Starting phenix.real_space_refine on Tue May 20 22:25:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vgk_43203/05_2025/8vgk_43203.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vgk_43203/05_2025/8vgk_43203.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vgk_43203/05_2025/8vgk_43203.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vgk_43203/05_2025/8vgk_43203.map" model { file = "/net/cci-nas-00/data/ceres_data/8vgk_43203/05_2025/8vgk_43203.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vgk_43203/05_2025/8vgk_43203.cif" } resolution = 2.4 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= -0.008 sd= 0.350 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 132 5.16 5 C 12912 2.51 5 N 3488 2.21 5 O 4035 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 20567 Number of models: 1 Model: "" Number of chains: 20 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: "E" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1613 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 204} Chain: "F" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1576 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Chain: "G" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1613 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 204} Chain: "H" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1576 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Chain: "I" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1613 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 204} Chain: "J" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1576 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Chain: "K" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1576 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Chain: "L" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1613 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 204} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 13.34, per 1000 atoms: 0.65 Number of scatterers: 20567 At special positions: 0 Unit cell: (183, 99, 111, 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 132 16.00 O 4035 8.00 N 3488 7.00 C 12912 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=56, symmetry=0 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 58 " distance=2.04 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 220 " distance=2.04 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 58 " distance=2.04 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 201 " distance=2.04 Simple disulfide: pdb=" SG CYS B 168 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 191 " - pdb=" SG CYS B 220 " distance=2.04 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 58 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 191 " - pdb=" SG CYS C 220 " distance=2.04 Simple disulfide: pdb=" SG CYS D 42 " - pdb=" SG CYS D 58 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS D 191 " - pdb=" SG CYS D 220 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.05 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 165 " distance=2.04 Simple disulfide: pdb=" SG CYS E 80 " - pdb=" SG CYS E 171 " distance=2.03 Simple disulfide: pdb=" SG CYS E 116 " - pdb=" SG CYS F 141 " distance=2.04 Simple disulfide: pdb=" SG CYS E 124 " - pdb=" SG CYS F 126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.04 Simple disulfide: pdb=" SG CYS F 11 " - pdb=" SG CYS F 151 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.04 Simple disulfide: pdb=" SG CYS F 108 " - pdb=" SG CYS F 153 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 201 " distance=2.04 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.05 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 165 " distance=2.04 Simple disulfide: pdb=" SG CYS G 80 " - pdb=" SG CYS G 171 " distance=2.03 Simple disulfide: pdb=" SG CYS G 116 " - pdb=" SG CYS H 141 " distance=2.04 Simple disulfide: pdb=" SG CYS G 124 " - pdb=" SG CYS H 126 " distance=2.04 Simple disulfide: pdb=" SG CYS G 134 " - pdb=" SG CYS G 194 " distance=2.04 Simple disulfide: pdb=" SG CYS H 11 " - pdb=" SG CYS H 151 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 108 " - pdb=" SG CYS H 153 " distance=2.03 Simple disulfide: pdb=" SG CYS H 144 " - pdb=" SG CYS H 201 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.05 Simple disulfide: pdb=" SG CYS I 40 " - pdb=" SG CYS I 165 " distance=2.04 Simple disulfide: pdb=" SG CYS I 80 " - pdb=" SG CYS I 171 " distance=2.03 Simple disulfide: pdb=" SG CYS I 116 " - pdb=" SG CYS J 141 " distance=2.04 Simple disulfide: pdb=" SG CYS I 124 " - pdb=" SG CYS J 126 " distance=2.04 Simple disulfide: pdb=" SG CYS I 134 " - pdb=" SG CYS I 194 " distance=2.04 Simple disulfide: pdb=" SG CYS J 11 " - pdb=" SG CYS J 151 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS J 108 " - pdb=" SG CYS J 153 " distance=2.03 Simple disulfide: pdb=" SG CYS J 144 " - pdb=" SG CYS J 201 " distance=2.04 Simple disulfide: pdb=" SG CYS K 11 " - pdb=" SG CYS K 151 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.04 Simple disulfide: pdb=" SG CYS K 108 " - pdb=" SG CYS K 153 " distance=2.03 Simple disulfide: pdb=" SG CYS K 126 " - pdb=" SG CYS L 124 " distance=2.04 Simple disulfide: pdb=" SG CYS K 141 " - pdb=" SG CYS L 116 " distance=2.04 Simple disulfide: pdb=" SG CYS K 144 " - pdb=" SG CYS K 201 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 Simple disulfide: pdb=" SG CYS L 40 " - pdb=" SG CYS L 165 " distance=2.04 Simple disulfide: pdb=" SG CYS L 80 " - pdb=" SG CYS L 171 " distance=2.03 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: 4.97 Conformation dependent library (CDL) restraints added in 2.7 seconds 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4912 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 52 sheets defined 7.9% alpha, 40.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.33 Creating SS restraints... 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 234 through 239 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 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 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 'E' and resid 79 through 83 Processing helix chain 'E' and resid 122 through 127 Processing helix chain 'E' and resid 183 through 187 Processing helix chain 'F' and resid 62 through 65 removed outlier: 3.570A 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 83 through 87 Processing helix chain 'F' and resid 161 through 163 No H-bonds generated for 'chain 'F' and resid 161 through 163' Processing helix chain 'F' and resid 190 through 194 Processing helix chain 'G' and resid 79 through 83 Processing helix chain 'G' and resid 122 through 127 Processing helix chain 'G' and resid 183 through 187 Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.566A 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 83 through 87 Processing helix chain 'H' and resid 161 through 163 No H-bonds generated for 'chain 'H' and resid 161 through 163' Processing helix chain 'H' and resid 190 through 194 Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'I' and resid 122 through 127 Processing helix chain 'I' and resid 183 through 187 Processing helix chain 'J' and resid 62 through 65 removed outlier: 3.570A 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 83 through 87 Processing helix chain 'J' and resid 161 through 163 No H-bonds generated for 'chain 'J' and resid 161 through 163' Processing helix chain 'J' and resid 190 through 194 Processing helix chain 'K' and resid 62 through 65 removed outlier: 