Starting phenix.real_space_refine on Wed Jun 18 03:32:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vgh_43200/06_2025/8vgh_43200.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vgh_43200/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8vgh_43200/06_2025/8vgh_43200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vgh_43200/06_2025/8vgh_43200.map" model { file = "/net/cci-nas-00/data/ceres_data/8vgh_43200/06_2025/8vgh_43200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vgh_43200/06_2025/8vgh_43200.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.011 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.57, per 1000 atoms: 0.66 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: 5.25 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 3.94 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: 8.55 Time building geometry restraints manager: 6.17 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: 0.14 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: 3.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.900 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 51.310 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:19.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.480 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (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 TRP 0.022 0.003 TRP D 27 HIS 0.008 0.003 HIS A 91 PHE 0.024 0.003 PHE C 153 TYR 0.029 0.004 TYR B 75 ARG 0.019 0.003 ARG F 97 Details of bonding type rmsd hydrogen bonds : bond 0.21246 ( 724) hydrogen bonds : angle 9.35744 ( 1980) SS BOND : bond 0.00673 ( 32) SS BOND : angle 1.42154 ( 64) covalent geometry : bond 0.01112 (21016) covalent geometry : angle 0.94076 (28688) *********************** 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 : 2.847 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: 0.8638 (m-40) REVERT: A 149 GLU cc_start: 0.9135 (mp0) cc_final: 0.8877 (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: 0.8630 (m-40) REVERT: B 149 GLU cc_start: 0.9208 (mp0) cc_final: 0.8741 (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: 0.8634 (m-40) REVERT: C 149 GLU cc_start: 0.9144 (mp0) cc_final: 0.8885 (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: 0.8663 (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 93 ASP cc_start: 0.9332 (t0) cc_final: 0.8897 (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: 0.8055 (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: 0.8157 (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: 0.8203 (pt0) REVERT: F 72 ASP cc_start: 0.8746 (t0) cc_final: 0.8525 (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 93 ASP cc_start: 0.9338 (t0) cc_final: 0.8905 (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: 0.8980 (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 93 ASP cc_start: 0.9342 (t0) cc_final: 0.8909 (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 93 ASP cc_start: 0.9341 (t0) cc_final: 0.8908 (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: 1.4721 time to fit residues: 1040.8702 Evaluate side-chains 376 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 373 time to evaluate : 4.233 ------------------------------------------------------------------------------- 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 222 optimal weight: 1.9990 chunk 200 optimal weight: 7.9990 chunk 111 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 134 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 206 optimal weight: 3.9990 chunk 80 optimal weight: 0.4980 chunk 125 optimal weight: 1.9990 chunk 154 optimal weight: 6.9990 chunk 239 optimal weight: 5.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 = 0.3515 r_free = 0.3515 target = 0.090068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.060474 restraints weight = 50553.417| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 3.97 r_work: 0.2747 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 21048 Z= 0.182 Angle : 0.763 7.235 28752 Z= 0.404 Chirality : 0.048 0.163 3224 Planarity : 0.006 0.056 3668 Dihedral : 6.472 45.955 2866 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.79 % Allowed : 13.35 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.16), residues: 2636 helix: -2.45 (0.33), residues: 144 sheet: 0.29 (0.17), residues: 880 loop : -0.39 (0.16), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 51 HIS 0.005 0.001 HIS D 173 PHE 0.029 0.003 PHE L 209 TYR 0.018 0.002 TYR F 180 ARG 0.012 0.001 ARG G 142 Details of bonding type rmsd hydrogen bonds : bond 0.03813 ( 724) hydrogen bonds : angle 6.75630 ( 1980) SS BOND : bond 0.00653 ( 32) SS BOND : angle 1.47999 ( 64) covalent geometry : bond 0.00398 (21016) covalent geometry : angle 0.76069 (28688) *********************** 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 543 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 479 time to evaluate : 2.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.9526 (tp30) cc_final: 0.9196 (tp30) REVERT: A 230 THR cc_start: 0.9674 (m) cc_final: 0.9302 (p) REVERT: B 109 GLU cc_start: 0.8801 (tp30) cc_final: 0.8485 (tp30) REVERT: B 128 GLU cc_start: 0.9515 (tp30) cc_final: 0.9183 (tp30) REVERT: B 229 THR cc_start: 0.9669 (m) cc_final: 0.9272 (p) REVERT: C 109 GLU cc_start: 0.8781 (tp30) cc_final: 0.8465 (tp30) REVERT: C 128 GLU cc_start: 0.9514 (tp30) cc_final: 0.9180 (tp30) REVERT: C 149 GLU cc_start: 0.9216 (mp0) cc_final: 0.9014 (mp0) REVERT: C 229 THR cc_start: 0.9661 (m) cc_final: 0.9284 (p) REVERT: D 109 GLU cc_start: 0.8806 (tp30) cc_final: 0.8488 (tp30) REVERT: D 128 GLU cc_start: 0.9511 (tp30) cc_final: 0.9176 (tp30) REVERT: D 149 GLU cc_start: 0.9215 (mp0) cc_final: 0.8954 (mp0) REVERT: D 229 THR cc_start: 0.9667 (m) cc_final: 0.9290 (p) REVERT: G 36 TYR cc_start: 0.8975 (m-80) cc_final: 0.8753 (m-80) REVERT: G 45 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8944 (ttpt) REVERT: G 67 SER cc_start: 0.9083 (m) cc_final: 0.8859 (p) REVERT: G 93 ASP cc_start: 0.9342 (t0) cc_final: 0.8974 (t70) REVERT: G 103 LYS cc_start: 0.9292 (mttt) cc_final: 0.8774 (mtpp) REVERT: G 106 ILE cc_start: 0.8860 (mt) cc_final: 0.8015 (pp) REVERT: H 3 GLN cc_start: 0.8891 (pm20) cc_final: 0.8505 (pm20) REVERT: H 46 GLU cc_start: 0.8902 (tt0) cc_final: 0.8445 (tt0) REVERT: H 72 ASP cc_start: 0.9026 (t0) cc_final: 0.8587 (OUTLIER) REVERT: H 77 GLN cc_start: 0.9105 (mt0) cc_final: 0.8424 (mm110) REVERT: H 86 ASP cc_start: 0.9097 (m-30) cc_final: 0.8657 (m-30) REVERT: H 94 ARG cc_start: 0.8631 (tmm-80) cc_final: 0.8306 (tmm-80) REVERT: H 95 ASP cc_start: 0.9509 (t0) cc_final: 0.8977 (t0) REVERT: H 100 LEU cc_start: 0.9712 (mt) cc_final: 0.9481 (mm) REVERT: H 105 GLN cc_start: 0.9370 (mt0) cc_final: 0.9146 (mm110) REVERT: H 199 ILE cc_start: 0.8508 (mm) cc_final: 0.8214 (tp) REVERT: F 3 GLN cc_start: 0.8885 (pm20) cc_final: 0.8498 (pm20) REVERT: F 46 GLU cc_start: 0.8898 (tt0) cc_final: 0.8442 (tt0) REVERT: F 72 ASP cc_start: 0.9035 (t0) cc_final: 0.8596 (OUTLIER) REVERT: F 77 GLN cc_start: 0.9109 (mt0) cc_final: 0.8438 (mm110) REVERT: F 86 ASP cc_start: 0.9071 (m-30) cc_final: 0.8626 (m-30) REVERT: F 94 ARG cc_start: 0.8620 (tmm-80) cc_final: 0.8301 (tmm-80) REVERT: F 95 ASP cc_start: 0.9513 (t0) cc_final: 0.8989 (t0) REVERT: F 100 LEU cc_start: 0.9714 (mt) cc_final: 0.9480 (mm) REVERT: F 105 GLN cc_start: 0.9362 (mt0) cc_final: 0.9140 (mm110) REVERT: J 3 GLN cc_start: 0.8889 (pm20) cc_final: 0.8508 (pm20) REVERT: J 46 GLU cc_start: 0.8890 (tt0) cc_final: 0.8434 (tt0) REVERT: J 72 ASP cc_start: 0.9018 (t0) cc_final: 0.8576 (OUTLIER) REVERT: J 77 GLN cc_start: 0.9076 (mt0) cc_final: 0.8432 (mm110) REVERT: J 86 ASP cc_start: 0.9084 (m-30) cc_final: 0.8642 (m-30) REVERT: J 95 ASP cc_start: 0.9516 (t0) cc_final: 0.8976 (t0) REVERT: J 100 LEU cc_start: 0.9716 (mt) cc_final: 0.9489 (mm) REVERT: J 105 GLN cc_start: 0.9352 (mt0) cc_final: 0.9126 (mm110) REVERT: J 199 ILE cc_start: 0.8576 (mm) cc_final: 0.8290 (tp) REVERT: K 3 GLN cc_start: 0.8878 (pm20) cc_final: 0.8493 (pm20) REVERT: K 46 GLU cc_start: 0.8893 (tt0) cc_final: 0.8436 (tt0) REVERT: K 72 ASP cc_start: 0.9017 (t0) cc_final: 0.8577 (OUTLIER) REVERT: K 77 GLN cc_start: 0.9077 (mt0) cc_final: 0.8429 (mm110) REVERT: K 86 ASP cc_start: 0.9075 (m-30) cc_final: 0.8633 (m-30) REVERT: K 94 ARG cc_start: 0.8602 (tmm-80) cc_final: 0.8238 (tmm-80) REVERT: K 95 ASP cc_start: 0.9509 (t0) cc_final: 0.8981 (t0) REVERT: K 100 LEU cc_start: 0.9716 (mt) cc_final: 0.9487 (mm) REVERT: K 105 GLN cc_start: 0.9361 (mt0) cc_final: 0.9134 (mm110) REVERT: K 149 TYR cc_start: 0.8071 (p90) cc_final: 0.7864 (p90) REVERT: E 36 TYR cc_start: 0.8969 (m-80) cc_final: 0.8744 (m-80) REVERT: E 45 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8949 (ttpt) REVERT: E 67 SER cc_start: 0.9088 (m) cc_final: 0.8864 (p) REVERT: E 93 ASP cc_start: 0.9334 (t0) cc_final: 0.8959 (t70) REVERT: E 103 LYS cc_start: 0.9294 (mttt) cc_final: 0.8764 (mtpp) REVERT: E 106 ILE cc_start: 0.8833 (mt) cc_final: 0.7977 (pp) REVERT: I 36 TYR cc_start: 0.8985 (m-80) cc_final: 0.8769 (m-80) REVERT: I 45 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8949 (ttpt) REVERT: I 67 SER cc_start: 0.9087 (m) cc_final: 0.8866 (p) REVERT: I 93 ASP cc_start: 0.9347 (t0) cc_final: 0.8979 (t70) REVERT: I 103 LYS cc_start: 0.9291 (mttt) cc_final: 0.8764 (mtpp) REVERT: I 106 ILE cc_start: 0.8852 (mt) cc_final: 0.7977 (pp) REVERT: L 36 TYR cc_start: 0.8977 (m-80) cc_final: 0.8762 (m-80) REVERT: L 45 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8954 (ttpt) REVERT: L 67 SER cc_start: 0.9093 (m) cc_final: 0.8866 (p) REVERT: L 92 PHE cc_start: 0.9254 (m-80) cc_final: 0.9054 (m-80) REVERT: L 93 ASP cc_start: 0.9332 (t0) cc_final: 0.8959 (t70) REVERT: L 103 LYS cc_start: 0.9290 (mttt) cc_final: 0.8752 (mtpp) REVERT: L 106 ILE cc_start: 0.8852 (mt) cc_final: 0.8004 (pp) outliers start: 64 outliers final: 22 residues processed: 500 average time/residue: 0.9993 time to fit residues: 583.7707 Evaluate side-chains 425 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 403 time to evaluate : 2.