.9715 (mt) cc_final: 0.9472 (mm) REVERT: F 105 GLN cc_start: 0.9368 (mt0) cc_final: 0.9140 (mm110) REVERT: F 149 TYR cc_start: 0.8000 (p90) cc_final: 0.7788 (p90) REVERT: J 3 GLN cc_start: 0.8885 (pm20) cc_final: 0.8506 (pm20) REVERT: J 46 GLU cc_start: 0.8901 (tt0) cc_final: 0.8454 (tt0) REVERT: J 72 ASP cc_start: 0.9017 (t0) cc_final: 0.8566 (OUTLIER) REVERT: J 77 GLN cc_start: 0.9095 (mt0) cc_final: 0.8416 (mm110) REVERT: J 86 ASP cc_start: 0.9079 (m-30) cc_final: 0.8640 (m-30) REVERT: J 95 ASP cc_start: 0.9503 (t0) cc_final: 0.8968 (t0) REVERT: J 100 LEU cc_start: 0.9721 (mt) cc_final: 0.9483 (mm) REVERT: J 105 GLN cc_start: 0.9354 (mt0) cc_final: 0.9125 (mm110) REVERT: J 149 TYR cc_start: 0.8051 (p90) cc_final: 0.7813 (p90) REVERT: J 199 ILE cc_start: 0.8536 (mm) cc_final: 0.8259 (tp) REVERT: K 3 GLN cc_start: 0.8870 (pm20) cc_final: 0.8490 (pm20) REVERT: K 46 GLU cc_start: 0.8895 (tt0) cc_final: 0.8447 (tt0) REVERT: K 72 ASP cc_start: 0.9028 (t0) cc_final: 0.8580 (OUTLIER) REVERT: K 77 GLN cc_start: 0.9097 (mt0) cc_final: 0.8414 (mm110) REVERT: K 86 ASP cc_start: 0.9077 (m-30) cc_final: 0.8642 (m-30) REVERT: K 95 ASP cc_start: 0.9501 (t0) cc_final: 0.8991 (t0) REVERT: K 100 LEU cc_start: 0.9717 (mt) cc_final: 0.9478 (mm) REVERT: K 105 GLN cc_start: 0.9361 (mt0) cc_final: 0.9132 (mm110) REVERT: K 149 TYR cc_start: 0.8005 (p90) cc_final: 0.7789 (p90) REVERT: E 36 TYR cc_start: 0.8957 (m-80) cc_final: 0.8727 (m-80) REVERT: E 45 LYS cc_start: 0.9177 (OUTLIER) cc_final: 0.8969 (ttpt) REVERT: E 67 SER cc_start: 0.9087 (m) cc_final: 0.8864 (p) REVERT: E 93 ASP cc_start: 0.9389 (t0) cc_final: 0.8985 (t70) REVERT: E 103 LYS cc_start: 0.9293 (mttt) cc_final: 0.8774 (mtpp) REVERT: E 106 ILE cc_start: 0.8886 (mt) cc_final: 0.8054 (pp) REVERT: I 36 TYR cc_start: 0.8965 (m-80) cc_final: 0.8740 (m-80) REVERT: I 45 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8974 (ttpt) REVERT: I 67 SER cc_start: 0.9091 (m) cc_final: 0.8870 (p) REVERT: I 93 ASP cc_start: 0.9411 (t0) cc_final: 0.9013 (t70) REVERT: I 103 LYS cc_start: 0.9290 (mttt) cc_final: 0.8771 (mtpp) REVERT: I 106 ILE cc_start: 0.8908 (mt) cc_final: 0.8068 (pp) REVERT: L 36 TYR cc_start: 0.8957 (m-80) cc_final: 0.8729 (m-80) REVERT: L 45 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8975 (ttpt) REVERT: L 67 SER cc_start: 0.9093 (m) cc_final: 0.8867 (p) REVERT: L 93 ASP cc_start: 0.9385 (t0) cc_final: 0.8954 (t0) REVERT: L 103 LYS cc_start: 0.9288 (mttt) cc_final: 0.8764 (mtpp) REVERT: L 106 ILE cc_start: 0.8880 (mt) cc_final: 0.8046 (pp) outliers start: 74 outliers final: 24 residues processed: 512 average time/residue: 0.4989 time to fit residues: 296.4962 Evaluate side-chains 441 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 413 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 209 PHE Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 209 PHE Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 209 PHE Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 209 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 170 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 138 optimal weight: 0.8980 chunk 163 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 254 optimal weight: 3.9990 chunk 154 optimal weight: 0.0570 chunk 206 optimal weight: 5.9990 chunk 193 optimal weight: 6.9990 chunk 229 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.5702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN A 209 GLN B 146 ASN B 209 GLN C 146 ASN C 209 GLN D 146 ASN D 209 GLN G 158 ASN H 76 ASN H 208 ASN F 76 ASN F 208 ASN J 76 ASN J 208 ASN K 76 ASN K 208 ASN E 158 ASN I 158 ASN L 158 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.088995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.059721 restraints weight = 51641.507| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 3.99 r_work: 0.2727 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 21048 Z= 0.219 Angle : 0.724 9.105 28752 Z= 0.370 Chirality : 0.048 0.248 3224 Planarity : 0.005 0.059 3668 Dihedral : 5.727 21.369 2860 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.88 % Allowed : 16.01 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.16), residues: 2636 helix: -2.08 (0.36), residues: 144 sheet: 0.42 (0.17), residues: 884 loop : -0.26 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 142 TYR 0.022 0.002 TYR K 180 PHE 0.030 0.003 PHE L 209 TRP 0.015 0.002 TRP H 158 HIS 0.004 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00494 (21016) covalent geometry : angle 0.72164 (28688) SS BOND : bond 0.00540 ( 32) SS BOND : angle 1.43722 ( 64) hydrogen bonds : bond 0.03581 ( 724) hydrogen bonds : angle 6.11165 ( 1980) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 421 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 GLU cc_start: 0.8919 (tp30) cc_final: 0.8440 (tt0) REVERT: A 110 GLU cc_start: 0.9031 (mp0) cc_final: 0.8768 (mp0) REVERT: A 128 GLU cc_start: 0.9535 (tp30) cc_final: 0.9205 (tp30) REVERT: A 194 ASP cc_start: 0.8672 (m-30) cc_final: 0.7938 (m-30) REVERT: B 109 GLU cc_start: 0.8918 (tp30) cc_final: 0.8222 (tt0) REVERT: B 128 GLU cc_start: 0.9542 (tp30) cc_final: 0.9203 (tp30) REVERT: B 194 ASP cc_start: 0.8622 (m-30) cc_final: 0.8017 (m-30) REVERT: C 109 GLU cc_start: 0.8930 (tp30) cc_final: 0.8217 (tt0) REVERT: C 128 GLU cc_start: 0.9523 (tp30) cc_final: 0.9189 (tp30) REVERT: C 194 ASP cc_start: 0.8688 (m-30) cc_final: 0.7929 (m-30) REVERT: D 109 GLU cc_start: 0.8875 (tp30) cc_final: 0.8098 (tt0) REVERT: D 128 GLU cc_start: 0.9533 (tp30) cc_final: 0.9192 (tp30) REVERT: D 149 GLU cc_start: 0.9288 (mp0) cc_final: 0.9049 (mp0) REVERT: D 194 ASP cc_start: 0.8671 (m-30) cc_final: 0.7886 (m-30) REVERT: G 45 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8931 (ttpt) REVERT: G 67 SER cc_start: 0.9122 (m) cc_final: 0.8889 (p) REVERT: G 93 ASP cc_start: 0.9341 (t0) cc_final: 0.8918 (t70) REVERT: G 103 LYS cc_start: 0.9304 (mttt) cc_final: 0.8791 (mtpp) REVERT: G 105 GLU cc_start: 0.7860 (tp30) cc_final: 0.7255 (tp30) REVERT: G 106 ILE cc_start: 0.8660 (mt) cc_final: 0.8134 (pp) REVERT: H 3 GLN cc_start: 0.9043 (pm20) cc_final: 0.8610 (pm20) REVERT: H 6 GLU cc_start: 0.8215 (mp0) cc_final: 0.7222 (mp0) REVERT: H 46 GLU cc_start: 0.8838 (tt0) cc_final: 0.8368 (pt0) REVERT: H 72 ASP cc_start: 0.8992 (t0) cc_final: 0.8561 (OUTLIER) REVERT: H 95 ASP cc_start: 0.9539 (t0) cc_final: 0.9101 (t0) REVERT: H 105 GLN cc_start: 0.9429 (mt0) cc_final: 0.9109 (pm20) REVERT: H 157 SER cc_start: 0.8307 (OUTLIER) cc_final: 0.8083 (t) REVERT: H 199 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8469 (tp) REVERT: F 3 GLN cc_start: 0.9029 (pm20) cc_final: 0.8630 (pm20) REVERT: F 6 GLU cc_start: 0.8233 (mp0) cc_final: 0.7109 (mp0) REVERT: F 46 GLU cc_start: 0.8825 (tt0) cc_final: 0.8354 (pt0) REVERT: F 72 ASP cc_start: 0.8995 (t0) cc_final: 0.8563 (OUTLIER) REVERT: F 95 ASP cc_start: 0.9530 (t0) cc_final: 0.9073 (t0) REVERT: F 105 GLN cc_start: 0.9420 (mt0) cc_final: 0.9116 (pm20) REVERT: F 157 SER cc_start: 0.8341 (OUTLIER) cc_final: 0.8118 (t) REVERT: F 213 LYS cc_start: 0.7469 (OUTLIER) cc_final: 0.6990 (ttpp) REVERT: J 3 GLN cc_start: 0.9035 (pm20) cc_final: 0.8640 (pm20) REVERT: J 6 GLU cc_start: 0.8211 (mp0) cc_final: 0.7073 (mp0) REVERT: J 46 GLU cc_start: 0.8828 (tt0) cc_final: 0.8359 (pt0) REVERT: J 72 ASP cc_start: 0.8992 (t0) cc_final: 0.8546 (OUTLIER) REVERT: J 95 ASP cc_start: 0.9526 (t0) cc_final: 0.9086 (t0) REVERT: J 100 LEU cc_start: 0.9706 (mt) cc_final: 0.9501 (mp) REVERT: J 105 GLN cc_start: 0.9416 (mt0) cc_final: 0.9111 (pm20) REVERT: J 157 SER cc_start: 0.8324 (OUTLIER) cc_final: 0.8104 (t) REVERT: J 199 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8441 (tp) REVERT: K 3 GLN cc_start: 0.9021 (pm20) cc_final: 0.8626 (pm20) REVERT: K 6 GLU cc_start: 0.8198 (mp0) cc_final: 0.7065 (mp0) REVERT: K 46 GLU cc_start: 0.8837 (tt0) cc_final: 0.8346 (pt0) REVERT: K 72 ASP cc_start: 0.8993 (t0) cc_final: 0.8561 (OUTLIER) REVERT: K 95 ASP cc_start: 0.9531 (t0) cc_final: 0.9095 (t0) REVERT: K 105 GLN cc_start: 0.9420 (mt0) cc_final: 0.9112 (pm20) REVERT: K 157 SER cc_start: 0.8354 (OUTLIER) cc_final: 0.8135 (t) REVERT: K 213 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.6984 (ttpp) REVERT: E 27 LYS cc_start: 0.9322 (OUTLIER) cc_final: 0.8863 (pmtt) REVERT: E 45 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8943 (ttpt) REVERT: E 67 SER cc_start: 0.9125 (m) cc_final: 0.8900 (p) REVERT: E 93 ASP cc_start: 0.9352 (t0) cc_final: 0.8950 (t70) REVERT: E 103 LYS cc_start: 0.9303 (mttt) cc_final: 0.8772 (mtpp) REVERT: E 105 GLU cc_start: 0.7895 (tp30) cc_final: 0.7299 (tp30) REVERT: E 106 ILE cc_start: 0.8661 (mt) cc_final: 0.8130 (pp) REVERT: E 185 ASP cc_start: 0.8096 (OUTLIER) cc_final: 0.7577 (p0) REVERT: I 45 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8933 (ttpt) REVERT: I 67 SER cc_start: 0.9117 (m) cc_final: 0.8883 (p) REVERT: I 93 ASP cc_start: 0.9346 (t0) cc_final: 0.8935 (t70) REVERT: I 103 LYS cc_start: 0.9307 (mttt) cc_final: 0.8779 (mtpp) REVERT: I 105 GLU cc_start: 0.7859 (tp30) cc_final: 0.7268 (tp30) REVERT: I 106 ILE cc_start: 0.8655 (mt) cc_final: 0.8138 (pp) REVERT: L 45 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8947 (ttpt) REVERT: L 67 SER cc_start: 0.9125 (m) cc_final: 0.8893 (p) REVERT: L 93 ASP cc_start: 0.9351 (t0) cc_final: 0.8948 (t70) REVERT: L 103 LYS cc_start: 0.9306 (mttt) cc_final: 0.8775 (mtpp) REVERT: L 105 GLU cc_start: 0.7864 (tp30) cc_final: 0.7268 (tp30) REVERT: L 106 ILE cc_start: 0.8655 (mt) cc_final: 0.8131 (pp) outliers start: 89 outliers final: 27 residues processed: 472 average time/residue: 0.4984 time to fit residues: 274.0209 Evaluate side-chains 435 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 398 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 209 PHE Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 157 SER Chi-restraints excluded: chain F residue 213 LYS Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 157 SER Chi-restraints excluded: chain J residue 199 ILE Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 213 LYS Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 