Starting phenix.real_space_refine on Wed May 21 00:09:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vgh_43200/05_2025/8vgh_43200.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vgh_43200/05_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_43200/05_2025/8vgh_43200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vgh_43200/05_2025/8vgh_43200.map" model { file = "/net/cci-nas-00/data/ceres_data/8vgh_43200/05_2025/8vgh_43200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vgh_43200/05_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-5687/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: 13.62, per 1000 atoms: 0.67 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: 5.32 Conformation dependent library (CDL) restraints added in 2.9 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: 3.53 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: 8.68 Time building geometry restraints manager: 6.24 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: 0.13 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: 13.290 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 52.100 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.120 ------------------------------------------------------------------------------- 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 : 2.210 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: 1.2329 time to fit residues: 867.4174 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 : 2.386 ------------------------------------------------------------------------------- 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 = 30)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.060494 restraints weight = 50553.421| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 3.95 r_work: 0.2746 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 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 : 2.328 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: 0.9525 (tp30) cc_final: 0.9195 (tp30) REVERT: A 149 GLU cc_start: 0.9226 (mp0) cc_final: 0.9026 (mp0) REVERT: A 230 THR cc_start: 0.9673 (m) cc_final: 0.9302 (p) REVERT: B 109 GLU cc_start: 0.8798 (tp30) cc_final: 0.8481 (tp30) REVERT: B 128 GLU cc_start: 0.9516 (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: 0.8780 (tp30) cc_final: 0.8465 (tp30) REVERT: C 128 GLU cc_start: 0.9513 (tp30) cc_final: 0.9177 (tp30) REVERT: C 149 GLU cc_start: 0.9217 (mp0) cc_final: 0.9016 (mp0) REVERT: C 229 THR cc_start: 0.9660 (m) cc_final: 0.9284 (p) REVERT: D 109 GLU cc_start: 0.8804 (tp30) cc_final: 0.8486 (tp30) REVERT: D 128 GLU cc_start: 0.9512 (tp30) cc_final: 0.9174 (tp30) REVERT: D 149 GLU cc_start: 0.9216 (mp0) cc_final: 0.8956 (mp0) REVERT: D 229 THR cc_start: 0.9667 (m) cc_final: 0.9290 (p) REVERT: G 36 TYR cc_start: 0.8973 (m-80) cc_final: 0.8753 (m-80) REVERT: G 45 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8943 (ttpt) REVERT: G 67 SER cc_start: 0.9080 (m) cc_final: 0.8856 (p) REVERT: G 93 ASP cc_start: 0.9342 (t0) cc_final: 0.8973 (t70) REVERT: G 103 LYS cc_start: 0.9290 (mttt) cc_final: 0.8771 (mtpp) REVERT: G 106 ILE cc_start: 0.8854 (mt) cc_final: 0.8010 (pp) REVERT: H 3 GLN cc_start: 0.8890 (pm20) cc_final: 0.8505 (pm20) REVERT: H 46 GLU cc_start: 0.8903 (tt0) cc_final: 0.8448 (tt0) REVERT: H 72 ASP cc_start: 0.9022 (t0) cc_final: 0.8582 (OUTLIER) REVERT: H 77 GLN cc_start: 0.9104 (mt0) cc_final: 0.8423 (mm110) REVERT: H 86 ASP cc_start: 0.9095 (m-30) cc_final: 0.8655 (m-30) REVERT: H 94 ARG cc_start: 0.8634 (tmm-80) cc_final: 0.8310 (tmm-80) REVERT: H 95 ASP cc_start: 0.9509 (t0) cc_final: 0.8977 (t0) REVERT: H 100 LEU cc_start: 0.9711 (mt) cc_final: 0.9481 (mm) REVERT: H 105 GLN cc_start: 0.9370 (mt0) cc_final: 0.9147 (mm110) REVERT: H 199 ILE cc_start: 0.8501 (mm) cc_final: 0.8208 (tp) REVERT: F 3 GLN cc_start: 0.8884 (pm20) cc_final: 0.8498 (pm20) REVERT: F 46 GLU cc_start: 0.8897 (tt0) cc_final: 0.8442 (tt0) REVERT: F 72 ASP cc_start: 0.9037 (t0) cc_final: 0.8598 (OUTLIER) REVERT: F 77 GLN cc_start: 0.9109 (mt0) cc_final: 0.8438 (mm110) REVERT: F 86 ASP cc_start: 0.9070 (m-30) cc_final: 0.8625 (m-30) REVERT: F 94 ARG cc_start: 0.8625 (tmm-80) cc_final: 0.8306 (tmm-80) REVERT: F 95 ASP cc_start: 0.9514 (t0) cc_final: 0.8991 (t0) REVERT: F 100 LEU cc_start: 0.9715 (mt) cc_final: 0.9482 (mm) REVERT: F 105 GLN cc_start: 0.9363 (mt0) cc_final: 0.9141 (mm110) REVERT: J 3 GLN cc_start: 0.8890 (pm20) cc_final: 0.8509 (pm20) REVERT: J 46 GLU cc_start: 0.8890 (tt0) cc_final: 0.8436 (tt0) REVERT: J 72 ASP cc_start: 0.9020 (t0) cc_final: 0.8577 (OUTLIER) REVERT: J 77 GLN cc_start: 0.9080 (mt0) cc_final: 0.8435 (mm110) REVERT: J 86 ASP cc_start: 0.9084 (m-30) cc_final: 0.8642 (m-30) REVERT: J 95 ASP cc_start: 0.9513 (t0) cc_final: 0.8975 (t0) REVERT: J 100 LEU cc_start: 0.9718 (mt) cc_final: 0.9491 (mm) REVERT: J 105 GLN cc_start: 0.9351 (mt0) cc_final: 0.9126 (mm110) REVERT: J 199 ILE cc_start: 0.8568 (mm) cc_final: 0.8283 (tp) REVERT: K 3 GLN cc_start: 0.8880 (pm20) cc_final: 0.8496 (pm20) REVERT: K 46 GLU cc_start: 0.8894 (tt0) cc_final: 0.8439 (tt0) REVERT: K 72 ASP cc_start: 0.9019 (t0) cc_final: 0.8578 (OUTLIER) REVERT: K 77 GLN cc_start: 0.9079 (mt0) cc_final: 0.8432 (mm110) REVERT: K 86 ASP cc_start: 0.9075 (m-30) cc_final: 0.8631 (m-30) REVERT: K 94 ARG cc_start: 0.8608 (tmm-80) cc_final: 0.8246 (tmm-80) REVERT: K 95 ASP cc_start: 0.9509 (t0) cc_final: 0.8982 (t0) REVERT: K 100 LEU cc_start: 0.9717 (mt) cc_final: 0.9489 (mm) REVERT: K 105 GLN cc_start: 0.9361 (mt0) cc_final: 0.9135 (mm110) REVERT: K 149 TYR cc_start: 0.8055 (p90) cc_final: 0.7855 (p90) REVERT: E 36 TYR cc_start: 0.8970 (m-80) cc_final: 0.8747 (m-80) REVERT: E 45 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8948 (ttpt) REVERT: E 67 SER cc_start: 0.9085 (m) cc_final: 0.8859 (p) REVERT: E 93 ASP cc_start: 0.9334 (t0) cc_final: 0.8958 (t70) REVERT: E 103 LYS cc_start: 0.9291 (mttt) cc_final: 0.8761 (mtpp) REVERT: E 106 ILE cc_start: 0.8828 (mt) cc_final: 0.7975 (pp) REVERT: I 36 TYR cc_start: 0.8985 (m-80) cc_final: 0.8767 (m-80) REVERT: I 45 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8948 (ttpt) REVERT: I 67 SER cc_start: 0.9083 (m) cc_final: 0.8861 (p) REVERT: I 93 ASP cc_start: 0.9347 (t0) cc_final: 0.8981 (t70) REVERT: I 103 LYS cc_start: 0.9288 (mttt) cc_final: 0.8760 (mtpp) REVERT: I 106 ILE cc_start: 0.8844 (mt) cc_final: 0.7969 (pp) REVERT: L 36 TYR cc_start: 0.8978 (m-80) cc_final: 0.8764 (m-80) REVERT: L 45 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8955 (ttpt) REVERT: L 67 SER cc_start: 0.9091 (m) cc_final: 0.8863 (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: 0.9289 (mttt) cc_final: 0.8751 (mtpp) REVERT: L 106 ILE cc_start: 0.8847 (mt) cc_final: 0.8000 (pp) outliers start: 64 outliers final: 22 residues processed: 500 average time/residue: 0.9837 time to fit residues: 574.8915 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 : 2.352 ------------------------------------------------------------------------------- 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: 0.8980 chunk 50 optimal weight: 0.9990 chunk 230 optimal weight: 1.9990 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: 0.7980 chunk 64 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.3501 r_free = 0.3501 target = 0.089565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.060114 restraints weight = 51147.671| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 4.01 r_work: 0.2744 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21048 Z= 0.176 Angle : 0.696 9.696 28752 Z= 0.358 Chirality : 0.047 0.236 3224 Planarity : 0.005 0.058 3668 Dihedral : 5.732 20.797 2860 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.14 % Allowed : 16.71 % Favored : 79.14 % 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: -0.25 (0.16), residues: 2636 helix: -2.03 (0.36), residues: 144 sheet: 0.49 (0.17), residues: 848 loop : -0.29 (0.16), residues: 1644 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 0.020 0.002 TYR K 180 ARG 0.009 0.001 ARG I 142 Details of bonding type rmsd hydrogen bonds : bond 0.03448 ( 724) hydrogen bonds : angle 6.18101 ( 1980) SS BOND : bond 0.00625 ( 32) SS BOND : angle 1.40422 ( 64) covalent geometry : bond 0.00398 (21016) covalent geometry : angle 0.69321 (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 536 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 441 time to evaluate : 2.274 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: 0.8857 (tp30) cc_final: 0.7911 (tt0) REVERT: A 110 GLU cc_start: 0.9034 (mp0) cc_final: 0.8758 (mp0) REVERT: A 128 GLU cc_start: 0.9534 (tp30) cc_final: 0.9198 (tp30) REVERT: A 164 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7550 (tm-30) REVERT: A 194 ASP cc_start: 0.8655 (m-30) cc_final: 0.7915 (m-30) REVERT: B 128 GLU cc_start: 0.9535 (tp30) cc_final: 0.9191 (tp30) REVERT: B 164 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7539 (tm-30) REVERT: C 109 GLU cc_start: 0.8842 (tp30) cc_final: 0.8611 (tp30) REVERT: C 128 GLU cc_start: 0.9522 (tp30) cc_final: 0.9179 (tp30) REVERT: C 164 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7545 (tm-30) REVERT: C 194 ASP cc_start: 0.8705 (m-30) cc_final: 0.7940 (m-30) REVERT: D 109 GLU cc_start: 0.8832 (tp30) cc_final: 0.8472 (mm-30) REVERT: D 128 GLU cc_start: 0.9533 (tp30) cc_final: 0.9185 (tp30) REVERT: D 164 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7534 (tm-30) REVERT: G 36 TYR cc_start: 0.9037 (m-80) cc_final: 0.8801 (m-80) REVERT: G 45 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8921 (ttpt) REVERT: G 67 SER cc_start: 0.9108 (m) cc_final: 0.8864 (p) REVERT: G 93 ASP cc_start: 0.9340 (t0) cc_final: 0.8969 (t70) REVERT: G 103 LYS cc_start: 0.9314 (mttt) cc_final: 0.8785 (mtpp) REVERT: G 105 GLU cc_start: 0.7871 (tp30) cc_final: 0.7308 (tp30) REVERT: G 106 ILE cc_start: 0.8594 (mt) cc_final: 0.8031 (pp) REVERT: H 3 GLN cc_start: 0.9008 (pm20) cc_final: 0.8574 (pm20) REVERT: H 6 GLU cc_start: 0.8163 (mp0) cc_final: 0.7329 (mp0) REVERT: H 38 ARG cc_start: 0.8540 (ttt-90) cc_final: 0.8231 (ttp80) REVERT: H 46 GLU cc_start: 0.8850 (tt0) cc_final: 0.8155 (pt0) REVERT: H 72 ASP cc_start: 0.8993 (t0) cc_final: 0.8561 (t0) REVERT: H 86 ASP cc_start: 0.9160 (m-30) cc_final: 0.8924 (m-30) REVERT: H 95 ASP cc_start: 0.9514 (t0) cc_final: 0.9076 (t0) REVERT: H 100 LEU cc_start: 0.9698 (mt) cc_final: 0.9437 (mm) REVERT: H 105 GLN cc_start: 0.9419 (mt0) cc_final: 