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain G residue 45 LYS 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 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 123 optimal weight: 1.9990 chunk 232 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 230 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 170 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 196 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.089350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.060077 restraints weight = 51281.421| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 3.99 r_work: 0.2736 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21048 Z= 0.191 Angle : 0.700 9.750 28752 Z= 0.361 Chirality : 0.047 0.242 3224 Planarity : 0.005 0.057 3668 Dihedral : 5.740 21.089 2860 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.14 % Allowed : 16.80 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.16), residues: 2636 helix: -2.04 (0.36), residues: 144 sheet: 0.39 (0.17), residues: 876 loop : -0.29 (0.16), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 158 HIS 0.004 0.001 HIS D 173 PHE 0.030 0.002 PHE L 209 TYR 0.021 0.002 TYR K 180 ARG 0.009 0.001 ARG E 142 Details of bonding type rmsd hydrogen bonds : bond 0.03471 ( 724) hydrogen bonds : angle 6.16723 ( 1980) SS BOND : bond 0.00528 ( 32) SS BOND : angle 1.50013 ( 64) covalent geometry : bond 0.00426 (21016) covalent geometry : angle 0.69723 (28688) *********************** 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 527 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 432 time to evaluate : 2.284 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 109 GLU cc_start: 0.8879 (tp30) cc_final: 0.8559 (tp30) REVERT: A 110 GLU cc_start: 0.9050 (mp0) cc_final: 0.8752 (mp0) REVERT: A 128 GLU cc_start: 0.9537 (tp30) cc_final: 0.9205 (tp30) REVERT: A 164 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7546 (tm-30) REVERT: A 194 ASP cc_start: 0.8669 (m-30) cc_final: 0.7930 (m-30) REVERT: B 128 GLU cc_start: 0.9538 (tp30) cc_final: 0.9198 (tp30) REVERT: B 164 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7556 (tm-30) REVERT: B 194 ASP cc_start: 0.8676 (m-30) cc_final: 0.7897 (m-30) REVERT: C 109 GLU cc_start: 0.8858 (tp30) cc_final: 0.8447 (tp30) REVERT: C 128 GLU cc_start: 0.9522 (tp30) cc_final: 0.9185 (tp30) REVERT: C 164 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7580 (tm-30) REVERT: C 194 ASP cc_start: 0.8713 (m-30) cc_final: 0.7918 (m-30) REVERT: D 109 GLU cc_start: 0.8837 (tp30) cc_final: 0.8427 (tp30) REVERT: D 128 GLU cc_start: 0.9538 (tp30) cc_final: 0.9194 (tp30) REVERT: D 164 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7532 (tm-30) REVERT: G 45 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8923 (ttpt) REVERT: G 67 SER cc_start: 0.9107 (m) cc_final: 0.8861 (p) REVERT: G 93 ASP cc_start: 0.9339 (t0) cc_final: 0.8979 (t70) REVERT: G 103 LYS cc_start: 0.9307 (mttt) cc_final: 0.8789 (mtpp) REVERT: G 105 GLU cc_start: 0.7882 (tp30) cc_final: 0.7317 (tp30) REVERT: G 106 ILE cc_start: 0.8591 (mt) cc_final: 0.8014 (pp) REVERT: H 3 GLN cc_start: 0.9038 (pm20) cc_final: 0.8611 (pm20) REVERT: H 6 GLU cc_start: 0.8156 (mp0) cc_final: 0.7323 (mp0) REVERT: H 46 GLU cc_start: 0.8842 (tt0) cc_final: 0.8354 (pt0) REVERT: H 72 ASP cc_start: 0.8991 (t0) cc_final: 0.8560 (t0) REVERT: H 95 ASP cc_start: 0.9522 (t0) cc_final: 0.9031 (t0) REVERT: H 100 LEU cc_start: 0.9700 (mt) cc_final: 0.9474 (mp) REVERT: H 105 GLN cc_start: 0.9422 (mt0) cc_final: 0.9093 (pm20) REVERT: H 157 SER cc_start: 0.8331 (OUTLIER) cc_final: 0.8105 (t) REVERT: H 199 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8496 (tp) REVERT: F 3 GLN cc_start: 0.9031 (pm20) cc_final: 0.8636 (pm20) REVERT: F 6 GLU cc_start: 0.8182 (mp0) cc_final: 0.7338 (mp0) REVERT: F 46 GLU cc_start: 0.8834 (tt0) cc_final: 0.8346 (pt0) REVERT: F 72 ASP cc_start: 0.8992 (t0) cc_final: 0.8562 (t0) REVERT: F 95 ASP cc_start: 0.9531 (t0) cc_final: 0.9097 (t0) REVERT: F 100 LEU cc_start: 0.9703 (mt) cc_final: 0.9496 (mp) REVERT: F 105 GLN cc_start: 0.9420 (mt0) cc_final: 0.9113 (pm20) REVERT: F 157 SER cc_start: 0.8464 (OUTLIER) cc_final: 0.8256 (t) REVERT: F 213 LYS cc_start: 0.7496 (OUTLIER) cc_final: 0.7028 (ttpp) REVERT: J 3 GLN cc_start: 0.9030 (pm20) cc_final: 0.8637 (pm20) REVERT: J 6 GLU cc_start: 0.8153 (mp0) cc_final: 0.7304 (mp0) REVERT: J 46 GLU cc_start: 0.8828 (tt0) cc_final: 0.8341 (pt0) REVERT: J 72 ASP cc_start: 0.9006 (t0) cc_final: 0.8579 (t0) REVERT: J 95 ASP cc_start: 0.9532 (t0) cc_final: 0.9003 (t0) REVERT: J 100 LEU cc_start: 0.9702 (mt) cc_final: 0.9499 (mp) REVERT: J 105 GLN cc_start: 0.9406 (mt0) cc_final: 0.9087 (pm20) REVERT: J 157 SER cc_start: 0.8361 (OUTLIER) cc_final: 0.8135 (t) REVERT: J 199 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8470 (tp) REVERT: K 3 GLN cc_start: 0.9018 (pm20) cc_final: 0.8624 (pm20) REVERT: K 6 GLU cc_start: 0.8150 (mp0) cc_final: 0.7308 (mp0) REVERT: K 46 GLU cc_start: 0.8839 (tt0) cc_final: 0.8327 (pt0) REVERT: K 72 ASP cc_start: 0.8998 (t0) cc_final: 0.8566 (t0) REVERT: K 95 ASP cc_start: 0.9536 (t0) cc_final: 0.9096 (t0) REVERT: K 100 LEU cc_start: 0.9704 (mt) cc_final: 0.9501 (mp) REVERT: K 105 GLN cc_start: 0.9421 (mt0) cc_final: 0.9102 (pm20) REVERT: K 149 TYR cc_start: 0.7924 (p90) cc_final: 0.7720 (p90) REVERT: K 213 LYS cc_start: 0.7477 (OUTLIER) cc_final: 0.7009 (ttpp) REVERT: E 45 LYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8927 (ttpt) REVERT: E 67 SER cc_start: 0.9112 (m) cc_final: 0.8865 (p) REVERT: E 93 ASP cc_start: 0.9334 (t0) cc_final: 0.8972 (t70) REVERT: E 103 LYS cc_start: 0.9307 (mttt) cc_final: 0.8784 (mtpp) REVERT: E 105 GLU cc_start: 0.7904 (tp30) cc_final: 0.7392 (tp30) REVERT: E 106 ILE cc_start: 0.8601 (mt) cc_final: 0.8016 (pp) REVERT: I 45 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8919 (ttpt) REVERT: I 67 SER cc_start: 0.9108 (m) cc_final: 0.8864 (p) REVERT: I 92 PHE cc_start: 0.9270 (m-80) cc_final: 0.9060 (m-80) REVERT: I 93 ASP cc_start: 0.9350 (t0) cc_final: 0.8987 (t70) REVERT: I 103 LYS cc_start: 0.9314 (mttt) cc_final: 0.8791 (mtpp) REVERT: I 105 GLU cc_start: 0.7869 (tp30) cc_final: 0.7309 (tp30) REVERT: I 106 ILE cc_start: 0.8604 (mt) cc_final: 0.8023 (pp) REVERT: L 45 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8932 (ttpt) REVERT: L 67 SER cc_start: 0.9105 (m) cc_final: 0.8865 (p) REVERT: L 92 PHE cc_start: 0.9323 (m-80) cc_final: 0.9045 (m-80) REVERT: L 93 ASP cc_start: 0.9338 (t0) cc_final: 0.8961 (t70) REVERT: L 103 LYS cc_start: 0.9304 (mttt) cc_final: 0.8776 (mtpp) REVERT: L 105 GLU cc_start: 0.7876 (tp30) cc_final: 0.7312 (tp30) REVERT: L 106 ILE cc_start: 0.8591 (mt) cc_final: 0.8013 (pp) outliers start: 95 outliers final: 17 residues processed: 478 average time/residue: 1.0134 time to fit residues: 568.0325 Evaluate side-chains 442 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 410 time to evaluate : 2.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 149 GLU 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 139 THR Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 45 LYS 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 213 LYS Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain I residue 17 ASP Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 45 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 69 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 221 optimal weight: 9.9990 chunk 257 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 178 optimal weight: 10.0000 chunk 163 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 141 optimal weight: 0.6980 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 77 GLN F 76 ASN F 77 GLN J 76 ASN J 77 GLN K 76 ASN K 77 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.089450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.059964 restraints weight = 50979.583| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 4.04 r_work: 0.2739 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 21048 Z= 0.180 Angle : 0.682 9.149 28752 Z= 0.352 Chirality : 0.046 0.154 3224 Planarity : 0.005 0.060 3668 Dihedral : 5.447 20.655 2860 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.14 % Allowed : 19.50 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.16), residues: 2636 helix: -1.87 (0.37), residues: 144 sheet: 0.60 (0.17), residues: 850 loop : -0.32 (0.16), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 158 HIS 0.004 0.001 HIS C 173 PHE 0.035 0.002 PHE L 209 TYR 0.019 0.002 TYR F 149 ARG 0.006 0.001 ARG L 142 Details of bonding type rmsd hydrogen bonds : bond 0.03275 ( 724) hydrogen bonds : angle 5.79734 ( 1980) SS BOND : bond 0.00553 ( 32) SS BOND : angle 1.54544 ( 64) covalent geometry : bond 0.00406 (21016) covalent geometry : angle 0.67858 (28688) *********************** 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 534 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 439 time to evaluate : 2.549 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: 0.9356 (OUTLIER) cc_final: 0.9002 (pm20) REVERT: A 109 GLU cc_start: 0.8871 (tp30) cc_final: 0.7935 (tt0) REVERT: A 110 GLU cc_start: 0.9007 (mp0) cc_final: 0.8786 (mp0) REVERT: A 128 GLU cc_start: 0.9534 (tp30) cc_final: 0.9221 (tp30) REVERT: A 164 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7636 (tm-30) REVERT: A 180 MET cc_start: 0.9228 (OUTLIER) cc_final: 0.9022 (mtm) REVERT: B 20 GLN cc_start: 0.9249 (OUTLIER) cc_final: 0.8814 (pm20) REVERT: B 109 GLU cc_start: 0.8871 (tp30) cc_final: 0.8309 (tt0) REVERT: B 128 GLU cc_start: 0.9538 (tp30) cc_final: 0.9219 (tp30) REVERT: B 164 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7633 (tm-30) REVERT: C 128 GLU cc_start: 0.9530 (tp30) cc_final: 0.9215 (tp30) REVERT: C 164 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7617 (tm-30) REVERT: D 128 GLU cc_start: 0.9537 (tp30) cc_final: 0.9216 (tp30) REVERT: D 149 GLU cc_start: 0.9236 (mp0) cc_final: 0.8973 (mp0) REVERT: D 164 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7598 (tm-30) REVERT: D 194 ASP cc_start: 0.8572 (m-30) cc_final: 0.7890 (m-30) REVERT: G 45 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8901 (ttpt) REVERT: G 49 TYR cc_start: 0.9293 (p90) cc_final: 0.8913 (p90) REVERT: G 50 GLU cc_start: 0.9337 (mt-10) cc_final: 0.8980 (mp0) REVERT: G 67 SER cc_start: 0.9148 (m) cc_final: 0.8909 (p) REVERT: G 93 ASP cc_start: 0.9347 (t0) cc_final: 0.8979 (t70) REVERT: G 103 LYS cc_start: 0.9285 (mttt) cc_final: 0.8771 (mtpp) REVERT: G 105 GLU cc_start: 0.7869 (tp30) cc_final: 0.7276 (tp30) REVERT: G 106 ILE cc_start: 0.8638 (mt) cc_final: 0.8010 (pp) REVERT: G 142 ARG cc_start: 0.9147 (ttm-80) cc_final: 0.8931 (ttm-80) REVERT: H 3 GLN cc_start: 0.9028 (pm20) cc_final: 0.8585 (pm20) REVERT: H 6 GLU cc_start: 0.8190 (mp0) cc_final: 0.7322 (mp0) REVERT: H 46 GLU cc_start: 0.8833 (tt0) cc_final: 0.8414 (pt0) REVERT: H 72 ASP cc_start: 0.8974 (t0) cc_final: 0.8549 (t0) REVERT: H 95 ASP cc_start: 0.9535 (t0) cc_final: 0.9086 (t0) REVERT: H 105 GLN cc_start: 0.9420 (mt0) cc_final: 0.9092 (pm20) REVERT: H 163 LEU cc_start: 0.9547 (mp) cc_final: 0.9315 (tm) REVERT: H 199 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8522 (tp) REVERT: F 3 GLN cc_start: 0.9077 (pm20) cc_final: 0.8693 (pm20) REVERT: F 6 GLU cc_start: 0.8163 (mp0) cc_final: 0.7299 (mp0) REVERT: F 46 GLU cc_start: 0.8860 (tt0) cc_final: 0.8434 (pt0) REVERT: F 72 ASP cc_start: 0.8974 (t0) cc_final: 0.8546 (t0) REVERT: F 95 ASP cc_start: 0.9540 (t0) cc_final: 0.9089 (t0) REVERT: F 100 LEU cc_start: 0.9737 (mt) cc_final: 0.9530 (mp) REVERT: F 105 GLN cc_start: 0.9417 (mt0) cc_final: 0.9088 (pm20) REVERT: J 3 GLN cc_start: 0.9080 (pm20) cc_final: 0.8697 (pm20) REVERT: J 6 GLU cc_start: 0.8178 (mp0) cc_final: 0.7322 (mp0) REVERT: J 46 GLU cc_start: 0.8833 (tt0) cc_final: 0.8409 (pt0) REVERT: J 72 ASP cc_start: 0.8985 (t0) cc_final: 0.8556 (t0) REVERT: J 95 ASP cc_start: 0.9525 (t0) cc_final: 0.9001 (t0) REVERT: J 100 LEU cc_start: 0.9737 (mt) cc_final: 0.9523 (mp) REVERT: J 105 GLN cc_start: 0.9411 (mt0) cc_final: 0.9077 (pm20) REVERT: J 163 LEU cc_start: 0.9545 (mp) cc_final: 0.9311 (tm) REVERT: J 199 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8494 (tp) REVERT: K 3 GLN cc_start: 0.9071 (pm20) cc_final: 0.8688 (pm20) REVERT: K 6 GLU cc_start: 0.8149 (mp0) cc_final: 0.7291 (mp0) REVERT: K 46 GLU cc_start: 0.8849 (tt0) cc_final: 0.8414 (pt0) REVERT: K 72 ASP cc_start: 0.8980 (t0) cc_final: 0.8552 (t0) REVERT: K 95 ASP cc_start: 0.9544 (t0) cc_final: 0.9093 (t0) REVERT: K 100 LEU cc_start: 0.9739 (mt) cc_final: 0.9534 (mp) REVERT: K 105 GLN cc_start: 0.9416 (mt0) cc_final: 0.9079 (pm20) REVERT: K 149 TYR cc_start: 0.7975 (p90) cc_final: 0.7772 (p90) REVERT: E 45 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8923 (ttpt) REVERT: E 49 TYR cc_start: 0.9297 (p90) cc_final: 0.8916 (p90) REVERT: E 50 GLU cc_start: 0.9332 (mt-10) cc_final: 0.8980 (mp0) REVERT: E 67 SER cc_start: 0.9134 (m) cc_final: 0.8896 (p) REVERT: E 93 ASP cc_start: 0.9336 (t0) cc_final: 0.8991 (t70) REVERT: E 103 LYS cc_start: 0.9289 (mttt) cc_final: 0.8770 (mtpp) REVERT: E 105 GLU cc_start: 0.7883 (tp30) cc_final: 0.7290 (tp30) REVERT: E 106 ILE cc_start: 0.8645 (mt) cc_final: 0.8007 (pp) REVERT: E 142 ARG cc_start: 0.9136 (ttm-80) cc_final: 0.8924 (ttm-80) REVERT: E 195 GLU cc_start: 0.5506 (OUTLIER) cc_final: 0.5238 (tm-30) REVERT: I 36 TYR cc_start: 0.9146 (m-80) cc_final: 0.8940 (m-80) REVERT: I 45 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8913 (ttpt) REVERT: I 49 TYR cc_start: 0.9302 (p90) cc_final: 0.8910 (p90) REVERT: I 50 GLU cc_start: 0.9325 (mt-10) cc_final: 0.8971 (mp0) REVERT: I 67 SER cc_start: 0.9138 (m) cc_final: 0.8895 (p) REVERT: I 93 ASP cc_start: 0.9360 (t0) cc_final: 0.8999 (t70) REVERT: I 103 LYS cc_start: 0.9297 (mttt) cc_final: 0.8784 (mtpp) REVERT: I 105 GLU cc_start: 0.7842 (tp30) cc_final: 0.7255 (tp30) REVERT: I 106 ILE cc_start: 0.8643 (mt) cc_final: 0.8014 (pp) REVERT: I 142 ARG cc_start: 0.9152 (ttm-80) cc_final: 0.8939 (ttm-80) REVERT: L 45 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8921 (ttpt) REVERT: L 49 TYR cc_start: 0.9298 (p90) cc_final: 0.8918 (p90) REVERT: L 50 GLU cc_start: 0.9328 (mt-10) cc_final: 0.8974 (mp0) REVERT: L 67 SER cc_start: 0.9152 (m) cc_final: 0.8911 (p) REVERT: L 92 PHE cc_start: 0.9311 (m-80) cc_final: 0.8991 (m-80) REVERT: L 93 ASP cc_start: 0.9330 (t0) cc_final: 0.8965 (t70) REVERT: L 103 LYS cc_start: 0.9294 (mttt) cc_final: 0.8786 (mtpp) REVERT: L 105 GLU cc_start: 0.7865 (tp30) cc_final: 0.7274 (tp30) REVERT: L 106 ILE cc_start: 0.8653 (mt) cc_final: 0.8013 (pp) REVERT: L 142 ARG cc_start: 0.9143 (ttm-80) cc_final: 0.8932 (ttm-80) REVERT: L 195 GLU cc_start: 0.5500 (OUTLIER) cc_final: 0.5227 (tm-30) outliers start: 95 outliers final: 32 residues processed: 493 average time/residue: 1.0625 time to fit residues: 607.3587 Evaluate side-chains 457 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 410 time to evaluate : 2.415 ------------------------------------------------------------------------------- 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 A residue 180 MET Chi-restraints excluded: chain B residue 20 GLN 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 139 THR Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 164 GLU 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 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 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 165 SER 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 E residue 195 GLU 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 45 LYS Chi-restraints excluded: chain L residue 159 SER Chi-restraints excluded: chain L residue 194 CYS Chi-restraints excluded: chain L residue 195 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 170 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 69 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 243 optimal weight: 2.9990 chunk 237 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 220 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 215 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 203 ASN H 208 ASN 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 Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.089390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.060178 restraints weight = 51511.910| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 4.03 r_work: 0.2736 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21048 Z= 0.194 Angle : 0.686 8.163 28752 Z= 0.354 Chirality : 0.046 0.152 3224 Planarity : 0.005 0.061 3668 Dihedral : 5.267 21.070 2860 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.80 % Allowed : 20.72 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.16), residues: 2636 helix: -1.70 (0.39), residues: 144 sheet: 0.49 (0.17), residues: 839 loop : -0.26 (0.16), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 158 HIS 0.004 0.001 HIS A 173 PHE 0.039 0.002 PHE L 209 TYR 0.026 0.002 TYR H 99 ARG 0.010 0.001 ARG H 26 Details of bonding type rmsd hydrogen bonds : bond 0.03159 ( 724) hydrogen bonds : angle 5.72341 ( 1980) SS BOND : bond 0.00559 ( 32) SS BOND : angle 1.15746 ( 64) covalent geometry : bond 0.00434 (21016) covalent geometry : angle 0.68419 (28688) *********************** 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 517 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 430 time to evaluate : 2.295 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: A 20 GLN cc_start: 0.9351 (OUTLIER) cc_final: 0.9033 (pm20) REVERT: A 109 GLU cc_start: 0.8971 (tp30) cc_final: 0.7915 (tt0) REVERT: A 110 GLU cc_start: 0.9037 (mp0) cc_final: 0.8825 (mp0) REVERT: A 128 GLU cc_start: 0.9533 (tp30) cc_final: 0.9224 (tp30) REVERT: A 164 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7638 (tm-30) REVERT: A 194 ASP cc_start: 0.8607 (m-30) cc_final: 0.7945 (m-30) REVERT: B 20 GLN cc_start: 0.9233 (OUTLIER) cc_final: 0.8829 (pm20) REVERT: B 109 GLU cc_start: 0.8905 (tp30) cc_final: 0.8550 (tp30) REVERT: B 128 GLU cc_start: 0.9533 (tp30) cc_final: 0.9215 (tp30) REVERT: B 164 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7591 (tm-30) REVERT: B 194 ASP cc_start: 0.8613 (m-30) cc_final: 0.7958 (m-30) REVERT: C 109 GLU cc_start: 0.8785 (tt0) cc_final: 0.7902 (tt0) REVERT: C 128 GLU cc_start: 0.9529 (tp30) cc_final: 0.9213 (tp30) REVERT: C 164 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7643 (tm-30) REVERT: C 180 MET cc_start: 0.9484 (mtm) cc_final: 0.9167 (mtm) REVERT: C 194 ASP cc_start: 0.8621 (m-30) cc_final: 0.7958 (m-30) REVERT: D 109 GLU cc_start: 0.8749 (tt0) cc_final: 0.7873 (tt0) REVERT: D 128 GLU cc_start: 0.9530 (tp30) cc_final: 0.9213 (tp30) REVERT: D 164 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7613 (tm-30) REVERT: D 180 MET cc_start: 0.9475 (mtm) cc_final: 0.9150 (mtm) REVERT: D 194 ASP cc_start: 0.8579 (m-30) cc_final: 0.7798 (m-30) REVERT: G 45 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8892 (ttpt) REVERT: G 49 TYR cc_start: 0.9293 (p90) cc_final: 0.8924 (p90) REVERT: G 50 GLU cc_start: 0.9329 (mt-10) cc_final: 0.8970 (mp0) REVERT: G 67 SER cc_start: 0.9152 (m) cc_final: 0.8923 (p) REVERT: G 93 ASP cc_start: 0.9351 (t0) cc_final: 0.8988 (t70) REVERT: G 103 LYS cc_start: 0.9273 (mttt) cc_final: 0.8748 (mtpp) REVERT: G 105 GLU cc_start: 0.7923 (tp30) cc_final: 0.7335 (tp30) REVERT: G 106 ILE cc_start: 0.8698 (mt) cc_final: 0.8165 (pp) REVERT: H 3 GLN cc_start: 0.9100 (pm20) cc_final: 0.8684 (pm20) REVERT: H 6 GLU cc_start: 0.8227 (mp0) cc_final: 0.7368 (mp0) REVERT: H 16 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8339 (pm20) REVERT: H 46 GLU cc_start: 0.8865 (tt0) cc_final: 0.8383 (tt0) REVERT: H 72 ASP cc_start: 0.8930 (t0) cc_final: 0.8474 (t0) REVERT: H 95 ASP cc_start: 0.9521 (t0) cc_final: 0.9075 (t0) REVERT: H 105 GLN cc_start: 0.9428 (mt0) cc_final: 0.9062 (pm20) REVERT: H 163 LEU cc_start: 0.9564 (mp) cc_final: 0.9345 (tm) REVERT: H 199 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8591 (tp) REVERT: F 3 GLN cc_start: 0.9115 (pm20) cc_final: 0.8810 (pm20) REVERT: F 6 GLU cc_start: 0.8199 (mp0) cc_final: 0.7361 (mp0) REVERT: F 16 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8358 (pm20) REVERT: F 46 GLU cc_start: 0.8886 (tt0) cc_final: 0.8411 (tt0) REVERT: F 72 ASP cc_start: 0.8923 (t0) cc_final: 0.8465 (t0) REVERT: F 95 ASP cc_start: 0.9532 (t0) cc_final: 0.9041 (t0) REVERT: F 99 TYR cc_start: 0.9171 (m-10) cc_final: 0.8641 (m-80) REVERT: F 100 LEU cc_start: 0.9733 (mt) cc_final: 0.9517 (mm) REVERT: F 105 GLN cc_start: 0.9430 (mt0) cc_final: 0.9059 (pm20) REVERT: F 213 LYS cc_start: 0.7637 (OUTLIER) cc_final: 0.7224 (ttpp) REVERT: J 3 GLN cc_start: 0.9099 (pm20) cc_final: 0.8796 (pm20) REVERT: J 6 GLU cc_start: 0.8178 (mp0) cc_final: 0.7334 (mp0) REVERT: J 46 GLU cc_start: 0.8842 (tt0) cc_final: 0.8355 (tt0) REVERT: J 72 ASP cc_start: 0.8932 (t0) cc_final: 0.8474 (t0) REVERT: J 95 ASP cc_start: 0.9516 (t0) cc_final: 0.9018 (t0) REVERT: J 99 TYR cc_start: 0.8876 (m-10) cc_final: 0.8519 (m-10) REVERT: J 100 LEU cc_start: 0.9733 (mt) cc_final: 0.9520 (mp) REVERT: J 105 GLN cc_start: 0.9419 (mt0) cc_final: 0.9050 (pm20) REVERT: J 108 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9092 (tm) REVERT: J 163 LEU cc_start: 0.9563 (mp) cc_final: 0.9339 (tm) REVERT: J 199 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8566 (tp) REVERT: K 3 GLN cc_start: 0.9101 (pm20) cc_final: 0.8797 (pm20) REVERT: K 6 GLU cc_start: 0.8156 (mp0) cc_final: 0.7323 (mp0) REVERT: K 46 GLU cc_start: 0.8860 (tt0) cc_final: 0.8376 (tt0) REVERT: K 72 ASP cc_start: 0.8921 (t0) cc_final: 0.8462 (t0) REVERT: K 95 ASP cc_start: 0.9530 (t0) cc_final: 0.8985 (t0) REVERT: K 99 TYR cc_start: 0.9167 (m-10) cc_final: 0.8640 (m-80) REVERT: K 105 GLN cc_start: 0.9427 (mt0) cc_final: 0.9075 (pm20) REVERT: K 108 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9072 (tm) REVERT: K 213 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7278 (ttpp) REVERT: E 45 LYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8912 (ttpt) REVERT: E 49 TYR cc_start: 0.9292 (p90) cc_final: 0.8934 (p90) REVERT: E 50 GLU cc_start: 0.9334 (mt-10) cc_final: 0.8980 (mp0) REVERT: E 67 SER cc_start: 0.9141 (m) cc_final: 0.8911 (p) REVERT: E 93 ASP cc_start: 0.9348 (t0) cc_final: 0.8999 (t70) REVERT: E 103 LYS cc_start: 0.9279 (mttt) cc_final: 0.8759 (mtpp) REVERT: E 105 GLU cc_start: 0.7926 (tp30) cc_final: 0.7341 (tp30) REVERT: E 106 ILE cc_start: 0.8699 (mt) cc_final: 0.8158 (pp) REVERT: E 195 GLU cc_start: 0.5731 (OUTLIER) cc_final: 0.5438 (tm-30) REVERT: E 196 VAL cc_start: 0.8948 (OUTLIER) cc_final: 0.8706 (m) REVERT: I 45 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8889 (ttpt) REVERT: I 49 TYR cc_start: 0.9292 (p90) cc_final: 0.8923 (p90) REVERT: I 50 GLU cc_start: 0.9325 (mt-10) cc_final: 0.8970 (mp0) REVERT: I 67 SER cc_start: 0.9143 (m) cc_final: 0.8914 (p) REVERT: I 93 ASP cc_start: 0.9371 (t0) cc_final: 0.8997 (t70) REVERT: I 103 LYS cc_start: 0.9284 (mttt) cc_final: 0.8768 (mtpp) REVERT: I 105 GLU cc_start: 0.7888 (tp30) cc_final: 0.7311 (tp30) REVERT: I 106 ILE cc_start: 0.8696 (mt) cc_final: 0.8162 (pp) REVERT: L 45 LYS cc_start: 0.9177 (OUTLIER) cc_final: 0.8906 (ttpt) REVERT: L 49 TYR cc_start: 0.9292 (p90) cc_final: 0.8936 (p90) REVERT: L 50 GLU cc_start: 0.9339 (mt-10) cc_final: 0.8983 (mp0) REVERT: L 67 SER cc_start: 0.9157 (m) cc_final: 0.8931 (p) REVERT: L 92 PHE cc_start: 0.9318 (m-80) cc_final: 0.8878 (m-80) REVERT: L 93 ASP cc_start: 0.9337 (t0) cc_final: 0.8980 (t70) REVERT: L 95 ASP cc_start: 0.8784 (m-30) cc_final: 0.8025 (p0) REVERT: L 103 LYS cc_start: 0.9281 (mttt) cc_final: 0.8767 (mtpp) REVERT: L 105 GLU cc_start: 0.7915 (tp30) cc_final: 0.7331 (tp30) REVERT: L 106 ILE cc_start: 0.8697 (mt) cc_final: 0.8155 (pp) REVERT: L 195 GLU cc_start: 0.5712 (OUTLIER) cc_final: 0.5421 (tm-30) REVERT: L 196 VAL cc_start: 0.8931 (OUTLIER) cc_final: 0.8684 (m) outliers start: 87 outliers final: 41 residues processed: 486 average time/residue: 1.1413 time to fit residues: 638.3282 Evaluate side-chains 458 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 397 time to evaluate : 2.545 ------------------------------------------------------------------------------- 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 149 GLU 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 149 GLU Chi-restraints excluded: chain D residue 164 GLU 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 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 199 ILE 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 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 199 ILE 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 45 LYS Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 183 LYS 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 45 LYS Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 194 CYS 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 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 155 optimal weight: 8.9990 chunk 39 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 196 optimal weight: 3.9990 chunk 204 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 chunk 187 optimal weight: 4.9990 chunk 180 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 252 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 124 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 F 203 ASN ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 GLN ** K 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 GLN K 203 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.088574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.059414 restraints weight = 51645.028| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 4.02 r_work: 0.2724 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 21048 Z= 0.227 Angle : 0.695 8.308 28752 Z= 0.358 Chirality : 0.046 0.157 3224 Planarity : 0.005 0.062 3668 Dihedral : 5.210 21.389 2860 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.28 % Allowed : 21.51 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.16), residues: 2636 helix: -1.51 (0.39), residues: 144 sheet: 0.55 (0.17), residues: 834 loop : -0.31 (0.16), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 158 HIS 0.004 0.001 HIS D 173 PHE 0.041 0.002 PHE E 209 TYR 0.021 0.002 TYR J 99 ARG 0.012 0.001 ARG E 142 Details of bonding type rmsd hydrogen bonds : bond 0.03181 ( 724) hydrogen bonds : angle 5.52940 ( 1980) SS BOND : bond 0.00594 ( 32) SS BOND : angle 1.26524 ( 64) covalent geometry : bond 0.00505 (21016) covalent geometry : angle 0.69366 (28688) *********************** 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 514 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 416 time to evaluate : 2.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLN cc_start: 0.9345 (OUTLIER) cc_final: 0.8970 (pm20) REVERT: A 109 GLU cc_start: 0.8959 (tp30) cc_final: 0.7894 (tt0) REVERT: A 110 GLU cc_start: 0.9033 (mp0) cc_final: 0.8830 (mp0) REVERT: A 128 GLU cc_start: 0.9535 (tp30) cc_final: 0.9239 (tp30) REVERT: A 164 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7676 (tm-30) REVERT: A 180 MET cc_start: 0.9236 (OUTLIER) cc_final: 0.8979 (mtm) REVERT: A 194 ASP cc_start: 0.8631 (m-30) cc_final: 0.7952 (m-30) REVERT: B 20 GLN cc_start: 0.9150 (OUTLIER) cc_final: 0.8732 (pm20) REVERT: B 128 GLU cc_start: 0.9539 (tp30) cc_final: 0.9231 (tp30) REVERT: B 134 MET cc_start: 0.9174 (tpp) cc_final: 0.8885 (mmp) REVERT: B 164 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7618 (tm-30) REVERT: B 180 MET cc_start: 0.9498 (mtm) cc_final: 0.9220 (mtm) REVERT: B 194 ASP cc_start: 0.8651 (m-30) cc_final: 0.7981 (m-30) REVERT: C 20 GLN cc_start: 0.9329 (OUTLIER) cc_final: 0.8943 (pm20) REVERT: C 109 GLU cc_start: 0.8757 (tt0) cc_final: 0.8060 (tt0) REVERT: C 128 GLU cc_start: 0.9538 (tp30) cc_final: 0.9231 (tp30) REVERT: C 164 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7667 (tm-30) REVERT: C 180 MET cc_start: 0.9500 (mtm) cc_final: 0.9224 (mtm) REVERT: C 194 ASP cc_start: 0.8622 (m-30) cc_final: 0.7940 (m-30) REVERT: D 20 GLN cc_start: 0.9305 (OUTLIER) cc_final: 0.8939 (pm20) REVERT: D 109 GLU cc_start: 0.8729 (tt0) cc_final: 0.8040 (tt0) REVERT: D 128 GLU cc_start: 0.9532 (tp30) cc_final: 0.9221 (tp30) REVERT: D 134 MET cc_start: 0.9180 (tpp) cc_final: 0.8896 (mmp) REVERT: D 164 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7665 (tm-30) REVERT: D 180 MET cc_start: 0.9501 (mtm) cc_final: 0.9197 (mtm) REVERT: D 194 ASP cc_start: 0.8613 (m-30) cc_final: 0.7876 (m-30) REVERT: G 49 TYR cc_start: 0.9279 (p90) cc_final: 0.8861 (p90) REVERT: G 50 GLU cc_start: 0.9356 (mt-10) cc_final: 0.8953 (mp0) REVERT: G 67 SER cc_start: 0.9174 (m) cc_final: 0.8930 (p) REVERT: G 93 ASP cc_start: 0.9356 (t0) cc_final: 0.8981 (t70) REVERT: G 103 LYS cc_start: 0.9282 (mttt) cc_final: 0.8744 (mtpp) REVERT: G 105 GLU cc_start: 0.8007 (tp30) cc_final: 0.7530 (tp30) REVERT: G 106 ILE cc_start: 0.8695 (mt) cc_final: 0.8185 (pp) REVERT: H 3 GLN cc_start: 0.9095 (pm20) cc_final: 0.8712 (pm20) REVERT: H 6 GLU cc_start: 0.8208 (mp0) cc_final: 0.7346 (mp0) REVERT: H 16 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8356 (pm20) REVERT: H 46 GLU cc_start: 0.8849 (tt0) cc_final: 0.8386 (tt0) REVERT: H 72 ASP cc_start: 0.8901 (t0) cc_final: 0.8451 (t0) REVERT: H 95 ASP cc_start: 0.9545 (t0) cc_final: 0.9121 (t0) REVERT: H 105 GLN cc_start: 0.9442 (mt0) cc_final: 0.9089 (pm20) REVERT: H 108 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9121 (tm) REVERT: H 163 LEU cc_start: 0.9600 (mp) cc_final: 0.9364 (tm) REVERT: H 199 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8564 (tp) REVERT: F 3 GLN cc_start: 0.9106 (pm20) cc_final: 0.8762 (pm20) REVERT: F 6 GLU cc_start: 0.8182 (mp0) cc_final: 0.7342 (mp0) REVERT: F 16 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8363 (pm20) REVERT: F 26 ARG cc_start: 0.8408 (tmm-80) cc_final: 0.8038 (tmm-80) REVERT: F 27 PHE cc_start: 0.8653 (OUTLIER) cc_final: 0.8335 (m-80) REVERT: F 46 GLU cc_start: 0.8856 (tt0) cc_final: 0.8394 (tt0) REVERT: F 72 ASP cc_start: 0.8901 (t0) cc_final: 0.8436 (t0) REVERT: F 95 ASP cc_start: 0.9531 (t0) cc_final: 0.9030 (t0) REVERT: F 105 GLN cc_start: 0.9446 (mt0) cc_final: 0.9089 (pm20) REVERT: F 108 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9108 (tm) REVERT: F 213 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7389 (tmmm) REVERT: J 3 GLN cc_start: 0.9099 (pm20) cc_final: 0.8757 (pm20) REVERT: J 6 GLU cc_start: 0.8192 (mp0) cc_final: 0.7333 (mp0) REVERT: J 16 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8301 (pm20) REVERT: J 26 ARG cc_start: 0.8409 (tmm-80) cc_final: 0.8042 (tmm-80) REVERT: J 27 PHE cc_start: 0.8651 (OUTLIER) cc_final: 0.8335 (m-80) REVERT: J 46 GLU cc_start: 0.8838 (tt0) cc_final: 0.8370 (tt0) REVERT: J 72 ASP cc_start: 0.8906 (t0) cc_final: 0.8453 (t0) REVERT: J 95 ASP cc_start: 0.9545 (t0) cc_final: 0.9095 (t0) REVERT: J 105 GLN cc_start: 0.9425 (mt0) cc_final: 0.9065 (pm20) REVERT: J 108 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9093 (tm) REVERT: J 163 LEU cc_start: 0.9600 (mp) cc_final: 0.9363 (tm) REVERT: J 199 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8569 (tp) REVERT: K 3 GLN cc_start: 0.9095 (pm20) cc_final: 0.8753 (pm20) REVERT: K 6 GLU cc_start: 0.8148 (mp0) cc_final: 0.7272 (mp0) REVERT: K 16 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8287 (pm20) REVERT: K 26 ARG cc_start: 0.8400 (tmm-80) cc_final: 0.8033 (tmm-80) REVERT: K 27 PHE cc_start: 0.8645 (OUTLIER) cc_final: 0.8326 (m-80) REVERT: K 46 GLU cc_start: 0.8848 (tt0) cc_final: 0.8386 (tt0) REVERT: K 72 ASP cc_start: 0.8904 (t0) cc_final: 0.8441 (t0) REVERT: K 95 ASP cc_start: 0.9501 (t0) cc_final: 0.9061 (t0) REVERT: K 105 GLN cc_start: 0.9425 (mt0) cc_final: 0.9065 (pm20) REVERT: K 108 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9090 (tm) REVERT: K 213 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7302 (ttpp) REVERT: E 49 TYR cc_start: 0.9273 (p90) cc_final: 0.8847 (p90) REVERT: E 50 GLU cc_start: 0.9349 (mt-10) cc_final: 0.8938 (mp0) REVERT: E 67 SER cc_start: 0.9158 (m) cc_final: 0.8918 (p) REVERT: E 93 ASP cc_start: 0.9336 (t0) cc_final: 0.8972 (t70) REVERT: E 103 LYS cc_start: 0.9297 (mttt) cc_final: 0.8765 (mtpp) REVERT: E 105 GLU cc_start: 0.7997 (tp30) cc_final: 0.7526 (tp30) REVERT: E 106 ILE cc_start: 0.8704 (mt) cc_final: 0.8184 (pp) REVERT: I 45 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8915 (ttpt) REVERT: I 49 TYR cc_start: 0.9277 (p90) cc_final: 0.8855 (p90) REVERT: I 50 GLU cc_start: 0.9347 (mt-10) cc_final: 0.8935 (mp0) REVERT: I 67 SER cc_start: 0.9156 (m) cc_final: 0.8918 (p) REVERT: I 93 ASP cc_start: 0.9340 (t0) cc_final: 0.9009 (t70) REVERT: I 103 LYS cc_start: 0.9295 (mttt) cc_final: 0.8758 (mtpp) REVERT: I 105 GLU cc_start: 0.7970 (tp30) cc_final: 0.7504 (tp30) REVERT: I 106 ILE cc_start: 0.8696 (mt) cc_final: 0.8188 (pp) REVERT: L 49 TYR cc_start: 0.9269 (p90) cc_final: 0.8850 (p90) REVERT: L 50 GLU cc_start: 0.9356 (mt-10) cc_final: 0.8941 (mp0) REVERT: L 67 SER cc_start: 0.9170 (m) cc_final: 0.8934 (p) REVERT: L 93 ASP cc_start: 0.9346 (t0) cc_final: 0.8966 (t70) REVERT: L 103 LYS cc_start: 0.9293 (mttt) cc_final: 0.8774 (mtpp) REVERT: L 105 GLU cc_start: 0.7981 (tp30) cc_final: 0.7509 (tp30) REVERT: L 106 ILE cc_start: 0.8700 (mt) cc_final: 0.8181 (pp) outliers start: 98 outliers final: 44 residues processed: 481 average time/residue: 1.0493 time to fit residues: 589.6607 Evaluate side-chains 461 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 396 time to evaluate : 2.319 ------------------------------------------------------------------------------- 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 A residue 180 MET 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 