209 PHE Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 209 PHE Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 209 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 210 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 221 optimal weight: 9.9990 chunk 176 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 191 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 233 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 165 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN A 209 GLN B 146 ASN B 209 GLN C 146 ASN C 209 GLN D 146 ASN D 209 GLN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 GLN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 GLN ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 GLN ** K 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.087779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.058402 restraints weight = 51867.094| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 4.04 r_work: 0.2701 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 21048 Z= 0.274 Angle : 0.742 8.381 28752 Z= 0.385 Chirality : 0.048 0.171 3224 Planarity : 0.005 0.059 3668 Dihedral : 5.589 21.565 2860 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.71 % Allowed : 18.32 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.16), residues: 2636 helix: -2.14 (0.35), residues: 144 sheet: 0.39 (0.16), residues: 924 loop : -0.32 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 142 TYR 0.023 0.002 TYR F 99 PHE 0.029 0.002 PHE I 209 TRP 0.015 0.002 TRP F 158 HIS 0.004 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00605 (21016) covalent geometry : angle 0.73866 (28688) SS BOND : bond 0.00621 ( 32) SS BOND : angle 1.66415 ( 64) hydrogen bonds : bond 0.03509 ( 724) hydrogen bonds : angle 5.83919 ( 1980) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 413 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLN cc_start: 0.9318 (OUTLIER) cc_final: 0.8961 (pm20) REVERT: A 109 GLU cc_start: 0.8930 (tp30) cc_final: 0.8519 (tp30) REVERT: A 110 GLU cc_start: 0.9062 (mp0) cc_final: 0.8790 (mp0) REVERT: A 128 GLU cc_start: 0.9545 (tp30) cc_final: 0.9240 (tp30) REVERT: A 149 GLU cc_start: 0.9227 (mp0) cc_final: 0.8998 (mp0) REVERT: A 164 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7641 (tm-30) REVERT: B 20 GLN cc_start: 0.9220 (OUTLIER) cc_final: 0.8839 (pm20) REVERT: B 109 GLU cc_start: 0.8946 (tp30) cc_final: 0.8296 (tt0) REVERT: B 128 GLU cc_start: 0.9545 (tp30) cc_final: 0.9238 (tp30) REVERT: B 164 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7592 (tm-30) REVERT: C 109 GLU cc_start: 0.8928 (tp30) cc_final: 0.8273 (tt0) REVERT: C 128 GLU cc_start: 0.9534 (tp30) cc_final: 0.9228 (tp30) REVERT: C 164 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7624 (tm-30) REVERT: D 109 GLU cc_start: 0.8910 (tp30) cc_final: 0.8266 (tt0) REVERT: D 128 GLU cc_start: 0.9537 (tp30) cc_final: 0.9207 (tp30) REVERT: D 164 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7607 (tm-30) REVERT: G 36 TYR cc_start: 0.9280 (m-80) cc_final: 0.8878 (m-80) REVERT: G 45 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8957 (ttpt) REVERT: G 67 SER cc_start: 0.9179 (m) cc_final: 0.8934 (p) REVERT: G 93 ASP cc_start: 0.9352 (t0) cc_final: 0.8921 (t70) REVERT: G 103 LYS cc_start: 0.9300 (mttt) cc_final: 0.8790 (mtpp) REVERT: G 105 GLU cc_start: 0.7914 (tp30) cc_final: 0.7249 (tp30) REVERT: G 106 ILE cc_start: 0.8660 (mt) cc_final: 0.8129 (pp) REVERT: H 3 GLN cc_start: 0.9062 (pm20) cc_final: 0.8616 (pm20) REVERT: H 6 GLU cc_start: 0.8222 (mp0) cc_final: 0.7196 (mp0) REVERT: H 16 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8367 (pm20) REVERT: H 46 GLU cc_start: 0.8842 (tt0) cc_final: 0.8415 (pt0) REVERT: H 72 ASP cc_start: 0.8930 (t0) cc_final: 0.8496 (t0) REVERT: H 95 ASP cc_start: 0.9539 (t0) cc_final: 0.9174 (t0) REVERT: H 100 LEU cc_start: 0.9675 (mp) cc_final: 0.9452 (mm) REVERT: H 105 GLN cc_start: 0.9445 (mt0) cc_final: 0.9117 (pm20) REVERT: H 199 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8572 (tp) REVERT: F 3 GLN cc_start: 0.9065 (pm20) cc_final: 0.8660 (pm20) REVERT: F 6 GLU cc_start: 0.8210 (mp0) cc_final: 0.7174 (mp0) REVERT: F 16 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8373 (pm20) REVERT: F 46 GLU cc_start: 0.8852 (tt0) cc_final: 0.8421 (pt0) REVERT: F 72 ASP cc_start: 0.8935 (t0) cc_final: 0.8490 (t0) REVERT: F 95 ASP cc_start: 0.9534 (t0) cc_final: 0.9160 (t0) REVERT: F 100 LEU cc_start: 0.9674 (mp) cc_final: 0.9460 (mm) REVERT: F 105 GLN cc_start: 0.9442 (mt0) cc_final: 0.9114 (pm20) REVERT: F 213 LYS cc_start: 0.7531 (OUTLIER) cc_final: 0.7132 (ttpp) REVERT: J 3 GLN cc_start: 0.9067 (pm20) cc_final: 0.8664 (pm20) REVERT: J 6 GLU cc_start: 0.8211 (mp0) cc_final: 0.7177 (mp0) REVERT: J 16 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8361 (pm20) REVERT: J 46 GLU cc_start: 0.8828 (tt0) cc_final: 0.8404 (pt0) REVERT: J 72 ASP cc_start: 0.8935 (t0) cc_final: 0.8498 (t0) REVERT: J 95 ASP cc_start: 0.9562 (t0) cc_final: 0.9134 (t0) REVERT: J 105 GLN cc_start: 0.9440 (mt0) cc_final: 0.9107 (pm20) REVERT: J 199 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8484 (tp) REVERT: K 3 GLN cc_start: 0.9065 (pm20) cc_final: 0.8661 (pm20) REVERT: K 6 GLU cc_start: 0.8196 (mp0) cc_final: 0.7163 (mp0) REVERT: K 46 GLU cc_start: 0.8853 (tt0) cc_final: 0.8419 (pt0) REVERT: K 72 ASP cc_start: 0.8940 (t0) cc_final: 0.8507 (t0) REVERT: K 95 ASP cc_start: 0.9539 (t0) cc_final: 0.9165 (t0) REVERT: K 100 LEU cc_start: 0.9670 (mp) cc_final: 0.9452 (mm) REVERT: K 105 GLN cc_start: 0.9440 (mt0) cc_final: 0.9109 (pm20) REVERT: K 213 LYS cc_start: 0.7538 (OUTLIER) cc_final: 0.7106 (ttpp) REVERT: E 27 LYS cc_start: 0.9375 (OUTLIER) cc_final: 0.8953 (pmtt) REVERT: E 36 TYR cc_start: 0.9281 (m-80) cc_final: 0.8884 (m-80) REVERT: E 45 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.8971 (ttpt) REVERT: E 67 SER cc_start: 0.9178 (m) cc_final: 0.8933 (p) REVERT: E 92 PHE cc_start: 0.9386 (m-10) cc_final: 0.9174 (m-10) REVERT: E 93 ASP cc_start: 0.9373 (t0) cc_final: 0.8940 (t70) REVERT: E 103 LYS cc_start: 0.9304 (mttt) cc_final: 0.8788 (mtpp) REVERT: E 105 GLU cc_start: 0.7931 (tp30) cc_final: 0.7344 (tp30) REVERT: E 106 ILE cc_start: 0.8665 (mt) cc_final: 0.8139 (pp) REVERT: I 36 TYR cc_start: 0.9174 (m-80) cc_final: 0.8949 (m-80) REVERT: I 45 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8959 (ttpt) REVERT: I 67 SER cc_start: 0.9153 (m) cc_final: 0.8914 (p) REVERT: I 93 ASP cc_start: 0.9376 (t0) cc_final: 0.8948 (t70) REVERT: I 103 LYS cc_start: 0.9311 (mttt) cc_final: 0.8801 (mtpp) REVERT: I 105 GLU cc_start: 0.7890 (tp30) cc_final: 0.7232 (tp30) REVERT: I 106 ILE cc_start: 0.8662 (mt) cc_final: 0.8157 (pp) REVERT: L 36 TYR cc_start: 0.9254 (m-80) cc_final: 0.8856 (m-80) REVERT: L 45 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8932 (ttpt) REVERT: L 67 SER cc_start: 0.9167 (m) cc_final: 0.8926 (p) REVERT: L 93 ASP cc_start: 0.9380 (t0) cc_final: 0.8950 (t70) REVERT: L 103 LYS cc_start: 0.9308 (mttt) cc_final: 0.8800 (mtpp) REVERT: L 105 GLU cc_start: 0.7900 (tp30) cc_final: 0.7311 (tp30) REVERT: L 106 ILE cc_start: 0.8664 (mt) cc_final: 0.8139 (pp) outliers start: 108 outliers final: 43 residues processed: 484 average time/residue: 0.5363 time to fit residues: 299.3254 Evaluate side-chains 442 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 384 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 194 CYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 213 LYS Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 199 ILE Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 213 LYS Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 194 CYS Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 194 CYS Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 159 SER Chi-restraints excluded: chain L residue 194 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 90 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 226 optimal weight: 3.9990 chunk 211 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN B 146 ASN C 146 ASN D 146 ASN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 GLN H 208 ASN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 GLN F 208 ASN ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 GLN J 208 ASN ** K 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 GLN K 208 ASN E 30 ASN I 30 ASN L 30 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.088584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.059548 restraints weight = 51364.475| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 3.98 r_work: 0.2721 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 21048 Z= 0.215 Angle : 0.706 8.279 28752 Z= 0.365 Chirality : 0.047 0.149 3224 Planarity : 0.005 0.060 3668 Dihedral : 5.411 21.022 2860 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.23 % Allowed : 20.16 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.16), residues: 2636 helix: -1.75 (0.37), residues: 144 sheet: 0.47 (0.17), residues: 884 loop : -0.36 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 142 TYR 0.020 0.002 TYR D 233 PHE 0.039 0.003 PHE E 209 TRP 0.014 0.001 TRP K 158 HIS 0.004 0.001 HIS C 173 Details of bonding type rmsd covalent geometry : bond 0.00479 (21016) covalent geometry : angle 0.70515 (28688) SS BOND : bond 0.00701 ( 32) SS BOND : angle 1.14119 ( 64) hydrogen bonds : bond 0.03297 ( 724) hydrogen bonds : angle 5.73879 ( 1980) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 415 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLN cc_start: 0.9340 (OUTLIER) cc_final: 0.8980 (pm20) REVERT: A 109 GLU cc_start: 0.8990 (tp30) cc_final: 0.8363 (tt0) REVERT: A 110 GLU cc_start: 0.9075 (mp0) cc_final: 0.8807 (mp0) REVERT: A 128 GLU cc_start: 0.9541 (tp30) cc_final: 0.9244 (tp30) REVERT: A 164 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7639 (tm-30) REVERT: A 194 ASP cc_start: 0.8576 (m-30) cc_final: 0.7899 (m-30) REVERT: B 20 GLN cc_start: 0.9230 (OUTLIER) cc_final: 0.8838 (pm20) REVERT: B 109 GLU cc_start: 0.8950 (tp30) cc_final: 0.8294 (tt0) REVERT: B 