0.9090 (pm20) REVERT: H 157 SER cc_start: 0.8338 (OUTLIER) cc_final: 0.8053 (p) REVERT: H 199 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8491 (tp) REVERT: F 3 GLN cc_start: 0.9020 (pm20) cc_final: 0.8627 (pm20) REVERT: F 6 GLU cc_start: 0.8176 (mp0) cc_final: 0.7328 (mp0) REVERT: F 38 ARG cc_start: 0.8534 (ttt-90) cc_final: 0.8230 (ttp80) REVERT: F 46 GLU cc_start: 0.8839 (tt0) cc_final: 0.8149 (pt0) REVERT: F 72 ASP cc_start: 0.8992 (t0) cc_final: 0.8562 (t0) REVERT: F 86 ASP cc_start: 0.9145 (m-30) cc_final: 0.8912 (m-30) REVERT: F 95 ASP cc_start: 0.9525 (t0) cc_final: 0.9074 (t0) REVERT: F 100 LEU cc_start: 0.9700 (mt) cc_final: 0.9440 (mm) REVERT: F 105 GLN cc_start: 0.9409 (mt0) cc_final: 0.9091 (pm20) REVERT: F 157 SER cc_start: 0.8387 (OUTLIER) cc_final: 0.8180 (t) REVERT: F 213 LYS cc_start: 0.7518 (OUTLIER) cc_final: 0.7060 (ttpp) REVERT: J 3 GLN cc_start: 0.9021 (pm20) cc_final: 0.8630 (pm20) REVERT: J 6 GLU cc_start: 0.8149 (mp0) cc_final: 0.7299 (mp0) REVERT: J 38 ARG cc_start: 0.8551 (ttt-90) cc_final: 0.8227 (ttp80) REVERT: J 46 GLU cc_start: 0.8833 (tt0) cc_final: 0.8153 (pt0) REVERT: J 72 ASP cc_start: 0.9011 (t0) cc_final: 0.8578 (t0) REVERT: J 86 ASP cc_start: 0.9148 (m-30) cc_final: 0.8912 (m-30) REVERT: J 95 ASP cc_start: 0.9524 (t0) cc_final: 0.9043 (t0) REVERT: J 100 LEU cc_start: 0.9701 (mt) cc_final: 0.9442 (mm) REVERT: J 105 GLN cc_start: 0.9404 (mt0) cc_final: 0.9082 (pm20) REVERT: J 157 SER cc_start: 0.8369 (OUTLIER) cc_final: 0.8082 (p) REVERT: J 199 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8462 (tp) REVERT: K 3 GLN cc_start: 0.9007 (pm20) cc_final: 0.8615 (pm20) REVERT: K 6 GLU cc_start: 0.8139 (mp0) cc_final: 0.7297 (mp0) REVERT: K 38 ARG cc_start: 0.8518 (ttt-90) cc_final: 0.8202 (ttp80) REVERT: K 46 GLU cc_start: 0.8847 (tt0) cc_final: 0.8145 (pt0) REVERT: K 72 ASP cc_start: 0.8995 (t0) cc_final: 0.8563 (t0) REVERT: K 86 ASP cc_start: 0.9139 (m-30) cc_final: 0.8932 (m-30) REVERT: K 95 ASP cc_start: 0.9530 (t0) cc_final: 0.9066 (t0) REVERT: K 99 TYR cc_start: 0.9073 (m-10) cc_final: 0.8614 (m-10) REVERT: K 100 LEU cc_start: 0.9701 (mt) cc_final: 0.9443 (mm) REVERT: K 105 GLN cc_start: 0.9410 (mt0) cc_final: 0.9082 (pm20) REVERT: K 157 SER cc_start: 0.8373 (OUTLIER) cc_final: 0.8169 (t) REVERT: K 213 LYS cc_start: 0.7498 (OUTLIER) cc_final: 0.7070 (ttpp) REVERT: E 36 TYR cc_start: 0.9018 (m-80) cc_final: 0.8778 (m-80) REVERT: E 45 LYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8929 (ttpt) REVERT: E 67 SER cc_start: 0.9111 (m) cc_final: 0.8866 (p) REVERT: E 93 ASP cc_start: 0.9336 (t0) cc_final: 0.8984 (t70) REVERT: E 103 LYS cc_start: 0.9312 (mttt) cc_final: 0.8779 (mtpp) REVERT: E 105 GLU cc_start: 0.7887 (tp30) cc_final: 0.7325 (tp30) REVERT: E 106 ILE cc_start: 0.8604 (mt) cc_final: 0.8032 (pp) REVERT: I 36 TYR cc_start: 0.9027 (m-80) cc_final: 0.8790 (m-80) REVERT: I 45 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8923 (ttpt) REVERT: I 67 SER cc_start: 0.9107 (m) cc_final: 0.8867 (p) REVERT: I 93 ASP cc_start: 0.9340 (t0) cc_final: 0.8991 (t70) REVERT: I 103 LYS cc_start: 0.9313 (mttt) cc_final: 0.8790 (mtpp) REVERT: I 105 GLU cc_start: 0.7855 (tp30) cc_final: 0.7297 (tp30) REVERT: I 106 ILE cc_start: 0.8607 (mt) cc_final: 0.8043 (pp) REVERT: L 36 TYR cc_start: 0.9021 (m-80) cc_final: 0.8784 (m-80) REVERT: L 45 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8935 (ttpt) REVERT: L 67 SER cc_start: 0.9098 (m) cc_final: 0.8861 (p) REVERT: L 92 PHE cc_start: 0.9318 (m-80) cc_final: 0.9050 (m-80) REVERT: L 93 ASP cc_start: 0.9340 (t0) cc_final: 0.8964 (t70) REVERT: L 103 LYS cc_start: 0.9319 (mttt) cc_final: 0.8779 (mtpp) REVERT: L 105 GLU cc_start: 0.7863 (tp30) cc_final: 0.7301 (tp30) REVERT: L 106 ILE cc_start: 0.8599 (mt) cc_final: 0.8034 (pp) outliers start: 95 outliers final: 19 residues processed: 487 average time/residue: 0.9935 time to fit residues: 565.5249 Evaluate side-chains 453 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 418 time to evaluate : 2.261 ------------------------------------------------------------------------------- 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 157 SER 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 E residue 209 PHE 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 Chi-restraints excluded: chain L residue 209 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 69 optimal weight: 0.3980 chunk 49 optimal weight: 2.9990 chunk 221 optimal weight: 7.9990 chunk 257 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 178 optimal weight: 9.9990 chunk 163 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 107 optimal weight: 0.2980 chunk 141 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.091393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.062040 restraints weight = 50518.637| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 4.03 r_work: 0.2783 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21048 Z= 0.129 Angle : 0.668 8.405 28752 Z= 0.342 Chirality : 0.046 0.149 3224 Planarity : 0.005 0.061 3668 Dihedral : 5.320 19.196 2860 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.18 % Allowed : 19.42 % Favored : 77.40 % 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: -0.13 (0.16), residues: 2636 helix: -1.71 (0.38), residues: 144 sheet: 0.68 (0.18), residues: 812 loop : -0.28 (0.16), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 158 HIS 0.004 0.001 HIS B 173 PHE 0.037 0.002 PHE G 209 TYR 0.020 0.001 TYR K 149 ARG 0.007 0.001 ARG L 142 Details of bonding type rmsd hydrogen bonds : bond 0.03141 ( 724) hydrogen bonds : angle 5.71589 ( 1980) SS BOND : bond 0.00483 ( 32) SS BOND : angle 1.42709 ( 64) covalent geometry : bond 0.00296 (21016) covalent geometry : angle 0.66553 (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 542 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 469 time to evaluate : 2.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLN cc_start: 0.9385 (OUTLIER) cc_final: 0.8999 (pm20) REVERT: A 109 GLU cc_start: 0.8987 (tp30) cc_final: 0.7814 (tt0) REVERT: A 110 GLU cc_start: 0.8988 (mp0) cc_final: 0.8780 (mp0) REVERT: A 128 GLU cc_start: 0.9524 (tp30) cc_final: 0.9237 (tp30) REVERT: A 164 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7540 (tm-30) REVERT: B 20 GLN cc_start: 0.9251 (OUTLIER) cc_final: 0.8843 (pm20) REVERT: B 109 GLU cc_start: 0.8927 (tp30) cc_final: 0.8244 (tt0) REVERT: B 128 GLU cc_start: 0.9531 (tp30) cc_final: 0.9236 (tp30) REVERT: B 149 GLU cc_start: 0.9253 (mp0) cc_final: 0.8963 (mp0) REVERT: B 164 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7505 (tm-30) REVERT: B 194 ASP cc_start: 0.8603 (m-30) cc_final: 0.7813 (m-30) REVERT: C 109 GLU cc_start: 0.8894 (tp30) cc_final: 0.8650 (tt0) REVERT: C 128 GLU cc_start: 0.9515 (tp30) cc_final: 0.9224 (tp30) REVERT: C 164 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7505 (tm-30) REVERT: D 70 GLU cc_start: 0.8144 (pp20) cc_final: 0.7934 (pp20) REVERT: D 109 GLU cc_start: 0.8856 (tp30) cc_final: 0.8501 (mm-30) REVERT: D 128 GLU cc_start: 0.9521 (tp30) cc_final: 0.9228 (tp30) REVERT: D 149 GLU cc_start: 0.9251 (mp0) cc_final: 0.8991 (mp0) REVERT: D 164 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7496 (tm-30) REVERT: D 194 ASP cc_start: 0.8604 (m-30) cc_final: 0.7872 (m-30) REVERT: G 18 ARG cc_start: 0.9113 (ppp80) cc_final: 0.8721 (ttp-110) REVERT: G 36 TYR cc_start: 0.9020 (m-80) cc_final: 0.8743 (m-80) REVERT: G 45 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8912 (ttpt) REVERT: G 49 TYR cc_start: 0.9250 (p90) cc_final: 0.8884 (p90) REVERT: G 50 GLU cc_start: 0.9319 (mt-10) cc_final: 0.8927 (mp0) REVERT: G 67 SER cc_start: 0.9125 (m) cc_final: 0.8882 (p) REVERT: G 93 ASP cc_start: 0.9303 (t0) cc_final: 0.8954 (t70) REVERT: G 103 LYS cc_start: 0.9258 (mttt) cc_final: 0.8732 (mtpp) REVERT: G 105 GLU cc_start: 0.7800 (tp30) cc_final: 0.7213 (tp30) REVERT: G 106 ILE cc_start: 0.8658 (mt) cc_final: 0.8071 (pp) REVERT: H 3 GLN cc_start: 0.9013 (pm20) cc_final: 0.8618 (pm20) REVERT: H 6 GLU cc_start: 0.8191 (mp0) cc_final: 0.7320 (mp0) REVERT: H 46 GLU cc_start: 0.8833 (tt0) cc_final: 0.8288 (pt0) REVERT: H 72 ASP cc_start: 0.8973 (t0) cc_final: 0.8527 (t0) REVERT: H 86 ASP cc_start: 0.9128 (m-30) cc_final: 0.8899 (m-30) REVERT: H 95 ASP cc_start: 0.9527 (t0) cc_final: 0.9012 (t0) REVERT: H 100 LEU cc_start: 0.9685 (mt) cc_final: 0.9400 (mm) REVERT: H 105 GLN cc_start: 0.9403 (mt0) cc_final: 0.9089 (pm20) REVERT: H 163 LEU cc_start: 0.9545 (mp) cc_final: 0.9323 (tm) REVERT: H 199 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8519 (tp) REVERT: F 3 GLN cc_start: 0.9065 (pm20) cc_final: 0.8698 (pm20) REVERT: F 6 GLU cc_start: 0.8163 (mp0) cc_final: 0.7292 (mp0) REVERT: F 46 GLU cc_start: 0.8846 (tt0) cc_final: 0.8256 (tt0) REVERT: F 72 ASP cc_start: 0.8961 (t0) cc_final: 0.8517 (t0) REVERT: F 86 ASP cc_start: 0.9119 (m-30) cc_final: 0.8822 (m-30) REVERT: F 95 ASP cc_start: 0.9519 (t0) cc_final: 0.8946 (t0) REVERT: F 100 LEU cc_start: 0.9684 (mt) cc_final: 0.9392 (mm) REVERT: F 105 GLN cc_start: 0.9405 (mt0) cc_final: 0.9080 (pm20) REVERT: F 199 ILE cc_start: 0.8472 (tp) cc_final: 0.8261 (tp) REVERT: J 3 GLN cc_start: 0.9065 (pm20) cc_final: 0.8699 (pm20) REVERT: J 6 GLU cc_start: 0.8168 (mp0) cc_final: 0.7311 (mp0) REVERT: J 46 GLU cc_start: 0.8822 (tt0) cc_final: 0.8228 (tt0) REVERT: J 72 ASP cc_start: 0.8984 (t0) cc_final: 0.8539 (t0) REVERT: J 86 ASP cc_start: 0.9106 (m-30) cc_final: 0.8807 (m-30) REVERT: J 95 ASP cc_start: 0.9499 (t0) cc_final: 0.8909 (t0) REVERT: J 100 LEU cc_start: 0.9686 (mt) cc_final: 0.9394 (mm) REVERT: J 105 GLN cc_start: 0.9400 (mt0) cc_final: 0.9075 (pm20) REVERT: J 163 LEU cc_start: 0.9545 (mp) cc_final: 0.9321 (tm) REVERT: J 199 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8492 (tp) REVERT: K 3 GLN cc_start: 0.9052 (pm20) cc_final: 0.8685 (pm20) REVERT: K 6 GLU cc_start: 0.8163 (mp0) cc_final: 0.7319 (mp0) REVERT: K 46 GLU cc_start: 0.8836 (tt0) cc_final: 0.8238 (tt0) REVERT: K 72 ASP cc_start: 0.8976 (t0) cc_final: 0.8534 (t0) REVERT: K 86 ASP cc_start: 0.9104 (m-30) cc_final: 0.8803 (m-30) REVERT: K 95 ASP cc_start: 0.9539 (t0) cc_final: 0.8920 (t0) REVERT: K 99 TYR cc_start: 0.9071 (m-10) cc_final: 0.8505 (m-10) REVERT: K 100 LEU cc_start: 0.9682 (mt) cc_final: 0.9395 (mm) REVERT: K 105 GLN cc_start: 0.9404 (mt0) cc_final: 0.9070 (pm20) REVERT: E 18 ARG cc_start: 0.9121 (ppp80) cc_final: 0.8727 (ttp-110) REVERT: E 36 TYR cc_start: 0.9021 (m-80) cc_final: 0.8720 (m-80) REVERT: E 45 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8917 (ttpt) REVERT: E 49 TYR cc_start: 0.9250 (p90) cc_final: 0.8892 (p90) REVERT: E 50 GLU cc_start: 0.9326 (mt-10) cc_final: 0.8936 (mp0) REVERT: E 67 SER cc_start: 0.9109 (m) cc_final: 0.8865 (p) REVERT: E 93 ASP cc_start: 0.9333 (t0) cc_final: 0.8972 (t70) REVERT: E 103 LYS cc_start: 0.9265 (mttt) cc_final: 0.8749 (mtpp) REVERT: E 105 GLU cc_start: 0.7807 (tp30) cc_final: 0.7221 (tp30) REVERT: E 106 ILE cc_start: 0.8674 (mt) cc_final: 0.8071 (pp) REVERT: E 195 GLU cc_start: 0.5464 (OUTLIER) cc_final: 0.5220 (tm-30) REVERT: I 18 ARG cc_start: 0.9116 (ppp80) cc_final: 0.8705 (ttp-110) REVERT: I 36 TYR cc_start: 0.9021 (m-80) cc_final: 0.8722 (m-80) REVERT: I 45 LYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8915 (ttpt) REVERT: I 49 TYR cc_start: 0.9255 (p90) cc_final: 0.8882 (p90) REVERT: I 50 GLU cc_start: 0.9308 (mt-10) cc_final: 0.8916 (mp0) REVERT: I 67 SER cc_start: 0.9118 (m) cc_final: 0.8870 (p) REVERT: I 93 ASP cc_start: 0.9314 (t0) cc_final: 0.8978 (t70) REVERT: I 103 LYS cc_start: 0.9279 (mttt) cc_final: 0.8767 (mtpp) REVERT: I 105 GLU cc_start: 0.7773 (tp30) cc_final: 0.7189 (tp30) REVERT: I 106 ILE cc_start: 0.8664 (mt) cc_final: 0.8082 (pp) REVERT: L 18 ARG cc_start: 0.9113 (ppp80) cc_final: 0.8726 (ttp-110) REVERT: L 36 TYR cc_start: 0.9015 (m-80) cc_final: 0.8718 (m-80) REVERT: L 45 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8923 (ttpt) REVERT: L 49 TYR cc_start: 0.9251 (p90) cc_final: 0.8887 (p90) REVERT: L 50 GLU cc_start: 0.9315 (mt-10) cc_final: 0.8925 (mp0) REVERT: L 67 SER cc_start: 0.9124 (m) cc_final: 0.8879 (p) REVERT: L 92 PHE cc_start: 0.9285 (m-80) cc_final: 0.8980 (m-80) REVERT: L 93 ASP cc_start: 0.9307 (t0) cc_final: 0.8942 (t70) REVERT: L 103 LYS cc_start: 0.9271 (mttt) cc_final: 0.8757 (mtpp) REVERT: L 105 GLU cc_start: 0.7800 (tp30) cc_final: 0.7213 (tp30) REVERT: L 106 ILE cc_start: 0.8685 (mt) cc_final: 0.8074 (pp) REVERT: L 195 GLU cc_start: 0.5438 (OUTLIER) cc_final: 0.5195 (tm-30) outliers start: 73 outliers final: 28 residues processed: 512 average time/residue: 1.0982 time to fit residues: 649.1442 Evaluate side-chains 468 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 426 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 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 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 194 CYS Chi-restraints excluded: chain E residue 195 GLU Chi-restraints excluded: chain I residue 17 ASP 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 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: 4.9990 chunk 128 optimal weight: 4.9990 chunk 243 optimal weight: 0.6980 chunk 237 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 220 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 C 209 GLN D 146 ASN D 209 GLN H 76 ASN H 77 GLN H 203 ASN 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 Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.089548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.060072 restraints weight = 51508.506| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 4.03 r_work: 0.2733 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 21048 Z= 0.224 Angle : 0.686 8.059 28752 Z= 0.354 Chirality : 0.046 0.141 3224 Planarity : 0.005 0.062 3668 Dihedral : 5.242 21.422 2860 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.36 % Allowed : 19.98 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.10 (0.16), residues: 2636 helix: -1.72 (0.39), residues: 144 sheet: 0.62 (0.17), residues: 875 loop : -0.25 (0.16), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 158 HIS 0.004 0.001 HIS C 48 PHE 0.038 0.002 PHE G 209 TYR 0.029 0.002 TYR H 99 ARG 0.009 0.001 ARG L 142 Details of bonding type rmsd hydrogen bonds : bond 0.03210 ( 724) hydrogen bonds : angle 5.57814 ( 1980) SS BOND : bond 0.00543 ( 32) SS BOND : angle 1.25832 ( 64) covalent geometry : bond 0.00498 (21016) covalent geometry : angle 0.68463 (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 534 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 434 time to evaluate : 2.361 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: 0.9354 (OUTLIER) cc_final: 0.8990 (pm20) REVERT: A 80 ASP cc_start: 0.8318 (m-30) cc_final: 0.7934 (m-30) REVERT: A 109 GLU cc_start: 0.8962 (tp30) cc_final: 0.7894 (tt0) REVERT: A 128 GLU cc_start: 0.9535 (tp30) cc_final: 0.9228 (tp30) REVERT: A 164 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7668 (tm-30) REVERT: A 180 MET cc_start: 0.9472 (mtm) cc_final: 0.9155 (mtm) REVERT: A 194 ASP cc_start: 0.8620 (m-30) cc_final: 0.7984 (m-30) REVERT: B 20 GLN cc_start: 0.9225 (OUTLIER) cc_final: 0.8806 (pm20) REVERT: B 109 GLU cc_start: 0.9038 (tp30) cc_final: 0.8628 (tp30) REVERT: B 128 GLU cc_start: 0.9540 (tp30) cc_final: 0.9219 (tp30) REVERT: B 134 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8815 (mmp) REVERT: B 164 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7628 (tm-30) REVERT: B 180 MET cc_start: 0.9463 (mtm) cc_final: 0.9184 (mtm) REVERT: B 194 ASP cc_start: 0.8613 (m-30) cc_final: 0.7930 (m-30) REVERT: C 109 GLU cc_start: 0.9012 (tp30) cc_final: 0.8669 (tt0) REVERT: C 128 GLU cc_start: 0.9538 (tp30) cc_final: 0.9222 (tp30) REVERT: C 164 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7664 (tm-30) REVERT: C 180 MET cc_start: 0.9473 (mtm) cc_final: 0.9164 (mtm) REVERT: C 194 ASP cc_start: 0.8656 (m-30) cc_final: 0.8007 (m-30) REVERT: D 109 GLU cc_start: 0.8822 (tp30) cc_final: 0.8256 (tp30) REVERT: D 128 GLU cc_start: 0.9532 (tp30) cc_final: 0.9215 (tp30) REVERT: D 134 MET cc_start: 0.9079 (OUTLIER) cc_final: 0.8836 (mmp) REVERT: D 164 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7632 (tm-30) REVERT: D 180 MET cc_start: 0.9463 (mtm) cc_final: 0.9143 (mtm) REVERT: D 194 ASP cc_start: 0.8574 (m-30) cc_final: 0.7864 (m-30) REVERT: G 45 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8902 (ttpt) REVERT: G 49 TYR cc_start: 0.9297 (p90) cc_final: 0.8861 (p90) REVERT: G 50 GLU cc_start: 0.9370 (mt-10) cc_final: 0.8915 (mp0) REVERT: G 67 SER cc_start: 0.9151 (m) cc_final: 0.8925 (p) REVERT: G 93 ASP cc_start: 0.9333 (t0) cc_final: 0.8970 (t70) REVERT: G 103 LYS cc_start: 0.9270 (mttt) cc_final: 0.8746 (mtpp) REVERT: G 105 GLU cc_start: 0.7876 (tp30) cc_final: 0.7514 (tp30) REVERT: G 106 ILE cc_start: 0.8700 (mt) cc_final: 0.8203 (pp) REVERT: G 161 GLU cc_start: 0.9162 (pm20) cc_final: 0.8569 (pp20) REVERT: H 3 GLN cc_start: 0.9139 (pm20) cc_final: 0.8759 (pm20) REVERT: H 6 GLU cc_start: 0.8200 (mp0) cc_final: 0.7342 (mp0) REVERT: H 46 GLU cc_start: 0.8836 (tt0) cc_final: 0.8413 (pt0) REVERT: H 72 ASP cc_start: 0.8918 (t0) cc_final: 0.8462 (t0) REVERT: H 95 ASP cc_start: 0.9546 (t0) cc_final: 0.9099 (t0) REVERT: H 105 GLN cc_start: 0.9434 (mt0) cc_final: 0.9062 (pm20) REVERT: H 163 LEU cc_start: 0.9580 (mp) cc_final: 0.9361 (tm) REVERT: H 199 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8576 (tp) REVERT: F 3 GLN cc_start: 0.9125 (pm20) cc_final: 0.8814 (pm20) REVERT: F 6 GLU cc_start: 0.8190 (mp0) cc_final: 0.7329 (mp0) REVERT: F 46 GLU cc_start: 0.8845 (tt0) cc_final: 0.8337 (pt0) REVERT: F 72 ASP cc_start: 0.8915 (t0) cc_final: 0.8459 (t0) REVERT: F 95 ASP cc_start: 0.9554 (t0) cc_final: 0.9080 (t0) REVERT: F 105 GLN cc_start: 0.9438 (mt0) cc_final: 0.9080 (pm20) REVERT: J 3 GLN cc_start: 0.9122 (pm20) cc_final: 0.8811 (pm20) REVERT: J 6 GLU cc_start: 0.8174 (mp0) cc_final: 0.7322 (mp0) REVERT: J 46 GLU cc_start: 0.8834 (tt0) cc_final: 0.8332 (pt0) REVERT: J 72 ASP cc_start: 0.8928 (t0) cc_final: 0.8455 (t0) REVERT: J 94 ARG cc_start: 0.8661 (tmm-80) cc_final: 0.8335 (tmm-80) REVERT: J 95 ASP cc_start: 0.9539 (t0) cc_final: 0.9081 (t0) REVERT: J 99 TYR cc_start: 0.8912 (m-10) cc_final: 0.8585 (m-80) REVERT: J 100 LEU cc_start: 0.9696 (mt) cc_final: 0.9487 (mp) REVERT: J 105 GLN cc_start: 0.9434 (mt0) cc_final: 0.9077 (pm20) REVERT: J 108 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9074 (tm) REVERT: J 163 LEU cc_start: 0.9581 (mp) cc_final: 0.9363 (tm) REVERT: J 199 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8558 (tp) REVERT: K 3 GLN cc_start: 0.9114 (pm20) cc_final: 0.8803 (pm20) REVERT: K 6 GLU cc_start: 0.8141 (mp0) cc_final: 0.7295 (mp0) REVERT: K 46 GLU cc_start: 0.8825 (tt0) cc_final: 0.8321 (pt0) REVERT: K 72 ASP cc_start: 0.8925 (t0) cc_final: 0.8466 (t0) REVERT: K 95 ASP cc_start: 0.9560 (t0) cc_final: 0.9088 (t0) REVERT: K 105 GLN cc_start: 0.9430 (mt0) cc_final: 0.9066 (pm20) REVERT: K 108 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9065 (tm) REVERT: E 45 LYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8915 (ttpt) REVERT: E 49 TYR cc_start: 0.9304 (p90) cc_final: 0.8900 (p90) REVERT: E 50 GLU cc_start: 0.9366 (mt-10) cc_final: 0.8965 (mp0) REVERT: E 67 SER cc_start: 0.9149 (m) cc_final: 0.8926 (p) REVERT: E 93 ASP cc_start: 0.9341 (t0) cc_final: 0.8980 (t70) REVERT: E 103 LYS cc_start: 0.9278 (mttt) cc_final: 0.8758 (mtpp) REVERT: E 105 GLU cc_start: 0.7890 (tp30) cc_final: 0.7529 (tp30) REVERT: E 106 ILE cc_start: 0.8705 (mt) cc_final: 0.8203 (pp) REVERT: E 161 GLU cc_start: 0.9160 (pm20) cc_final: 0.8554 (pp20) REVERT: I 45 LYS cc_start: 0.9177 (OUTLIER) cc_final: 0.8905 (ttpt) REVERT: I 49 TYR cc_start: 0.9304 (p90) cc_final: 0.8890 (p90) REVERT: I 50 GLU cc_start: 0.9351 (mt-10) cc_final: 0.8948 (mp0) REVERT: I 67 SER cc_start: 0.9136 (m) cc_final: 0.8911 (p) REVERT: I 93 ASP cc_start: 0.9350 (t0) cc_final: 0.8997 (t70) REVERT: I 103 LYS cc_start: 0.9287 (mttt) cc_final: 0.8777 (mtpp) REVERT: I 105 GLU cc_start: 0.7868 (tp30) cc_final: 0.7519 (tp30) REVERT: I 106 ILE cc_start: 0.8702 (mt) cc_final: 0.8215 (pp) REVERT: I 161 GLU cc_start: 0.9161 (pm20) cc_final: 0.8571 (pp20) REVERT: L 45 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8915 (ttpt) REVERT: L 49 TYR cc_start: 0.9297 (p90) cc_final: 0.8899 (p90) REVERT: L 50 GLU cc_start: 0.9366 (mt-10) cc_final: 0.8963 (mp0) REVERT: L 67 SER cc_start: 0.9144 (m) cc_final: 0.8919 (p) REVERT: L 92 PHE cc_start: 0.9299 (m-80) cc_final: 0.8971 (m-80) REVERT: L 93 ASP cc_start: 0.9350 (t0) cc_final: 0.8961 (t70) REVERT: L 103 LYS cc_start: 0.9281 (mttt) cc_final: 0.8768 (mtpp) REVERT: L 105 GLU cc_start: 0.7865 (tp30) cc_final: 0.7510 (tp30) REVERT: L 106 ILE cc_start: 0.8698 (mt) cc_final: 