3.566A 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 83 through 87 Processing helix chain 'K' and resid 161 through 163 No H-bonds generated for 'chain 'K' and resid 161 through 163' Processing helix chain 'K' and resid 190 through 194 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'L' and resid 122 through 127 Processing helix chain 'L' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 67 removed outlier: 3.717A pdb=" N CYS A 42 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL A 35 " --> pdb=" O HIS A 40 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N HIS A 40 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TRP A 51 " --> pdb=" O ILE A 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 156 through 160 removed outlier: 4.311A pdb=" N CYS A 136 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR A 139 " --> pdb=" O PRO A 198 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU A 199 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL A 213 " --> pdb=" O THR A 229 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N THR A 229 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N CYS A 182 " --> pdb=" O MET A 163 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 20 through 21 removed outlier: 4.328A pdb=" N CYS B 136 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR B 139 " --> pdb=" O PRO B 198 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU B 199 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL B 213 " --> pdb=" O THR B 229 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N THR B 229 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N CYS B 182 " --> pdb=" O MET B 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 64 through 67 removed outlier: 3.710A pdb=" N CYS B 42 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL B 35 " --> pdb=" O HIS B 40 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N HIS B 40 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TRP B 51 " --> pdb=" O ILE B 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 64 through 67 removed outlier: 3.719A pdb=" N CYS C 42 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL C 35 " --> pdb=" O HIS C 40 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N HIS C 40 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TRP C 51 " --> pdb=" O ILE C 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 156 through 160 removed outlier: 4.306A pdb=" N CYS C 136 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR C 139 " --> pdb=" O PRO C 198 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU C 199 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N VAL C 213 " --> pdb=" O THR C 229 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N THR C 229 " --> pdb=" O VAL C 213 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N CYS C 182 " --> pdb=" O MET C 163 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 64 through 67 removed outlier: 3.719A pdb=" N CYS D 42 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL D 35 " --> pdb=" O HIS D 40 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N HIS D 40 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N TRP D 51 " --> pdb=" O ILE D 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 156 through 160 removed outlier: 4.312A pdb=" N CYS D 136 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THR D 139 " --> pdb=" O PRO D 198 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU D 199 " --> pdb=" O ALA D 210 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N VAL D 213 " --> pdb=" O THR D 229 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N THR D 229 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N CYS D 182 " --> pdb=" O MET D 163 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 14 removed outlier: 6.719A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N LYS E 107 " --> pdb=" O LEU E 11 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA E 13 " --> pdb=" O LYS E 107 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA E 84 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 14 removed outlier: 6.719A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N LYS E 107 " --> pdb=" O LEU E 11 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA E 13 " --> pdb=" O LYS E 107 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA E 84 " --> pdb=" O VAL E 104 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 114 through 118 removed outlier: 3.931A pdb=" N VAL E 133 " --> pdb=" O PHE E 118 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N TYR E 173 " --> pdb=" O ASN E 138 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN E 160 " --> pdb=" O THR E 178 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 153 through 154 Processing sheet with id=AB5, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AB6, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.707A pdb=" N ALA F 33 " --> pdb=" O ASP F 95 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.870A pdb=" N LEU F 102 " --> pdb=" O ARG F 94 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 124 through 128 removed outlier: 5.391A pdb=" N TYR F 181 " --> pdb=" O ASP F 148 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 124 through 128 removed outlier: 5.391A pdb=" N TYR F 181 " --> pdb=" O ASP F 148 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 156 through 159 Processing sheet with id=AC2, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AC3, first strand: chain 'G' and resid 10 through 14 removed outlier: 6.717A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N LYS G 107 " --> pdb=" O LEU G 11 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA G 13 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA G 84 " --> pdb=" O VAL G 104 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 10 through 14 removed outlier: 6.717A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N LYS G 107 " --> pdb=" O LEU G 11 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA G 13 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA G 84 " --> pdb=" O VAL G 104 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 114 through 118 removed outlier: 4.061A pdb=" N VAL G 133 " --> pdb=" O PHE G 118 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N TYR G 173 " --> pdb=" O ASN G 138 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN G 160 " --> pdb=" O THR G 178 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 153 through 154 Processing sheet with id=AC7, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AC8, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.707A pdb=" N ALA H 33 " --> pdb=" O ASP H 95 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.873A pdb=" N LEU H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 124 through 128 removed outlier: 5.397A pdb=" N TYR H 181 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 124 through 128 removed outlier: 5.397A pdb=" N TYR H 181 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 156 through 159 removed outlier: 3.515A pdb=" N THR H 156 " --> pdb=" O ASN H 204 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AD5, first strand: chain 'I' and resid 10 through 14 removed outlier: 6.723A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LYS I 107 " --> pdb=" O LEU I 11 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA I 13 " --> pdb=" O LYS I 107 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA I 84 " --> pdb=" O VAL I 104 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 