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 20 GLN 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 164 GLU 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 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 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 165 SER Chi-restraints excluded: chain F residue 213 LYS 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 108 LEU Chi-restraints excluded: chain J residue 199 ILE Chi-restraints excluded: chain J residue 213 LYS 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 108 LEU Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 213 LYS Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 194 CYS 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 45 LYS Chi-restraints excluded: chain L residue 159 SER Chi-restraints excluded: chain L residue 183 LYS Chi-restraints excluded: chain L residue 194 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 37 optimal weight: 4.9990 chunk 158 optimal weight: 7.9990 chunk 2 optimal weight: 0.0170 chunk 169 optimal weight: 0.9990 chunk 210 optimal weight: 2.9990 chunk 257 optimal weight: 4.9990 chunk 246 optimal weight: 2.9990 chunk 202 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 227 optimal weight: 1.9990 overall best weight: 1.2026 ------------------------------------------------------------------------------- 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 D 146 ASN H 76 ASN 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 203 ASN K 208 ASN E 124 GLN L 124 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.089323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.060217 restraints weight = 50752.736| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 4.01 r_work: 0.2745 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21048 Z= 0.176 Angle : 0.685 8.014 28752 Z= 0.351 Chirality : 0.046 0.153 3224 Planarity : 0.005 0.062 3668 Dihedral : 5.103 20.804 2860 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.01 % Allowed : 21.73 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.16), residues: 2636 helix: -1.30 (0.40), residues: 144 sheet: 0.71 (0.18), residues: 830 loop : -0.37 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 158 HIS 0.004 0.001 HIS C 173 PHE 0.043 0.002 PHE E 209 TYR 0.015 0.001 TYR K 149 ARG 0.011 0.001 ARG I 142 Details of bonding type rmsd hydrogen bonds : bond 0.03020 ( 724) hydrogen bonds : angle 5.36953 ( 1980) SS BOND : bond 0.00490 ( 32) SS BOND : angle 1.07424 ( 64) covalent geometry : bond 0.00399 (21016) covalent geometry : angle 0.68394 (28688) *********************** 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 512 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 420 time to evaluate : 2.293 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: 0.9360 (OUTLIER) cc_final: 0.9027 (pm20) REVERT: A 31 VAL cc_start: 0.9662 (OUTLIER) cc_final: 0.9461 (p) REVERT: A 109 GLU cc_start: 0.8986 (tp30) cc_final: 0.7917 (tt0) REVERT: A 128 GLU cc_start: 0.9538 (tp30) cc_final: 0.9306 (tp30) REVERT: A 164 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7708 (tm-30) REVERT: A 180 MET cc_start: 0.9218 (OUTLIER) cc_final: 0.8965 (mtm) REVERT: A 194 ASP cc_start: 0.8628 (m-30) cc_final: 0.7933 (m-30) REVERT: B 20 GLN cc_start: 0.9125 (OUTLIER) cc_final: 0.8720 (pm20) REVERT: B 109 GLU cc_start: 0.8921 (tp30) cc_final: 0.8152 (tt0) REVERT: B 128 GLU cc_start: 0.9533 (tp30) cc_final: 0.9294 (tp30) REVERT: B 149 GLU cc_start: 0.9093 (mp0) cc_final: 0.8800 (mp0) REVERT: B 164 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7653 (tm-30) REVERT: B 180 MET cc_start: 0.9469 (mtm) cc_final: 0.9205 (mtm) REVERT: B 194 ASP cc_start: 0.8619 (m-30) cc_final: 0.7904 (m-30) REVERT: C 20 GLN cc_start: 0.9351 (OUTLIER) cc_final: 0.8967 (pm20) REVERT: C 109 GLU cc_start: 0.8719 (tt0) cc_final: 0.8056 (tt0) REVERT: C 128 GLU cc_start: 0.9537 (tp30) cc_final: 0.9294 (tp30) REVERT: C 164 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7695 (tm-30) REVERT: C 180 MET cc_start: 0.9505 (mtm) cc_final: 0.9203 (mtm) REVERT: C 194 ASP cc_start: 0.8610 (m-30) cc_final: 0.7914 (m-30) REVERT: D 20 GLN cc_start: 0.9327 (OUTLIER) cc_final: 0.8924 (pm20) REVERT: D 109 GLU cc_start: 0.8727 (tt0) cc_final: 0.8119 (tt0) REVERT: D 128 GLU cc_start: 0.9530 (tp30) cc_final: 0.9283 (tp30) REVERT: D 164 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7661 (tm-30) REVERT: D 180 MET cc_start: 0.9513 (mtm) cc_final: 0.9228 (mtm) REVERT: D 194 ASP cc_start: 0.8592 (m-30) cc_final: 0.7851 (m-30) REVERT: G 24 GLN cc_start: 0.8697 (mt0) cc_final: 0.8452 (mp10) REVERT: G 49 TYR cc_start: 0.9270 (p90) cc_final: 0.8934 (p90) REVERT: G 50 GLU cc_start: 0.9337 (mt-10) cc_final: 0.8952 (mp0) REVERT: G 67 SER cc_start: 0.9159 (m) cc_final: 0.8920 (p) REVERT: G 93 ASP cc_start: 0.9304 (t0) cc_final: 0.8987 (t70) REVERT: G 103 LYS cc_start: 0.9275 (mttt) cc_final: 0.8727 (mtpp) REVERT: H 3 GLN cc_start: 0.9085 (pm20) cc_final: 0.8708 (pm20) REVERT: H 6 GLU cc_start: 0.8222 (mp0) cc_final: 0.7393 (mp0) REVERT: H 16 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8391 (pm20) REVERT: H 46 GLU cc_start: 0.8843 (tt0) cc_final: 0.8370 (tt0) REVERT: H 72 ASP cc_start: 0.8900 (t0) cc_final: 0.8450 (t0) REVERT: H 95 ASP cc_start: 0.9519 (t0) cc_final: 0.9020 (t0) REVERT: H 100 LEU cc_start: 0.9540 (mt) cc_final: 0.9243 (mt) REVERT: H 105 GLN cc_start: 0.9443 (mt0) cc_final: 0.9089 (pm20) REVERT: H 108 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9097 (tm) REVERT: H 163 LEU cc_start: 0.9608 (mp) cc_final: 0.9363 (tm) REVERT: H 213 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7476 (ttpp) REVERT: F 3 GLN cc_start: 0.9081 (pm20) cc_final: 0.8714 (pm20) REVERT: F 6 GLU cc_start: 0.8184 (mp0) cc_final: 0.7332 (mp0) REVERT: F 16 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8386 (pm20) REVERT: F 26 ARG cc_start: 0.8457 (tmm-80) cc_final: 0.8074 (tmm-80) REVERT: F 27 PHE cc_start: 0.8676 (OUTLIER) cc_final: 0.8330 (m-80) REVERT: F 46 GLU cc_start: 0.8855 (tt0) cc_final: 0.8384 (tt0) REVERT: F 72 ASP cc_start: 0.8895 (t0) cc_final: 0.8444 (t0) REVERT: F 95 ASP cc_start: 0.9482 (t0) cc_final: 0.9003 (t0) REVERT: F 105 GLN cc_start: 0.9436 (mt0) cc_final: 0.9088 (pm20) REVERT: F 108 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9077 (tm) REVERT: F 203 ASN cc_start: 0.8812 (m-40) cc_final: 0.8534 (t0) REVERT: J 3 GLN cc_start: 0.9076 (pm20) cc_final: 0.8709 (pm20) REVERT: J 6 GLU cc_start: 0.8211 (mp0) cc_final: 0.7366 (mp0) REVERT: J 16 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8403 (pm20) REVERT: J 26 ARG cc_start: 0.8449 (tmm-80) cc_final: 0.8064 (tmm-80) REVERT: J 27 PHE cc_start: 0.8676 (OUTLIER) cc_final: 0.8336 (m-80) REVERT: J 46 GLU cc_start: 0.8852 (tt0) cc_final: 0.8377 (tt0) REVERT: J 72 ASP cc_start: 0.8909 (t0) cc_final: 0.8451 (t0) REVERT: J 95 ASP cc_start: 0.9503 (t0) cc_final: 0.9072 (t0) REVERT: J 105 GLN cc_start: 0.9441 (mt0) cc_final: 0.9073 (pm20) REVERT: J 108 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9074 (tm) REVERT: J 163 LEU cc_start: 0.9631 (mp) cc_final: 0.9366 (tm) REVERT: J 199 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8537 (tp) REVERT: K 3 GLN cc_start: 0.9071 (pm20) cc_final: 0.8706 (pm20) REVERT: K 6 GLU cc_start: 0.8177 (mp0) cc_final: 0.7306 (mp0) REVERT: K 16 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8395 (pm20) REVERT: K 26 ARG cc_start: 0.8452 (tmm-80) cc_final: 0.8074 (tmm-80) REVERT: K 27 PHE cc_start: 0.8679 (OUTLIER) cc_final: 0.8335 (m-80) REVERT: K 46 GLU cc_start: 0.8855 (tt0) cc_final: 0.8387 (tt0) REVERT: K 72 ASP cc_start: 0.8897 (t0) cc_final: 0.8445 (t0) REVERT: K 95 ASP cc_start: 0.9523 (t0) cc_final: 0.9076 (t0) REVERT: K 105 GLN cc_start: 0.9426 (mt0) cc_final: 0.9078 (pm20) REVERT: K 108 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9062 (tm) REVERT: E 49 TYR cc_start: 0.9267 (p90) cc_final: 0.8911 (p90) REVERT: E 50 GLU cc_start: 0.9341 (mt-10) cc_final: 0.8929 (mp0) REVERT: E 67 SER cc_start: 0.9152 (m) cc_final: 0.8918 (p) REVERT: E 93 ASP cc_start: 0.9351 (t0) cc_final: 0.9005 (t70) REVERT: E 103 LYS cc_start: 0.9281 (mttt) cc_final: 0.8732 (mtpp) REVERT: E 105 GLU cc_start: 0.8075 (tp30) cc_final: 0.7674 (tp30) REVERT: E 106 ILE cc_start: 0.8767 (mt) cc_final: 0.8277 (pp) REVERT: I 49 TYR cc_start: 0.9260 (p90) cc_final: 0.8916 (p90) REVERT: I 50 GLU cc_start: 0.9333 (mt-10) cc_final: 0.8913 (mp0) REVERT: I 67 SER cc_start: 0.9150 (m) cc_final: 0.8912 (p) REVERT: I 93 ASP cc_start: 0.9342 (t0) cc_final: 0.9032 (t70) REVERT: I 103 LYS cc_start: 0.9286 (mttt) cc_final: 0.8741 (mtpp) REVERT: I 105 GLU cc_start: 0.8052 (tp30) cc_final: 0.7668 (tp30) REVERT: I 106 ILE cc_start: 0.8750 (mt) cc_final: 0.8275 (pp) REVERT: L 49 TYR cc_start: 0.9265 (p90) cc_final: 0.8929 (p90) REVERT: L 50 GLU cc_start: 0.9352 (mt-10) cc_final: 0.8937 (mp0) REVERT: L 67 SER cc_start: 0.9158 (m) cc_final: 0.8925 (p) REVERT: L 93 ASP cc_start: 0.9331 (t0) cc_final: 0.8957 (t70) REVERT: L 103 LYS cc_start: 0.9281 (mttt) cc_final: 0.8738 (mtpp) outliers start: 92 outliers final: 42 residues processed: 480 average time/residue: 1.0100 time to fit residues: 565.8309 Evaluate side-chains 466 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 405 time to evaluate : 2.270 ------------------------------------------------------------------------------- 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 145 ASP Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 180 MET 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 164 GLU Chi-restraints excluded: chain C residue 20 GLN 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 121 VAL Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 164 GLU 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 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 100 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 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 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 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 100 LEU Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 194 CYS 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 45 LYS Chi-restraints excluded: chain L residue 159 SER Chi-restraints excluded: chain L residue 183 LYS Chi-restraints excluded: chain L residue 194 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 66 optimal weight: 0.0270 chunk 186 optimal weight: 4.9990 chunk 233 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 174 optimal weight: 9.9990 chunk 75 optimal weight: 0.2980 chunk 105 optimal weight: 4.9990 chunk 258 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 222 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 overall best weight: 0.