0.8203 (pp) REVERT: L 161 GLU cc_start: 0.9167 (pm20) cc_final: 0.8560 (pp20) outliers start: 100 outliers final: 42 residues processed: 500 average time/residue: 1.0383 time to fit residues: 602.1142 Evaluate side-chains 459 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 401 time to evaluate : 2.618 ------------------------------------------------------------------------------- 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 134 MET Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 134 MET 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 108 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 108 LEU Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 27 PHE Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 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 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 17 ASP Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 183 LYS Chi-restraints excluded: chain I residue 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=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: 1.9990 chunk 196 optimal weight: 6.9990 chunk 204 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 252 optimal weight: 0.6980 chunk 161 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN B 146 ASN C 146 ASN G 30 ASN G 124 GLN H 77 GLN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 GLN ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 GLN ** K 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 GLN K 203 ASN E 30 ASN I 30 ASN L 30 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.088522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.059145 restraints weight = 51738.761| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 4.03 r_work: 0.2720 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3739 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= 0.245 Angle : 0.700 8.227 28752 Z= 0.363 Chirality : 0.047 0.186 3224 Planarity : 0.005 0.061 3668 Dihedral : 5.208 21.635 2860 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.36 % Allowed : 20.11 % Favored : 75.52 % 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: -0.21 (0.16), residues: 2636 helix: -1.58 (0.39), residues: 144 sheet: 0.54 (0.17), residues: 858 loop : -0.33 (0.16), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 158 HIS 0.004 0.001 HIS B 173 PHE 0.041 0.002 PHE L 209 TYR 0.024 0.002 TYR H 99 ARG 0.010 0.001 ARG L 142 Details of bonding type rmsd hydrogen bonds : bond 0.03186 ( 724) hydrogen bonds : angle 5.50458 ( 1980) SS BOND : bond 0.00527 ( 32) SS BOND : angle 1.20545 ( 64) covalent geometry : bond 0.00540 (21016) covalent geometry : angle 0.69797 (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 512 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 412 time to evaluate : 3.375 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: 0.9375 (OUTLIER) cc_final: 0.9043 (pm20) REVERT: A 109 GLU cc_start: 0.8875 (tp30) cc_final: 0.8157 (tt0) REVERT: A 128 GLU cc_start: 0.9546 (tp30) cc_final: 0.9250 (tp30) REVERT: A 164 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7651 (tm-30) REVERT: A 180 MET cc_start: 0.9484 (mtm) cc_final: 0.9197 (mtm) REVERT: A 194 ASP cc_start: 0.8641 (m-30) cc_final: 0.7987 (m-30) REVERT: B 20 GLN cc_start: 0.9157 (OUTLIER) cc_final: 0.8768 (pm20) REVERT: B 128 GLU cc_start: 0.9548 (tp30) cc_final: 0.9243 (tp30) REVERT: B 164 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7602 (tm-30) REVERT: B 180 MET cc_start: 0.9475 (mtm) cc_final: 0.9198 (mtm) REVERT: B 194 ASP cc_start: 0.8579 (m-30) cc_final: 0.7914 (m-30) REVERT: C 20 GLN cc_start: 0.9317 (OUTLIER) cc_final: 0.8919 (pm20) REVERT: C 109 GLU cc_start: 0.9043 (tp30) cc_final: 0.8687 (tt0) REVERT: C 128 GLU cc_start: 0.9549 (tp30) cc_final: 0.9250 (tp30) REVERT: C 164 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7656 (tm-30) REVERT: C 180 MET cc_start: 0.9485 (mtm) cc_final: 0.9207 (mtm) REVERT: C 194 ASP cc_start: 0.8622 (m-30) cc_final: 0.7955 (m-30) REVERT: D 20 GLN cc_start: 0.9245 (OUTLIER) cc_final: 0.8981 (pm20) REVERT: D 109 GLU cc_start: 0.8824 (tp30) cc_final: 0.8233 (tp30) REVERT: D 128 GLU cc_start: 0.9546 (tp30) cc_final: 0.9239 (tp30) REVERT: D 164 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7628 (tm-30) REVERT: D 180 MET cc_start: 0.9475 (mtm) cc_final: 0.9186 (mtm) REVERT: D 194 ASP cc_start: 0.8603 (m-30) cc_final: 0.7880 (m-30) REVERT: G 36 TYR cc_start: 0.9295 (m-80) cc_final: 0.9024 (m-80) REVERT: G 45 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8910 (ttpt) REVERT: G 49 TYR cc_start: 0.9309 (p90) cc_final: 0.8926 (p90) REVERT: G 50 GLU cc_start: 0.9363 (mt-10) cc_final: 0.8998 (mp0) REVERT: G 67 SER cc_start: 0.9162 (m) cc_final: 0.8922 (p) REVERT: G 93 ASP cc_start: 0.9334 (t0) cc_final: 0.8972 (t70) REVERT: G 103 LYS cc_start: 0.9274 (mttt) cc_final: 0.8754 (mtpp) REVERT: G 105 GLU cc_start: 0.8179 (tp30) cc_final: 0.7767 (tp30) REVERT: G 106 ILE cc_start: 0.8721 (mt) cc_final: 0.8242 (pp) REVERT: G 161 GLU cc_start: 0.9167 (pm20) cc_final: 0.8594 (pp20) REVERT: H 3 GLN cc_start: 0.9134 (pm20) cc_final: 0.8734 (pm20) REVERT: H 6 GLU cc_start: 0.8210 (mp0) cc_final: 0.7345 (mp0) REVERT: H 46 GLU cc_start: 0.8836 (tt0) cc_final: 0.8408 (pt0) REVERT: H 72 ASP cc_start: 0.8897 (t0) cc_final: 0.8428 (t0) REVERT: H 95 ASP cc_start: 0.9537 (t0) cc_final: 0.9143 (t0) REVERT: H 105 GLN cc_start: 0.9446 (mt0) cc_final: 0.9039 (pm20) REVERT: H 163 LEU cc_start: 0.9602 (mp) cc_final: 0.9369 (tm) REVERT: H 199 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8600 (tp) REVERT: F 3 GLN cc_start: 0.9091 (pm20) cc_final: 0.8752 (pm20) REVERT: F 6 GLU cc_start: 0.8226 (mp0) cc_final: 0.7381 (mp0) REVERT: F 26 ARG cc_start: 0.8442 (tmm-80) cc_final: 0.8056 (tmm-80) REVERT: F 27 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.8282 (m-80) REVERT: F 46 GLU cc_start: 0.8854 (tt0) cc_final: 0.8352 (pt0) REVERT: F 72 ASP cc_start: 0.8903 (t0) cc_final: 0.8446 (t0) REVERT: F 95 ASP cc_start: 0.9522 (t0) cc_final: 0.9113 (t0) REVERT: F 105 GLN cc_start: 0.9446 (mt0) cc_final: 0.9048 (pm20) REVERT: F 213 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.7442 (tmmm) REVERT: J 3 GLN cc_start: 0.9094 (pm20) cc_final: 0.8755 (pm20) REVERT: J 6 GLU cc_start: 0.8212 (mp0) cc_final: 0.7369 (mp0) REVERT: J 16 GLU cc_start: 0.7794 (pm20) cc_final: 0.7588 (pm20) REVERT: J 26 ARG cc_start: 0.8456 (tmm-80) cc_final: 0.8047 (tmm-80) REVERT: J 27 PHE cc_start: 0.8620 (OUTLIER) cc_final: 0.8291 (m-80) REVERT: J 46 GLU cc_start: 0.8826 (tt0) cc_final: 0.8323 (pt0) REVERT: J 72 ASP cc_start: 0.8909 (t0) cc_final: 0.8455 (t0) REVERT: J 94 ARG cc_start: 0.8689 (tmm-80) cc_final: 0.8365 (tmm-80) REVERT: J 95 ASP cc_start: 0.9558 (t0) cc_final: 0.9110 (t0) REVERT: J 105 GLN cc_start: 0.9432 (mt0) cc_final: 0.9023 (pm20) REVERT: J 108 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9149 (tm) REVERT: J 110 THR cc_start: 0.9508 (m) cc_final: 0.9250 (p) REVERT: J 163 LEU cc_start: 0.9605 (mp) cc_final: 0.9371 (tm) REVERT: J 199 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8579 (tp) REVERT: K 3 GLN cc_start: 0.9084 (pm20) cc_final: 0.8744 (pm20) REVERT: K 6 GLU cc_start: 0.8154 (mp0) cc_final: 0.7316 (mp0) REVERT: K 26 ARG cc_start: 0.8463 (tmm-80) cc_final: 0.8052 (tmm-80) REVERT: K 27 PHE cc_start: 0.8612 (OUTLIER) cc_final: 0.8283 (m-80) REVERT: K 46 GLU cc_start: 0.8846 (tt0) cc_final: 0.8368 (pt0) REVERT: K 72 ASP cc_start: 0.8902 (t0) cc_final: 0.8451 (t0) REVERT: K 95 ASP cc_start: 0.9530 (t0) cc_final: 0.9123 (t0) REVERT: K 105 GLN cc_start: 0.9445 (mt0) cc_final: 0.9046 (pm20) REVERT: K 108 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9132 (tm) REVERT: K 110 THR cc_start: 0.9505 (m) cc_final: 0.9245 (p) REVERT: K 213 LYS cc_start: 0.7688 (OUTLIER) cc_final: 0.7428 (tmmm) REVERT: E 36 TYR cc_start: 0.9275 (m-80) cc_final: 0.9000 (m-80) REVERT: E 45 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8919 (ttpt) REVERT: E 49 TYR cc_start: 0.9317 (p90) cc_final: 0.8923 (p90) REVERT: E 50 GLU cc_start: 0.9367 (mt-10) cc_final: 0.9001 (mp0) REVERT: E 67 SER cc_start: 0.9159 (m) cc_final: 0.8927 (p) REVERT: E 93 ASP cc_start: 0.9332 (t0) cc_final: 0.8987 (t70) REVERT: E 103 LYS cc_start: 0.9282 (mttt) cc_final: 0.8742 (mtpp) REVERT: E 105 GLU cc_start: 0.8179 (tp30) cc_final: 0.7771 (tp30) REVERT: E 106 ILE cc_start: 0.8730 (mt) cc_final: 0.8246 (pp) REVERT: E 161 GLU cc_start: 0.9166 (pm20) cc_final: 0.8595 (pp20) REVERT: E 195 GLU cc_start: 0.5751 (OUTLIER) cc_final: 0.5443 (tm-30) REVERT: I 45 LYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8915 (ttpt) REVERT: I 49 TYR cc_start: 0.9318 (p90) cc_final: 0.8924 (p90) REVERT: I 50 GLU cc_start: 0.9361 (mt-10) cc_final: 0.8993 (mp0) REVERT: I 67 SER cc_start: 0.9163 (m) cc_final: 0.8928 (p) REVERT: I 93 ASP cc_start: 0.9359 (t0) cc_final: 0.9012 (t70) REVERT: I 103 LYS cc_start: 0.9285 (mttt) cc_final: 0.8758 (mtpp) REVERT: I 105 GLU cc_start: 0.8147 (tp30) cc_final: 0.7749 (tp30) REVERT: I 106 ILE cc_start: 0.8732 (mt) cc_final: 0.8250 (pp) REVERT: I 161 GLU cc_start: 0.9167 (pm20) cc_final: 0.8592 (pp20) REVERT: L 36 TYR cc_start: 0.9280 (m-80) cc_final: 0.9008 (m-80) REVERT: L 45 LYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8919 (ttpt) REVERT: L 49 TYR cc_start: 0.9309 (p90) cc_final: 0.8921 (p90) REVERT: L 50 GLU cc_start: 0.9370 (mt-10) cc_final: 0.8996 (mp0) REVERT: L 67 SER cc_start: 0.9168 (m) cc_final: 0.8933 (p) REVERT: L 93 ASP cc_start: 0.9345 (t0) cc_final: 0.8971 (t70) REVERT: L 103 LYS cc_start: 0.9287 (mttt) cc_final: 0.8771 (mtpp) REVERT: L 105 GLU cc_start: 0.8157 (tp30) cc_final: 0.7753 (tp30) REVERT: L 106 ILE cc_start: 0.8719 (mt) cc_final: 0.8239 (pp) REVERT: L 161 GLU cc_start: 0.9170 (pm20) cc_final: 0.8600 (pp20) REVERT: L 195 GLU cc_start: 0.5741 (OUTLIER) cc_final: 0.5435 (tm-30) outliers start: 100 outliers final: 38 residues processed: 473 average time/residue: 1.0263 time to fit residues: 569.5219 Evaluate side-chains 450 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 389 time to evaluate : 2.396 ------------------------------------------------------------------------------- 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 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 165 SER 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 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 165 SER 