10 through 14 removed outlier: 6.723A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LYS I 107 " --> pdb=" O LEU I 11 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA I 13 " --> pdb=" O LYS I 107 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA I 84 " --> pdb=" O VAL I 104 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 114 through 118 removed outlier: 4.076A pdb=" N VAL I 133 " --> pdb=" O PHE I 118 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N TYR I 173 " --> pdb=" O ASN I 138 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN I 160 " --> pdb=" O THR I 178 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 153 through 154 Processing sheet with id=AD9, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AE1, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.697A pdb=" N ALA J 33 " --> pdb=" O ASP J 95 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.873A pdb=" N LEU J 102 " --> pdb=" O ARG J 94 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 124 through 128 removed outlier: 5.392A pdb=" N TYR J 181 " --> pdb=" O ASP J 148 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 124 through 128 removed outlier: 5.392A pdb=" N TYR J 181 " --> pdb=" O ASP J 148 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 156 through 159 Processing sheet with id=AE6, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AE7, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.699A pdb=" N ALA K 33 " --> pdb=" O ASP K 95 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.870A pdb=" N LEU K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 124 through 128 removed outlier: 5.394A pdb=" N TYR K 181 " --> pdb=" O ASP K 148 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 124 through 128 removed outlier: 5.394A pdb=" N TYR K 181 " --> pdb=" O ASP K 148 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 156 through 159 Processing sheet with id=AF3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AF4, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.719A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N LYS L 107 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ALA L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.719A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N LYS L 107 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ALA L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 114 through 118 removed outlier: 4.067A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN L 160 " --> pdb=" O THR L 178 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 153 through 154 793 hydrogen bonds defined for protein. 1995 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: 7.81 Time building geometry restraints manager: 5.88 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: 6547 1.34 - 1.47: 5263 1.47 - 1.59: 8998 1.59 - 1.72: 0 1.72 - 1.85: 152 Bond restraints: 20960 Sorted by residual: bond pdb=" C ALA L 111 " pdb=" N ALA L 112 " ideal model delta sigma weight residual 1.331 1.418 -0.087 2.07e-02 2.33e+03 1.77e+01 bond pdb=" C VAL J 12 " pdb=" N LYS J 13 " ideal model delta sigma weight residual 1.331 1.380 -0.049 2.07e-02 2.33e+03 5.63e+00 bond pdb=" C VAL K 12 " pdb=" N LYS K 13 " ideal model delta sigma weight residual 1.331 1.380 -0.049 2.07e-02 2.33e+03 5.55e+00 bond pdb=" C VAL F 12 " pdb=" N LYS F 13 " ideal model delta sigma weight residual 1.331 1.379 -0.048 2.07e-02 2.33e+03 5.27e+00 bond pdb=" C VAL H 12 " pdb=" N LYS H 13 " ideal model delta sigma weight residual 1.331 1.377 -0.046 2.07e-02 2.33e+03 5.03e+00 ... (remaining 20955 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 26713 2.00 - 4.01: 1643 4.01 - 6.01: 194 6.01 - 8.02: 34 8.02 - 10.02: 8 Bond angle restraints: 28592 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 110.70 120.72 -10.02 1.22e+00 6.72e-01 6.75e+01 angle pdb=" N PRO D 152A" pdb=" CA PRO D 152A" pdb=" C PRO D 152A" ideal model delta sigma weight residual 110.70 120.44 -9.74 1.22e+00 6.72e-01 6.38e+01 angle pdb=" N PRO A 152A" pdb=" CA PRO A 152A" pdb=" C PRO A 152A" ideal model delta sigma weight residual 110.70 120.06 -9.36 1.22e+00 6.72e-01 5.88e+01 angle pdb=" N PRO C 152A" pdb=" CA PRO C 152A" pdb=" C PRO C 152A" ideal model delta sigma weight residual 110.70 119.97 -9.27 1.22e+00 6.72e-01 5.78e+01 angle pdb=" CA PRO B 152A" pdb=" C PRO B 152A" pdb=" N PRO B 152B" ideal model delta sigma weight residual 117.93 124.06 -6.13 1.20e+00 6.94e-01 2.61e+01 ... (remaining 28587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 11534 17.87 - 35.73: 837 35.73 - 53.60: 114 53.60 - 71.47: 41 71.47 - 89.33: 34 Dihedral angle restraints: 12560 sinusoidal: 4884 harmonic: 7676 Sorted by residual: dihedral pdb=" CA GLU K 152 " pdb=" C GLU K 152 " pdb=" N CYS K 153 " pdb=" CA CYS K 153 " ideal model delta harmonic sigma weight residual -180.00 -151.10 -28.90 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA GLU J 152 " pdb=" C GLU J 152 " pdb=" N CYS J 153 " pdb=" CA CYS J 153 " ideal model delta harmonic sigma weight residual 180.00 -151.14 -28.86 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA CYS E 124 " pdb=" C CYS E 124 " pdb=" N LEU E 125 " pdb=" CA LEU E 125 " ideal model delta harmonic sigma weight residual 180.00 151.22 28.78 0 5.00e+00 4.00e-02 3.31e+01 ... (remaining 12557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2173 0.055 - 0.111: 831 0.111 - 0.166: 192 0.166 - 0.222: 20 0.222 - 0.277: 4 Chirality restraints: 3220 Sorted by residual: chirality pdb=" CA PRO B 152A" pdb=" N PRO B 152A" pdb=" C PRO B 152A" pdb=" CB PRO B 152A" both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA PRO D 152A" pdb=" N PRO D 152A" pdb=" C PRO D 152A" pdb=" CB PRO D 152A" both_signs ideal model delta sigma weight residual False 2.72 2.44 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA PRO A 152A" pdb=" N PRO A 152A" pdb=" C PRO A 152A" pdb=" CB PRO A 152A" both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 3217 not shown) Planarity restraints: 3648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 181 " -0.008 2.00e-02 2.50e+03 2.42e-02 1.17e+01 pdb=" CG TYR H 181 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR H 181 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR H 181 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR H 181 " -0.033 2.00e-02 2.50e+03 pdb=" CE2 TYR H 181 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR H 181 " -0.035 2.00e-02 2.50e+03 pdb=" OH TYR H 181 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 181 " -0.008 2.00e-02 2.50e+03 2.36e-02 1.11e+01 pdb=" CG TYR F 181 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR F 181 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR F 181 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR F 181 " -0.032 2.00e-02 2.50e+03 pdb=" CE2 TYR F 181 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR F 181 " -0.034 2.00e-02 2.50e+03 pdb=" OH TYR F 181 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 181 " 0.007 2.00e-02 2.50e+03 2.32e-02 1.08e+01 pdb=" CG TYR J 181 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR J 181 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR J 181 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR J 181 " 0.031 2.00e-02 2.50e+03 pdb=" CE2 TYR J 181 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR J 181 " 0.034 2.00e-02 2.50e+03 pdb=" OH TYR J 181 " -0.032 2.00e-02 2.50e+03 ... (remaining 3645 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 291 2.66 - 3.22: 18633 3.22 - 3.78: 