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 146 ASN H 76 ASN H 77 GLN F 76 ASN F 77 GLN J 76 ASN J 77 GLN K 76 ASN K 77 GLN K 203 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.090777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.061603 restraints weight = 51325.299| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 4.08 r_work: 0.2772 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4146 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= 0.133 Angle : 0.691 8.885 28752 Z= 0.350 Chirality : 0.045 0.203 3224 Planarity : 0.005 0.062 3668 Dihedral : 4.938 19.611 2860 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.18 % Allowed : 23.04 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.16), residues: 2636 helix: -1.04 (0.40), residues: 144 sheet: 0.81 (0.18), residues: 834 loop : -0.35 (0.16), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 158 HIS 0.003 0.001 HIS D 173 PHE 0.047 0.002 PHE G 209 TYR 0.014 0.001 TYR K 149 ARG 0.012 0.001 ARG G 142 Details of bonding type rmsd hydrogen bonds : bond 0.02897 ( 724) hydrogen bonds : angle 5.23123 ( 1980) SS BOND : bond 0.00435 ( 32) SS BOND : angle 0.94589 ( 64) covalent geometry : bond 0.00311 (21016) covalent geometry : angle 0.69044 (28688) *********************** 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 528 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 455 time to evaluate : 2.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLN cc_start: 0.9391 (OUTLIER) cc_final: 0.9054 (pm20) REVERT: A 109 GLU cc_start: 0.8866 (tp30) cc_final: 0.8162 (tt0) REVERT: A 128 GLU cc_start: 0.9526 (tp30) cc_final: 0.9262 (tp30) REVERT: A 164 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7647 (tm-30) REVERT: A 180 MET cc_start: 0.9087 (OUTLIER) cc_final: 0.8859 (mtm) REVERT: A 194 ASP cc_start: 0.8554 (m-30) cc_final: 0.7824 (m-30) REVERT: B 109 GLU cc_start: 0.8946 (tp30) cc_final: 0.8135 (tt0) REVERT: B 128 GLU cc_start: 0.9526 (tp30) cc_final: 0.9244 (tp30) REVERT: B 164 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7617 (tm-30) REVERT: B 180 MET cc_start: 0.9442 (mtm) cc_final: 0.9177 (mtm) REVERT: B 194 ASP cc_start: 0.8583 (m-30) cc_final: 0.7849 (m-30) REVERT: C 20 GLN cc_start: 0.9387 (OUTLIER) cc_final: 0.8979 (pm20) REVERT: C 109 GLU cc_start: 0.8674 (tt0) cc_final: 0.8248 (tt0) REVERT: C 128 GLU cc_start: 0.9533 (tp30) cc_final: 0.9193 (tp30) REVERT: C 164 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7594 (tm-30) REVERT: C 180 MET cc_start: 0.9472 (mtm) cc_final: 0.9217 (mtm) REVERT: C 194 ASP cc_start: 0.8532 (m-30) cc_final: 0.7773 (m-30) REVERT: D 20 GLN cc_start: 0.9376 (OUTLIER) cc_final: 0.8992 (pm20) REVERT: D 109 GLU cc_start: 0.8702 (tt0) cc_final: 0.8289 (tt0) REVERT: D 128 GLU cc_start: 0.9519 (tp30) cc_final: 0.9242 (tp30) REVERT: D 164 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7575 (tm-30) REVERT: D 180 MET cc_start: 0.9478 (mtm) cc_final: 0.9205 (mtm) REVERT: D 194 ASP cc_start: 0.8542 (m-30) cc_final: 0.7936 (m-30) REVERT: G 24 GLN cc_start: 0.8713 (mt0) cc_final: 0.8481 (mp10) REVERT: G 45 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8873 (ttpt) REVERT: G 49 TYR cc_start: 0.9241 (p90) cc_final: 0.8896 (p90) REVERT: G 50 GLU cc_start: 0.9300 (mt-10) cc_final: 0.8943 (mp0) REVERT: G 67 SER cc_start: 0.9147 (m) cc_final: 0.8915 (p) REVERT: G 93 ASP cc_start: 0.9314 (t0) cc_final: 0.8995 (t70) REVERT: G 103 LYS cc_start: 0.9247 (mttt) cc_final: 0.8718 (mtpp) REVERT: G 105 GLU cc_start: 0.8029 (tp30) cc_final: 0.7652 (tp30) REVERT: G 106 ILE cc_start: 0.8755 (mt) cc_final: 0.7946 (pp) REVERT: G 118 PHE cc_start: 0.8023 (m-80) cc_final: 0.7729 (m-80) REVERT: G 167 ASP cc_start: 0.8778 (t70) cc_final: 0.8356 (t70) REVERT: G 173 TYR cc_start: 0.7468 (m-80) cc_final: 0.7026 (m-10) REVERT: G 185 ASP cc_start: 0.7942 (m-30) cc_final: 0.7519 (p0) REVERT: H 3 GLN cc_start: 0.9042 (pm20) cc_final: 0.8722 (pm20) REVERT: H 6 GLU cc_start: 0.8193 (mp0) cc_final: 0.7275 (mp0) REVERT: H 16 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8490 (pm20) REVERT: H 38 ARG cc_start: 0.8654 (ttt-90) cc_final: 0.8451 (ttp80) REVERT: H 46 GLU cc_start: 0.8854 (tt0) cc_final: 0.8379 (tt0) REVERT: H 72 ASP cc_start: 0.8900 (t0) cc_final: 0.8477 (t0) REVERT: H 76 ASN cc_start: 0.8680 (t0) cc_final: 0.8417 (t0) REVERT: H 77 GLN cc_start: 0.9040 (mt0) cc_final: 0.8823 (mt0) REVERT: H 95 ASP cc_start: 0.9470 (t0) cc_final: 0.8917 (t0) REVERT: H 100 LEU cc_start: 0.9457 (mt) cc_final: 0.9208 (mt) REVERT: H 105 GLN cc_start: 0.9444 (mt0) cc_final: 0.9089 (pm20) REVERT: H 108 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9158 (tm) REVERT: H 203 ASN cc_start: 0.8772 (m-40) cc_final: 0.8507 (t0) REVERT: F 3 GLN cc_start: 0.9044 (pm20) cc_final: 0.8687 (pm20) REVERT: F 6 GLU cc_start: 0.8194 (mp0) cc_final: 0.7506 (mp0) REVERT: F 16 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8501 (pm20) REVERT: F 26 ARG cc_start: 0.8488 (tmm-80) cc_final: 0.8169 (tmm-80) REVERT: F 27 PHE cc_start: 0.8666 (OUTLIER) cc_final: 0.8347 (m-80) REVERT: F 46 GLU cc_start: 0.8863 (tt0) cc_final: 0.8387 (tt0) REVERT: F 72 ASP cc_start: 0.8909 (t0) cc_final: 0.8482 (t0) REVERT: F 76 ASN cc_start: 0.8737 (t0) cc_final: 0.8428 (t0) REVERT: F 77 GLN cc_start: 0.9047 (mt0) cc_final: 0.8829 (mt0) REVERT: F 92 CYS cc_start: 0.7117 (p) cc_final: 0.6645 (p) REVERT: F 95 ASP cc_start: 0.9468 (t0) cc_final: 0.8942 (t0) REVERT: F 105 GLN cc_start: 0.9444 (mt0) cc_final: 0.9082 (pm20) REVERT: F 108 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.9144 (tm) REVERT: F 186 VAL cc_start: 0.9431 (t) cc_final: 0.9212 (m) REVERT: F 203 ASN cc_start: 0.8804 (m-40) cc_final: 0.8522 (t0) REVERT: J 3 GLN cc_start: 0.9033 (pm20) cc_final: 0.8679 (pm20) REVERT: J 6 GLU cc_start: 0.8173 (mp0) cc_final: 0.7466 (mp0) REVERT: J 16 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8519 (pm20) REVERT: J 26 ARG cc_start: 0.8474 (tmm-80) cc_final: 0.8154 (tmm-80) REVERT: J 27 PHE cc_start: 0.8661 (OUTLIER) cc_final: 0.8342 (m-80) REVERT: J 38 ARG cc_start: 0.8673 (ttt-90) cc_final: 0.8470 (ttp80) REVERT: J 46 GLU cc_start: 0.8858 (tt0) cc_final: 0.8375 (tt0) REVERT: J 72 ASP cc_start: 0.8907 (t0) cc_final: 0.8477 (t0) REVERT: J 76 ASN cc_start: 0.8738 (t0) cc_final: 0.8420 (t0) REVERT: J 77 GLN cc_start: 0.9035 (mt0) cc_final: 0.8813 (mt0) REVERT: J 92 CYS cc_start: 0.7176 (p) cc_final: 0.6770 (p) REVERT: J 95 ASP cc_start: 0.9502 (t0) cc_final: 0.9005 (t0) REVERT: J 100 LEU cc_start: 0.9670 (mt) cc_final: 0.9382 (mt) REVERT: J 105 GLN cc_start: 0.9438 (mt0) cc_final: 0.9077 (pm20) REVERT: J 108 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9145 (tm) REVERT: J 163 LEU cc_start: 0.9633 (mp) cc_final: 0.9399 (tm) REVERT: J 203 ASN cc_start: 0.8731 (m-40) cc_final: 0.8425 (t0) REVERT: K 3 GLN cc_start: 0.9031 (pm20) cc_final: 0.8676 (pm20) REVERT: K 6 GLU cc_start: 0.8176 (mp0) cc_final: 0.7255 (mp0) REVERT: K 16 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8486 (pm20) REVERT: K 26 ARG cc_start: 0.8483 (tmm-80) cc_final: 0.8164 (tmm-80) REVERT: K 27 PHE cc_start: 0.8669 (OUTLIER) cc_final: 0.8353 (m-80) REVERT: K 38 ARG cc_start: 0.8675 (ttt-90) cc_final: 0.8445 (ttp80) REVERT: K 46 GLU cc_start: 0.8862 (tt0) cc_final: 0.8375 (tt0) REVERT: K 72 ASP cc_start: 0.8903 (t0) cc_final: 0.8475 (t0) REVERT: K 76 ASN cc_start: 0.8747 (t0) cc_final: 0.8438 (t0) REVERT: K 77 GLN cc_start: 0.9046 (mt0) cc_final: 0.8825 (mt0) REVERT: K 95 ASP cc_start: 0.9506 (t0) cc_final: 0.9011 (t0) REVERT: K 100 LEU cc_start: 0.9670 (mt) cc_final: 0.9389 (mt) REVERT: K 105 GLN cc_start: 0.9438 (mt0) cc_final: 0.9081 (pm20) REVERT: K 108 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9183 (tm) REVERT: K 110 THR cc_start: 0.9481 (m) cc_final: 0.9188 (p) REVERT: K 203 ASN cc_start: 0.8772 (m110) cc_final: 0.8525 (t0) REVERT: E 24 GLN cc_start: 0.8689 (mt0) cc_final: 0.8459 (mp10) REVERT: E 45 LYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8891 (ttpt) REVERT: E 49 TYR cc_start: 0.9231 (p90) cc_final: 0.8918 (p90) REVERT: E 50 GLU cc_start: 0.9295 (mt-10) cc_final: 0.8938 (mp0) REVERT: E 67 SER cc_start: 0.9138 (m) cc_final: 0.8907 (p) REVERT: E 93 ASP cc_start: 0.9296 (t0) cc_final: 0.8958 (t70) REVERT: E 103 LYS cc_start: 0.9255 (mttt) cc_final: 0.8728 (mtpp) REVERT: E 118 PHE cc_start: 0.8000 (m-80) cc_final: 0.7718 (m-80) REVERT: E 167 ASP cc_start: 0.8768 (t70) cc_final: 0.8342 (t70) REVERT: E 173 TYR cc_start: 0.7419 (m-80) cc_final: 0.6825 (m-10) REVERT: E 185 ASP cc_start: 0.7940 (m-30) cc_final: 0.7594 (p0) REVERT: I 24 GLN cc_start: 0.8692 (mt0) cc_final: 0.8457 (mp10) REVERT: I 45 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8886 (ttpt) REVERT: I 49 TYR cc_start: 0.9232 (p90) cc_final: 0.8921 (p90) REVERT: I 50 GLU cc_start: 0.9274 (mt-10) cc_final: 0.8924 (mp0) REVERT: I 67 SER cc_start: 0.9144 (m) cc_final: 0.8908 (p) REVERT: I 93 ASP cc_start: 0.9336 (t0) cc_final: 0.9030 (t70) REVERT: I 103 LYS cc_start: 0.9255 (mttt) cc_final: 0.8732 (mtpp) REVERT: I 118 PHE cc_start: 0.8020 (m-80) cc_final: 0.7722 (m-80) REVERT: I 167 ASP cc_start: 0.8773 (t70) cc_final: 0.8359 (t70) REVERT: I 173 TYR cc_start: 0.7403 (m-80) cc_final: 0.6843 (m-10) REVERT: L 45 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8879 (ttpt) REVERT: L 49 TYR cc_start: 0.9225 (p90) cc_final: 0.8924 (p90) REVERT: L 50 GLU cc_start: 0.9292 (mt-10) cc_final: 0.8936 (mp0) REVERT: L 67 SER cc_start: 0.9155 (m) cc_final: 0.8927 (p) REVERT: L 93 ASP cc_start: 0.9352 (t0) cc_final: 0.8956 (t70) REVERT: L 103 LYS cc_start: 0.9254 (mttt) cc_final: 0.8741 (mtpp) REVERT: L 105 GLU cc_start: 0.7981 (tp30) cc_final: 0.7545 (tp30) REVERT: L 106 ILE cc_start: 0.8719 (mt) cc_final: 0.7889 (pp) REVERT: L 118 PHE cc_start: 0.8015 (m-80) cc_final: 0.7732 (m-80) REVERT: L 167 ASP cc_start: 0.8784 (t70) cc_final: 0.8369 (t70) REVERT: L 173 TYR cc_start: 0.7492 (m-80) cc_final: 0.7049 (m-10) outliers start: 73 outliers final: 33 residues processed: 496 average time/residue: 1.0990 time to fit residues: 629.3549 Evaluate side-chains 476 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 424 time to evaluate : 2.554 ------------------------------------------------------------------------------- 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 A residue 180 MET Chi-restraints excluded: chain B residue 139 THR 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 45 LYS Chi-restraints excluded: chain G residue 194 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 11 LEU 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 F residue 2 VAL Chi-restraints excluded: chain F residue 11 LEU 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 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 108 LEU Chi-restraints excluded: chain J residue 186 VAL 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 108 LEU Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 194 CYS Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 194 CYS Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 183 LYS 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 177 optimal weight: 8.9990 chunk 258 optimal weight: 4.9990 chunk 