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 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 I residue 45 LYS Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 183 LYS Chi-restraints excluded: chain I residue 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 37 optimal weight: 1.9990 chunk 158 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 210 optimal weight: 1.9990 chunk 257 optimal weight: 7.9990 chunk 246 optimal weight: 0.7980 chunk 202 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 227 optimal weight: 0.0470 overall best weight: 1.3684 ------------------------------------------------------------------------------- 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 77 GLN H 208 ASN F 76 ASN F 77 GLN F 208 ASN J 76 ASN J 77 GLN J 208 ASN K 76 ASN K 77 GLN K 203 ASN K 208 ASN E 124 GLN I 124 GLN L 124 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.089410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.060133 restraints weight = 51138.151| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 3.99 r_work: 0.2735 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21048 Z= 0.188 Angle : 0.677 8.273 28752 Z= 0.348 Chirality : 0.046 0.149 3224 Planarity : 0.005 0.061 3668 Dihedral : 5.068 21.049 2860 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.71 % Allowed : 21.38 % Favored : 74.91 % 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: -0.16 (0.16), residues: 2636 helix: -1.35 (0.39), residues: 144 sheet: 0.61 (0.17), residues: 852 loop : -0.34 (0.16), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 158 HIS 0.003 0.001 HIS C 173 PHE 0.044 0.002 PHE L 209 TYR 0.018 0.002 TYR H 99 ARG 0.009 0.001 ARG L 142 Details of bonding type rmsd hydrogen bonds : bond 0.03003 ( 724) hydrogen bonds : angle 5.28531 ( 1980) SS BOND : bond 0.00459 ( 32) SS BOND : angle 1.09876 ( 64) covalent geometry : bond 0.00421 (21016) covalent geometry : angle 0.67597 (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 503 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 418 time to evaluate : 2.658 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: 0.9375 (OUTLIER) cc_final: 0.9068 (pm20) REVERT: A 80 ASP cc_start: 0.8254 (m-30) cc_final: 0.7750 (m-30) REVERT: A 109 GLU cc_start: 0.8958 (tp30) cc_final: 0.8129 (tt0) REVERT: A 128 GLU cc_start: 0.9556 (tp30) cc_final: 0.9293 (tp30) REVERT: A 164 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7701 (tm-30) REVERT: A 180 MET cc_start: 0.9491 (mtm) cc_final: 0.9199 (mtm) REVERT: A 194 ASP cc_start: 0.8638 (m-30) cc_final: 0.7940 (m-30) REVERT: B 20 GLN cc_start: 0.9106 (OUTLIER) cc_final: 0.8693 (pm20) REVERT: B 109 GLU cc_start: 0.8984 (tp30) cc_final: 0.8742 (tp30) REVERT: B 128 GLU cc_start: 0.9554 (tp30) cc_final: 0.9296 (tp30) REVERT: B 164 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7612 (tm-30) REVERT: B 180 MET cc_start: 0.9470 (mtm) cc_final: 0.9197 (mtm) REVERT: B 194 ASP cc_start: 0.8604 (m-30) cc_final: 0.7878 (m-30) REVERT: C 20 GLN cc_start: 0.9328 (OUTLIER) cc_final: 0.8920 (pm20) REVERT: C 109 GLU cc_start: 0.9005 (tp30) cc_final: 0.8699 (tt0) REVERT: C 128 GLU cc_start: 0.9558 (tp30) cc_final: 0.9285 (tp30) REVERT: C 164 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7690 (tm-30) REVERT: C 180 MET cc_start: 0.9494 (mtm) cc_final: 0.9219 (mtm) REVERT: C 194 ASP cc_start: 0.8617 (m-30) cc_final: 0.7909 (m-30) REVERT: D 20 GLN cc_start: 0.9300 (OUTLIER) cc_final: 0.8894 (pm20) REVERT: D 128 GLU cc_start: 0.9542 (tp30) cc_final: 0.9292 (tp30) REVERT: D 164 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7653 (tm-30) REVERT: D 180 MET cc_start: 0.9487 (mtm) cc_final: 0.9194 (mtm) REVERT: D 194 ASP cc_start: 0.8552 (m-30) cc_final: 0.7764 (m-30) REVERT: G 24 GLN cc_start: 0.8699 (mt0) cc_final: 0.8460 (mp10) REVERT: G 36 TYR cc_start: 0.9181 (m-80) cc_final: 0.8962 (m-80) REVERT: G 45 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8911 (ttpt) REVERT: G 49 TYR cc_start: 0.9261 (p90) cc_final: 0.8846 (p90) REVERT: G 50 GLU cc_start: 0.9358 (mt-10) cc_final: 0.8944 (mp0) REVERT: G 67 SER cc_start: 0.9161 (m) cc_final: 0.8927 (p) REVERT: G 93 ASP cc_start: 0.9298 (t0) cc_final: 0.8989 (t70) REVERT: G 103 LYS cc_start: 0.9258 (mttt) cc_final: 0.8704 (mtpp) REVERT: G 161 GLU cc_start: 0.9162 (pm20) cc_final: 0.8639 (pp20) REVERT: H 3 GLN cc_start: 0.9097 (pm20) cc_final: 0.8695 (pm20) REVERT: H 6 GLU cc_start: 0.8175 (mp0) cc_final: 0.7345 (mp0) REVERT: H 26 ARG cc_start: 0.8645 (tmm-80) cc_final: 0.7930 (tmm-80) REVERT: H 27 PHE cc_start: 0.8533 (OUTLIER) cc_final: 0.8210 (m-80) REVERT: H 46 GLU cc_start: 0.8814 (tt0) cc_final: 0.8385 (pt0) REVERT: H 72 ASP cc_start: 0.8936 (t0) cc_final: 0.8491 (t0) REVERT: H 95 ASP cc_start: 0.9541 (t0) cc_final: 0.9065 (t0) REVERT: H 105 GLN cc_start: 0.9443 (mt0) cc_final: 0.9089 (pm20) REVERT: H 110 THR cc_start: 0.9505 (m) cc_final: 0.9281 (p) REVERT: H 163 LEU cc_start: 0.9616 (mp) cc_final: 0.9377 (tm) REVERT: H 199 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8584 (tp) REVERT: F 3 GLN cc_start: 0.9062 (pm20) cc_final: 0.8692 (pm20) REVERT: F 6 GLU cc_start: 0.8166 (mp0) cc_final: 0.7329 (mp0) REVERT: F 16 GLU cc_start: 0.7811 (pm20) cc_final: 0.7513 (pm20) REVERT: F 26 ARG cc_start: 0.8498 (tmm-80) cc_final: 0.8072 (tmm-80) REVERT: F 27 PHE cc_start: 0.8639 (OUTLIER) cc_final: 0.8309 (m-80) REVERT: F 46 GLU cc_start: 0.8855 (tt0) cc_final: 0.8362 (tt0) REVERT: F 72 ASP cc_start: 0.8911 (t0) cc_final: 0.8471 (t0) REVERT: F 95 ASP cc_start: 0.9525 (t0) cc_final: 0.9083 (t0) REVERT: F 105 GLN cc_start: 0.9448 (mt0) cc_final: 0.9092 (pm20) REVERT: F 108 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9190 (tm) REVERT: F 110 THR cc_start: 0.9491 (m) cc_final: 0.9257 (p) REVERT: F 203 ASN cc_start: 0.8792 (m-40) cc_final: 0.8538 (t0) REVERT: J 3 GLN cc_start: 0.9077 (pm20) cc_final: 0.8706 (pm20) REVERT: J 6 GLU cc_start: 0.8216 (mp0) cc_final: 0.7348 (mp0) REVERT: J 16 GLU cc_start: 0.7816 (pm20) cc_final: 0.7287 (pm20) REVERT: J 26 ARG cc_start: 0.8513 (tmm-80) cc_final: 0.8123 (tmm-80) REVERT: J 27 PHE cc_start: 0.8653 (OUTLIER) cc_final: 0.8337 (m-80) REVERT: J 46 GLU cc_start: 0.8840 (tt0) cc_final: 0.8344 (pt0) REVERT: J 72 ASP cc_start: 0.8915 (t0) cc_final: 0.8472 (t0) REVERT: J 95 ASP cc_start: 0.9486 (t0) cc_final: 0.9065 (t0) REVERT: J 105 GLN cc_start: 0.9437 (mt0) cc_final: 0.9075 (pm20) REVERT: J 108 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9212 (tm) REVERT: J 110 THR cc_start: 0.9527 (m) cc_final: 0.9276 (p) REVERT: J 163 LEU cc_start: 0.9617 (mp) cc_final: 0.9376 (tm) REVERT: J 199 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8608 (tp) REVERT: J 213 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7585 (ttpp) REVERT: K 3 GLN cc_start: 0.9049 (pm20) cc_final: 0.8678 (pm20) REVERT: K 6 GLU cc_start: 0.8188 (mp0) cc_final: 0.7290 (mp0) REVERT: K 26 ARG cc_start: 0.8517 (tmm-80) cc_final: 0.8129 (tmm-80) REVERT: K 27 PHE cc_start: 0.8653 (OUTLIER) cc_final: 0.8329 (m-80) REVERT: K 46 GLU cc_start: 0.8840 (tt0) cc_final: 0.8369 (pt0) REVERT: K 72 ASP cc_start: 0.8905 (t0) cc_final: 0.8462 (t0) REVERT: K 95 ASP cc_start: 0.9544 (t0) cc_final: 0.9097 (t0) REVERT: K 105 GLN cc_start: 0.9443 (mt0) cc_final: 0.9088 (pm20) REVERT: K 108 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9196 (tm) REVERT: K 110 THR cc_start: 0.9516 (m) cc_final: 0.9274 (p) REVERT: K 203 ASN cc_start: 0.8787 (m110) cc_final: 0.8528 (t0) REVERT: K 213 LYS cc_start: 0.7683 (OUTLIER) cc_final: 0.7428 (tmmm) REVERT: E 36 TYR cc_start: 0.9172 (m-80) cc_final: 0.8958 (m-80) REVERT: E 45 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8927 (ttpt) REVERT: E 49 TYR cc_start: 0.9274 (p90) cc_final: 0.8846 (p90) REVERT: E 50 GLU cc_start: 0.9353 (mt-10) cc_final: 0.8938 (mp0) REVERT: E 67 SER cc_start: 0.9164 (m) cc_final: 0.8930 (p) REVERT: E 81 GLU cc_start: 0.9315 (mp0) cc_final: 0.9110 (pm20) REVERT: E 93 ASP cc_start: 0.9360 (t0) cc_final: 0.9023 (t70) REVERT: E 103 LYS cc_start: 0.9261 (mttt) cc_final: 0.8716 (mtpp) REVERT: E 161 GLU cc_start: 0.9159 (pm20) cc_final: 0.8639 (pp20) REVERT: I 45 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8902 (ttpt) REVERT: I 49 TYR cc_start: 0.9267 (p90) cc_final: 0.8840 (p90) REVERT: I 50 GLU cc_start: 0.9345 (mt-10) cc_final: 0.8922 (mp0) REVERT: I 67 SER cc_start: 0.9163 (m) cc_final: 0.8931 (p) REVERT: I 81 GLU cc_start: 0.9318 (mp0) cc_final: 0.9114 (pm20) REVERT: I 93 ASP cc_start: 0.9313 (t0) cc_final: 0.9006 (t70) REVERT: I 103 LYS cc_start: 0.9267 (mttt) cc_final: 0.8728 (mtpp) REVERT: I 161 GLU cc_start: 0.9152 (pm20) cc_final: 0.8635 (pp20) REVERT: L 36 TYR cc_start: 0.9198 (m-80) cc_final: 0.8978 (m-80) REVERT: L 45 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8922 (ttpt) REVERT: L 49 TYR cc_start: 0.9273 (p90) cc_final: 0.8855 (p90) REVERT: L 50 GLU cc_start: 0.9359 (mt-10) cc_final: 0.8939 (mp0) REVERT: L 67 SER cc_start: 0.9165 (m) cc_final: 0.8939 (p) REVERT: L 81 GLU cc_start: 0.9317 (mp0) cc_final: 0.9115 (pm20) REVERT: L 93 ASP cc_start: 0.9345 (t0) cc_final: 0.8967 (t70) REVERT: L 103 LYS cc_start: 0.9267 (mttt) cc_final: 0.8722 (mtpp) REVERT: L 161 GLU cc_start: 0.9159 (pm20) cc_final: 0.8645 (pp20) outliers start: 85 outliers final: 37 residues processed: 475 average time/residue: 0.9822 time to fit residues: 546.1968 Evaluate side-chains 463 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 403 time to evaluate : 2.221 ------------------------------------------------------------------------------- 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 145 ASP Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain C residue 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 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 2 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain 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 108 LEU Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 11 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 J residue 213 LYS Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 27 PHE Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 213 LYS Chi-restraints excluded: chain E residue 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 183 LYS 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: 5.9990 chunk 186 optimal weight: 0.7980 chunk 233 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 174 optimal weight: 9.9990 