128 GLU cc_start: 0.9537 (tp30) cc_final: 0.9234 (tp30) REVERT: B 164 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7619 (tm-30) REVERT: B 194 ASP cc_start: 0.8605 (m-30) cc_final: 0.7921 (m-30) REVERT: C 20 GLN cc_start: 0.9297 (OUTLIER) cc_final: 0.8926 (pm20) REVERT: C 70 GLU cc_start: 0.8252 (pp20) cc_final: 0.8013 (pp20) REVERT: C 109 GLU cc_start: 0.8938 (tp30) cc_final: 0.8256 (tt0) REVERT: C 128 GLU cc_start: 0.9536 (tp30) cc_final: 0.9234 (tp30) REVERT: C 164 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7621 (tm-30) REVERT: C 194 ASP cc_start: 0.8605 (m-30) cc_final: 0.7895 (m-30) REVERT: D 20 GLN cc_start: 0.9293 (OUTLIER) cc_final: 0.8920 (pm20) REVERT: D 109 GLU cc_start: 0.8916 (tp30) cc_final: 0.8214 (tt0) REVERT: D 128 GLU cc_start: 0.9528 (tp30) cc_final: 0.9217 (tp30) REVERT: D 149 GLU cc_start: 0.9231 (mp0) cc_final: 0.8978 (mp0) REVERT: D 164 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7604 (tm-30) REVERT: D 194 ASP cc_start: 0.8593 (m-30) cc_final: 0.7910 (m-30) REVERT: G 36 TYR cc_start: 0.9266 (m-80) cc_final: 0.8932 (m-80) REVERT: G 45 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8912 (ttpt) REVERT: G 49 TYR cc_start: 0.9279 (p90) cc_final: 0.8965 (p90) REVERT: G 50 GLU cc_start: 0.9340 (mt-10) cc_final: 0.9007 (mp0) REVERT: G 67 SER cc_start: 0.9179 (m) cc_final: 0.8942 (p) REVERT: G 93 ASP cc_start: 0.9341 (t0) cc_final: 0.8926 (t70) REVERT: G 103 LYS cc_start: 0.9288 (mttt) cc_final: 0.8775 (mtpp) REVERT: G 105 GLU cc_start: 0.7840 (tp30) cc_final: 0.7461 (tp30) REVERT: G 106 ILE cc_start: 0.8738 (mt) cc_final: 0.8252 (pp) REVERT: G 185 ASP cc_start: 0.7804 (OUTLIER) cc_final: 0.7367 (p0) REVERT: H 3 GLN cc_start: 0.9106 (pm20) cc_final: 0.8710 (pm20) REVERT: H 6 GLU cc_start: 0.8225 (mp0) cc_final: 0.7186 (mp0) REVERT: H 46 GLU cc_start: 0.8859 (tt0) cc_final: 0.8473 (pt0) REVERT: H 72 ASP cc_start: 0.8916 (t0) cc_final: 0.8444 (t0) REVERT: H 95 ASP cc_start: 0.9530 (t0) cc_final: 0.9092 (t0) REVERT: H 105 GLN cc_start: 0.9432 (mt0) cc_final: 0.9092 (pm20) REVERT: H 163 LEU cc_start: 0.9558 (mp) cc_final: 0.9251 (tm) REVERT: H 199 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8555 (tp) REVERT: H 213 LYS cc_start: 0.7606 (OUTLIER) cc_final: 0.7323 (ttpp) REVERT: F 3 GLN cc_start: 0.9123 (pm20) cc_final: 0.8790 (pm20) REVERT: F 6 GLU cc_start: 0.8204 (mp0) cc_final: 0.7186 (mp0) REVERT: F 46 GLU cc_start: 0.8861 (tt0) cc_final: 0.8457 (pt0) REVERT: F 72 ASP cc_start: 0.8924 (t0) cc_final: 0.8455 (t0) REVERT: F 95 ASP cc_start: 0.9529 (t0) cc_final: 0.9086 (t0) REVERT: F 105 GLN cc_start: 0.9440 (mt0) cc_final: 0.9088 (pm20) REVERT: J 3 GLN cc_start: 0.9103 (pm20) cc_final: 0.8774 (pm20) REVERT: J 6 GLU cc_start: 0.8218 (mp0) cc_final: 0.7188 (mp0) REVERT: J 26 ARG cc_start: 0.8643 (tmm-80) cc_final: 0.7926 (tmm-80) REVERT: J 27 PHE cc_start: 0.8545 (OUTLIER) cc_final: 0.8252 (m-80) REVERT: J 46 GLU cc_start: 0.8836 (tt0) cc_final: 0.8435 (pt0) REVERT: J 72 ASP cc_start: 0.8924 (t0) cc_final: 0.8471 (t0) REVERT: J 95 ASP cc_start: 0.9527 (t0) cc_final: 0.9117 (t0) REVERT: J 105 GLN cc_start: 0.9433 (mt0) cc_final: 0.9081 (pm20) REVERT: J 163 LEU cc_start: 0.9557 (mp) cc_final: 0.9252 (tm) REVERT: J 199 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8539 (tp) REVERT: J 213 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7383 (ttpp) REVERT: K 3 GLN cc_start: 0.9093 (pm20) cc_final: 0.8761 (pm20) REVERT: K 6 GLU cc_start: 0.8191 (mp0) cc_final: 0.7173 (mp0) REVERT: K 26 ARG cc_start: 0.8655 (tmm-80) cc_final: 0.7941 (tmm-80) REVERT: K 27 PHE cc_start: 0.8542 (OUTLIER) cc_final: 0.8248 (m-80) REVERT: K 46 GLU cc_start: 0.8850 (tt0) cc_final: 0.8450 (pt0) REVERT: K 72 ASP cc_start: 0.8916 (t0) cc_final: 0.8443 (t0) REVERT: K 95 ASP cc_start: 0.9531 (t0) cc_final: 0.9088 (t0) REVERT: K 105 GLN cc_start: 0.9434 (mt0) cc_final: 0.9079 (pm20) REVERT: E 27 LYS cc_start: 0.9397 (OUTLIER) cc_final: 0.8989 (pmtt) REVERT: E 36 TYR cc_start: 0.9262 (m-80) cc_final: 0.8925 (m-80) REVERT: E 45 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8925 (ttpt) REVERT: E 49 TYR cc_start: 0.9282 (p90) cc_final: 0.8960 (p90) REVERT: E 50 GLU cc_start: 0.9344 (mt-10) cc_final: 0.8989 (mp0) REVERT: E 67 SER cc_start: 0.9162 (m) cc_final: 0.8925 (p) REVERT: E 93 ASP cc_start: 0.9380 (t0) cc_final: 0.8960 (t70) REVERT: E 103 LYS cc_start: 0.9286 (mttt) cc_final: 0.8765 (mtpp) REVERT: E 105 GLU cc_start: 0.7839 (tp30) cc_final: 0.7358 (tp30) REVERT: E 106 ILE cc_start: 0.8717 (mt) cc_final: 0.8230 (pp) REVERT: E 185 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7655 (p0) REVERT: E 195 GLU cc_start: 0.5558 (OUTLIER) cc_final: 0.5207 (tm-30) REVERT: E 196 VAL cc_start: 0.8997 (OUTLIER) cc_final: 0.8754 (m) REVERT: I 36 TYR cc_start: 0.9286 (m-80) cc_final: 0.8979 (m-80) REVERT: I 45 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8917 (ttpt) REVERT: I 49 TYR cc_start: 0.9291 (p90) cc_final: 0.8965 (p90) REVERT: I 50 GLU cc_start: 0.9334 (mt-10) cc_final: 0.8999 (mp0) REVERT: I 67 SER cc_start: 0.9161 (m) cc_final: 0.8917 (p) REVERT: I 93 ASP cc_start: 0.9383 (t0) cc_final: 0.8970 (t70) REVERT: I 103 LYS cc_start: 0.9300 (mttt) cc_final: 0.8793 (mtpp) REVERT: I 105 GLU cc_start: 0.7818 (tp30) cc_final: 0.7453 (tp30) REVERT: I 106 ILE cc_start: 0.8743 (mt) cc_final: 0.8262 (pp) REVERT: I 185 ASP cc_start: 0.7839 (OUTLIER) cc_final: 0.7369 (p0) REVERT: L 36 TYR cc_start: 0.9250 (m-80) cc_final: 0.8899 (m-80) REVERT: L 45 LYS cc_start: 0.9177 (OUTLIER) cc_final: 0.8924 (ttpt) REVERT: L 49 TYR cc_start: 0.9283 (p90) cc_final: 0.8963 (p90) REVERT: L 50 GLU cc_start: 0.9340 (mt-10) cc_final: 0.8985 (mp0) REVERT: L 67 SER cc_start: 0.9183 (m) cc_final: 0.8950 (p) REVERT: L 93 ASP cc_start: 0.9383 (t0) cc_final: 0.8967 (t70) REVERT: L 103 LYS cc_start: 0.9295 (mttt) cc_final: 0.8793 (mtpp) REVERT: L 105 GLU cc_start: 0.7827 (tp30) cc_final: 0.7343 (tp30) REVERT: L 106 ILE cc_start: 0.8713 (mt) cc_final: 0.8228 (pp) REVERT: L 185 ASP cc_start: 0.7846 (OUTLIER) cc_final: 0.7368 (p0) REVERT: L 195 GLU cc_start: 0.5538 (OUTLIER) cc_final: 0.5190 (tm-30) REVERT: L 196 VAL cc_start: 0.8995 (OUTLIER) cc_final: 0.8752 (m) outliers start: 97 outliers final: 40 residues processed: 476 average time/residue: 0.5139 time to fit residues: 280.8277 Evaluate side-chains 449 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 382 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain D residue 20 GLN Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 194 CYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain H residue 213 LYS Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 27 PHE Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 199 ILE Chi-restraints excluded: chain J residue 213 LYS Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 27 PHE Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 194 CYS Chi-restraints excluded: chain E residue 195 GLU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 194 CYS Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 159 SER Chi-restraints excluded: chain L residue 185 ASP Chi-restraints excluded: chain L residue 194 CYS Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 182 optimal weight: 5.9990 chunk 202 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 237 optimal weight: 2.9990 chunk 158 optimal weight: 7.9990 chunk 201 optimal weight: 0.9980 chunk 188 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 200 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN B 146 ASN C 146 ASN D 146 ASN G 124 GLN H 76 ASN H 77 GLN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 GLN F 203 ASN J 76 ASN J 77 GLN K 76 ASN K 77 GLN K 203 ASN E 124 GLN I 124 GLN L 124 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.088098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.059070 restraints weight = 51484.550| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 3.99 r_work: 0.2709 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 21048 Z= 0.232 Angle : 0.699 8.189 28752 Z= 0.361 Chirality : 0.047 0.167 3224 Planarity : 0.005 0.060 3668 Dihedral : 5.314 20.983 2860 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.89 % Allowed : 19.90 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.16), residues: 2636 helix: -1.72 (0.38), residues: 144 sheet: 0.59 (0.17), residues: 804 loop : -0.40 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 150 TYR 0.019 0.002 TYR D 233 PHE 0.042 0.002 PHE L 209 TRP 0.015 0.001 TRP K 158 HIS 0.004 0.001 HIS C 173 Details of bonding type rmsd covalent geometry : bond 0.00516 (21016) covalent geometry : angle 0.69703 (28688) SS BOND : bond 0.00683 ( 32) SS BOND : angle 1.24480 ( 64) hydrogen bonds : bond 0.03256 ( 724) hydrogen bonds : angle 5.63479 ( 1980) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 401 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLN cc_start: 0.9347 (OUTLIER) cc_final: 0.8982 (pm20) REVERT: A 109 GLU cc_start: 0.8983 (tp30) cc_final: 0.8355 (tt0) REVERT: A 110 GLU cc_start: 0.9072 (mp0) cc_final: 0.8785 (mp0) REVERT: A 128 GLU cc_start: 0.9542 (tp30) cc_final: 0.9249 (tp30) REVERT: A 164 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7592 (tm-30) REVERT: A 180 MET cc_start: 0.9514 (mtm) cc_final: 0.9198 (mtm) REVERT: A 194 ASP cc_start: 0.8623 (m-30) cc_final: 0.7913 (m-30) REVERT: B 20 GLN cc_start: 0.9249 (OUTLIER) cc_final: 0.8871 (pm20) REVERT: B 109 GLU cc_start: 0.8956 (tp30) cc_final: 0.8351 (tt0) REVERT: B 128 GLU cc_start: 0.9545 (tp30) cc_final: 0.9247 (tp30) REVERT: B 164 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7591 (tm-30) REVERT: B 180 MET cc_start: 0.9491 (mtm) cc_final: 0.9185 (mtm) REVERT: B 194 ASP cc_start: 0.8630 (m-30) cc_final: 0.7896 (m-30) REVERT: C 20 GLN cc_start: 0.9305 (OUTLIER) cc_final: 0.8893 (pm20) REVERT: C 70 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8158 (pp20) REVERT: C 109 GLU cc_start: 0.8938 (tp30) cc_final: 0.8274 (tt0) REVERT: C 128 GLU cc_start: 0.9539 (tp30) cc_final: 0.9238 (tp30) REVERT: C 164 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7587 (tm-30) REVERT: C 180 