31089 3.78 - 4.34: 45901 4.34 - 4.90: 72755 Nonbonded interactions: 168669 Sorted by model distance: nonbonded pdb=" OE1 GLN D 192 " pdb=" O HOH D 301 " model vdw 2.099 3.040 nonbonded pdb=" OD1 ASP L 170 " pdb=" OG1 THR L 172 " model vdw 2.142 3.040 nonbonded pdb=" OD1 ASP I 170 " pdb=" OG1 THR I 172 " model vdw 2.149 3.040 nonbonded pdb=" O HOH C 330 " pdb=" O HOH C 339 " model vdw 2.150 3.040 nonbonded pdb=" OD1 ASP E 170 " pdb=" OG1 THR E 172 " model vdw 2.152 3.040 ... (remaining 168664 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.150 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: 0.020 Extract box with map and model: 0.830 Check model and map are aligned: 0.140 Set scattering table: 0.210 Process input model: 49.730 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 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 : 0.005 0.087 21016 Z= 0.256 Angle : 1.044 10.021 28704 Z= 0.594 Chirality : 0.060 0.277 3220 Planarity : 0.010 0.096 3648 Dihedral : 13.841 89.332 7480 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.61 % Allowed : 7.05 % Favored : 92.35 % Rotamer: Outliers : 0.65 % Allowed : 3.91 % Favored : 95.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.15), residues: 2640 helix: -2.54 (0.34), residues: 152 sheet: 0.46 (0.16), residues: 876 loop : -1.15 (0.14), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP F 159 HIS 0.011 0.003 HIS D 72 PHE 0.022 0.003 PHE G 92 TYR 0.035 0.008 TYR H 181 ARG 0.025 0.004 ARG H 97 Details of bonding type rmsd hydrogen bonds : bond 0.20065 ( 709) hydrogen bonds : angle 9.17229 ( 1995) SS BOND : bond 0.01013 ( 56) SS BOND : angle 1.89601 ( 112) covalent geometry : bond 0.00544 (20960) covalent geometry : angle 1.03976 (28592) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 618 time to evaluate : 2.256 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 181 TYR cc_start: 0.8747 (m-80) cc_final: 0.8250 (m-80) REVERT: G 138 ASN cc_start: 0.7702 (m110) cc_final: 0.7246 (m110) REVERT: G 139 PHE cc_start: 0.8407 (p90) cc_final: 0.8080 (p90) REVERT: G 173 TYR cc_start: 0.7482 (p90) cc_final: 0.6147 (p90) REVERT: G 211 ARG cc_start: 0.7401 (ttp80) cc_final: 0.7168 (ttp-170) REVERT: H 6 GLU cc_start: 0.6801 (mp0) cc_final: 0.6598 (mp0) REVERT: H 128 LEU cc_start: 0.7857 (tp) cc_final: 0.7545 (tp) REVERT: H 181 TYR cc_start: 0.8707 (m-80) cc_final: 0.8223 (m-80) REVERT: I 211 ARG cc_start: 0.7434 (ttp80) cc_final: 0.7186 (ttp-170) REVERT: J 128 LEU cc_start: 0.7718 (tp) cc_final: 0.7478 (tp) REVERT: K 128 LEU cc_start: 0.7776 (tp) cc_final: 0.7466 (tp) REVERT: K 149 TYR cc_start: 0.7574 (p90) cc_final: 0.7330 (p90) REVERT: K 181 TYR cc_start: 0.8732 (m-80) cc_final: 0.8373 (m-80) outliers start: 15 outliers final: 3 residues processed: 633 average time/residue: 1.4532 time to fit residues: 1024.0601 Evaluate side-chains 390 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 387 time to evaluate : 2.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain L residue 123 GLU Chi-restraints excluded: chain L residue 170 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 4.9990 chunk 200 optimal weight: 0.6980 chunk 111 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 206 optimal weight: 2.9990 chunk 80 optimal weight: 0.1980 chunk 125 optimal weight: 0.9980 chunk 154 optimal weight: 0.9980 chunk 239 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN B 20 GLN B 79 GLN B 192 GLN C 192 GLN D 79 GLN D 192 GLN E 3 GLN E 189 HIS F 209 ASN G 3 GLN G 189 HIS H 160 ASN H 209 ASN I 3 GLN I 189 HIS J 76 ASN ** J 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 209 ASN K 76 ASN K 209 ASN L 3 GLN L 189 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.119362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.067778 restraints weight = 36086.248| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 3.11 r_work: 0.2605 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2470 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21016 Z= 0.194 Angle : 0.834 12.661 28704 Z= 0.437 Chirality : 0.051 0.208 3220 Planarity : 0.006 0.073 3648 Dihedral : 6.722 48.394 2872 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.13 % Allowed : 14.02 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.06 (0.17), residues: 2640 helix: -0.56 (0.51), residues: 124 sheet: 0.99 (0.17), residues: 888 loop : -0.59 (0.16), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 215 HIS 0.004 0.001 HIS B 173 PHE 0.022 0.002 PHE L 139 TYR 0.024 0.002 TYR I 140 ARG 0.010 0.001 ARG L 61 Details of bonding type rmsd hydrogen bonds : bond 0.04083 ( 709) hydrogen bonds : angle 6.49661 ( 1995) SS BOND : bond 0.00697 ( 56) SS BOND : angle 1.34073 ( 112) covalent geometry : bond 0.00436 (20960) covalent geometry : angle 0.83102 (28592) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 469 time to evaluate : 2.286 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: 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: 0.9119 (tp30) cc_final: 0.8767 (tp30) REVERT: A 134 MET cc_start: 0.8735 (tpp) cc_final: 0.8027 (mpp) REVERT: A 164 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8082 (mm-30) REVERT: B 109 GLU cc_start: 0.9129 (tp30) cc_final: 0.8793 (tp30) REVERT: B 150 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.8793 (mmp80) REVERT: B 164 GLU cc_start: 0.8393 (mm-30) cc_final: 0.7962 (mm-30) REVERT: C 109 GLU cc_start: 0.9101 (tp30) cc_final: 0.8750 (tp30) REVERT: C 145 ASP cc_start: 0.8342 (OUTLIER) cc_final: 0.7499 (p0) REVERT: C 149 GLU cc_start: 0.8393 (mp0) cc_final: 0.8094 (mp0) REVERT: C 164 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8029 (mm-30) REVERT: D 109 GLU cc_start: 0.9152 (tp30) cc_final: 0.8802 (tp30) REVERT: D 134 MET cc_start: 0.8679 (tpp) cc_final: 0.7974 (mpp) REVERT: D 164 GLU cc_start: 0.8377 (mm-30) cc_final: 0.7964 (mm-30) REVERT: E 78 LEU cc_start: 0.9174 (mt) cc_final: 0.8889 (tm) REVERT: E 139 PHE cc_start: 0.8261 (p90) cc_final: 0.8014 (p90) REVERT: E 148 TRP cc_start: 0.6869 (m100) cc_final: 0.6621 (m100) REVERT: E 167 ASP cc_start: 0.7670 (t0) cc_final: 0.7456 (t0) REVERT: E 173 TYR cc_start: 0.5921 (OUTLIER) cc_final: 0.5044 (p90) REVERT: F 3 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.8187 (pm20) REVERT: F 6 GLU cc_start: 0.7788 (mp0) cc_final: 0.7335 (mp0) REVERT: F 46 GLU cc_start: 0.8989 (pt0) cc_final: 0.8734 (pt0) REVERT: F 72 ASP cc_start: 0.8305 (t0) cc_final: 0.8025 (t0) REVERT: F 86 ASP cc_start: 0.9079 (m-30) cc_final: 0.8851 (m-30) REVERT: F 105 GLN cc_start: 0.8580 (pm20) cc_final: 0.8247 (pm20) REVERT: F 152 GLU cc_start: 0.8377 (pm20) cc_final: 0.8022 (pm20) REVERT: F 160 ASN cc_start: 0.8889 (m-40) cc_final: 0.8470 (m110) REVERT: F 209 ASN cc_start: 0.9186 (m110) cc_final: 0.8948 (m-40) REVERT: G 78 LEU cc_start: 0.9167 (mt) cc_final: 0.8892 (tm) REVERT: G 139 PHE cc_start: 0.8257 (p90) cc_final: 0.8009 (p90) REVERT: G 148 TRP cc_start: 0.6710 (m100) cc_final: 0.5922 (m100) REVERT: G 155 GLN cc_start: 0.8379 (mm-40) cc_final: 0.8050 (mp10) REVERT: G 173 TYR cc_start: 0.5838 (OUTLIER) cc_final: 0.4977 (p90) REVERT: H 3 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8160 (pm20) REVERT: H 6 GLU cc_start: 0.7377 (mp0) cc_final: 0.6521 (mp0) REVERT: H 46 GLU cc_start: 0.8968 (pt0) cc_final: 0.8709 (pt0) REVERT: H 72 ASP cc_start: 0.8319 (t0) cc_final: 0.8027 (t0) REVERT: H 86 ASP cc_start: 0.9084 (m-30) cc_final: 0.8853 (m-30) REVERT: H 105 GLN cc_start: 0.8312 (pm20) cc_final: 0.7617 (pm20) REVERT: H 128 LEU cc_start: 0.7153 (tp) cc_final: 0.6888 (tp) REVERT: H 152 GLU cc_start: 0.8498 (pm20) cc_final: 0.8151 (pm20) REVERT: H 213 ASP cc_start: 0.8689 (t0) cc_final: 0.8365 (t0) REVERT: H 214 LYS cc_start: 0.5761 (OUTLIER) cc_final: 0.5504 (ttpp) REVERT: I 78 LEU cc_start: 0.9140 (mt) cc_final: 0.8865 (tm) REVERT: I 139 PHE cc_start: 0.8239 (p90) cc_final: 0.7949 (p90) REVERT: I 148 TRP cc_start: 0.6810 (m100) cc_final: 0.5733 (m100) REVERT: I 155 GLN cc_start: 0.8398 (mm-40) cc_final: 0.8008 (mp10) REVERT: I 167 ASP cc_start: 0.7649 (t0) cc_final: 0.7447 (t0) REVERT: I 173 TYR cc_start: 0.5845 (OUTLIER) cc_final: 0.4988 (p90) REVERT: J 3 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.8170 (pm20) REVERT: J 6 GLU cc_start: 0.7768 (mp0) cc_final: 0.7342 (mp0) REVERT: J 43 LYS cc_start: 0.8794 (mmtm) cc_final: 0.8458 (mppt) REVERT: J 46 GLU cc_start: 0.8979 (pt0) cc_final: 0.8728 (pt0) REVERT: J 72 ASP cc_start: 0.8345 (t0) cc_final: 0.7948 (t0) REVERT: J 86 ASP cc_start: 0.9073 (m-30) cc_final: 0.8851 (m-30) REVERT: J 105 GLN cc_start: 0.8617 (pm20) cc_final: 0.8289 (pm20) REVERT: J 117 LYS cc_start: 0.8701 (ttpp) cc_final: 0.8390 (ptmm) REVERT: J 152 GLU cc_start: 0.8423 (pm20) cc_final: 0.7880 (pm20) REVERT: J 160 ASN cc_start: 0.8988 (m-40) cc_final: 0.8558 (m110) REVERT: J 206 LYS cc_start: 0.9252 (mmpt) cc_final: 0.8928 (mmmt) REVERT: K 3 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8171 (pm20) REVERT: K 6 GLU cc_start: 0.7767 (mp0) cc_final: 0.7333 (mp0) REVERT: K 46 GLU cc_start: 0.8959 (pt0) cc_final: 0.8707 (pt0) REVERT: K 72 ASP cc_start: 0.8327 (t0) cc_final: 0.8051 (t0) REVERT: K 86 ASP cc_start: 0.9085 (m-30) cc_final: 0.8856 (m-30) REVERT: K 105 GLN cc_start: 0.8602 (pm20) cc_final: 0.8274 (pm20) REVERT: K 128 LEU cc_start: 0.7135 (tp) cc_final: 0.6671 (tp) REVERT: K 152 GLU cc_start: 0.8112 (pm20) cc_final: 0.7907 (pm20) REVERT: K 160 ASN cc_start: 0.8997 (m-40) cc_final: 0.8510 (m110) REVERT: K 171 PHE cc_start: 0.7819 (m-80) cc_final: 0.7616 (m-80) REVERT: K 209 ASN cc_start: 0.9158 (m110) cc_final: 0.8951 (m-40) REVERT: L 78 LEU cc_start: 0.9156 (mt) cc_final: 0.8865 (tm) REVERT: L 123 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6657 (tt0) REVERT: L 139 PHE cc_start: 0.8148 (p90) cc_final: 0.7895 (p90) REVERT: L 145 LYS cc_start: 0.8644 (mttp) cc_final: 0.8427 (mmtt) REVERT: L 148 TRP cc_start: 0.6847 (m100) cc_final: 0.6643 (m100) REVERT: L 167 ASP cc_start: 0.7648 (t0) cc_final: 0.7437 (t0) outliers start: 49 outliers final: 13 residues processed: 506 average time/residue: 1.1872 time to fit residues: 685.6470 Evaluate side-chains 423 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 399 time to evaluate : 2.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 11 CYS Chi-restraints excluded: chain F residue 108 CYS Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain G residue 173 TYR Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 214 LYS Chi-restraints excluded: chain I residue 173 TYR Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 11 CYS Chi-restraints excluded: chain J residue 108 CYS Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 11 CYS Chi-restraints excluded: chain K residue 108 CYS Chi-restraints excluded: chain K residue 156 THR Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain L residue 123 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 88 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 189 optimal weight: 4.9990 chunk 225 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.117193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.065597 restraints weight = 36135.013| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 3.10 r_work: 0.2567 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2434 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 21016 Z= 0.206 Angle : 0.773 10.784 28704 Z= 0.401 Chirality : 0.049 0.166 3220 Planarity : 0.006 0.072 3648 Dihedral : 6.106 49.349 2867 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.04 % Allowed : 16.54 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.17), residues: 2640 helix: -0.51 (0.50), residues: 124 sheet: 1.16 (0.17), residues: 916 loop : -0.63 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 215 HIS 0.004 0.001 HIS L 189 PHE 0.017 0.002 PHE B 153 TYR 0.020 0.002 TYR J 181 ARG 0.005 0.001 ARG E 61 Details of bonding type rmsd hydrogen bonds : bond 0.03878 ( 709) hydrogen bonds : angle 6.04127 ( 1995) SS BOND : bond 0.00810 ( 56) SS BOND : angle 1.39467 ( 112) covalent geometry : bond 0.00479 (20960) covalent geometry : angle 0.76955 (28592) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 425 time to evaluate : 2.513 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: symmetry clash revert: symmetry clash REVERT: B 109 GLU cc_start: 0.9163 (tp30) cc_final: 0.8776 (tp30) REVERT: B 134 MET cc_start: 0.8829 (tpp) cc_final: 0.8306 (mpp) REVERT: B 150 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8678 (mmp80) REVERT: B 164 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8007 (mm-30) REVERT: C 134 MET cc_start: 0.8978 (tpp) cc_final: 0.8488 (mpp) REVERT: C 149 GLU cc_start: 0.8358 (mp0) cc_final: 0.7947 (mp0) REVERT: C 164 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8091 (mm-30) REVERT: D 109 GLU cc_start: 0.9137 (tp30) cc_final: 0.8761 (tp30) REVERT: D 150 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8556 (mmp80) REVERT: D 164 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8099 (mm-30) REVERT: E 17 ASP cc_start: 0.8596 (t0) cc_final: 0.8117 (m-30) REVERT: E 78 LEU cc_start: 0.9245 (mt) cc_final: 0.9004 (tm) REVERT: E 82 ASP cc_start: 0.8351 (m-30) cc_final: 0.8092 (m-30) REVERT: E 108 ARG cc_start: 0.6705 (tmm-80) cc_final: 0.6329 (tmm-80) REVERT: E 139 PHE cc_start: 0.8345 (p90) cc_final: 0.7987 (p90) REVERT: E 148 TRP cc_start: 0.6998 (m100) cc_final: 0.6165 (m100) REVERT: E 155 GLN cc_start: 0.8430 (mm-40) cc_final: 0.8145 (mp10) REVERT: E 167 ASP cc_start: 0.7616 (t0) cc_final: 0.7402 (t0) REVERT: E 173 TYR cc_start: 0.5794 (p90) cc_final: 0.5133 (p90) REVERT: E 211 ARG cc_start: 0.7389 (ttp-170) cc_final: 0.7186 (ptm160) REVERT: F 3 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8243 (pm20) REVERT: F 6 GLU cc_start: 0.7764 (mp0) cc_final: 0.6988 (mp0) REVERT: F 72 ASP cc_start: 0.8358 (t0) cc_final: 0.7965 (t0) REVERT: F 86 ASP cc_start: 0.9027 (m-30) cc_final: 0.8737 (m-30) REVERT: F 105 GLN cc_start: 0.8486 (pm20) cc_final: 0.8098 (pm20) REVERT: F 128 LEU cc_start: 0.8921 (mp) cc_final: 0.8464 (mm) REVERT: G 17 ASP cc_start: 0.8639 (t0) cc_final: 0.8153 (m-30) REVERT: G 78 LEU cc_start: 0.9227 (mt) cc_final: 0.8986 (tm) REVERT: G 82 ASP cc_start: 0.8328 (m-30) cc_final: 0.8073 (m-30) REVERT: G 123 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7043 (tt0) REVERT: G 139 PHE cc_start: 0.8158 (p90) cc_final: 0.7888 (p90) REVERT: G 148 TRP cc_start: 0.6858 (m100) cc_final: 0.6039 (m100) REVERT: G 155 GLN cc_start: 0.8404 (mm-40) cc_final: 0.8096 (mp10) REVERT: G 173 TYR cc_start: 0.5814 (OUTLIER) cc_final: 0.5030 (p90) REVERT: H 3 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8170 (pm20) REVERT: H 6 GLU cc_start: 0.7461 (mp0) cc_final: 0.6409 (mp0) REVERT: H 22 CYS cc_start: 0.8583 (t) cc_final: 0.8291 (t) REVERT: H 72 ASP cc_start: 0.8336 (t0) cc_final: 0.7947 (t0) REVERT: H 86 ASP cc_start: 0.9025 (m-30) cc_final: 0.8743 (m-30) REVERT: H 105 GLN cc_start: 0.8317 (pm20) cc_final: 0.7714 (pm20) REVERT: H 128 LEU cc_start: 0.7181 (tp) cc_final: 0.6791 (tp) REVERT: H 152 GLU cc_start: 0.7836 (pm20) cc_final: 