chunk 75 optimal weight: 0.2980 chunk 105 optimal weight: 3.9990 chunk 258 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 222 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN D 146 ASN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 GLN F 76 ASN F 77 GLN F 203 ASN J 76 ASN J 77 GLN K 76 ASN K 77 GLN I 30 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.089638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.060340 restraints weight = 51359.133| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 4.04 r_work: 0.2746 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21048 Z= 0.170 Angle : 0.684 10.719 28752 Z= 0.351 Chirality : 0.045 0.210 3224 Planarity : 0.005 0.062 3668 Dihedral : 4.987 20.476 2860 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.97 % Allowed : 21.68 % Favored : 74.35 % 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: -0.11 (0.16), residues: 2636 helix: -1.03 (0.39), residues: 144 sheet: 0.78 (0.18), residues: 796 loop : -0.38 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 158 HIS 0.003 0.001 HIS C 173 PHE 0.046 0.002 PHE G 209 TYR 0.017 0.002 TYR I 173 ARG 0.010 0.001 ARG I 142 Details of bonding type rmsd hydrogen bonds : bond 0.02966 ( 724) hydrogen bonds : angle 5.19407 ( 1980) SS BOND : bond 0.00474 ( 32) SS BOND : angle 1.12739 ( 64) covalent geometry : bond 0.00389 (21016) covalent geometry : angle 0.68301 (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 519 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 428 time to evaluate : 2.051 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: 0.9408 (OUTLIER) cc_final: 0.9005 (pm20) REVERT: A 109 GLU cc_start: 0.8945 (tp30) cc_final: 0.8140 (tt0) REVERT: A 128 GLU cc_start: 0.9558 (tp30) cc_final: 0.9314 (tp30) REVERT: A 164 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7701 (tm-30) REVERT: A 180 MET cc_start: 0.9484 (mtm) cc_final: 0.9195 (mtm) REVERT: A 194 ASP cc_start: 0.8589 (m-30) cc_final: 0.7868 (m-30) REVERT: B 109 GLU cc_start: 0.8992 (tp30) cc_final: 0.8513 (mm-30) REVERT: B 128 GLU cc_start: 0.9551 (tp30) cc_final: 0.9298 (tp30) REVERT: B 164 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7604 (tm-30) REVERT: B 180 MET cc_start: 0.9468 (mtm) cc_final: 0.9213 (mtm) REVERT: B 194 ASP cc_start: 0.8609 (m-30) cc_final: 0.7891 (m-30) REVERT: C 20 GLN cc_start: 0.9351 (OUTLIER) cc_final: 0.8946 (pm20) REVERT: C 109 GLU cc_start: 0.9011 (tp30) cc_final: 0.8726 (tt0) REVERT: C 128 GLU cc_start: 0.9559 (tp30) cc_final: 0.9308 (tp30) REVERT: C 164 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7689 (tm-30) REVERT: C 180 MET cc_start: 0.9490 (mtm) cc_final: 0.9213 (mtm) REVERT: C 194 ASP cc_start: 0.8578 (m-30) cc_final: 0.7851 (m-30) REVERT: D 20 GLN cc_start: 0.9339 (OUTLIER) cc_final: 0.8954 (pm20) REVERT: D 109 GLU cc_start: 0.8723 (tt0) cc_final: 0.7821 (tt0) REVERT: D 128 GLU cc_start: 0.9543 (tp30) cc_final: 0.9297 (tp30) REVERT: D 164 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7657 (tm-30) REVERT: D 180 MET cc_start: 0.9475 (mtm) cc_final: 0.9184 (mtm) REVERT: D 194 ASP cc_start: 0.8559 (m-30) cc_final: 0.7955 (m-30) REVERT: D 217 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8694 (mt-10) REVERT: G 24 GLN cc_start: 0.8709 (mt0) cc_final: 0.8477 (mp10) REVERT: G 45 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8898 (ttpt) REVERT: G 49 TYR cc_start: 0.9264 (p90) cc_final: 0.8874 (p90) REVERT: G 50 GLU cc_start: 0.9315 (mt-10) cc_final: 0.8948 (mp0) REVERT: G 67 SER cc_start: 0.9156 (m) cc_final: 0.8920 (p) REVERT: G 93 ASP cc_start: 0.9308 (t0) cc_final: 0.8988 (t70) REVERT: G 103 LYS cc_start: 0.9255 (mttt) cc_final: 0.8709 (mtpp) REVERT: G 118 PHE cc_start: 0.8044 (m-80) cc_final: 0.7770 (m-80) REVERT: G 161 GLU cc_start: 0.9147 (pm20) cc_final: 0.8649 (pp20) REVERT: G 185 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7576 (p0) REVERT: H 3 GLN cc_start: 0.9078 (pm20) cc_final: 0.8693 (pm20) REVERT: H 6 GLU cc_start: 0.8211 (mp0) cc_final: 0.7340 (mp0) REVERT: H 46 GLU cc_start: 0.8815 (tt0) cc_final: 0.8389 (pt0) REVERT: H 72 ASP cc_start: 0.8932 (t0) cc_final: 0.8491 (t0) REVERT: H 95 ASP cc_start: 0.9515 (t0) cc_final: 0.8934 (t0) REVERT: H 105 GLN cc_start: 0.9446 (mt0) cc_final: 0.9110 (pm20) REVERT: H 110 THR cc_start: 0.9492 (m) cc_final: 0.9243 (p) REVERT: H 163 LEU cc_start: 0.9627 (mp) cc_final: 0.9390 (tm) REVERT: H 199 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8590 (tp) REVERT: H 213 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7638 (ttpp) REVERT: F 3 GLN cc_start: 0.9047 (pm20) cc_final: 0.8679 (pm20) REVERT: F 6 GLU cc_start: 0.8220 (mp0) cc_final: 0.7341 (mp0) REVERT: F 16 GLU cc_start: 0.7876 (pm20) cc_final: 0.7630 (pm20) REVERT: F 26 ARG cc_start: 0.8498 (tmm-80) cc_final: 0.7979 (tmm-80) REVERT: F 27 PHE cc_start: 0.8659 (OUTLIER) cc_final: 0.8289 (m-80) REVERT: F 46 GLU cc_start: 0.8845 (tt0) cc_final: 0.8356 (tt0) REVERT: F 72 ASP cc_start: 0.8937 (t0) cc_final: 0.8503 (t0) REVERT: F 76 ASN cc_start: 0.8774 (t0) cc_final: 0.8466 (t0) REVERT: F 95 ASP cc_start: 0.9518 (t0) cc_final: 0.8976 (t0) REVERT: F 105 GLN cc_start: 0.9450 (mt0) cc_final: 0.9098 (pm20) REVERT: F 110 THR cc_start: 0.9485 (m) cc_final: 0.9244 (p) REVERT: F 203 ASN cc_start: 0.8789 (m110) cc_final: 0.8529 (t0) REVERT: F 213 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.7379 (ttpp) REVERT: J 3 GLN cc_start: 0.9045 (pm20) cc_final: 0.8679 (pm20) REVERT: J 6 GLU cc_start: 0.8227 (mp0) cc_final: 0.7359 (mp0) REVERT: J 26 ARG cc_start: 0.8507 (tmm-80) cc_final: 0.8111 (tmm-80) REVERT: J 27 PHE cc_start: 0.8658 (OUTLIER) cc_final: 0.8317 (m-80) REVERT: J 46 GLU cc_start: 0.8811 (tt0) cc_final: 0.8330 (tt0) REVERT: J 72 ASP cc_start: 0.8907 (t0) cc_final: 0.8474 (t0) REVERT: J 76 ASN cc_start: 0.8769 (t0) cc_final: 0.8466 (t0) REVERT: J 95 ASP cc_start: 0.9524 (t0) cc_final: 0.9050 (t0) REVERT: J 99 TYR cc_start: 0.8973 (m-10) cc_final: 0.8528 (m-10) REVERT: J 105 GLN cc_start: 0.9445 (mt0) cc_final: 0.9090 (pm20) REVERT: J 108 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.9226 (tm) REVERT: J 110 THR cc_start: 0.9508 (m) cc_final: 0.9225 (p) REVERT: J 163 LEU cc_start: 0.9629 (mp) cc_final: 0.9401 (tm) REVERT: J 199 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8581 (tp) REVERT: K 3 GLN cc_start: 0.9036 (pm20) cc_final: 0.8673 (pm20) REVERT: K 6 GLU cc_start: 0.8164 (mp0) cc_final: 0.7300 (mp0) REVERT: K 26 ARG cc_start: 0.8512 (tmm-80) cc_final: 0.8113 (tmm-80) REVERT: K 27 PHE cc_start: 0.8650 (OUTLIER) cc_final: 0.8309 (m-80) REVERT: K 46 GLU cc_start: 0.8825 (tt0) cc_final: 0.8333 (tt0) REVERT: K 72 ASP cc_start: 0.8927 (t0) cc_final: 0.8492 (t0) REVERT: K 76 ASN cc_start: 0.8764 (t0) cc_final: 0.8462 (t0) REVERT: K 95 ASP cc_start: 0.9517 (t0) cc_final: 0.9026 (t0) REVERT: K 99 TYR cc_start: 0.9139 (m-10) cc_final: 0.8684 (m-10) REVERT: K 105 GLN cc_start: 0.9446 (mt0) cc_final: 0.9093 (pm20) REVERT: K 108 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9206 (tm) REVERT: K 110 THR cc_start: 0.9504 (m) cc_final: 0.9221 (p) REVERT: K 203 ASN cc_start: 0.8773 (m110) cc_final: 0.8528 (t0) REVERT: E 24 GLN cc_start: 0.8702 (mt0) cc_final: 0.8460 (mp10) REVERT: E 45 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8918 (ttpt) REVERT: E 49 TYR cc_start: 0.9270 (p90) cc_final: 0.8866 (p90) REVERT: E 50 GLU cc_start: 0.9317 (mt-10) cc_final: 0.8946 (mp0) REVERT: E 67 SER cc_start: 0.9156 (m) cc_final: 0.8926 (p) REVERT: E 81 GLU cc_start: 0.9311 (mp0) cc_final: 0.9095 (pm20) REVERT: E 93 ASP cc_start: 0.9325 (t0) cc_final: 0.8997 (t70) REVERT: E 103 LYS cc_start: 0.9261 (mttt) cc_final: 0.8714 (mtpp) REVERT: E 118 PHE cc_start: 0.8030 (m-80) cc_final: 0.7755 (m-80) REVERT: E 161 GLU cc_start: 0.9145 (pm20) cc_final: 0.8645 (pp20) REVERT: E 185 ASP cc_start: 0.7940 (OUTLIER) cc_final: 0.7613 (p0) REVERT: I 24 GLN cc_start: 0.8693 (mt0) cc_final: 0.8458 (mp10) REVERT: I 49 TYR cc_start: 0.9277 (p90) cc_final: 0.8853 (p90) REVERT: I 50 GLU cc_start: 0.9318 (mt-10) cc_final: 0.8924 (mp0) REVERT: I 67 SER cc_start: 0.9166 (m) cc_final: 0.8932 (p) REVERT: I 81 GLU cc_start: 0.9317 (mp0) cc_final: 0.9100 (pm20) REVERT: I 93 ASP cc_start: 0.9316 (t0) cc_final: 0.9002 (t70) REVERT: I 103 LYS cc_start: 0.9267 (mttt) cc_final: 0.8730 (mtpp) REVERT: I 118 PHE cc_start: 0.8032 (m-80) cc_final: 0.7756 (m-80) REVERT: I 161 GLU cc_start: 0.9147 (pm20) cc_final: 0.8651 (pp20) REVERT: L 45 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8913 (ttpt) REVERT: L 49 TYR cc_start: 0.9268 (p90) cc_final: 0.8878 (p90) REVERT: L 50 GLU cc_start: 0.9338 (mt-10) cc_final: 0.8945 (mp0) REVERT: L 67 SER cc_start: 0.9171 (m) cc_final: 0.8938 (p) REVERT: L 81 GLU cc_start: 0.9311 (mp0) cc_final: 0.9096 (pm20) REVERT: L 93 ASP cc_start: 0.9326 (t0) cc_final: 0.8967 (t70) REVERT: L 103 LYS cc_start: 0.9264 (mttt) cc_final: 0.8735 (mtpp) REVERT: L 118 PHE cc_start: 0.8030 (m-80) cc_final: 0.7756 (m-80) REVERT: L 161 GLU cc_start: 0.9142 (pm20) cc_final: 0.8648 (pp20) outliers start: 91 outliers final: 34 residues processed: 481 average time/residue: 0.9770 time to fit residues: 549.5007 Evaluate side-chains 464 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 409 time to evaluate : 2.