178 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 204 optimal weight: 4.9990 chunk 162 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 175 optimal weight: 3.9990 chunk 121 optimal weight: 0.0980 chunk 140 optimal weight: 2.9990 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 D 146 ASN H 208 ASN F 208 ASN J 208 ASN K 208 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.089017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.059760 restraints weight = 51840.828| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 4.03 r_work: 0.2721 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 21048 Z= 0.237 Angle : 0.720 10.233 28752 Z= 0.368 Chirality : 0.046 0.206 3224 Planarity : 0.005 0.063 3668 Dihedral : 5.006 21.155 2860 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.88 % Allowed : 23.30 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.16), residues: 2636 helix: -0.83 (0.41), residues: 144 sheet: 0.75 (0.17), residues: 879 loop : -0.40 (0.16), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 158 HIS 0.004 0.001 HIS C 173 PHE 0.020 0.002 PHE L 92 TYR 0.015 0.002 TYR H 99 ARG 0.013 0.001 ARG I 142 Details of bonding type rmsd hydrogen bonds : bond 0.03115 ( 724) hydrogen bonds : angle 5.27251 ( 1980) SS BOND : bond 0.00574 ( 32) SS BOND : angle 1.24331 ( 64) covalent geometry : bond 0.00532 (21016) covalent geometry : angle 0.71828 (28688) *********************** 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 498 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 409 time to evaluate : 2.469 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: 0.9364 (OUTLIER) cc_final: 0.8973 (pm20) REVERT: A 109 GLU cc_start: 0.8962 (tp30) cc_final: 0.8178 (tt0) REVERT: A 128 GLU cc_start: 0.9565 (tp30) cc_final: 0.9293 (tp30) REVERT: A 164 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7683 (tm-30) REVERT: A 194 ASP cc_start: 0.8593 (m-30) cc_final: 0.7859 (m-30) REVERT: B 20 GLN cc_start: 0.9072 (OUTLIER) cc_final: 0.8639 (pm20) REVERT: B 109 GLU cc_start: 0.8951 (tp30) cc_final: 0.8308 (tt0) REVERT: B 128 GLU cc_start: 0.9541 (tp30) cc_final: 0.9206 (tp30) REVERT: B 134 MET cc_start: 0.9026 (tpp) cc_final: 0.8719 (mmp) REVERT: B 164 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7638 (tm-30) REVERT: B 180 MET cc_start: 0.9486 (mtm) cc_final: 0.9222 (mtm) REVERT: B 194 ASP cc_start: 0.8604 (m-30) cc_final: 0.7861 (m-30) REVERT: C 20 GLN cc_start: 0.9353 (OUTLIER) cc_final: 0.9011 (pm20) REVERT: C 109 GLU cc_start: 0.8769 (tt0) cc_final: 0.8413 (tt0) REVERT: C 128 GLU cc_start: 0.9553 (tp30) cc_final: 0.9234 (tp30) REVERT: C 164 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7673 (tm-30) REVERT: C 180 MET cc_start: 0.9518 (mtm) cc_final: 0.9247 (mtm) REVERT: C 194 ASP cc_start: 0.8613 (m-30) cc_final: 0.7855 (m-30) REVERT: D 20 GLN cc_start: 0.9341 (OUTLIER) cc_final: 0.8947 (pm20) REVERT: D 109 GLU cc_start: 0.8825 (tt0) cc_final: 0.8464 (tt0) REVERT: D 128 GLU cc_start: 0.9551 (tp30) cc_final: 0.9264 (tp30) REVERT: D 134 MET cc_start: 0.9035 (tpp) cc_final: 0.8747 (mmp) REVERT: D 164 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7625 (tm-30) REVERT: D 180 MET cc_start: 0.9518 (mtm) cc_final: 0.9254 (mtm) REVERT: D 194 ASP cc_start: 0.8587 (m-30) cc_final: 0.7916 (m-30) REVERT: G 24 GLN cc_start: 0.8707 (mt0) cc_final: 0.8452 (mp10) REVERT: G 49 TYR cc_start: 0.9266 (p90) cc_final: 0.8950 (p90) REVERT: G 50 GLU cc_start: 0.9331 (mt-10) cc_final: 0.8941 (mp0) REVERT: G 67 SER cc_start: 0.9154 (m) cc_final: 0.8921 (p) REVERT: G 93 ASP cc_start: 0.9288 (t0) cc_final: 0.8966 (t70) REVERT: G 103 LYS cc_start: 0.9288 (mttt) cc_final: 0.8755 (mtpp) REVERT: G 105 GLU cc_start: 0.8305 (tp30) cc_final: 0.7981 (tp30) REVERT: G 106 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.7958 (pp) REVERT: G 118 PHE cc_start: 0.8094 (m-80) cc_final: 0.7886 (m-80) REVERT: G 161 GLU cc_start: 0.9131 (pm20) cc_final: 0.8619 (pp20) REVERT: G 185 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7576 (p0) REVERT: H 3 GLN cc_start: 0.9034 (pm20) cc_final: 0.8648 (pm20) REVERT: H 6 GLU cc_start: 0.8169 (mp0) cc_final: 0.7233 (mp0) REVERT: H 16 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8493 (pm20) REVERT: H 46 GLU cc_start: 0.8843 (tt0) cc_final: 0.8362 (tt0) REVERT: H 72 ASP cc_start: 0.8900 (t0) cc_final: 0.8454 (t0) REVERT: H 76 ASN cc_start: 0.8756 (t0) cc_final: 0.8406 (t0) REVERT: H 95 ASP cc_start: 0.9531 (t0) cc_final: 0.9064 (t0) REVERT: H 100 LEU cc_start: 0.9517 (mt) cc_final: 0.9203 (mt) REVERT: H 105 GLN cc_start: 0.9452 (mt0) cc_final: 0.9060 (pm20) REVERT: H 108 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9170 (tm) REVERT: H 203 ASN cc_start: 0.8763 (m-40) cc_final: 0.8462 (t0) REVERT: F 3 GLN cc_start: 0.9023 (pm20) cc_final: 0.8656 (pm20) REVERT: F 6 GLU cc_start: 0.8121 (mp0) cc_final: 0.7172 (mp0) REVERT: F 16 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8494 (pm20) REVERT: F 26 ARG cc_start: 0.8509 (tmm-80) cc_final: 0.8028 (tmm-80) REVERT: F 27 PHE cc_start: 0.8706 (OUTLIER) cc_final: 0.8318 (m-80) REVERT: F 46 GLU cc_start: 0.8835 (tt0) cc_final: 0.8356 (tt0) REVERT: F 72 ASP cc_start: 0.8909 (t0) cc_final: 0.8450 (t0) REVERT: F 76 ASN cc_start: 0.8796 (t0) cc_final: 0.8394 (t0) REVERT: F 95 ASP cc_start: 0.9510 (t0) cc_final: 0.9104 (t0) REVERT: F 105 GLN cc_start: 0.9454 (mt0) cc_final: 0.9053 (pm20) REVERT: F 108 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9154 (tm) REVERT: F 203 ASN cc_start: 0.8744 (m-40) cc_final: 0.8474 (t0) REVERT: J 3 GLN cc_start: 0.9023 (pm20) cc_final: 0.8657 (pm20) REVERT: J 6 GLU cc_start: 0.8153 (mp0) cc_final: 0.7189 (mp0) REVERT: J 16 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8484 (pm20) REVERT: J 26 ARG cc_start: 0.8518 (tmm-80) cc_final: 0.8037 (tmm-80) REVERT: J 27 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.8285 (m-80) REVERT: J 46 GLU cc_start: 0.8855 (tt0) cc_final: 0.8444 (pt0) REVERT: J 72 ASP cc_start: 0.8922 (t0) cc_final: 0.8472 (t0) REVERT: J 76 ASN cc_start: 0.8798 (t0) cc_final: 0.8396 (t0) REVERT: J 95 ASP cc_start: 0.9528 (t0) cc_final: 0.9022 (t0) REVERT: J 100 LEU cc_start: 0.9521 (mt) cc_final: 0.9249 (mt) REVERT: J 105 GLN cc_start: 0.9454 (mt0) cc_final: 0.9053 (pm20) REVERT: J 108 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9173 (tm) REVERT: J 163 LEU cc_start: 0.9637 (mp) cc_final: 0.9430 (tm) REVERT: J 203 ASN cc_start: 0.8751 (m-40) cc_final: 0.8442 (t0) REVERT: K 3 GLN cc_start: 0.9018 (pm20) cc_final: 0.8656 (pm20) REVERT: K 6 GLU cc_start: 0.8116 (mp0) cc_final: 0.7159 (mp0) REVERT: K 16 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8487 (pm20) REVERT: K 26 ARG cc_start: 0.8528 (tmm-80) cc_final: 0.8047 (tmm-80) REVERT: K 27 PHE cc_start: 0.8702 (OUTLIER) cc_final: 0.8316 (m-80) REVERT: K 46 GLU cc_start: 0.8838 (tt0) cc_final: 0.8434 (pt0) REVERT: K 72 ASP cc_start: 0.8910 (t0) cc_final: 0.8463 (t0) REVERT: K 76 ASN cc_start: 0.8803 (t0) cc_final: 0.8406 (t0) REVERT: K 95 ASP cc_start: 0.9548 (t0) cc_final: 0.9054 (t0) REVERT: K 100 LEU cc_start: 0.9529 (mt) cc_final: 0.9238 (mt) REVERT: K 105 GLN cc_start: 0.9443 (mt0) cc_final: 0.9049 (pm20) REVERT: K 108 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9100 (tm) REVERT: K 203 ASN cc_start: 0.8755 (m110) cc_final: 0.8507 (t0) REVERT: E 49 TYR cc_start: 0.9268 (p90) cc_final: 0.8942 (p90) REVERT: E 50 GLU cc_start: 0.9334 (mt-10) cc_final: 0.8930 (mp0) REVERT: E 67 SER cc_start: 0.9146 (m) cc_final: 0.8917 (p) REVERT: E 93 ASP cc_start: 0.9266 (t0) cc_final: 0.8936 (t70) REVERT: E 103 LYS cc_start: 0.9290 (mttt) cc_final: 0.8755 (mtpp) REVERT: E 118 PHE cc_start: 0.7997 (m-80) cc_final: 0.7742 (m-80) REVERT: E 161 GLU cc_start: 0.9121 (pm20) cc_final: 0.8589 (pp20) REVERT: E 185 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.7568 (p0) REVERT: I 49 TYR cc_start: 0.9263 (p90) cc_final: 0.8958 (p90) REVERT: I 50 GLU cc_start: 0.9322 (mt-10) cc_final: 0.8931 (mp0) REVERT: I 67 SER cc_start: 0.9150 (m) cc_final: 0.8916 (p) REVERT: I 93 ASP cc_start: 0.9349 (t0) cc_final: 0.9039 (t70) REVERT: I 103 LYS cc_start: 0.9290 (mttt) cc_final: 0.8757 (mtpp) REVERT: I 105 GLU cc_start: 0.8187 (tp30) cc_final: 0.7815 (tp30) REVERT: I 106 ILE cc_start: 0.8737 (mt) cc_final: 0.7891 (pp) REVERT: I 118 PHE cc_start: 0.8079 (m-80) cc_final: 0.7833 (m-80) REVERT: I 161 GLU cc_start: 0.9119 (pm20) cc_final: 0.8591 (pp20) REVERT: L 49 TYR cc_start: 0.9260 (p90) cc_final: 0.8963 (p90) REVERT: L 50 GLU cc_start: 0.9331 (mt-10) cc_final: 0.8949 (mp0) REVERT: L 67 SER cc_start: 0.9163 (m) cc_final: 0.8936 (p) REVERT: L 93 ASP cc_start: 0.9343 (t0) cc_final: 0.8947 (t70) REVERT: L 103 LYS cc_start: 0.9290 (mttt) cc_final: 0.8762 (mtpp) REVERT: L 105 GLU cc_start: 0.8265 (tp30) cc_final: 0.7945 (tp30) REVERT: L 106 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.7855 (pp) REVERT: L 118 PHE cc_start: 0.8021 (m-80) cc_final: 0.7771 (m-80) REVERT: L 161 GLU cc_start: 0.9121 (pm20) cc_final: 0.8594 (pp20) outliers start: 89 outliers final: 46 residues processed: 471 average time/residue: 1.0198 time to fit residues: 567.3378 Evaluate side-chains 463 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 398 time to evaluate : 2.307 ------------------------------------------------------------------------------- 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 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 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 121 VAL Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 106 ILE 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 2 VAL Chi-restraints excluded: chain H residue 11 LEU 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 F residue 2 VAL Chi-restraints excluded: chain F residue 11 LEU 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 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 100 LEU Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 11 LEU 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 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 45 LYS Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 194 CYS Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain L residue 159 SER Chi-restraints excluded: chain L residue 183 LYS 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 4 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 chunk 107 optimal weight: 0.0000 chunk 143 optimal weight: 0.7980 chunk 200 optimal weight: 5.9990 chunk 73 optimal weight: 0.5980 chunk 167 optimal weight: 6.9990 chunk 238 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- 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 D 146 ASN H 77 GLN F 77 GLN F 203 ASN J 77 GLN K 77 GLN E 79 GLN I 79 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.090287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.060897 restraints weight = 51269.891| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 4.06 r_work: 0.2749 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21048 