0.7606 (pm20) REVERT: I 17 ASP cc_start: 0.8602 (t0) cc_final: 0.8147 (m-30) REVERT: I 78 LEU cc_start: 0.9206 (mt) cc_final: 0.8970 (tm) REVERT: I 82 ASP cc_start: 0.8359 (m-30) cc_final: 0.8107 (m-30) REVERT: I 139 PHE cc_start: 0.8276 (p90) cc_final: 0.8033 (p90) REVERT: I 148 TRP cc_start: 0.6937 (m100) cc_final: 0.6123 (m100) REVERT: I 155 GLN cc_start: 0.8379 (mm-40) cc_final: 0.8041 (mp10) REVERT: I 167 ASP cc_start: 0.7595 (t0) cc_final: 0.7373 (t0) REVERT: J 3 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.8168 (pm20) REVERT: J 6 GLU cc_start: 0.7720 (mp0) cc_final: 0.7012 (mp0) REVERT: J 13 LYS cc_start: 0.8936 (mttt) cc_final: 0.8678 (mttm) REVERT: J 72 ASP cc_start: 0.8497 (t0) cc_final: 0.8044 (t0) REVERT: J 75 LYS cc_start: 0.9415 (mttm) cc_final: 0.9213 (mttm) REVERT: J 86 ASP cc_start: 0.9018 (m-30) cc_final: 0.8731 (m-30) REVERT: J 105 GLN cc_start: 0.8495 (pm20) cc_final: 0.8117 (pm20) REVERT: J 171 PHE cc_start: 0.7693 (m-80) cc_final: 0.7069 (m-80) REVERT: J 176 GLN cc_start: 0.6258 (mp10) cc_final: 0.5957 (mp10) REVERT: J 204 ASN cc_start: 0.7315 (p0) cc_final: 0.6807 (p0) REVERT: K 3 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8178 (pm20) REVERT: K 6 GLU cc_start: 0.7746 (mp0) cc_final: 0.7023 (mp0) REVERT: K 72 ASP cc_start: 0.8357 (t0) cc_final: 0.7972 (t0) REVERT: K 86 ASP cc_start: 0.9031 (m-30) cc_final: 0.8743 (m-30) REVERT: K 105 GLN cc_start: 0.8481 (pm20) cc_final: 0.8105 (pm20) REVERT: K 128 LEU cc_start: 0.7129 (tp) cc_final: 0.6732 (tp) REVERT: L 17 ASP cc_start: 0.8596 (t0) cc_final: 0.8120 (m-30) REVERT: L 78 LEU cc_start: 0.9230 (mt) cc_final: 0.8990 (tm) REVERT: L 82 ASP cc_start: 0.8370 (m-30) cc_final: 0.8115 (m-30) REVERT: L 123 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6815 (tt0) REVERT: L 139 PHE cc_start: 0.8274 (p90) cc_final: 0.8018 (p90) REVERT: L 145 LYS cc_start: 0.8825 (mttp) cc_final: 0.8608 (mmtt) REVERT: L 167 ASP cc_start: 0.7605 (t0) cc_final: 0.7375 (t0) outliers start: 47 outliers final: 24 residues processed: 457 average time/residue: 1.2094 time to fit residues: 630.0519 Evaluate side-chains 411 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 378 time to evaluate : 2.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain D residue 150 ARG Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 11 CYS Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 108 CYS Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 173 TYR Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 11 CYS Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 108 CYS Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 11 CYS Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 108 CYS Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 202 ASN Chi-restraints excluded: chain L residue 123 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 234 optimal weight: 0.0770 chunk 226 optimal weight: 3.9990 chunk 184 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 176 optimal weight: 6.9990 chunk 83 optimal weight: 0.0870 chunk 60 optimal weight: 0.9990 chunk 238 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 227 optimal weight: 2.9990 overall best weight: 1.4322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.116419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.065030 restraints weight = 36453.239| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 3.12 r_work: 0.2562 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2429 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 21016 Z= 0.199 Angle : 0.749 11.370 28704 Z= 0.390 Chirality : 0.048 0.160 3220 Planarity : 0.006 0.067 3648 Dihedral : 5.880 51.364 2867 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.95 % Allowed : 17.45 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.00 (0.17), residues: 2640 helix: -0.81 (0.47), residues: 124 sheet: 1.13 (0.16), residues: 936 loop : -0.65 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 148 HIS 0.004 0.001 HIS L 189 PHE 0.023 0.002 PHE F 27 TYR 0.025 0.002 TYR H 181 ARG 0.008 0.001 ARG I 142 Details of bonding type rmsd hydrogen bonds : bond 0.03621 ( 709) hydrogen bonds : angle 5.83954 ( 1995) SS BOND : bond 0.00690 ( 56) SS BOND : angle 1.27499 ( 112) covalent geometry : bond 0.00466 (20960) covalent geometry : angle 0.74656 (28592) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 395 time to evaluate : 2.399 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 109 GLU cc_start: 0.9156 (tp30) cc_final: 0.8884 (tp30) REVERT: A 134 MET cc_start: 0.9080 (tpp) cc_final: 0.8539 (mpp) REVERT: B 134 MET cc_start: 0.8841 (tpp) cc_final: 0.8369 (mpp) REVERT: B 150 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.8614 (mmp80) REVERT: B 164 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8064 (mm-30) REVERT: C 109 GLU cc_start: 0.9134 (tp30) cc_final: 0.8860 (tp30) REVERT: C 134 MET cc_start: 0.9000 (tpp) cc_final: 0.8537 (mpp) REVERT: C 149 GLU cc_start: 0.8450 (mp0) cc_final: 0.7993 (mp0) REVERT: C 164 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8088 (mm-30) REVERT: D 134 MET cc_start: 0.8995 (tpp) cc_final: 0.8485 (mpp) REVERT: D 150 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8513 (mmp80) REVERT: D 164 GLU cc_start: 0.8398 (mm-30) cc_final: 0.8117 (mm-30) REVERT: E 4 MET cc_start: 0.8887 (mtp) cc_final: 0.7994 (mtp) REVERT: E 17 ASP cc_start: 0.8712 (t0) cc_final: 0.8199 (m-30) REVERT: E 78 LEU cc_start: 0.9206 (mt) cc_final: 0.8998 (tm) REVERT: E 82 ASP cc_start: 0.8321 (m-30) cc_final: 0.7929 (m-30) REVERT: E 108 ARG cc_start: 0.6750 (tmm-80) cc_final: 0.5882 (tmm-80) REVERT: E 139 PHE cc_start: 0.8214 (p90) cc_final: 0.7890 (p90) REVERT: E 167 ASP cc_start: 0.7702 (t0) cc_final: 0.7457 (t0) REVERT: E 173 TYR cc_start: 0.6431 (OUTLIER) cc_final: 0.5911 (p90) REVERT: F 3 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8167 (pm20) REVERT: F 6 GLU cc_start: 0.7689 (mp0) cc_final: 0.6724 (mp0) REVERT: F 22 CYS cc_start: 0.8689 (t) cc_final: 0.8194 (t) REVERT: F 26 ARG cc_start: 0.8526 (pmm-80) cc_final: 0.7945 (pmm-80) REVERT: F 72 ASP cc_start: 0.8400 (t0) cc_final: 0.7960 (t0) REVERT: F 86 ASP cc_start: 0.9008 (m-30) cc_final: 0.8669 (m-30) REVERT: F 105 GLN cc_start: 0.8494 (pm20) cc_final: 0.8093 (pm20) REVERT: F 128 LEU cc_start: 0.8946 (mp) cc_final: 0.8578 (mm) REVERT: F 171 PHE cc_start: 0.7757 (m-80) cc_final: 0.7163 (m-80) REVERT: G 4 MET cc_start: 0.8902 (mtp) cc_final: 0.8066 (mtp) REVERT: G 17 ASP cc_start: 0.8800 (t0) cc_final: 0.8310 (m-30) REVERT: G 78 LEU cc_start: 0.9238 (mt) cc_final: 0.9031 (tm) REVERT: G 139 PHE cc_start: 0.8154 (p90) cc_final: 0.7568 (p90) REVERT: G 148 TRP cc_start: 0.7006 (m100) cc_final: 0.6206 (m100) REVERT: G 155 GLN cc_start: 0.8387 (mm-40) cc_final: 0.8071 (mp10) REVERT: G 173 TYR cc_start: 0.6159 (OUTLIER) cc_final: 0.5846 (p90) REVERT: H 3 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8202 (pm20) REVERT: H 6 GLU cc_start: 0.7462 (mp0) cc_final: 0.6293 (mp0) REVERT: H 22 CYS cc_start: 0.8551 (t) cc_final: 0.8146 (t) REVERT: H 72 ASP cc_start: 0.8369 (t0) cc_final: 0.7930 (t0) REVERT: H 86 ASP cc_start: 0.8997 (m-30) cc_final: 0.8662 (m-30) REVERT: H 105 GLN cc_start: 0.8346 (pm20) cc_final: 0.7576 (pm20) REVERT: I 4 MET cc_start: 0.8874 (mtp) cc_final: 0.7967 (mtp) REVERT: I 17 ASP cc_start: 0.8711 (t0) cc_final: 0.8232 (m-30) REVERT: I 82 ASP cc_start: 0.8331 (m-30) cc_final: 0.7940 (m-30) REVERT: I 139 PHE cc_start: 0.8117 (p90) cc_final: 0.7866 (p90) REVERT: I 148 TRP cc_start: 0.6978 (m100) cc_final: 