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain B residue 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 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 185 ASP Chi-restraints excluded: chain G residue 194 CYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain H residue 213 LYS Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 100 LEU 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 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 108 LEU 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 183 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 177 optimal weight: 10.0000 chunk 258 optimal weight: 6.9990 chunk 178 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 135 optimal weight: 0.0670 chunk 204 optimal weight: 0.8980 chunk 162 optimal weight: 0.0060 chunk 39 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 overall best weight: 0.7936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN C 146 ASN H 76 ASN H 77 GLN H 208 ASN F 77 GLN F 208 ASN J 77 GLN J 208 ASN K 77 GLN K 208 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.090524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.061209 restraints weight = 51387.624| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 4.07 r_work: 0.2760 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21048 Z= 0.145 Angle : 0.690 10.666 28752 Z= 0.348 Chirality : 0.045 0.149 3224 Planarity : 0.005 0.062 3668 Dihedral : 4.914 19.758 2860 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.10 % Allowed : 22.82 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.82 (0.40), residues: 144 sheet: 0.82 (0.18), residues: 824 loop : -0.38 (0.16), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP H 158 HIS 0.003 0.001 HIS D 173 PHE 0.045 0.002 PHE G 209 TYR 0.016 0.001 TYR I 173 ARG 0.009 0.001 ARG L 142 Details of bonding type rmsd hydrogen bonds : bond 0.02897 ( 724) hydrogen bonds : angle 5.09154 ( 1980) SS BOND : bond 0.00403 ( 32) SS BOND : angle 1.03857 ( 64) covalent geometry : bond 0.00336 (21016) covalent geometry : angle 0.68884 (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 511 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 440 time to evaluate : 2.269 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: 0.9412 (OUTLIER) cc_final: 0.9107 (pm20) REVERT: A 109 GLU cc_start: 0.8920 (tp30) cc_final: 0.8204 (tt0) REVERT: A 128 GLU cc_start: 0.9555 (tp30) cc_final: 0.9283 (tp30) REVERT: A 164 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7653 (tm-30) REVERT: A 180 MET cc_start: 0.9473 (mtm) cc_final: 0.9194 (mtm) REVERT: A 194 ASP cc_start: 0.8584 (m-30) cc_final: 0.7798 (m-30) REVERT: B 20 GLN cc_start: 0.9121 (OUTLIER) cc_final: 0.8693 (pm20) REVERT: B 109 GLU cc_start: 0.8972 (tp30) cc_final: 0.8271 (tt0) REVERT: B 128 GLU cc_start: 0.9548 (tp30) cc_final: 0.9263 (tp30) REVERT: B 164 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7617 (tm-30) REVERT: B 180 MET cc_start: 0.9454 (mtm) cc_final: 0.9216 (mtm) REVERT: B 194 ASP cc_start: 0.8593 (m-30) cc_final: 0.7942 (m-30) REVERT: C 20 GLN cc_start: 0.9360 (OUTLIER) cc_final: 0.8984 (pm20) REVERT: C 109 GLU cc_start: 0.9015 (tp30) cc_final: 0.8731 (tt0) REVERT: C 128 GLU cc_start: 0.9555 (tp30) cc_final: 0.9276 (tp30) REVERT: C 164 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7644 (tm-30) REVERT: C 180 MET cc_start: 0.9481 (mtm) cc_final: 0.9208 (mtm) REVERT: C 194 ASP cc_start: 0.8563 (m-30) cc_final: 0.7832 (m-30) REVERT: D 20 GLN cc_start: 0.9351 (OUTLIER) cc_final: 0.8974 (pm20) REVERT: D 109 GLU cc_start: 0.8738 (tt0) cc_final: 0.8017 (tt0) REVERT: D 128 GLU cc_start: 0.9541 (tp30) cc_final: 0.9268 (tp30) REVERT: D 164 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7613 (tm-30) REVERT: D 180 MET cc_start: 0.9468 (mtm) cc_final: 0.9191 (mtm) REVERT: D 194 ASP cc_start: 0.8567 (m-30) cc_final: 0.7958 (m-30) REVERT: D 217 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8620 (mt-10) REVERT: G 24 GLN cc_start: 0.8697 (mt0) cc_final: 0.8458 (mp10) REVERT: G 45 LYS cc_start: 0.9135 (OUTLIER) cc_final: 0.8860 (ttpt) REVERT: G 49 TYR cc_start: 0.9256 (p90) cc_final: 0.8883 (p90) REVERT: G 50 GLU cc_start: 0.9275 (mt-10) cc_final: 0.8897 (mp0) REVERT: G 67 SER cc_start: 0.9161 (m) cc_final: 0.8933 (p) REVERT: G 93 ASP cc_start: 0.9297 (t0) cc_final: 0.8990 (t70) REVERT: G 103 LYS cc_start: 0.9243 (mttt) cc_final: 0.8705 (mtpp) REVERT: G 118 PHE cc_start: 0.8247 (m-80) cc_final: 0.8019 (m-80) REVERT: G 161 GLU cc_start: 0.9127 (pm20) cc_final: 0.8653 (pp20) REVERT: G 167 ASP cc_start: 0.8783 (t70) cc_final: 0.8371 (t70) REVERT: G 185 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7522 (p0) REVERT: H 3 GLN cc_start: 0.9050 (pm20) cc_final: 0.8690 (pm20) REVERT: H 6 GLU cc_start: 0.8166 (mp0) cc_final: 0.7278 (mp0) REVERT: H 46 GLU cc_start: 0.8833 (tt0) cc_final: 0.8406 (pt0) REVERT: H 72 ASP cc_start: 0.8928 (t0) cc_final: 0.8490 (t0) REVERT: H 76 ASN cc_start: 0.8827 (t0) cc_final: 0.8505 (t0) REVERT: H 95 ASP cc_start: 0.9466 (t0) cc_final: 0.8911 (t0) REVERT: H 105 GLN cc_start: 0.9451 (mt0) cc_final: 0.9103 (pm20) REVERT: H 163 LEU cc_start: 0.9634 (mp) cc_final: 0.9410 (tm) REVERT: F 3 GLN cc_start: 0.9012 (pm20) cc_final: 0.8647 (pm20) REVERT: F 6 GLU cc_start: 0.8121 (mp0) cc_final: 0.7265 (mp0) REVERT: F 16 GLU cc_start: 0.7978 (pm20) cc_final: 0.7718 (pm20) REVERT: F 27 PHE cc_start: 0.8660 (OUTLIER) cc_final: 0.8363 (t80) REVERT: F 46 GLU cc_start: 0.8865 (tt0) cc_final: 0.8392 (tt0) REVERT: F 72 ASP cc_start: 0.8935 (t0) cc_final: 0.8499 (t0) REVERT: F 76 ASN cc_start: 0.8799 (t0) cc_final: 0.8416 (t0) REVERT: F 95 ASP cc_start: 0.9482 (t0) cc_final: 0.8923 (t0) REVERT: F 105 GLN cc_start: 0.9448 (mt0) cc_final: 0.9124 (pm20) REVERT: F 110 THR cc_start: 0.9499 (m) cc_final: 0.9247 (p) REVERT: F 186 VAL cc_start: 0.9435 (t) cc_final: 0.9190 (m) REVERT: F 203 ASN cc_start: 0.8802 (m110) cc_final: 0.8569 (t0) REVERT: J 3 GLN cc_start: 0.9003 (pm20) cc_final: 0.8636 (pm20) REVERT: J 6 GLU cc_start: 0.8171 (mp0) cc_final: 0.7248 (mp0) REVERT: J 27 PHE cc_start: 0.8610 (OUTLIER) cc_final: 0.8353 (t80) REVERT: J 46 GLU cc_start: 0.8833 (tt0) cc_final: 0.8360 (tt0) REVERT: J 72 ASP cc_start: 0.8938 (t0) cc_final: 0.8498 (t0) REVERT: J 76 ASN cc_start: 0.8792 (t0) cc_final: 0.8422 (t0) REVERT: J 95 ASP cc_start: 0.9475 (t0) cc_final: 0.8901 (t0) REVERT: J 105 GLN cc_start: 0.9449 (mt0) cc_final: 0.9087 (pm20) REVERT: J 108 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9166 (tm) REVERT: J 163 LEU cc_start: 0.9638 (mp) cc_final: 0.9407 (tm) REVERT: K 3 GLN cc_start: 0.9003 (pm20) cc_final: 0.8642 (pm20) REVERT: K 6 GLU cc_start: 0.8114 (mp0) cc_final: 0.7185 (mp0) REVERT: K 27 PHE cc_start: 0.8605 (OUTLIER) cc_final: 0.8350 (t80) REVERT: K 46 GLU cc_start: 0.8831 (tt0) cc_final: 0.8361 (tt0) REVERT: K 72 ASP cc_start: 0.8927 (t0) cc_final: 0.8489 (t0) REVERT: K 76 ASN cc_start: 0.8793 (t0) cc_final: 0.8427 (t0) REVERT: K 95 ASP cc_start: 0.9484 (t0) cc_final: 0.8933 (t0) REVERT: K 105 GLN cc_start: 0.9457 (mt0) cc_final: 0.9090 (pm20) REVERT: K 108 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9155 (tm) REVERT: K 186 VAL cc_start: 0.9445 (t) cc_final: 0.9205 (m) REVERT: K 203 ASN cc_start: 0.8758 (m110) cc_final: 0.8502 (t0) REVERT: K 213 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7456 (ttpp) REVERT: E 24 GLN cc_start: 0.8698 (mt0) cc_final: 0.8462 (mp10) REVERT: E 45 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8876 (ttpt) REVERT: E 49 TYR cc_start: 0.9261 (p90) cc_final: 0.8953 (p90) REVERT: E 50 GLU cc_start: 0.9305 (mt-10) cc_final: 0.8983 (mp0) REVERT: E 67 SER cc_start: 0.9153 (m) cc_final: 0.8923 (p) REVERT: E 81 GLU cc_start: 0.9301 (mp0) cc_final: 0.9039 (pm20) REVERT: E 93 ASP cc_start: 0.9289 (t0) cc_final: 0.8968 (t70) REVERT: E 103 LYS cc_start: 0.9272 (mttt) cc_final: 0.8723 (mtpp) REVERT: E 118 PHE cc_start: 0.8118 (m-80) cc_final: 0.7840 (m-80) REVERT: E 161 GLU cc_start: 0.9127 (pm20) cc_final: 0.8650 (pp20) REVERT: E 167 ASP cc_start: 0.8768 (t70) cc_final: 0.8356 (t70) REVERT: E 185 ASP cc_start: 0.7941 (OUTLIER) cc_final: 0.7598 (p0) REVERT: I 24 GLN cc_start: 0.8695 (mt0) cc_final: 0.8456 (mp10) REVERT: I 45 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8894 (ttpt) REVERT: I 49 TYR cc_start: 0.9253 (p90) cc_final: 0.8917 (p90) REVERT: I 50 GLU cc_start: 0.9260 (mt-10) cc_final: 0.8874 (mp0) REVERT: I 67 SER cc_start: 0.9149 (m) cc_final: 0.8918 (p) REVERT: I 81 GLU cc_start: 0.9308 (mp0) cc_final: 0.9070 (pm20) REVERT: I 93 ASP cc_start: 0.9313 (t0) cc_final: 0.9007 (t70) REVERT: I 103 LYS cc_start: 0.9276 (mttt) cc_final: 0.8737 (mtpp) REVERT: I 118 PHE cc_start: 0.8237 (m-80) cc_final: 0.7965 (m-80) REVERT: I 161 GLU cc_start: 0.9118 (pm20) cc_final: 0.8651 (pp20) REVERT: I 167 ASP cc_start: 0.8762 (t70) cc_final: 0.8362 (t70) REVERT: L 45 LYS cc_start: 0.9133 (OUTLIER) cc_final: 0.8858 (ttpt) REVERT: L 49 TYR cc_start: 0.9248 (p90) cc_final: 0.8889 (p90) REVERT: L 50 GLU cc_start: 0.9275 (mt-10) cc_final: 0.8936 (mp0) REVERT: L 67 SER cc_start: 0.9173 (m) cc_final: 0.8951 (p) REVERT: L 81 GLU cc_start: 0.9304 (mp0) cc_final: 0.9042 (pm20) REVERT: L 93 ASP cc_start: 0.9324 (t0) cc_final: 0.8939 (t70) REVERT: L 103 LYS cc_start: 0.9270 (mttt) cc_final: 0.8736 (mtpp) REVERT: L 118 PHE cc_start: 0.8130 (m-80) cc_final: 0.7848 (m-80) REVERT: L 161 GLU cc_start: 0.9123 (pm20) cc_final: 0.8654 (pp20) REVERT: L 167 ASP cc_start: 0.8778 (t70) cc_final: 0.8377 (t70) REVERT: L 185 ASP cc_start: 0.7936 (m-30) cc_final: 0.7578 (p0) outliers start: 71 outliers final: 35 residues processed: 485 average time/residue: 1.0507 time to fit residues: 596.8335 Evaluate side-chains 472 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 417 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 145 ASP Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain C residue 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 185 ASP Chi-restraints excluded: chain G residue 194 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain 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 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 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 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 183 LYS 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 4 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 107 optimal weight: 0.3980 chunk 143 optimal weight: 0.7980 chunk 200 optimal weight: 3.9990 chunk 73 optimal weight: 0.4980 chunk 167 optimal weight: 8.9990 chunk 238 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.090560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.061118 restraints weight = 51424.383| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 4.06 r_work: 0.2759 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21048 Z= 0.156 Angle : 0.699 10.703 28752 Z= 0.354 Chirality : 0.046 0.231 3224 Planarity : 0.005 0.063 3668 Dihedral : 4.899 19.738 2860 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.97 % Allowed : 23.47 % Favored : 73.56 % 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: -0.70 (0.41), residues: 144 sheet: 0.83 (0.18), residues: 824 loop : -0.36 (0.16), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP H 158 HIS 0.003 0.001 HIS C 173 PHE 0.044 0.002 PHE L 209 TYR 0.014 0.001 TYR G 173 ARG 0.008 0.001 ARG E 142 Details of bonding type rmsd hydrogen bonds : bond 0.02900 ( 724) hydrogen bonds : angle 5.11776 ( 1980) SS BOND : bond 0.00420 ( 32) SS BOND : angle 1.12683 ( 64) covalent geometry : bond 0.00357 (21016) covalent