MET cc_start: 0.9518 (mtm) cc_final: 0.9200 (mtm) REVERT: C 194 ASP cc_start: 0.8659 (m-30) cc_final: 0.7939 (m-30) REVERT: D 20 GLN cc_start: 0.9309 (OUTLIER) cc_final: 0.8886 (pm20) REVERT: D 109 GLU cc_start: 0.8921 (tp30) cc_final: 0.8281 (tt0) REVERT: D 128 GLU cc_start: 0.9530 (tp30) cc_final: 0.9223 (tp30) REVERT: D 164 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7571 (tm-30) REVERT: D 180 MET cc_start: 0.9531 (mtm) cc_final: 0.9204 (mtm) REVERT: D 194 ASP cc_start: 0.8617 (m-30) cc_final: 0.7879 (m-30) REVERT: G 36 TYR cc_start: 0.9203 (m-80) cc_final: 0.8965 (m-80) REVERT: G 45 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8930 (ttpt) REVERT: G 49 TYR cc_start: 0.9299 (p90) cc_final: 0.8983 (p90) REVERT: G 50 GLU cc_start: 0.9387 (mt-10) cc_final: 0.8990 (mp0) REVERT: G 67 SER cc_start: 0.9197 (m) cc_final: 0.8949 (p) REVERT: G 81 GLU cc_start: 0.9339 (mp0) cc_final: 0.9096 (pm20) REVERT: G 93 ASP cc_start: 0.9336 (t0) cc_final: 0.8945 (t0) REVERT: G 103 LYS cc_start: 0.9331 (mttt) cc_final: 0.8794 (mtpp) REVERT: G 105 GLU cc_start: 0.8128 (tp30) cc_final: 0.7694 (tp30) REVERT: G 106 ILE cc_start: 0.8768 (mt) cc_final: 0.8300 (pp) REVERT: G 185 ASP cc_start: 0.7919 (OUTLIER) cc_final: 0.7507 (p0) REVERT: H 3 GLN cc_start: 0.9086 (pm20) cc_final: 0.8711 (pm20) REVERT: H 6 GLU cc_start: 0.8212 (mp0) cc_final: 0.7175 (mp0) REVERT: H 46 GLU cc_start: 0.8856 (tt0) cc_final: 0.8449 (pt0) REVERT: H 72 ASP cc_start: 0.8905 (t0) cc_final: 0.8468 (t0) REVERT: H 95 ASP cc_start: 0.9553 (t0) cc_final: 0.9137 (t0) REVERT: H 105 GLN cc_start: 0.9428 (mt0) cc_final: 0.9095 (pm20) REVERT: H 163 LEU cc_start: 0.9589 (mp) cc_final: 0.9291 (tm) REVERT: H 199 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8597 (tp) REVERT: H 213 LYS cc_start: 0.7752 (OUTLIER) cc_final: 0.7458 (ttpp) REVERT: F 3 GLN cc_start: 0.9113 (pm20) cc_final: 0.8773 (pm20) REVERT: F 6 GLU cc_start: 0.8212 (mp0) cc_final: 0.7216 (mp0) REVERT: F 26 ARG cc_start: 0.8434 (tmm-80) cc_final: 0.8046 (tmm-80) REVERT: F 27 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.8377 (m-80) REVERT: F 46 GLU cc_start: 0.8865 (tt0) cc_final: 0.8449 (pt0) REVERT: F 72 ASP cc_start: 0.8923 (t0) cc_final: 0.8487 (t0) REVERT: F 95 ASP cc_start: 0.9552 (t0) cc_final: 0.9099 (t0) REVERT: F 105 GLN cc_start: 0.9421 (mt0) cc_final: 0.9066 (pm20) REVERT: J 3 GLN cc_start: 0.9130 (pm20) cc_final: 0.8787 (pm20) REVERT: J 6 GLU cc_start: 0.8233 (mp0) cc_final: 0.7205 (mp0) REVERT: J 46 GLU cc_start: 0.8852 (tt0) cc_final: 0.8441 (pt0) REVERT: J 72 ASP cc_start: 0.8918 (t0) cc_final: 0.8478 (t0) REVERT: J 95 ASP cc_start: 0.9564 (t0) cc_final: 0.9063 (t0) REVERT: J 105 GLN cc_start: 0.9431 (mt0) cc_final: 0.9087 (pm20) REVERT: J 163 LEU cc_start: 0.9594 (mp) cc_final: 0.9305 (tm) REVERT: J 199 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8593 (tp) REVERT: K 3 GLN cc_start: 0.9114 (pm20) cc_final: 0.8769 (pm20) REVERT: K 6 GLU cc_start: 0.8190 (mp0) cc_final: 0.7169 (mp0) REVERT: K 46 GLU cc_start: 0.8857 (tt0) cc_final: 0.8455 (pt0) REVERT: K 72 ASP cc_start: 0.8912 (t0) cc_final: 0.8476 (t0) REVERT: K 95 ASP cc_start: 0.9553 (t0) cc_final: 0.9099 (t0) REVERT: K 105 GLN cc_start: 0.9438 (mt0) cc_final: 0.9087 (pm20) REVERT: E 27 LYS cc_start: 0.9449 (OUTLIER) cc_final: 0.9075 (pmtt) REVERT: E 36 TYR cc_start: 0.9198 (m-80) cc_final: 0.8966 (m-80) REVERT: E 45 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8935 (ttpt) REVERT: E 49 TYR cc_start: 0.9306 (p90) cc_final: 0.8980 (p90) REVERT: E 50 GLU cc_start: 0.9389 (mt-10) cc_final: 0.8991 (mp0) REVERT: E 67 SER cc_start: 0.9190 (m) cc_final: 0.8941 (p) REVERT: E 81 GLU cc_start: 0.9336 (mp0) cc_final: 0.9104 (pm20) REVERT: E 93 ASP cc_start: 0.9390 (t0) cc_final: 0.8968 (t70) REVERT: E 103 LYS cc_start: 0.9337 (mttt) cc_final: 0.8799 (mtpp) REVERT: E 105 GLU cc_start: 0.8038 (tp30) cc_final: 0.7644 (tp30) REVERT: E 106 ILE cc_start: 0.8777 (mt) cc_final: 0.8319 (pp) REVERT: E 185 ASP cc_start: 0.7982 (OUTLIER) cc_final: 0.7504 (p0) REVERT: E 196 VAL cc_start: 0.8966 (OUTLIER) cc_final: 0.8757 (m) REVERT: I 36 TYR cc_start: 0.9195 (m-80) cc_final: 0.8936 (m-80) REVERT: I 45 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8924 (ttpt) REVERT: I 49 TYR cc_start: 0.9307 (p90) cc_final: 0.8969 (p90) REVERT: I 50 GLU cc_start: 0.9371 (mt-10) cc_final: 0.8973 (mp0) REVERT: I 67 SER cc_start: 0.9189 (m) cc_final: 0.8938 (p) REVERT: I 81 GLU cc_start: 0.9347 (mp0) cc_final: 0.9114 (pm20) REVERT: I 93 ASP cc_start: 0.9395 (t0) cc_final: 0.8974 (t70) REVERT: I 103 LYS cc_start: 0.9369 (mttt) cc_final: 0.8838 (mtpp) REVERT: I 105 GLU cc_start: 0.8128 (tp30) cc_final: 0.7707 (tp30) REVERT: I 106 ILE cc_start: 0.8768 (mt) cc_final: 0.8305 (pp) REVERT: I 185 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7507 (p0) REVERT: L 36 TYR cc_start: 0.9169 (m-80) cc_final: 0.8938 (m-80) REVERT: L 49 TYR cc_start: 0.9299 (p90) cc_final: 0.8980 (p90) REVERT: L 50 GLU cc_start: 0.9380 (mt-10) cc_final: 0.8989 (mp0) REVERT: L 67 SER cc_start: 0.9190 (m) cc_final: 0.8943 (p) REVERT: L 81 GLU cc_start: 0.9341 (mp0) cc_final: 0.9110 (pm20) REVERT: L 93 ASP cc_start: 0.9402 (t0) cc_final: 0.8982 (t70) REVERT: L 103 LYS cc_start: 0.9362 (mttt) cc_final: 0.8829 (mtpp) REVERT: L 105 GLU cc_start: 0.8030 (tp30) cc_final: 0.7635 (tp30) REVERT: L 106 ILE cc_start: 0.8774 (mt) cc_final: 0.8317 (pp) REVERT: L 185 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.7506 (p0) REVERT: L 196 VAL cc_start: 0.8964 (OUTLIER) cc_final: 0.8757 (m) outliers start: 112 outliers final: 56 residues processed: 479 average time/residue: 0.5335 time to fit residues: 295.4343 Evaluate side-chains 462 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 383 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain D residue 20 GLN Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 183 LYS Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 194 CYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain H residue 213 LYS Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 213 LYS Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 27 PHE Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain J residue 199 ILE Chi-restraints excluded: chain J residue 213 LYS Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 27 PHE Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 213 LYS Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 194 CYS Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 183 LYS Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 194 CYS Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 159 SER Chi-restraints excluded: chain L residue 183 LYS Chi-restraints excluded: chain L residue 185 ASP Chi-restraints excluded: chain L residue 194 CYS Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 156 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 146 optimal weight: 0.4980 chunk 116 optimal weight: 0.6980 chunk 91 optimal weight: 0.0170 chunk 10 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 122 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 157 optimal weight: 4.9990 chunk 258 optimal weight: 7.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN B 146 ASN C 146 ASN G 30 ASN G 79 GLN H 76 ASN H 77 GLN H 208 ASN F 76 ASN F 77 GLN F 208 ASN J 76 ASN J 77 GLN J 208 ASN K 76 ASN K 77 GLN K 208 ASN E 30 ASN E 79 GLN I 79 GLN L 30 ASN L 79 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.090215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.061223 restraints weight = 50916.111| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 3.99 r_work: 0.2760 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21048 Z= 0.132 Angle : 0.680 8.117 28752 Z= 0.349 Chirality : 0.046 0.180 3224 Planarity : 0.005 0.061 3668 Dihedral : 5.092 19.333 2860 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.32 % Allowed : 21.03 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.16), residues: 2636 helix: -1.32 (0.39), residues: 144 sheet: 0.65 (0.17), residues: 860 loop : -0.29 (0.16), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 142 TYR 0.019 0.001 TYR D 233 PHE 0.045 0.002 PHE G 209 TRP 0.015 0.001 TRP K 158 HIS 0.003 0.001 HIS C 173 Details of bonding type rmsd covalent geometry : bond 0.00303 (21016) covalent geometry : angle 0.67872 (28688) SS BOND : bond 0.00634 ( 32) SS BOND : angle 0.99823 ( 64) hydrogen bonds : bond 0.02956 ( 724) hydrogen bonds : angle 5.31552 ( 1980) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 434 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLN cc_start: 0.9401 (OUTLIER) cc_final: 0.9015 (pm20) REVERT: A 31 VAL cc_start: 0.9680 (OUTLIER) cc_final: 0.9463 (p) REVERT: A 109 GLU cc_start: 0.8993 (tp30) cc_final: 0.8260 (tt0) REVERT: A 110 GLU cc_start: 0.9024 (mp0) cc_final: 0.8786 (mp0) REVERT: A 128 GLU cc_start: 0.9533 (tp30) cc_final: 0.9229 (tp30) REVERT: A 164 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7651 (tm-30) REVERT: A 180 MET cc_start: 0.9476 (mtm) cc_final: 0.9209 (mtm) REVERT: A 194 ASP cc_start: 0.8550 (m-30) cc_final: 0.7982 (m-30) REVERT: A 217 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8637 (mt-10) REVERT: B 20 GLN cc_start: 0.9330 (OUTLIER) cc_final: 0.8907 (pm20) REVERT: B 109 GLU cc_start: 0.8919 (tp30) cc_final: 0.8534 (tp30) REVERT: B 128 GLU cc_start: 0.9538 (tp30) cc_final: 0.9230 (tp30) REVERT: B 164 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7597 (tm-30) REVERT: B 180 MET cc_start: 0.9465 (mtm) cc_final: 0.9197 (mtm) REVERT: B 194 ASP cc_start: 0.8575 (m-30) cc_final: 0.7950 (m-30) REVERT: B 217 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8690 (mt-10) REVERT: C 109 GLU cc_start: 0.8903 (tp30) cc_final: 0.8471 (tp30) REVERT: C 128 GLU cc_start: 0.9531 (tp30) cc_final: 0.9218 (tp30) REVERT: C 164 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7644 (tm-30) REVERT: C 180 MET cc_start: 0.9482 (mtm) cc_final: 0.9215 (mtm) REVERT: C 194 ASP cc_start: 0.8564 (m-30) cc_final: 0.7828 (m-30) REVERT: D 109 GLU cc_start: 0.8906 (tp30) cc_final: 0.8468 (tp30) REVERT: D 128 GLU cc_start: 0.9525 (tp30) cc_final: 