0.6203 (m100) REVERT: I 155 GLN cc_start: 0.8406 (mm-40) cc_final: 0.8128 (mp10) REVERT: I 167 ASP cc_start: 0.7700 (t0) cc_final: 0.7451 (t0) REVERT: I 173 TYR cc_start: 0.6312 (OUTLIER) cc_final: 0.5688 (p90) REVERT: I 195 GLU cc_start: 0.8829 (tt0) cc_final: 0.8629 (tm-30) REVERT: J 3 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8177 (pm20) REVERT: J 6 GLU cc_start: 0.7720 (mp0) cc_final: 0.6779 (mp0) REVERT: J 22 CYS cc_start: 0.8716 (t) cc_final: 0.8276 (t) REVERT: J 72 ASP cc_start: 0.8532 (t0) cc_final: 0.8090 (t0) REVERT: J 86 ASP cc_start: 0.9026 (m-30) cc_final: 0.8692 (m-30) REVERT: J 105 GLN cc_start: 0.8509 (pm20) cc_final: 0.8097 (pm20) REVERT: J 171 PHE cc_start: 0.7675 (m-80) cc_final: 0.6984 (m-80) REVERT: J 215 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8765 (tmtt) REVERT: J 217 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8172 (tm-30) REVERT: K 3 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8182 (pm20) REVERT: K 6 GLU cc_start: 0.7709 (mp0) cc_final: 0.6756 (mp0) REVERT: K 22 CYS cc_start: 0.8748 (t) cc_final: 0.8313 (t) REVERT: K 72 ASP cc_start: 0.8382 (t0) cc_final: 0.7948 (t0) REVERT: K 86 ASP cc_start: 0.9021 (m-30) cc_final: 0.8679 (m-30) REVERT: K 105 GLN cc_start: 0.8488 (pm20) cc_final: 0.8084 (pm20) REVERT: K 128 LEU cc_start: 0.7169 (tp) cc_final: 0.6843 (tp) REVERT: K 171 PHE cc_start: 0.7576 (m-80) cc_final: 0.7022 (m-80) REVERT: L 4 MET cc_start: 0.9032 (mtp) cc_final: 0.8115 (mtp) REVERT: L 17 ASP cc_start: 0.8774 (t0) cc_final: 0.8303 (m-30) REVERT: L 78 LEU cc_start: 0.9208 (mt) cc_final: 0.8991 (tm) REVERT: L 108 ARG cc_start: 0.6678 (tmm-80) cc_final: 0.6399 (tmm-80) REVERT: L 123 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6871 (tt0) REVERT: L 139 PHE cc_start: 0.8390 (p90) cc_final: 0.8076 (p90) REVERT: L 145 LYS cc_start: 0.8886 (mttp) cc_final: 0.8661 (mmtt) REVERT: L 167 ASP cc_start: 0.7725 (t0) cc_final: 0.7493 (t0) outliers start: 45 outliers final: 21 residues processed: 422 average time/residue: 1.1518 time to fit residues: 556.9220 Evaluate side-chains 399 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 367 time to evaluate : 2.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain D residue 150 ARG Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 11 CYS Chi-restraints excluded: chain F residue 108 CYS Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 173 TYR Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 173 TYR Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 11 CYS Chi-restraints excluded: chain J residue 108 CYS Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain J residue 215 LYS Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 11 CYS Chi-restraints excluded: chain K residue 108 CYS Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 123 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 27 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 218 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 195 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 118 optimal weight: 4.9990 chunk 174 optimal weight: 6.9990 chunk 139 optimal weight: 7.9990 chunk 193 optimal weight: 10.0000 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 137 ASN ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 GLN ** G 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 176 GLN I 137 ASN ** J 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.116482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.065403 restraints weight = 36300.906| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 3.09 r_work: 0.2572 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2438 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21016 Z= 0.168 Angle : 0.728 11.357 28704 Z= 0.373 Chirality : 0.047 0.169 3220 Planarity : 0.006 0.065 3648 Dihedral : 5.691 54.847 2867 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.47 % Allowed : 17.49 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 0.00 (0.17), residues: 2640 helix: -0.92 (0.47), residues: 124 sheet: 1.18 (0.16), residues: 936 loop : -0.68 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 148 HIS 0.003 0.001 HIS G 189 PHE 0.013 0.002 PHE B 153 TYR 0.025 0.002 TYR H 181 ARG 0.011 0.001 ARG L 142 Details of bonding type rmsd hydrogen bonds : bond 0.03403 ( 709) hydrogen bonds : angle 5.73448 ( 1995) SS BOND : bond 0.00677 ( 56) SS BOND : angle 1.75538 ( 112) covalent geometry : bond 0.00393 (20960) covalent geometry : angle 0.72104 (28592) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 386 time to evaluate : 2.287 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 134 MET cc_start: 0.9090 (tpp) cc_final: 0.8708 (mpp) REVERT: B 164 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8084 (mm-30) REVERT: C 149 GLU cc_start: 0.8535 (mp0) cc_final: 0.8050 (mp0) REVERT: C 164 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8127 (mm-30) REVERT: D 134 MET cc_start: 0.9015 (tpp) cc_final: 0.8604 (mpp) REVERT: D 150 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.8601 (mmp80) REVERT: D 164 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8153 (mm-30) REVERT: E 17 ASP cc_start: 0.8901 (t0) cc_final: 0.8405 (m-30) REVERT: E 23 CYS cc_start: 0.7260 (t) cc_final: 0.6058 (t) REVERT: E 78 LEU cc_start: 0.9179 (mt) cc_final: 0.8902 (tm) REVERT: E 139 PHE cc_start: 0.8322 (p90) cc_final: 0.7577 (p90) REVERT: E 167 ASP cc_start: 0.7752 (t0) cc_final: 0.7457 (t0) REVERT: E 173 TYR cc_start: 0.6762 (OUTLIER) cc_final: 0.6326 (p90) REVERT: E 211 ARG cc_start: 0.7780 (ttp-170) cc_final: 0.7488 (ptm160) REVERT: F 3 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8178 (pm20) REVERT: F 6 GLU cc_start: 0.7707 (mp0) cc_final: 0.6876 (mp0) REVERT: F 22 CYS cc_start: 0.8663 (t) cc_final: 0.8168 (t) REVERT: F 26 ARG cc_start: 0.8519 (pmm-80) cc_final: 0.8186 (pmm-80) REVERT: F 27 PHE cc_start: 0.8339 (m-80) cc_final: 0.8125 (m-80) REVERT: F 72 ASP cc_start: 0.8430 (t0) cc_final: 0.7959 (t0) REVERT: F 86 ASP cc_start: 0.9016 (m-30) cc_final: 0.8660 (m-30) REVERT: F 105 GLN cc_start: 0.8501 (pm20) cc_final: 0.8159 (pm20) REVERT: F 128 LEU cc_start: 0.8933 (mp) cc_final: 0.8547 (mm) REVERT: F 171 PHE cc_start: 0.7841 (m-80) cc_final: 0.7214 (m-80) REVERT: G 17 ASP cc_start: 0.8869 (t0) cc_final: 0.8376 (m-30) REVERT: G 23 CYS cc_start: 0.7057 (t) cc_final: 0.6598 (t) REVERT: G 78 LEU cc_start: 0.9262 (mt) cc_final: 0.9058 (tm) REVERT: G 139 PHE cc_start: 0.8217 (p90) cc_final: 0.7514 (p90) REVERT: G 148 TRP cc_start: 0.7117 (m100) cc_final: 0.6195 (m100) REVERT: G 155 GLN cc_start: 0.8420 (mm-40) cc_final: 0.8121 (mp10) REVERT: G 173 TYR cc_start: 0.6296 (OUTLIER) cc_final: 0.5744 (p90) REVERT: H 3 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8239 (pm20) REVERT: H 6 GLU cc_start: 0.7564 (mp0) cc_final: 0.6248 (mp0) REVERT: H 72 ASP cc_start: 0.8414 (t0) cc_final: 0.7942 (t0) REVERT: H 86 ASP cc_start: 0.8995 (m-30) cc_final: 0.8642 (m-30) REVERT: H 105 GLN cc_start: 0.8350 (pm20) cc_final: 0.7529 (pm20) REVERT: H 171 PHE cc_start: 0.7758 (m-80) cc_final: 0.7172 (m-80) REVERT: I 17 ASP cc_start: 0.9005 (t0) cc_final: 0.8365 (m-30) REVERT: I 23 CYS cc_start: 0.7040 (t) cc_final: 0.5921 (t) REVERT: I 139 PHE cc_start: 0.8312 (p90) cc_final: 0.7600 (p90) REVERT: I 148 TRP cc_start: 0.7121 (m100) cc_final: 0.6359 (m100) REVERT: I 155 GLN cc_start: 0.8453 (mm-40) cc_final: 0.8199 (mp10) REVERT: I 167 ASP cc_start: 0.7747 (t0) cc_final: 0.7447 (t0) REVERT: I 173 TYR cc_start: 0.6604 (OUTLIER) cc_final: 