geometry : angle 0.69821 (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: 68 poor density : 432 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLN cc_start: 0.9421 (OUTLIER) cc_final: 0.9128 (pm20) REVERT: A 109 GLU cc_start: 0.8900 (tp30) cc_final: 0.8135 (tt0) REVERT: A 128 GLU cc_start: 0.9552 (tp30) cc_final: 0.9273 (tp30) REVERT: A 164 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7641 (tm-30) REVERT: A 180 MET cc_start: 0.9471 (mtm) cc_final: 0.9175 (mtm) REVERT: A 194 ASP cc_start: 0.8605 (m-30) cc_final: 0.7817 (m-30) REVERT: B 20 GLN cc_start: 0.9106 (OUTLIER) cc_final: 0.8679 (pm20) REVERT: B 128 GLU cc_start: 0.9551 (tp30) cc_final: 0.9262 (tp30) REVERT: B 164 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7613 (tm-30) REVERT: B 180 MET cc_start: 0.9455 (mtm) cc_final: 0.9198 (mtm) REVERT: B 194 ASP cc_start: 0.8626 (m-30) cc_final: 0.7978 (m-30) REVERT: C 20 GLN cc_start: 0.9360 (OUTLIER) cc_final: 0.8996 (pm20) REVERT: C 109 GLU cc_start: 0.9020 (tp30) cc_final: 0.8729 (tt0) REVERT: C 128 GLU cc_start: 0.9557 (tp30) cc_final: 0.9270 (tp30) REVERT: C 164 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7631 (tm-30) REVERT: C 180 MET cc_start: 0.9482 (mtm) cc_final: 0.9195 (mtm) REVERT: C 194 ASP cc_start: 0.8586 (m-30) cc_final: 0.7849 (m-30) REVERT: D 20 GLN cc_start: 0.9367 (OUTLIER) cc_final: 0.9009 (pm20) REVERT: D 109 GLU cc_start: 0.8675 (tt0) cc_final: 0.8155 (tt0) REVERT: D 128 GLU cc_start: 0.9539 (tp30) cc_final: 0.9264 (tp30) REVERT: D 164 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7620 (tm-30) REVERT: D 180 MET cc_start: 0.9464 (mtm) cc_final: 0.9161 (mtm) REVERT: D 194 ASP cc_start: 0.8579 (m-30) cc_final: 0.7904 (m-30) REVERT: D 217 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8603 (mt-10) REVERT: G 24 GLN cc_start: 0.8692 (mt0) cc_final: 0.8450 (mp10) REVERT: G 45 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8856 (ttpt) REVERT: G 49 TYR cc_start: 0.9242 (p90) cc_final: 0.8936 (p90) REVERT: G 50 GLU cc_start: 0.9276 (mt-10) cc_final: 0.8945 (mp0) REVERT: G 67 SER cc_start: 0.9161 (m) cc_final: 0.8932 (p) REVERT: G 93 ASP cc_start: 0.9262 (t0) cc_final: 0.8966 (t70) REVERT: G 103 LYS cc_start: 0.9261 (mttt) cc_final: 0.8723 (mtpp) REVERT: G 118 PHE cc_start: 0.8228 (m-80) cc_final: 0.8001 (m-80) REVERT: G 143 GLU cc_start: 0.8892 (mp0) cc_final: 0.8606 (pm20) REVERT: G 161 GLU cc_start: 0.9105 (pm20) cc_final: 0.8638 (pp20) REVERT: G 167 ASP cc_start: 0.8797 (t70) cc_final: 0.8349 (t0) REVERT: G 185 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7618 (p0) REVERT: H 3 GLN cc_start: 0.9013 (pm20) cc_final: 0.8636 (pm20) REVERT: H 6 GLU cc_start: 0.8142 (mp0) cc_final: 0.7260 (mp0) REVERT: H 46 GLU cc_start: 0.8829 (tt0) cc_final: 0.8407 (pt0) REVERT: H 72 ASP cc_start: 0.8923 (t0) cc_final: 0.8493 (t0) REVERT: H 76 ASN cc_start: 0.8717 (t0) cc_final: 0.8490 (t0) REVERT: H 95 ASP cc_start: 0.9481 (t0) cc_final: 0.8905 (t0) REVERT: H 105 GLN cc_start: 0.9465 (mt0) cc_final: 0.9105 (pm20) REVERT: F 3 GLN cc_start: 0.9025 (pm20) cc_final: 0.8667 (pm20) REVERT: F 6 GLU cc_start: 0.8137 (mp0) cc_final: 0.7262 (mp0) REVERT: F 26 ARG cc_start: 0.8394 (tmm-80) cc_final: 0.7783 (tmm-80) REVERT: F 27 PHE cc_start: 0.8614 (OUTLIER) cc_final: 0.8349 (m-80) REVERT: F 46 GLU cc_start: 0.8877 (tt0) cc_final: 0.8403 (tt0) REVERT: F 72 ASP cc_start: 0.8928 (t0) cc_final: 0.8492 (t0) REVERT: F 76 ASN cc_start: 0.8696 (t0) cc_final: 0.8410 (t0) REVERT: F 95 ASP cc_start: 0.9490 (t0) cc_final: 0.8976 (t0) REVERT: F 105 GLN cc_start: 0.9466 (mt0) cc_final: 0.9102 (pm20) REVERT: F 186 VAL cc_start: 0.9446 (t) cc_final: 0.9208 (m) REVERT: F 203 ASN cc_start: 0.8759 (m110) cc_final: 0.8511 (t0) REVERT: J 3 GLN cc_start: 0.9014 (pm20) cc_final: 0.8654 (pm20) REVERT: J 6 GLU cc_start: 0.8130 (mp0) cc_final: 0.7229 (mp0) REVERT: J 26 ARG cc_start: 0.8417 (tmm-80) cc_final: 0.7807 (tmm-80) REVERT: J 27 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.8343 (m-80) REVERT: J 46 GLU cc_start: 0.8844 (tt0) cc_final: 0.8360 (tt0) REVERT: J 72 ASP cc_start: 0.8922 (t0) cc_final: 0.8482 (t0) REVERT: J 76 ASN cc_start: 0.8681 (t0) cc_final: 0.8410 (t0) REVERT: J 95 ASP cc_start: 0.9451 (t0) cc_final: 0.8866 (t0) REVERT: J 99 TYR cc_start: 0.8877 (m-10) cc_final: 0.8498 (m-10) REVERT: J 105 GLN cc_start: 0.9454 (mt0) cc_final: 0.9091 (pm20) REVERT: J 108 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9178 (tm) REVERT: K 3 GLN cc_start: 0.9023 (pm20) cc_final: 0.8665 (pm20) REVERT: K 6 GLU cc_start: 0.8088 (mp0) cc_final: 0.7177 (mp0) REVERT: K 26 ARG cc_start: 0.8413 (tmm-80) cc_final: 0.7805 (tmm-80) REVERT: K 27 PHE cc_start: 0.8605 (OUTLIER) cc_final: 0.8339 (m-80) REVERT: K 46 GLU cc_start: 0.8846 (tt0) cc_final: 0.8365 (tt0) REVERT: K 72 ASP cc_start: 0.8923 (t0) cc_final: 0.8483 (t0) REVERT: K 76 ASN cc_start: 0.8693 (t0) cc_final: 0.8423 (t0) REVERT: K 95 ASP cc_start: 0.9465 (t0) cc_final: 0.8923 (t0) REVERT: K 105 GLN cc_start: 0.9457 (mt0) cc_final: 0.9096 (pm20) REVERT: K 108 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9166 (tm) REVERT: K 186 VAL cc_start: 0.9455 (t) cc_final: 0.9222 (m) REVERT: K 203 ASN cc_start: 0.8766 (m110) cc_final: 0.8508 (t0) REVERT: K 213 LYS cc_start: 0.7711 (OUTLIER) cc_final: 0.7506 (ttpp) REVERT: E 24 GLN cc_start: 0.8696 (mt0) cc_final: 0.8452 (mp10) REVERT: E 45 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8874 (ttpt) REVERT: E 49 TYR cc_start: 0.9246 (p90) cc_final: 0.8957 (p90) REVERT: E 50 GLU cc_start: 0.9274 (mt-10) cc_final: 0.8949 (mp0) REVERT: E 67 SER cc_start: 0.9153 (m) cc_final: 0.8929 (p) REVERT: E 81 GLU cc_start: 0.9306 (mp0) cc_final: 0.9045 (pm20) REVERT: E 93 ASP cc_start: 0.9259 (t0) cc_final: 0.8951 (t70) REVERT: E 103 LYS cc_start: 0.9267 (mttt) cc_final: 0.8723 (mtpp) REVERT: E 118 PHE cc_start: 0.8232 (m-80) cc_final: 0.7972 (m-80) REVERT: E 143 GLU cc_start: 0.8851 (mp0) cc_final: 0.8563 (pm20) REVERT: E 161 GLU cc_start: 0.9100 (pm20) cc_final: 0.8627 (pp20) REVERT: E 167 ASP cc_start: 0.8779 (t70) cc_final: 0.8339 (t0) REVERT: E 185 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7522 (p0) REVERT: I 24 GLN cc_start: 0.8694 (mt0) cc_final: 0.8453 (mp10) REVERT: I 45 LYS cc_start: 0.9152 (OUTLIER) cc_final: 0.8872 (ttpt) REVERT: I 49 TYR cc_start: 0.9247 (p90) cc_final: 0.8932 (p90) REVERT: I 50 GLU cc_start: 0.9262 (mt-10) cc_final: 0.8928 (mp0) REVERT: I 67 SER cc_start: 0.9157 (m) cc_final: 0.8931 (p) REVERT: I 75 ILE cc_start: 0.9441 (mt) cc_final: 0.8916 (tp) REVERT: I 81 GLU cc_start: 0.9316 (mp0) cc_final: 0.9067 (pm20) REVERT: I 93 ASP cc_start: 0.9287 (t0) cc_final: 0.8983 (t70) REVERT: I 103 LYS cc_start: 0.9268 (mttt) cc_final: 0.8730 (mtpp) REVERT: I 118 PHE cc_start: 0.8207 (m-80) cc_final: 0.7949 (m-80) REVERT: I 161 GLU cc_start: 0.9095 (pm20) cc_final: 0.8612 (pp20) REVERT: I 167 ASP cc_start: 0.8777 (t70) cc_final: 0.8352 (t70) REVERT: L 21 ILE cc_start: 0.9459 (mt) cc_final: 0.9253 (mp) REVERT: L 45 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8861 (ttpt) REVERT: L 49 TYR cc_start: 0.9242 (p90) cc_final: 0.8945 (p90) REVERT: L 50 GLU cc_start: 0.9276 (mt-10) cc_final: 0.8946 (mp0) REVERT: L 67 SER cc_start: 0.9159 (m) cc_final: 0.8935 (p) REVERT: L 81 GLU cc_start: 0.9305 (mp0) cc_final: 0.9045 (pm20) REVERT: L 93 ASP cc_start: 0.9323 (t0) cc_final: 0.8937 (t70) REVERT: L 103 LYS cc_start: 0.9265 (mttt) cc_final: 0.8733 (mtpp) REVERT: L 118 PHE cc_start: 0.8230 (m-80) cc_final: 0.7967 (m-80) REVERT: L 143 GLU cc_start: 0.8851 (mp0) cc_final: 0.8564 (pm20) REVERT: L 161 GLU cc_start: 0.9095 (pm20) cc_final: 0.8629 (pp20) REVERT: L 167 ASP cc_start: 0.8804 (t70) cc_final: 0.8381 (t70) REVERT: L 185 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7517 (p0) outliers start: 68 outliers final: 33 residues processed: 471 average time/residue: 0.9577 time to fit residues: 527.3136 Evaluate side-chains 472 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 418 time to evaluate : 2.190 ------------------------------------------------------------------------------- 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 110 GLU 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 185 ASP Chi-restraints excluded: chain G residue 194 CYS Chi-restraints excluded: chain H residue 11 LEU 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 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 J residue 2 VAL Chi-restraints excluded: chain J residue 11 LEU 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 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 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 183 LYS 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 185 ASP Chi-restraints excluded: chain L residue 194 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 122 optimal weight: 0.6980 chunk 165 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 150 optimal weight: 7.9990 chunk 202 optimal weight: 0.9990 chunk 196 optimal weight: 0.9990 chunk 164 optimal weight: 0.5980 chunk 207 optimal weight: 7.9990 chunk 136 optimal weight: 7.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN B 209 GLN C 146 ASN D 146 ASN G 79 GLN H 208 ASN F 208 ASN J 208 ASN K 208 ASN E 79 GLN I 79 GLN L 79 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.090935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.061699 restraints weight = 51394.517| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 4.06 r_work: 0.2767 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21048 Z= 0.145 Angle : 0.706 10.737 28752 Z= 0.355 Chirality : 0.045 0.160 3224 Planarity : 0.005 0.063 3668 Dihedral : 4.846 19.748 2860 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.32 % Allowed : 23.65 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.59 (0.41), residues: 144 sheet: 0.83 (0.18), residues: 824 loop : -0.37 (0.16), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP H 158 HIS 0.003 0.001 HIS C 173 PHE 0.047 0.002 PHE I 209 TYR 0.016 0.001 TYR K 32 ARG 0.008 0.001 ARG I 142 Details of bonding type rmsd hydrogen bonds : bond 0.02845 ( 724) hydrogen bonds : angle 5.09941 ( 1980) SS BOND : bond 0.00368 ( 32) SS BOND : angle 1.25509 ( 64) covalent geometry : bond 0.00337 (21016) covalent geometry : angle 0.70477 (28688) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15946.35 seconds wall clock time: 275 minutes 24.15 seconds (16524.15 seconds total)