0.9209 (tp30) REVERT: D 164 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7612 (tm-30) REVERT: D 180 MET cc_start: 0.9484 (mtm) cc_final: 0.9172 (mtm) REVERT: D 194 ASP cc_start: 0.8544 (m-30) cc_final: 0.7793 (m-30) REVERT: D 217 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8628 (mt-10) REVERT: G 36 TYR cc_start: 0.9139 (m-80) cc_final: 0.8796 (m-80) REVERT: G 45 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8931 (ttpt) REVERT: G 49 TYR cc_start: 0.9227 (p90) cc_final: 0.8915 (p90) REVERT: G 50 GLU cc_start: 0.9321 (mt-10) cc_final: 0.8918 (mp0) REVERT: G 67 SER cc_start: 0.9176 (m) cc_final: 0.8926 (p) REVERT: G 81 GLU cc_start: 0.9340 (mp0) cc_final: 0.9100 (pm20) REVERT: G 93 ASP cc_start: 0.9322 (t0) cc_final: 0.8939 (t70) REVERT: G 103 LYS cc_start: 0.9270 (mttt) cc_final: 0.8747 (mtpp) REVERT: G 167 ASP cc_start: 0.8744 (t70) cc_final: 0.8341 (t70) REVERT: G 185 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.7544 (p0) REVERT: H 3 GLN cc_start: 0.9065 (pm20) cc_final: 0.8718 (pm20) REVERT: H 6 GLU cc_start: 0.8273 (mp0) cc_final: 0.7566 (mp0) REVERT: H 46 GLU cc_start: 0.8837 (tt0) cc_final: 0.8488 (pt0) REVERT: H 72 ASP cc_start: 0.8918 (t0) cc_final: 0.8488 (t0) REVERT: H 92 CYS cc_start: 0.7201 (p) cc_final: 0.6705 (p) REVERT: H 95 ASP cc_start: 0.9544 (t0) cc_final: 0.8975 (t0) REVERT: H 100 LEU cc_start: 0.9574 (mt) cc_final: 0.9363 (mt) REVERT: H 105 GLN cc_start: 0.9408 (mt0) cc_final: 0.9077 (pm20) REVERT: H 163 LEU cc_start: 0.9606 (mp) cc_final: 0.9353 (tm) REVERT: H 199 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8575 (tp) REVERT: H 203 ASN cc_start: 0.8805 (m-40) cc_final: 0.8530 (t0) REVERT: F 3 GLN cc_start: 0.9063 (pm20) cc_final: 0.8704 (pm20) REVERT: F 6 GLU cc_start: 0.8251 (mp0) cc_final: 0.7573 (mp0) REVERT: F 26 ARG cc_start: 0.8481 (tmm-80) cc_final: 0.8169 (tmm-80) REVERT: F 27 PHE cc_start: 0.8688 (OUTLIER) cc_final: 0.8387 (m-80) REVERT: F 46 GLU cc_start: 0.8856 (tt0) cc_final: 0.8494 (pt0) REVERT: F 72 ASP cc_start: 0.8934 (t0) cc_final: 0.8505 (t0) REVERT: F 92 CYS cc_start: 0.7195 (p) cc_final: 0.6704 (p) REVERT: F 95 ASP cc_start: 0.9524 (t0) cc_final: 0.9013 (t0) REVERT: F 105 GLN cc_start: 0.9420 (mt0) cc_final: 0.9072 (pm20) REVERT: F 186 VAL cc_start: 0.9436 (OUTLIER) cc_final: 0.9197 (m) REVERT: F 203 ASN cc_start: 0.8763 (m-40) cc_final: 0.8516 (t0) REVERT: J 3 GLN cc_start: 0.9085 (pm20) cc_final: 0.8712 (pm20) REVERT: J 6 GLU cc_start: 0.8249 (mp0) cc_final: 0.7535 (mp0) REVERT: J 26 ARG cc_start: 0.8416 (tmm-80) cc_final: 0.8030 (tmm-80) REVERT: J 27 PHE cc_start: 0.8654 (OUTLIER) cc_final: 0.8368 (m-80) REVERT: J 46 GLU cc_start: 0.8843 (tt0) cc_final: 0.8467 (pt0) REVERT: J 72 ASP cc_start: 0.8927 (t0) cc_final: 0.8494 (t0) REVERT: J 77 GLN cc_start: 0.9047 (mt0) cc_final: 0.8847 (mt0) REVERT: J 92 CYS cc_start: 0.7217 (p) cc_final: 0.6720 (p) REVERT: J 95 ASP cc_start: 0.9509 (t0) cc_final: 0.8991 (t0) REVERT: J 105 GLN cc_start: 0.9407 (mt0) cc_final: 0.9067 (pm20) REVERT: J 163 LEU cc_start: 0.9613 (mp) cc_final: 0.9354 (tm) REVERT: J 199 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8569 (tp) REVERT: J 203 ASN cc_start: 0.8791 (m-40) cc_final: 0.8517 (t0) REVERT: K 3 GLN cc_start: 0.9074 (pm20) cc_final: 0.8702 (pm20) REVERT: K 6 GLU cc_start: 0.8221 (mp0) cc_final: 0.7539 (mp0) REVERT: K 26 ARG cc_start: 0.8426 (tmm-80) cc_final: 0.8035 (tmm-80) REVERT: K 27 PHE cc_start: 0.8660 (OUTLIER) cc_final: 0.8371 (m-80) REVERT: K 38 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8332 (ttp80) REVERT: K 46 GLU cc_start: 0.8860 (tt0) cc_final: 0.8379 (tt0) REVERT: K 72 ASP cc_start: 0.8929 (t0) cc_final: 0.8496 (t0) REVERT: K 77 GLN cc_start: 0.9060 (mt0) cc_final: 0.8860 (mt0) REVERT: K 92 CYS cc_start: 0.7163 (p) cc_final: 0.6665 (p) REVERT: K 95 ASP cc_start: 0.9528 (t0) cc_final: 0.9011 (t0) REVERT: K 105 GLN cc_start: 0.9421 (mt0) cc_final: 0.9070 (pm20) REVERT: K 186 VAL cc_start: 0.9436 (OUTLIER) cc_final: 0.9197 (m) REVERT: K 203 ASN cc_start: 0.8799 (m-40) cc_final: 0.8551 (t0) REVERT: E 18 ARG cc_start: 0.9083 (ppp80) cc_final: 0.8796 (ttp-110) REVERT: E 27 LYS cc_start: 0.9457 (OUTLIER) cc_final: 0.9074 (pmtt) REVERT: E 36 TYR cc_start: 0.9128 (m-80) cc_final: 0.8791 (m-80) REVERT: E 45 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8938 (ttpt) REVERT: E 49 TYR cc_start: 0.9236 (p90) cc_final: 0.8923 (p90) REVERT: E 50 GLU cc_start: 0.9333 (mt-10) cc_final: 0.8927 (mp0) REVERT: E 67 SER cc_start: 0.9169 (m) cc_final: 0.8918 (p) REVERT: E 81 GLU cc_start: 0.9338 (mp0) cc_final: 0.9119 (pm20) REVERT: E 93 ASP cc_start: 0.9365 (t0) cc_final: 0.8962 (t70) REVERT: E 103 LYS cc_start: 0.9282 (mttt) cc_final: 0.8735 (mtpp) REVERT: E 167 ASP cc_start: 0.8748 (t70) cc_final: 0.8338 (t70) REVERT: E 185 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7649 (p0) REVERT: E 195 GLU cc_start: 0.5419 (OUTLIER) cc_final: 0.5111 (tm-30) REVERT: I 18 ARG cc_start: 0.9080 (ppp80) cc_final: 0.8785 (ttp-110) REVERT: I 45 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8929 (ttpt) REVERT: I 49 TYR cc_start: 0.9239 (p90) cc_final: 0.8916 (p90) REVERT: I 50 GLU cc_start: 0.9323 (mt-10) cc_final: 0.8910 (mp0) REVERT: I 67 SER cc_start: 0.9172 (m) cc_final: 0.8926 (p) REVERT: I 81 GLU cc_start: 0.9345 (mp0) cc_final: 0.9116 (pm20) REVERT: I 93 ASP cc_start: 0.9372 (t0) cc_final: 0.8988 (t70) REVERT: I 103 LYS cc_start: 0.9284 (mttt) cc_final: 0.8760 (mtpp) REVERT: I 185 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7541 (p0) REVERT: L 36 TYR cc_start: 0.9104 (m-80) cc_final: 0.8848 (m-80) REVERT: L 45 LYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8937 (ttpt) REVERT: L 49 TYR cc_start: 0.9230 (p90) cc_final: 0.8926 (p90) REVERT: L 50 GLU cc_start: 0.9333 (mt-10) cc_final: 0.8927 (mp0) REVERT: L 67 SER cc_start: 0.9178 (m) cc_final: 0.8933 (p) REVERT: L 81 GLU cc_start: 0.9335 (mp0) cc_final: 0.9129 (pm20) REVERT: L 93 ASP cc_start: 0.9377 (t0) cc_final: 0.8993 (t70) REVERT: L 103 LYS cc_start: 0.9282 (mttt) cc_final: 0.8742 (mtpp) REVERT: L 167 ASP cc_start: 0.8772 (t70) cc_final: 0.8376 (t70) REVERT: L 185 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7543 (p0) REVERT: L 195 GLU cc_start: 0.5423 (OUTLIER) cc_final: 0.5119 (tm-30) outliers start: 99 outliers final: 41 residues processed: 495 average time/residue: 0.4390 time to fit residues: 254.6948 Evaluate side-chains 469 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 402 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 183 LYS Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 194 CYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 27 PHE Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain J residue 199 ILE Chi-restraints excluded: chain J residue 213 LYS Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 27 PHE Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 194 CYS Chi-restraints excluded: chain E residue 195 GLU Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 183 LYS Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 194 CYS Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 183 LYS Chi-restraints excluded: chain L residue 185 ASP Chi-restraints excluded: chain L residue 194 CYS Chi-restraints excluded: chain L residue 195 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 228 optimal weight: 0.0370 chunk 57 optimal weight: 0.9980 chunk 157 optimal weight: 7.9990 chunk 21 optimal weight: 0.0030 chunk 90 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 219 optimal weight: 0.9980 chunk 194 optimal weight: 3.9990 chunk 180 optimal weight: 0.7980 chunk 148 optimal weight: 3.9990 overall best weight: 0.5668 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN B 146 ASN C 146 ASN D 146 ASN H 76 ASN F 76 ASN J 76 ASN K 76 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.090430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.061424 restraints weight = 50685.519| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 4.03 r_work: 0.2774 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21048 Z= 0.137 Angle : 0.692 10.538 28752 Z= 0.351 Chirality : 0.045 0.152 3224 Planarity : 0.005 0.062 3668 Dihedral : 4.975 18.986 2860 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.93 % Allowed : 22.34 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.16), residues: 2636 helix: -1.13 (0.39), residues: 144 sheet: 0.73 (0.17), residues: 860 loop : -0.28 (0.16), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 142 TYR 0.015 0.001 TYR I 173 PHE 0.046 0.002 PHE L 209 TRP 0.015 0.001 TRP K 158 HIS 0.003 0.001 HIS C 173 Details of bonding type rmsd covalent geometry : bond 0.00322 (21016) covalent geometry : angle 0.69108 (28688) SS BOND : bond 0.00503 ( 32) SS BOND : angle 0.97366 ( 64) hydrogen bonds : bond 0.02920 ( 724) hydrogen bonds : angle 5.19580 ( 1980) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 419 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLN cc_start: 0.9416 (OUTLIER) cc_final: 0.9048 (pm20) REVERT: A 109 GLU cc_start: 0.8986 (tp30) cc_final: 0.8721 (tt0) REVERT: A 128 GLU cc_start: 0.9532 (tp30) cc_final: 0.9226 (tp30) REVERT: A 164 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7630 (tm-30) REVERT: A 180 MET cc_start: 0.9470 (mtm) cc_final: 0.9199 (mtm) REVERT: A 194 ASP cc_start: 0.8557 (m-30) cc_final: 0.7984 (m-30) REVERT: A 217 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8614 (mt-10) REVERT: B 20 GLN cc_start: 0.9347 (OUTLIER) cc_final: 0.8943 (pm20) REVERT: B 109 GLU cc_start: 0.8914 (tp30) cc_final: 0.8488 (tp30) REVERT: B 128 GLU cc_start: 0.9535 (tp30) cc_final: 0.9220 (tp30) REVERT: B 164 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7590 (tm-30) REVERT: B 180 MET cc_start: 0.9462 (mtm) cc_final: 0.9187 (mtm) REVERT: B 194 ASP cc_start: 0.8563 (m-30) cc_final: 0.7936 (m-30) REVERT: B 217 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8679 (mt-10) REVERT: C 20 GLN cc_start: 0.9368 (OUTLIER) cc_final: 0.8964 (pm20) REVERT: C 109 GLU cc_start: 0.8898 (tp30) cc_final: 0.8472 (tp30) REVERT: C 128 GLU cc_start: 0.9525 (tp30) cc_final: 