Z= 0.168 Angle : 0.709 10.303 28752 Z= 0.359 Chirality : 0.045 0.152 3224 Planarity : 0.006 0.074 3668 Dihedral : 4.963 19.977 2860 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.36 % Allowed : 24.00 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.16), residues: 2636 helix: -0.74 (0.41), residues: 144 sheet: 0.93 (0.18), residues: 855 loop : -0.45 (0.16), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP H 158 HIS 0.004 0.001 HIS C 173 PHE 0.047 0.002 PHE I 209 TYR 0.035 0.002 TYR G 173 ARG 0.019 0.001 ARG I 142 Details of bonding type rmsd hydrogen bonds : bond 0.02950 ( 724) hydrogen bonds : angle 5.20276 ( 1980) SS BOND : bond 0.00463 ( 32) SS BOND : angle 1.20012 ( 64) covalent geometry : bond 0.00386 (21016) covalent geometry : angle 0.70744 (28688) ********************** 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 500 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 423 time to evaluate : 2.314 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: 0.9389 (OUTLIER) cc_final: 0.8984 (pm20) REVERT: A 109 GLU cc_start: 0.8915 (tp30) cc_final: 0.8135 (tt0) REVERT: A 128 GLU cc_start: 0.9557 (tp30) cc_final: 0.9265 (tp30) REVERT: A 164 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7641 (tm-30) REVERT: A 194 ASP cc_start: 0.8580 (m-30) cc_final: 0.7835 (m-30) REVERT: B 20 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.8674 (pm20) REVERT: B 109 GLU cc_start: 0.8936 (tp30) cc_final: 0.8314 (tt0) REVERT: B 128 GLU cc_start: 0.9546 (tp30) cc_final: 0.9246 (tp30) REVERT: B 164 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7649 (tm-30) REVERT: B 180 MET cc_start: 0.9459 (mtm) cc_final: 0.9195 (mtm) REVERT: B 194 ASP cc_start: 0.8611 (m-30) cc_final: 0.7846 (m-30) REVERT: C 20 GLN cc_start: 0.9367 (OUTLIER) cc_final: 0.8989 (pm20) REVERT: C 109 GLU cc_start: 0.8760 (tt0) cc_final: 0.8403 (tt0) REVERT: C 128 GLU cc_start: 0.9558 (tp30) cc_final: 0.9254 (tp30) REVERT: C 164 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7641 (tm-30) REVERT: C 180 MET cc_start: 0.9510 (mtm) cc_final: 0.9236 (mtm) REVERT: C 194 ASP cc_start: 0.8574 (m-30) cc_final: 0.7800 (m-30) REVERT: D 20 GLN cc_start: 0.9361 (OUTLIER) cc_final: 0.9012 (pm20) REVERT: D 109 GLU cc_start: 0.8791 (tt0) cc_final: 0.8368 (tt0) REVERT: D 128 GLU cc_start: 0.9553 (tp30) cc_final: 0.9296 (tp30) REVERT: D 164 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7617 (tm-30) REVERT: D 180 MET cc_start: 0.9516 (mtm) cc_final: 0.9250 (mtm) REVERT: G 24 GLN cc_start: 0.8683 (mt0) cc_final: 0.8434 (mp10) REVERT: G 49 TYR cc_start: 0.9262 (p90) cc_final: 0.8952 (p90) REVERT: G 50 GLU cc_start: 0.9307 (mt-10) cc_final: 0.8962 (mp0) REVERT: G 67 SER cc_start: 0.9160 (m) cc_final: 0.8927 (p) REVERT: G 93 ASP cc_start: 0.9283 (t0) cc_final: 0.8981 (t70) REVERT: G 103 LYS cc_start: 0.9239 (mttt) cc_final: 0.8695 (mtpp) REVERT: G 118 PHE cc_start: 0.8211 (m-80) cc_final: 0.7908 (m-80) REVERT: G 161 GLU cc_start: 0.9132 (pm20) cc_final: 0.8598 (pp20) REVERT: G 167 ASP cc_start: 0.8751 (t70) cc_final: 0.8348 (t70) REVERT: G 185 ASP cc_start: 0.7921 (m-30) cc_final: 0.7605 (p0) REVERT: H 3 GLN cc_start: 0.8993 (pm20) cc_final: 0.8596 (pm20) REVERT: H 6 GLU cc_start: 0.8126 (mp0) cc_final: 0.7188 (mp0) REVERT: H 16 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8543 (pm20) REVERT: H 46 GLU cc_start: 0.8841 (tt0) cc_final: 0.8470 (pt0) REVERT: H 72 ASP cc_start: 0.8892 (t0) cc_final: 0.8454 (t0) REVERT: H 76 ASN cc_start: 0.8671 (t0) cc_final: 0.8403 (t0) REVERT: H 77 GLN cc_start: 0.8989 (mt0) cc_final: 0.8785 (mt0) REVERT: H 95 ASP cc_start: 0.9493 (t0) cc_final: 0.8966 (t0) REVERT: H 100 LEU cc_start: 0.9477 (mt) cc_final: 0.9179 (mt) REVERT: H 105 GLN cc_start: 0.9444 (mt0) cc_final: 0.9095 (pm20) REVERT: H 108 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9177 (tm) REVERT: H 203 ASN cc_start: 0.8733 (m-40) cc_final: 0.8438 (t0) REVERT: F 3 GLN cc_start: 0.9007 (pm20) cc_final: 0.8619 (pm20) REVERT: F 6 GLU cc_start: 0.8089 (mp0) cc_final: 0.7101 (mp0) REVERT: F 16 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8540 (pm20) REVERT: F 27 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.8464 (t80) REVERT: F 46 GLU cc_start: 0.8826 (tt0) cc_final: 0.8346 (tt0) REVERT: F 72 ASP cc_start: 0.8897 (t0) cc_final: 0.8459 (t0) REVERT: F 76 ASN cc_start: 0.8723 (t0) cc_final: 0.8438 (t0) REVERT: F 77 GLN cc_start: 0.9001 (mt0) cc_final: 0.8795 (mt0) REVERT: F 95 ASP cc_start: 0.9499 (t0) cc_final: 0.8941 (t0) REVERT: F 100 LEU cc_start: 0.9517 (mt) cc_final: 0.9244 (mt) REVERT: F 105 GLN cc_start: 0.9456 (mt0) cc_final: 0.9092 (pm20) REVERT: F 108 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9165 (tm) REVERT: F 186 VAL cc_start: 0.9428 (OUTLIER) cc_final: 0.9212 (m) REVERT: F 203 ASN cc_start: 0.8722 (m110) cc_final: 0.8450 (t0) REVERT: J 3 GLN cc_start: 0.8998 (pm20) cc_final: 0.8612 (pm20) REVERT: J 6 GLU cc_start: 0.8092 (mp0) cc_final: 0.7132 (mp0) REVERT: J 16 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8540 (pm20) REVERT: J 27 PHE cc_start: 0.8721 (OUTLIER) cc_final: 0.8466 (t80) REVERT: J 46 GLU cc_start: 0.8852 (tt0) cc_final: 0.8362 (tt0) REVERT: J 72 ASP cc_start: 0.8905 (t0) cc_final: 0.8463 (t0) REVERT: J 76 ASN cc_start: 0.8743 (t0) cc_final: 0.8453 (t0) REVERT: J 77 GLN cc_start: 0.8980 (mt0) cc_final: 0.8767 (mt0) REVERT: J 95 ASP cc_start: 0.9463 (t0) cc_final: 0.8891 (t0) REVERT: J 100 LEU cc_start: 0.9457 (mt) cc_final: 0.9197 (mt) REVERT: J 105 GLN cc_start: 0.9449 (mt0) cc_final: 0.9048 (pm20) REVERT: J 108 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9179 (tm) REVERT: K 3 GLN cc_start: 0.9000 (pm20) cc_final: 0.8619 (pm20) REVERT: K 6 GLU cc_start: 0.8060 (mp0) cc_final: 0.7136 (mp0) REVERT: K 16 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8534 (pm20) REVERT: K 27 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.8459 (t80) REVERT: K 46 GLU cc_start: 0.8842 (tt0) cc_final: 0.8356 (tt0) REVERT: K 72 ASP cc_start: 0.8905 (t0) cc_final: 0.8466 (t0) REVERT: K 76 ASN cc_start: 0.8739 (t0) cc_final: 0.8459 (t0) REVERT: K 77 GLN cc_start: 0.8994 (mt0) cc_final: 0.8784 (mt0) REVERT: K 95 ASP cc_start: 0.9495 (t0) cc_final: 0.8987 (t0) REVERT: K 100 LEU cc_start: 0.9479 (mt) cc_final: 0.9211 (mt) REVERT: K 105 GLN cc_start: 0.9448 (mt0) cc_final: 0.9089 (pm20) REVERT: K 108 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9159 (tm) REVERT: K 186 VAL cc_start: 0.9448 (t) cc_final: 0.9236 (m) REVERT: K 203 ASN cc_start: 0.8740 (m110) cc_final: 0.8492 (t0) REVERT: E 49 TYR cc_start: 0.9257 (p90) cc_final: 0.8959 (p90) REVERT: E 50 GLU cc_start: 0.9291 (mt-10) cc_final: 0.8934 (mp0) REVERT: E 67 SER cc_start: 0.9153 (m) cc_final: 0.8920 (p) REVERT: E 93 ASP cc_start: 0.9254 (t0) cc_final: 0.8936 (t70) REVERT: E 103 LYS cc_start: 0.9269 (mttt) cc_final: 0.8721 (mtpp) REVERT: E 118 PHE cc_start: 0.8160 (m-80) cc_final: 0.7889 (m-80) REVERT: E 161 GLU cc_start: 0.9143 (pm20) cc_final: 0.8628 (pp20) REVERT: E 167 ASP cc_start: 0.8741 (t70) cc_final: 0.8304 (t0) REVERT: E 185 ASP cc_start: 0.7947 (m-30) cc_final: 0.7598 (p0) REVERT: I 49 TYR cc_start: 0.9258 (p90) cc_final: 0.8952 (p90) REVERT: I 50 GLU cc_start: 0.9293 (mt-10) cc_final: 0.8923 (mp0) REVERT: I 67 SER cc_start: 0.9158 (m) cc_final: 0.8925 (p) REVERT: I 93 ASP cc_start: 0.9345 (t0) cc_final: 0.9049 (t70) REVERT: I 103 LYS cc_start: 0.9246 (mttt) cc_final: 0.8705 (mtpp) REVERT: I 118 PHE cc_start: 0.8216 (m-80) cc_final: 0.7907 (m-80) REVERT: I 161 GLU cc_start: 0.9117 (pm20) cc_final: 0.8607 (pp20) REVERT: I 167 ASP cc_start: 0.8742 (t70) cc_final: 0.8340 (t70) REVERT: L 21 ILE cc_start: 0.9466 (mt) cc_final: 0.9259 (mp) REVERT: L 49 TYR cc_start: 0.9251 (p90) cc_final: 0.8953 (p90) REVERT: L 50 GLU cc_start: 0.9307 (mt-10) cc_final: 0.8956 (mp0) REVERT: L 67 SER cc_start: 0.9173 (m) cc_final: 0.8942 (p) REVERT: L 93 ASP cc_start: 0.9297 (t0) cc_final: 0.8938 (t70) REVERT: L 103 LYS cc_start: 0.9247 (mttt) cc_final: 0.8715 (mtpp) REVERT: L 118 PHE cc_start: 0.8179 (m-80) cc_final: 0.7915 (m-80) REVERT: L 161 GLU cc_start: 0.9146 (pm20) cc_final: 0.8629 (pp20) REVERT: L 167 ASP cc_start: 0.8735 (t70) cc_final: 0.8338 (t70) outliers start: 77 outliers final: 36 residues processed: 471 average time/residue: 0.9886 time to fit residues: 545.4869 Evaluate side-chains 472 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 420 time to evaluate : 2.434 ------------------------------------------------------------------------------- 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 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 139 THR Chi-restraints excluded: chain C residue 145 ASP 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 45 LYS Chi-restraints excluded: chain G residue 159 SER 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 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 165 SER 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 J residue 186 VAL 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 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 45 LYS Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 194 CYS Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 183 LYS 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 122 optimal weight: 0.4980 chunk 165 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 150 optimal weight: 5.9990 chunk 202 optimal weight: 0.9990 chunk 196 optimal weight: 8.9990 chunk 164 optimal weight: 0.1980 chunk 207 optimal weight: 7.9990 chunk 136 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 D 146 ASN G 79 GLN ** G 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 208 ASN F 208 ASN J 208 ASN K 208 ASN L 79 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.089778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.060356 restraints weight = 51641.393| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 4.06 r_work: 0.2742 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.4359 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= 0.193 Angle : 0.720 10.492 28752 Z= 0.366 Chirality : 0.046 0.159 3224 Planarity : 0.006 0.063 3668 Dihedral : 4.947 20.358 2860 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.27 % Allowed : 24.21 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.16), residues: 2636 helix: -0.67 (0.41), residues: 144 sheet: 0.90 (0.18), residues: 845 loop : -0.47 (0.16), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP H 158 HIS 0.004 0.001 HIS C 173 PHE 0.020 0.002 PHE L 92 TYR 0.025 0.002 TYR L 173 ARG 0.017 0.001 ARG E 142 Details of bonding type rmsd hydrogen bonds : bond 0.02964 ( 724) hydrogen bonds : angle 5.23524 ( 1980) SS BOND : bond 0.00460 ( 32) SS BOND : angle 1.38868 ( 64) covalent geometry : bond 0.00439 (21016) covalent geometry : angle 0.71820 (28688) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15898.74 seconds wall clock time: 273 minutes 50.31 seconds (16430.31 seconds total)