0.9220 (tp30) REVERT: C 164 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7623 (tm-30) REVERT: C 180 MET cc_start: 0.9479 (mtm) cc_final: 0.9201 (mtm) REVERT: C 194 ASP cc_start: 0.8565 (m-30) cc_final: 0.7970 (m-30) REVERT: D 20 GLN cc_start: 0.9368 (OUTLIER) cc_final: 0.8991 (pm20) REVERT: D 109 GLU cc_start: 0.8893 (tp30) cc_final: 0.8419 (tp30) REVERT: D 128 GLU cc_start: 0.9529 (tp30) cc_final: 0.9210 (tp30) REVERT: D 164 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7586 (tm-30) REVERT: D 180 MET cc_start: 0.9460 (mtm) cc_final: 0.9170 (mtm) REVERT: D 194 ASP cc_start: 0.8535 (m-30) cc_final: 0.7949 (m-30) REVERT: D 217 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8616 (mt-10) REVERT: G 36 TYR cc_start: 0.9129 (m-80) cc_final: 0.8878 (m-80) REVERT: G 45 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8903 (ttpt) REVERT: G 49 TYR cc_start: 0.9199 (p90) cc_final: 0.8968 (p90) REVERT: G 50 GLU cc_start: 0.9306 (mt-10) cc_final: 0.8920 (mp0) REVERT: G 67 SER cc_start: 0.9168 (m) cc_final: 0.8919 (p) REVERT: G 81 GLU cc_start: 0.9323 (mp0) cc_final: 0.9060 (pm20) REVERT: G 93 ASP cc_start: 0.9303 (t0) cc_final: 0.8936 (t70) REVERT: G 103 LYS cc_start: 0.9266 (mttt) cc_final: 0.8745 (mtpp) REVERT: G 118 PHE cc_start: 0.8016 (m-80) cc_final: 0.7713 (m-80) REVERT: G 167 ASP cc_start: 0.8764 (t70) cc_final: 0.8349 (t70) REVERT: G 185 ASP cc_start: 0.7859 (OUTLIER) cc_final: 0.7502 (p0) REVERT: H 3 GLN cc_start: 0.9029 (pm20) cc_final: 0.8707 (pm20) REVERT: H 6 GLU cc_start: 0.8193 (mp0) cc_final: 0.7220 (mp0) REVERT: H 46 GLU cc_start: 0.8850 (tt0) cc_final: 0.8369 (tt0) REVERT: H 72 ASP cc_start: 0.8919 (t0) cc_final: 0.8492 (t0) REVERT: H 76 ASN cc_start: 0.8659 (t0) cc_final: 0.8386 (t0) REVERT: H 95 ASP cc_start: 0.9522 (t0) cc_final: 0.9009 (t0) REVERT: H 100 LEU cc_start: 0.9555 (mt) cc_final: 0.9337 (mt) REVERT: H 105 GLN cc_start: 0.9401 (mt0) cc_final: 0.9081 (pm20) REVERT: H 163 LEU cc_start: 0.9621 (mp) cc_final: 0.9363 (tm) REVERT: H 203 ASN cc_start: 0.8760 (m-40) cc_final: 0.8456 (t0) REVERT: F 3 GLN cc_start: 0.9071 (pm20) cc_final: 0.8731 (pm20) REVERT: F 6 GLU cc_start: 0.8201 (mp0) cc_final: 0.7252 (mp0) REVERT: F 26 ARG cc_start: 0.8485 (tmm-80) cc_final: 0.8183 (tmm-80) REVERT: F 27 PHE cc_start: 0.8676 (OUTLIER) cc_final: 0.8365 (m-80) REVERT: F 46 GLU cc_start: 0.8875 (tt0) cc_final: 0.8400 (tt0) REVERT: F 72 ASP cc_start: 0.8923 (t0) cc_final: 0.8495 (t0) REVERT: F 76 ASN cc_start: 0.8704 (t0) cc_final: 0.8407 (t0) REVERT: F 95 ASP cc_start: 0.9518 (t0) cc_final: 0.8991 (t0) REVERT: F 105 GLN cc_start: 0.9416 (mt0) cc_final: 0.9077 (pm20) REVERT: F 186 VAL cc_start: 0.9443 (OUTLIER) cc_final: 0.9214 (m) REVERT: F 203 ASN cc_start: 0.8811 (m-40) cc_final: 0.8560 (t0) REVERT: J 3 GLN cc_start: 0.9061 (pm20) cc_final: 0.8700 (pm20) REVERT: J 6 GLU cc_start: 0.8253 (mp0) cc_final: 0.7273 (mp0) REVERT: J 26 ARG cc_start: 0.8460 (tmm-80) cc_final: 0.8088 (tmm-80) REVERT: J 27 PHE cc_start: 0.8640 (OUTLIER) cc_final: 0.8332 (m-80) REVERT: J 46 GLU cc_start: 0.8852 (tt0) cc_final: 0.8384 (tt0) REVERT: J 72 ASP cc_start: 0.8932 (t0) cc_final: 0.8506 (t0) REVERT: J 76 ASN cc_start: 0.8701 (t0) cc_final: 0.8407 (t0) REVERT: J 95 ASP cc_start: 0.9504 (t0) cc_final: 0.8997 (t0) REVERT: J 100 LEU cc_start: 0.9673 (mt) cc_final: 0.9354 (mt) REVERT: J 105 GLN cc_start: 0.9405 (mt0) cc_final: 0.9074 (pm20) REVERT: J 163 LEU cc_start: 0.9624 (mp) cc_final: 0.9361 (tm) REVERT: J 199 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8602 (tp) REVERT: J 203 ASN cc_start: 0.8746 (m-40) cc_final: 0.8446 (t0) REVERT: K 3 GLN cc_start: 0.9047 (pm20) cc_final: 0.8688 (pm20) REVERT: K 6 GLU cc_start: 0.8216 (mp0) cc_final: 0.7264 (mp0) REVERT: K 26 ARG cc_start: 0.8467 (tmm-80) cc_final: 0.8090 (tmm-80) REVERT: K 27 PHE cc_start: 0.8641 (OUTLIER) cc_final: 0.8333 (m-80) REVERT: K 46 GLU cc_start: 0.8867 (tt0) cc_final: 0.8376 (tt0) REVERT: K 72 ASP cc_start: 0.8922 (t0) cc_final: 0.8496 (t0) REVERT: K 76 ASN cc_start: 0.8716 (t0) cc_final: 0.8421 (t0) REVERT: K 77 GLN cc_start: 0.9037 (mt0) cc_final: 0.8819 (mt0) REVERT: K 95 ASP cc_start: 0.9519 (t0) cc_final: 0.8989 (t0) REVERT: K 100 LEU cc_start: 0.9552 (mt) cc_final: 0.9338 (mt) REVERT: K 105 GLN cc_start: 0.9418 (mt0) cc_final: 0.9074 (pm20) REVERT: K 186 VAL cc_start: 0.9450 (OUTLIER) cc_final: 0.9225 (m) REVERT: K 203 ASN cc_start: 0.8793 (m-40) cc_final: 0.8545 (t0) REVERT: E 36 TYR cc_start: 0.9077 (m-80) cc_final: 0.8857 (m-80) REVERT: E 45 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8899 (ttpt) REVERT: E 49 TYR cc_start: 0.9205 (p90) cc_final: 0.8941 (p90) REVERT: E 50 GLU cc_start: 0.9320 (mt-10) cc_final: 0.8920 (mp0) REVERT: E 67 SER cc_start: 0.9162 (m) cc_final: 0.8915 (p) REVERT: E 81 GLU cc_start: 0.9321 (mp0) cc_final: 0.9063 (pm20) REVERT: E 93 ASP cc_start: 0.9334 (t0) cc_final: 0.8966 (t70) REVERT: E 103 LYS cc_start: 0.9264 (mttt) cc_final: 0.8727 (mtpp) REVERT: E 118 PHE cc_start: 0.8036 (m-80) cc_final: 0.7762 (m-80) REVERT: E 167 ASP cc_start: 0.8760 (t70) cc_final: 0.8353 (t70) REVERT: E 185 ASP cc_start: 0.7952 (OUTLIER) cc_final: 0.7583 (p0) REVERT: I 45 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8915 (ttpt) REVERT: I 49 TYR cc_start: 0.9215 (p90) cc_final: 0.8964 (p90) REVERT: I 50 GLU cc_start: 0.9301 (mt-10) cc_final: 0.8870 (mp0) REVERT: I 67 SER cc_start: 0.9167 (m) cc_final: 0.8922 (p) REVERT: I 81 GLU cc_start: 0.9324 (mp0) cc_final: 0.9065 (pm20) REVERT: I 93 ASP cc_start: 0.9337 (t0) cc_final: 0.8972 (t70) REVERT: I 103 LYS cc_start: 0.9272 (mttt) cc_final: 0.8739 (mtpp) REVERT: I 118 PHE cc_start: 0.7996 (m-80) cc_final: 0.7691 (m-80) REVERT: I 167 ASP cc_start: 0.8745 (t70) cc_final: 0.8329 (t70) REVERT: I 185 ASP cc_start: 0.7861 (OUTLIER) cc_final: 0.7500 (p0) REVERT: L 36 TYR cc_start: 0.9084 (m-80) cc_final: 0.8854 (m-80) REVERT: L 45 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8911 (ttpt) REVERT: L 49 TYR cc_start: 0.9204 (p90) cc_final: 0.8976 (p90) REVERT: L 50 GLU cc_start: 0.9315 (mt-10) cc_final: 0.8919 (mp0) REVERT: L 67 SER cc_start: 0.9182 (m) cc_final: 0.8943 (p) REVERT: L 81 GLU cc_start: 0.9323 (mp0) cc_final: 0.9068 (pm20) REVERT: L 93 ASP cc_start: 0.9339 (t0) cc_final: 0.8961 (t70) REVERT: L 103 LYS cc_start: 0.9274 (mttt) cc_final: 0.8734 (mtpp) REVERT: L 118 PHE cc_start: 0.8084 (m-80) cc_final: 0.7820 (m-80) REVERT: L 167 ASP cc_start: 0.8792 (t70) cc_final: 0.8379 (t70) REVERT: L 185 ASP cc_start: 0.7865 (OUTLIER) cc_final: 0.7509 (p0) outliers start: 90 outliers final: 37 residues processed: 471 average time/residue: 0.4794 time to fit residues: 261.4445 Evaluate side-chains 455 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 396 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain D residue 20 GLN Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 183 LYS Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 194 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 27 PHE Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain J residue 199 ILE Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 27 PHE Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 194 CYS Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 183 LYS Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 194 CYS Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 183 LYS Chi-restraints excluded: chain L residue 185 ASP Chi-restraints excluded: chain L residue 194 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 147 optimal weight: 0.5980 chunk 149 optimal weight: 0.9990 chunk 172 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 chunk 117 optimal weight: 0.4980 chunk 248 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 203 optimal weight: 0.6980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN B 146 ASN C 146 ASN D 146 ASN H 208 ASN F 208 ASN J 208 ASN K 208 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.090368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.061199 restraints weight = 50875.572| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 4.03 r_work: 0.2761 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21048 Z= 0.158 Angle : 0.708 10.529 28752 Z= 0.358 Chirality : 0.046 0.204 3224 Planarity : 0.005 0.063 3668 Dihedral : 4.924 19.399 2860 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.32 % Allowed : 23.30 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.16), residues: 2636 helix: -0.88 (0.41), residues: 144 sheet: 0.84 (0.18), residues: 780 loop : -0.33 (0.15), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 142 TYR 0.014 0.001 TYR G 173 PHE 0.022 0.002 PHE E 92 TRP 0.015 0.001 TRP F 158 HIS 0.003 0.001 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00367 (21016) covalent geometry : angle 0.70681 (28688) SS BOND : bond 0.00469 ( 32) SS BOND : angle 1.00396 ( 64) hydrogen bonds : bond 0.02935 ( 724) hydrogen bonds : angle 5.13737 ( 1980) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 421 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLN cc_start: 0.9429 (OUTLIER) cc_final: 0.9134 (pm20) REVERT: A 109 GLU cc_start: 0.8926 (tp30) cc_final: 0.8723 (tt0) REVERT: A 128 GLU cc_start: 0.9538 (tp30) cc_final: 0.9304 (tp30) REVERT: A 164 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7634 (tm-30) REVERT: A 180 MET cc_start: 0.9486 (mtm) cc_final: 0.9208 (mtm) REVERT: A 194 ASP cc_start: 0.8617 (m-30) cc_final: 0.7885 (m-30) REVERT: A 217 GLU cc_start: 0.8947 (mt-10) cc_final: 0.8621 (mt-10) REVERT: B 20 GLN cc_start: 0.9352 (OUTLIER) cc_final: 0.8978 (pm20) REVERT: B 109 GLU cc_start: 0.8954 (tp30) cc_final: 0.8249 (tt0) REVERT: B 128 GLU cc_start: 0.9535 (tp30) cc_final: 0.9299 (tp30) REVERT: B 164 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7599 (tm-30) REVERT: B 180 MET cc_start: 0.9477 (mtm) cc_final: 0.9206 (mtm) REVERT: B 217 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8665 (mt-10) REVERT: C 20 GLN cc_start: 0.9381 (OUTLIER) cc_final: 0.9013 (pm20) REVERT: C 109 GLU cc_start: 0.8909 (tp30) cc_final: 0.8529 (tp30) REVERT: C 128 GLU cc_start: 0.9538 (tp30) cc_final: 0.9297 (tp30) REVERT: C 164 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7617 (tm-30) REVERT: C 180 MET cc_start: 0.9490 (mtm) cc_final: 0.9206 (mtm) REVERT: C 194 ASP cc_start: 0.8620 (m-30) cc_final: 0.7857 (m-30) REVERT: D 20 GLN cc_start: 0.9370 (OUTLIER) cc_final: 0.9006 (pm20) REVERT: D 109 GLU cc_start: 0.8898 (tp30) cc_final: 0.8462 (tp30) REVERT: D 128 GLU cc_start: 0.9524 (tp30) cc_final: 0.9279 (tp30) REVERT: D 164 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7578 (tm-30) REVERT: D 180 MET cc_start: 0.9461 (mtm) cc_final: 0.9160 (mtm) REVERT: D 194 ASP cc_start: 0.8612 (m-30) cc_final: 0.8009 (m-30) REVERT: D 217 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8603 (mt-10) REVERT: G 45 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8870 (ttpt) REVERT: G 49 TYR cc_start: 0.9189 (p90) cc_final: 0.8970 (p90) REVERT: G 50 GLU cc_start: 0.9263 (mt-10) cc_final: 0.8926 (mp0) REVERT: G 67 SER cc_start: 0.9162 (m) cc_final: 0.8925 (p) REVERT: G 81 GLU cc_start: 0.9330 (mp0) cc_final: 0.9068 (pm20) REVERT: G 93 ASP cc_start: 0.9310 (t0) cc_final: 0.8956 (t70) REVERT: G 103 LYS cc_start: 0.9284 (mttt) cc_final: 0.8746 (mtpp) REVERT: G 167 ASP cc_start: 0.8772 (t70) cc_final: 0.8358 (t70) REVERT: G 185 ASP cc_start: 0.7822 (OUTLIER) cc_final: 0.7479 (p0) REVERT: H 3 GLN cc_start: 0.8982 (pm20) cc_final: 0.8608 (pm20) REVERT: H 6 GLU cc_start: 0.8172 (mp0) cc_final: 0.7219 (mp0) REVERT: H 26 ARG cc_start: 0.8264 (tmm-80) cc_final: 0.6601 (tmm-80) REVERT: H 27 PHE cc_start: 0.8528 (OUTLIER) cc_final: 0.8030 (m-10) REVERT: H 46 GLU cc_start: 0.8852 (tt0) cc_final: 0.8372 (tt0) REVERT: H 72 ASP cc_start: 0.8918 (t0) cc_final: 0.8470 (t0) REVERT: H 76 ASN cc_start: 0.8705 (t0) cc_final: 0.8359 (t0) REVERT: H 94 ARG cc_start: 0.8491 (tmm-80) cc_final: 0.8280 (tmm-80) REVERT: H 95 ASP cc_start: 0.9515 (t0) cc_final: 0.8832 (t0) REVERT: H 105 GLN cc_start: 0.9432 (mt0) cc_final: 0.9107 (pm20) REVERT: H 108 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9110 (tm) REVERT: H 163 LEU cc_start: 0.9649 (mp) cc_final: 0.9412 (tm) REVERT: H 175 GLN cc_start: 0.8300 (mt0) cc_final: 0.7715 (mt0) REVERT: H 203 ASN cc_start: 0.8765 (m-40) cc_final: 0.8458 (t0) REVERT: F 3 GLN cc_start: 0.9033 (pm20) cc_final: 0.8687 (pm20) REVERT: F 6 GLU cc_start: 0.8156 (mp0) cc_final: 0.7206 (mp0) REVERT: F 27 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.8360 (t80) REVERT: F 46 GLU cc_start: 0.8859 (tt0) cc_final: 0.8392 (tt0) REVERT: F 72 ASP cc_start: 0.8904 (t0) cc_final: 0.8462 (t0) REVERT: F 76 ASN cc_start: 0.8748 (t0) cc_final: 0.8388 (t0) REVERT: F 95 ASP cc_start: 0.9525 (t0) cc_final: 0.9020 (t0) REVERT: F 105 GLN cc_start: 0.9443 (mt0) cc_final: 0.9105 (pm20) REVERT: F 108 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9109 (tm) REVERT: F 175 GLN cc_start: 0.8319 (mt0) cc_final: 0.7740 (mt0) REVERT: F 186 VAL cc_start: 0.9425 (OUTLIER) cc_final: 0.9220 (m) REVERT: F 203 ASN cc_start: 0.8808 (m-40) cc_final: 0.8533 (t0) REVERT: J 3 GLN cc_start: 0.9042 (pm20) cc_final: 0.8687 (pm20) REVERT: J 6 GLU cc_start: 0.8168 (mp0) cc_final: 0.7207 (mp0) REVERT: J 26 ARG cc_start: 0.8506 (tmm-80) cc_final: 0.8168 (tmm-80) REVERT: J 27 PHE cc_start: 0.8588 (OUTLIER) cc_final: 0.8280 (m-80) REVERT: J 46 GLU cc_start: 0.8861 (tt0) cc_final: 0.8385 (tt0) REVERT: J 72 ASP cc_start: 0.8891 (t0) cc_final: 0.8445 (t0) REVERT: J 76 ASN cc_start: 0.8719 (t0) cc_final: 0.8386 (t0) REVERT: J 95 ASP cc_start: 0.9517 (t0) cc_final: 0.8965 (t0) REVERT: J 100 LEU cc_start: 0.9497 (mt) cc_final: 0.9224 (mt) REVERT: J 105 GLN cc_start: 0.9433 (mt0) cc_final: 0.9107 (pm20) REVERT: J 108 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9102 (tm) REVERT: J 163 LEU cc_start: 0.9631 (mp) cc_final: 0.9370 (tm) REVERT: J 175 GLN cc_start: 0.8285 (mt0) cc_final: 0.7720 (mt0) REVERT: J 203 ASN cc_start: 0.8742 (m-40) cc_final: 0.8435 (t0) REVERT: K 3 GLN cc_start: 0.9029 (pm20) cc_final: 0.8674 (pm20) REVERT: K 6 GLU cc_start: 0.8161 (mp0) cc_final: 0.7214 (mp0) REVERT: K 26 ARG cc_start: 0.8516 (tmm-80) cc_final: 0.8174 (tmm-80) REVERT: K 27 PHE cc_start: 0.8590 (OUTLIER) cc_final: 0.8278 (m-80) REVERT: K 46 GLU cc_start: 0.8851 (tt0) cc_final: 0.8358 (tt0) REVERT: K 72 ASP cc_start: 0.8903 (t0) cc_final: 0.8475 (t0) REVERT: K 76 ASN cc_start: 0.8765 (t0) cc_final: 0.8425 (t0) REVERT: K 77 GLN cc_start: 0.9007 (mt0) cc_final: 0.8771 (mt0) REVERT: K 95 ASP cc_start: 0.9531 (t0) cc_final: 0.9023 (t0) REVERT: K 100 LEU cc_start: 0.9554 (mt) cc_final: 0.9323 (mt) REVERT: K 105 GLN cc_start: 0.9434 (mt0) cc_final: 0.9099 (pm20) REVERT: K 108 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9105 (tm) REVERT: K 175 GLN cc_start: 0.8306 (mt0) cc_final: 0.7735 (mt0) REVERT: K 184 SER cc_start: 0.8476 (t) cc_final: 0.8273 (p) REVERT: K 186 VAL cc_start: 0.9453 (OUTLIER) cc_final: 0.9226 (m) REVERT: K 203 ASN cc_start: 0.8787 (m-40) cc_final: 0.8536 (t0) REVERT: E 45 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8880 (ttpt) REVERT: E 49 TYR cc_start: 0.9188 (p90) cc_final: 0.8987 (p90) REVERT: E 50 GLU cc_start: 0.9298 (mt-10) cc_final: 0.8929 (mp0) REVERT: E 67 SER cc_start: 0.9160 (m) cc_final: 0.8924 (p) REVERT: E 81 GLU cc_start: 0.9339 (mp0) cc_final: 0.9078 (pm20) REVERT: E 93 ASP cc_start: 0.9343 (t0) cc_final: 0.8963 (t70) REVERT: E 103 LYS cc_start: 0.9321 (mttt) cc_final: 0.8780 (mtpp) REVERT: E 118 PHE cc_start: 0.8107 (m-80) cc_final: 0.7858 (m-80) REVERT: E 167 ASP cc_start: 0.8774 (t70) cc_final: 0.8360 (t70) REVERT: E 185 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.7584 (p0) REVERT: I 45 LYS cc_start: 0.9181 (OUTLIER) cc_final: 0.8888 (ttpt) REVERT: I 50 GLU cc_start: 0.9263 (mt-10) cc_final: 0.8910 (mp0) REVERT: I 67 SER cc_start: 0.9159 (m) cc_final: 0.8924 (p) REVERT: I 81 GLU cc_start: 0.9336 (mp0) cc_final: 0.9071 (pm20) REVERT: I 93 ASP cc_start: 0.9336 (t0) cc_final: 0.8984 (t70) REVERT: I 103 LYS cc_start: 0.9306 (mttt) cc_final: 0.8772 (mtpp) REVERT: I 118 PHE cc_start: 0.8175 (m-80) cc_final: 0.7943 (m-80) REVERT: I 167 ASP cc_start: 0.8760 (t70) cc_final: 0.8351 (t70) REVERT: I 185 ASP cc_start: 0.7871 (OUTLIER) cc_final: 0.7497 (p0) REVERT: L 45 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8866 (ttpt) REVERT: L 49 TYR cc_start: 0.9187 (p90) cc_final: 0.8986 (p90) REVERT: L 50 GLU cc_start: 0.9288 (mt-10) cc_final: 0.8920 (mp0) REVERT: L 67 SER cc_start: 0.9167 (m) cc_final: 0.8931 (p) REVERT: L 81 GLU cc_start: 0.9338 (mp0) cc_final: 0.9078 (pm20) REVERT: L 93 ASP cc_start: 0.9345 (t0) cc_final: 0.8995 (t70) REVERT: L 103 LYS cc_start: 0.9321 (mttt) cc_final: 0.8789 (mtpp) REVERT: L 118 PHE cc_start: 0.8157 (m-80) cc_final: 0.7907 (m-80) REVERT: L 167 ASP cc_start: 0.8782 (t70) cc_final: 0.8374 (t70) REVERT: L 185 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7495 (p0) outliers start: 76 outliers final: 37 residues processed: 472 average time/residue: 0.4962 time to fit residues: 271.0853 Evaluate side-chains 464 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 401 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain D residue 20 GLN Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 183 LYS Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 194 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 213 LYS Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 27 PHE Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 27 PHE Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 194 CYS Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 183 LYS Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 194 CYS Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 159 SER Chi-restraints excluded: chain L residue 183 LYS Chi-restraints excluded: chain L residue 185 ASP Chi-restraints excluded: chain L residue 194 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 101 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 209 optimal weight: 0.9980 chunk 134 optimal weight: 3.9990 chunk 193 optimal weight: 0.9990 chunk 19 optimal weight: 0.0000 chunk 56 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 154 optimal weight: 0.5980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN B 146 ASN C 146 ASN D 146 ASN G 124 GLN H 203 ASN K 203 ASN I 124 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.091609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.062472 restraints weight = 50821.466| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 4.03 r_work: 0.2787 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21048 Z= 0.135 Angle : 0.708 9.989 28752 Z= 0.357 Chirality : 0.045 0.266 3224 Planarity : 0.005 0.062 3668 Dihedral : 4.833 19.711 2860 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.14 % Allowed : 23.82 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.17), residues: 2636 helix: -0.81 (0.41), residues: 144 sheet: 0.81 (0.17), residues: 860 loop : -0.25 (0.16), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 142 TYR 0.016 0.001 TYR I 173 PHE 0.049 0.002 PHE I 209 TRP 0.036 0.001 TRP F 158 HIS 0.003 0.001 HIS C 173 Details of bonding type rmsd covalent geometry : bond 0.00318 (21016) covalent geometry : angle 0.70740 (28688) SS BOND : bond 0.00495 ( 32) SS BOND : angle 1.07822 ( 64) hydrogen bonds : bond 0.02876 ( 724) hydrogen bonds : angle 5.05879 ( 1980) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 433 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLN cc_start: 0.9421 (OUTLIER) cc_final: 0.9068 (pm20) REVERT: A 109 GLU cc_start: 0.9043 (tp30) cc_final: 0.8757 (tt0) REVERT: A 128 GLU cc_start: 0.9513 (tp30) cc_final: 0.9240 (tp30) REVERT: A 164 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7595 (tm-30) REVERT: A 180 MET cc_start: 0.9468 (mtm) cc_final: 0.9207 (mtm) REVERT: A 194 ASP cc_start: 0.8579 (m-30) cc_final: 0.7972 (m-30) REVERT: A 217 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8636 (mt-10) REVERT: B 20 GLN cc_start: 0.9344 (OUTLIER) cc_final: 0.8980 (pm20) REVERT: B 109 GLU cc_start: 0.8931 (tp30) cc_final: 0.8500 (tp30) REVERT: B 128 GLU cc_start: 0.9514 (tp30) cc_final: 0.9248 (tp30) REVERT: B 164 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7575 (tm-30) REVERT: B 180 MET cc_start: 0.9461 (mtm) cc_final: 0.9203 (mtm) REVERT: B 194 ASP cc_start: 0.8614 (m-30) cc_final: 0.7992 (m-30) REVERT: B 217 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8606 (mt-10) REVERT: C 20 GLN cc_start: 0.9364 (OUTLIER) cc_final: 0.8968 (pm20) REVERT: C 109 GLU cc_start: 0.8936 (tp30) cc_final: 0.8518 (tp30) REVERT: C 128 GLU cc_start: 0.9519 (tp30) cc_final: 0.9243 (tp30) REVERT: C 164 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7518 (tm-30) REVERT: C 180 MET cc_start: 0.9466 (mtm) cc_final: 0.9201 (mtm) REVERT: C 194 ASP cc_start: 0.8566 (m-30) cc_final: 0.7733 (m-30) REVERT: D 20 GLN cc_start: 0.9357 (OUTLIER) cc_final: 0.8960 (pm20) REVERT: D 109 GLU cc_start: 0.8912 (tp30) cc_final: 0.8536 (tp30) REVERT: D 128 GLU cc_start: 0.9510 (tp30) cc_final: 0.9232 (tp30) REVERT: D 164 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7460 (tm-30) REVERT: D 180 MET cc_start: 0.9433 (mtm) cc_final: 0.9145 (mtm) REVERT: D 194 ASP cc_start: 0.8572 (m-30) cc_final: 0.7722 (m-30) REVERT: D 217 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8524 (mt-10) REVERT: G 45 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8818 (ttpt) REVERT: G 49 TYR cc_start: 0.9158 (p90) cc_final: 0.8894 (p90) REVERT: G 50 GLU cc_start: 0.9205 (mt-10) cc_final: 0.8867 (mp0) REVERT: G 67 SER cc_start: 0.9158 (m) cc_final: 0.8918 (p) REVERT: G 81 GLU cc_start: 0.9340 (mp0) cc_final: 0.9063 (pm20) REVERT: G 93 ASP cc_start: 0.9321 (t0) cc_final: 0.8964 (t70) REVERT: G 103 LYS cc_start: 0.9257 (mttt) cc_final: 0.8723 (mtpp) REVERT: G 143 GLU cc_start: 0.8911 (mp0) cc_final: 0.8585 (pm20) REVERT: G 161 GLU cc_start: 0.9113 (pm20) cc_final: 0.8543 (pp20) REVERT: G 167 ASP cc_start: 0.8810 (t70) cc_final: 0.8390 (t70) REVERT: G 185 ASP cc_start: 0.7843 (OUTLIER) cc_final: 0.7491 (p0) REVERT: H 3 GLN cc_start: 0.8948 (pm20) cc_final: 0.8603 (pm20) REVERT: H 6 GLU cc_start: 0.8164 (mp0) cc_final: 0.7204 (mp0) REVERT: H 16 GLU cc_start: 0.8008 (pm20) cc_final: 0.7732 (pm20) REVERT: H 26 ARG cc_start: 0.8358 (tmm-80) cc_final: 0.6798 (tmm-80) REVERT: H 27 PHE cc_start: 0.8528 (OUTLIER) cc_final: 0.8023 (m-10) REVERT: H 46 GLU cc_start: 0.8888 (tt0) cc_final: 0.8393 (tt0) REVERT: H 51 ILE cc_start: 0.9436 (tt) cc_final: 0.9142 (tp) REVERT: H 72 ASP cc_start: 0.8932 (t0) cc_final: 0.8514 (t0) REVERT: H 76 ASN cc_start: 0.8567 (t0) cc_final: 0.8337 (t0) REVERT: H 95 ASP cc_start: 0.9438 (t0) cc_final: 0.8734 (t0) REVERT: H 105 GLN cc_start: 0.9431 (mt0) cc_final: 0.9056 (pm20) REVERT: H 163 LEU cc_start: 0.9644 (mp) cc_final: 0.9406 (tm) REVERT: H 175 GLN cc_start: 0.8253 (mt0) cc_final: 0.7700 (mt0) REVERT: H 203 ASN cc_start: 0.8748 (m110) cc_final: 0.8448 (t0) REVERT: F 3 GLN cc_start: 0.8990 (pm20) cc_final: 0.8658 (pm20) REVERT: F 6 GLU cc_start: 0.8155 (mp0) cc_final: 0.7217 (mp0) REVERT: F 16 GLU cc_start: 0.8012 (pm20) cc_final: 0.7738 (pm20) REVERT: F 26 ARG cc_start: 0.8363 (tmm-80) cc_final: 0.7847 (tmm-80) REVERT: F 27 PHE cc_start: 0.8655 (OUTLIER) cc_final: 0.8396 (m-80) REVERT: F 46 GLU cc_start: 0.8887 (tt0) cc_final: 0.8390 (tt0) REVERT: F 72 ASP cc_start: 0.8931 (t0) cc_final: 0.8505 (t0) REVERT: F 76 ASN cc_start: 0.8620 (t0) cc_final: 0.8355 (t0) REVERT: F 95 ASP cc_start: 0.9495 (t0) cc_final: 0.8876 (t0) REVERT: F 105 GLN cc_start: 0.9440 (mt0) cc_final: 0.9054 (pm20) REVERT: F 175 GLN cc_start: 0.8282 (mt0) cc_final: 0.7726 (mt0) REVERT: F 186 VAL cc_start: 0.9467 (OUTLIER) cc_final: 0.9232 (m) REVERT: F 203 ASN cc_start: 0.8813 (m-40) cc_final: 0.8573 (t0) REVERT: J 3 GLN cc_start: 0.8991 (pm20) cc_final: 0.8629 (pm20) REVERT: J 6 GLU cc_start: 0.8176 (mp0) cc_final: 0.7214 (mp0) REVERT: J 16 GLU cc_start: 0.8027 (pm20) cc_final: 0.7750 (pm20) REVERT: J 27 PHE cc_start: 0.8588 (OUTLIER) cc_final: 0.8382 (t80) REVERT: J 46 GLU cc_start: 0.8885 (tt0) cc_final: 0.8371 (tt0) REVERT: J 72 ASP cc_start: 0.8931 (t0) cc_final: 0.8496 (t0) REVERT: J 76 ASN cc_start: 0.8608 (t0) cc_final: 0.8346 (t0) REVERT: J 95 ASP cc_start: 0.9480 (t0) cc_final: 0.8946 (t0) REVERT: J 100 LEU cc_start: 0.9470 (mt) cc_final: 0.9187 (mt) REVERT: J 105 GLN cc_start: 0.9428 (mt0) cc_final: 0.9062 (pm20) REVERT: J 163 LEU cc_start: 0.9651 (mp) cc_final: 0.9443 (tm) REVERT: J 175 GLN cc_start: 0.8284 (mt0) cc_final: 0.7717 (mt0) REVERT: J 203 ASN cc_start: 0.8746 (m-40) cc_final: 0.8436 (t0) REVERT: K 3 GLN cc_start: 0.8989 (pm20) cc_final: 0.8628 (pm20) REVERT: K 6 GLU cc_start: 0.8188 (mp0) cc_final: 0.7272 (mp0) REVERT: K 27 PHE cc_start: 0.8577 (OUTLIER) cc_final: 0.8372 (t80) REVERT: K 46 GLU cc_start: 0.8858 (tt0) cc_final: 0.8363 (tt0) REVERT: K 72 ASP cc_start: 0.8916 (t0) cc_final: 0.8494 (t0) REVERT: K 76 ASN cc_start: 0.8668 (t0) cc_final: 0.8411 (t0) REVERT: K 95 ASP cc_start: 0.9492 (t0) cc_final: 0.8867 (t0) REVERT: K 100 LEU cc_start: 0.9480 (mt) cc_final: 0.9225 (mt) REVERT: K 105 GLN cc_start: 0.9437 (mt0) cc_final: 0.9049 (pm20) REVERT: K 175 GLN cc_start: 0.8297 (mt0) cc_final: 0.7715 (mt0) REVERT: K 186 VAL cc_start: 0.9435 (OUTLIER) cc_final: 0.9230 (m) REVERT: K 203 ASN cc_start: 0.8783 (m110) cc_final: 0.8527 (t0) REVERT: E 45 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8828 (ttpt) REVERT: E 49 TYR cc_start: 0.9174 (p90) cc_final: 0.8919 (p90) REVERT: E 50 GLU cc_start: 0.9197 (mt-10) cc_final: 0.8873 (mp0) REVERT: E 67 SER cc_start: 0.9151 (m) cc_final: 0.8909 (p) REVERT: E 81 GLU cc_start: 0.9344 (mp0) cc_final: 0.9077 (pm20) REVERT: E 93 ASP cc_start: 0.9345 (t0) cc_final: 0.8980 (t70) REVERT: E 103 LYS cc_start: 0.9269 (mttt) cc_final: 0.8720 (mtpp) REVERT: E 105 GLU cc_start: 0.8497 (tp30) cc_final: 0.7941 (tp30) REVERT: E 118 PHE cc_start: 0.8246 (m-80) cc_final: 0.7982 (m-80) REVERT: E 142 ARG cc_start: 0.9290 (ttm110) cc_final: 0.8760 (mtm-85) REVERT: E 161 GLU cc_start: 0.9111 (pm20) cc_final: 0.8539 (pp20) REVERT: E 167 ASP cc_start: 0.8793 (t70) cc_final: 0.8353 (t0) REVERT: E 185 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.7505 (p0) REVERT: I 45 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8823 (ttpt) REVERT: I 49 TYR cc_start: 0.9228 (p90) cc_final: 0.8803 (p90) REVERT: I 50 GLU cc_start: 0.9180 (mt-10) cc_final: 0.8829 (mp0) REVERT: I 67 SER cc_start: 0.9128 (m) cc_final: 0.8886 (p) REVERT: I 81 GLU cc_start: 0.9340 (mp0) cc_final: 0.9066 (pm20) REVERT: I 93 ASP cc_start: 0.9347 (t0) cc_final: 0.8992 (t70) REVERT: I 103 LYS cc_start: 0.9283 (mttt) cc_final: 0.8742 (mtpp) REVERT: I 118 PHE cc_start: 0.8259 (m-80) cc_final: 0.8030 (m-80) REVERT: I 143 GLU cc_start: 0.8911 (mp0) cc_final: 0.8586 (pm20) REVERT: I 161 GLU cc_start: 0.9111 (pm20) cc_final: 0.8541 (pp20) REVERT: I 167 ASP cc_start: 0.8800 (t70) cc_final: 0.8381 (t70) REVERT: I 185 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7492 (p0) REVERT: L 45 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8823 (ttpt) REVERT: L 49 TYR cc_start: 0.9170 (p90) cc_final: 0.8922 (p90) REVERT: L 50 GLU cc_start: 0.9188 (mt-10) cc_final: 0.8860 (mp0) REVERT: L 67 SER cc_start: 0.9151 (m) cc_final: 0.8910 (p) REVERT: L 81 GLU cc_start: 0.9337 (mp0) cc_final: 0.9071 (pm20) REVERT: L 93 ASP cc_start: 0.9358 (t0) cc_final: 0.9002 (t70) REVERT: L 103 LYS cc_start: 0.9267 (mttt) cc_final: 0.8726 (mtpp) REVERT: L 118 PHE cc_start: 0.8256 (m-80) cc_final: 0.7983 (m-80) REVERT: L 142 ARG cc_start: 0.9290 (ttm110) cc_final: 0.8919 (ttm-80) REVERT: L 161 GLU cc_start: 0.9114 (pm20) cc_final: 0.8544 (pp20) REVERT: L 167 ASP cc_start: 0.8802 (t70) cc_final: 0.8389 (t0) REVERT: L 185 ASP cc_start: 0.7852 (OUTLIER) cc_final: 0.7489 (p0) outliers start: 72 outliers final: 33 residues processed: 472 average time/residue: 0.4870 time to fit residues: 266.4612 Evaluate side-chains 469 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 414 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain D residue 20 GLN Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 183 LYS Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 194 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 27 PHE Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 27 PHE Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 194 CYS Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 183 LYS Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 194 CYS Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 159 SER Chi-restraints excluded: chain L residue 185 ASP Chi-restraints excluded: chain L residue 194 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 257 optimal weight: 4.9990 chunk 46 optimal weight: 0.0970 chunk 259 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 235 optimal weight: 0.9990 chunk 207 optimal weight: 8.9990 chunk 111 optimal weight: 0.8980 chunk 255 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN B 146 ASN C 146 ASN D 146 ASN H 208 ASN F 208 ASN J 208 ASN K 208 ASN E 124 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.091294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.061951 restraints weight = 51082.958| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 4.07 r_work: 0.2773 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21048 Z= 0.145 Angle : 0.706 10.339 28752 Z= 0.356 Chirality : 0.046 0.161 3224 Planarity : 0.005 0.063 3668 Dihedral : 4.778 20.757 2860 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.01 % Allowed : 24.56 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.17), residues: 2636 helix: -0.70 (0.41), residues: 144 sheet: 0.96 (0.17), residues: 880 loop : -0.27 (0.16), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 142 TYR 0.013 0.001 TYR H 32 PHE 0.022 0.002 PHE E 92 TRP 0.036 0.002 TRP J 158 HIS 0.003 0.001 HIS B 173 Details of bonding type rmsd covalent geometry : bond 0.00339 (21016) covalent geometry : angle 0.70431 (28688) SS BOND : bond 0.00485 ( 32) SS BOND : angle 1.13247 ( 64) hydrogen bonds : bond 0.02884 ( 724) hydrogen bonds : angle 5.05792 ( 1980) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7897.84 seconds wall clock time: 135 minutes 19.57 seconds (8119.57 seconds total)