0.6246 (p90) REVERT: J 3 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8206 (pm20) REVERT: J 6 GLU cc_start: 0.7746 (mp0) cc_final: 0.6875 (mp0) REVERT: J 22 CYS cc_start: 0.8662 (t) cc_final: 0.8234 (t) REVERT: J 72 ASP cc_start: 0.8591 (t0) cc_final: 0.8036 (t0) REVERT: J 75 LYS cc_start: 0.9455 (OUTLIER) cc_final: 0.9156 (mttm) REVERT: J 86 ASP cc_start: 0.9009 (m-30) cc_final: 0.8649 (m-30) REVERT: J 105 GLN cc_start: 0.8473 (pm20) cc_final: 0.8129 (pm20) REVERT: J 128 LEU cc_start: 0.7809 (mm) cc_final: 0.6940 (mm) REVERT: J 171 PHE cc_start: 0.7796 (m-80) cc_final: 0.7192 (m-80) REVERT: J 217 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8260 (tm-30) REVERT: K 3 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8217 (pm20) REVERT: K 6 GLU cc_start: 0.7705 (mp0) cc_final: 0.6828 (mp0) REVERT: K 22 CYS cc_start: 0.8653 (t) cc_final: 0.8229 (t) REVERT: K 72 ASP cc_start: 0.8426 (t0) cc_final: 0.7954 (t0) REVERT: K 86 ASP cc_start: 0.9014 (m-30) cc_final: 0.8651 (m-30) REVERT: K 105 GLN cc_start: 0.8470 (pm20) cc_final: 0.8126 (pm20) REVERT: K 171 PHE cc_start: 0.7672 (m-80) cc_final: 0.7054 (m-80) REVERT: L 17 ASP cc_start: 0.8866 (t0) cc_final: 0.8369 (m-30) REVERT: L 108 ARG cc_start: 0.6745 (tmm-80) cc_final: 0.5859 (tmm-80) REVERT: L 123 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7116 (tt0) REVERT: L 139 PHE cc_start: 0.8393 (p90) cc_final: 0.8170 (p90) REVERT: L 145 LYS cc_start: 0.8988 (mttp) cc_final: 0.8709 (mmtt) REVERT: L 167 ASP cc_start: 0.7758 (t0) cc_final: 0.7502 (t0) REVERT: L 173 TYR cc_start: 0.6044 (p90) cc_final: 0.4898 (p90) outliers start: 57 outliers final: 23 residues processed: 431 average time/residue: 1.1568 time to fit residues: 575.6060 Evaluate side-chains 394 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 361 time to evaluate : 2.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain D residue 150 ARG Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 131 SER Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 11 CYS Chi-restraints excluded: chain F residue 108 CYS Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 88 CYS Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 173 TYR Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 88 CYS Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 173 TYR Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 11 CYS Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 108 CYS Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 11 CYS Chi-restraints excluded: chain K residue 108 CYS Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain K residue 202 ASN Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 123 GLU Chi-restraints excluded: chain L residue 197 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 239 optimal weight: 3.9990 chunk 38 optimal weight: 0.0030 chunk 232 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 255 optimal weight: 6.9990 chunk 179 optimal weight: 8.9990 chunk 187 optimal weight: 3.9990 chunk 208 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 79 GLN E 137 ASN ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 GLN ** G 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 176 GLN I 79 GLN I 137 ASN J 76 ASN ** J 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 GLN L 79 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.117019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.066605 restraints weight = 36146.530| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 3.05 r_work: 0.2590 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2455 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21016 Z= 0.139 Angle : 0.718 12.936 28704 Z= 0.364 Chirality : 0.047 0.164 3220 Planarity : 0.006 0.064 3648 Dihedral : 5.498 58.923 2867 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.82 % Allowed : 18.53 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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 (0.17), residues: 2640 helix: -1.02 (0.48), residues: 124 sheet: 1.34 (0.16), residues: 936 loop : -0.66 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 148 HIS 0.003 0.001 HIS L 198 PHE 0.026 0.002 PHE J 27 TYR 0.030 0.002 TYR H 181 ARG 0.009 0.001 ARG G 211 Details of bonding type rmsd hydrogen bonds : bond 0.03215 ( 709) hydrogen bonds : angle 5.57438 ( 1995) SS BOND : bond 0.00583 ( 56) SS BOND : angle 1.63932 ( 112) covalent geometry : bond 0.00319 (20960) covalent geometry : angle 0.71177 (28592) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 380 time to evaluate : 2.315 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 134 MET cc_start: 0.9056 (tpp) cc_final: 0.8763 (mtt) REVERT: B 134 MET cc_start: 0.8884 (tpp) cc_final: 0.8520 (mtt) REVERT: B 150 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.8655 (mmp80) REVERT: B 164 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8080 (mm-30) REVERT: C 134 MET cc_start: 0.9077 (tpp) cc_final: 0.8694 (mtt) REVERT: C 149 GLU cc_start: 0.8584 (mp0) cc_final: 0.8088 (mp0) REVERT: C 164 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8099 (mm-30) REVERT: D 134 MET cc_start: 0.8972 (tpp) cc_final: 0.8685 (mtt) REVERT: D 150 ARG cc_start: 0.9087 (OUTLIER) cc_final: 0.8602 (mmp80) REVERT: D 164 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8096 (mm-30) REVERT: E 4 MET cc_start: 0.8547 (ttm) cc_final: 0.8274 (ttm) REVERT: E 17 ASP cc_start: 0.8920 (t0) cc_final: 0.8492 (m-30) REVERT: E 50 GLU cc_start: 0.9343 (mt-10) cc_final: 0.8704 (pp20) REVERT: E 108 ARG cc_start: 0.6558 (tmm-80) cc_final: 0.6243 (tmm-80) REVERT: E 136 LEU cc_start: 0.8844 (mp) cc_final: 0.8550 (pt) REVERT: E 139 PHE cc_start: 0.8282 (p90) cc_final: 0.7345 (p90) REVERT: E 155 GLN cc_start: 0.8416 (mm-40) cc_final: 0.8138 (mp10) REVERT: E 173 TYR cc_start: 0.6755 (OUTLIER) cc_final: 0.6023 (p90) REVERT: E 211 ARG cc_start: 0.7858 (ttp-170) cc_final: 0.7564 (ptm160) REVERT: F 3 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8188 (pm20) REVERT: F 6 GLU cc_start: 0.7622 (mp0) cc_final: 0.6741 (mp0) REVERT: F 22 CYS cc_start: 0.8641 (t) cc_final: 0.8175 (t) REVERT: F 26 ARG cc_start: 0.8502 (pmm-80) cc_final: 0.8132 (pmm-80) REVERT: F 72 ASP cc_start: 0.8438 (t0) cc_final: 0.7970 (t0) REVERT: F 86 ASP cc_start: 0.8989 (m-30) cc_final: 0.8622 (m-30) REVERT: F 105 GLN cc_start: 0.8525 (pm20) cc_final: 0.8132 (pm20) REVERT: F 128 LEU cc_start: 0.8889 (mp) cc_final: 0.8539 (mm) REVERT: F 171 PHE cc_start: 0.7766 (m-80) cc_final: 0.7123 (m-80) REVERT: G 4 MET cc_start: 0.8723 (ttm) cc_final: 0.8067 (ttm) REVERT: G 17 ASP cc_start: 0.8859 (t0) cc_final: 0.8436 (m-30) REVERT: G 50 GLU cc_start: 0.9342 (mt-10) cc_final: 0.8707 (pp20) REVERT: G 117 ILE cc_start: 0.7607 (OUTLIER) cc_final: 0.7403 (mt) REVERT: G 139 PHE cc_start: 0.8166 (p90) cc_final: 0.7482 (p90) REVERT: G 148 TRP cc_start: 0.7013 (m100) cc_final: 0.6199 (m100) REVERT: G 155 GLN cc_start: 0.8434 (mm-40) cc_final: 0.8181 (mp10) REVERT: G 173 TYR cc_start: 0.6001 (OUTLIER) cc_final: 0.5678 (p90) REVERT: H 3 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8194 (pm20) REVERT: H 6 GLU cc_start: 0.7485 (mp0) cc_final: 0.6213 (mp0) REVERT: H 72 ASP cc_start: 0.8414 (t0) cc_final: 0.7924 (t0) REVERT: H 79 SER cc_start: 0.9399 (m) cc_final: 0.8823 (p) REVERT: H 86 ASP cc_start: 0.8974 (m-30) cc_final: 0.8612 (m-30) REVERT: H 105 GLN cc_start: 0.8291 (pm20) cc_final: 0.7536 (pm20) REVERT: H 128 LEU cc_start: 0.7705 (mm) cc_final: 0.6909 (mm) REVERT: I 4 MET cc_start: 0.8687 (ttm) cc_final: 0.8047 (ttm) REVERT: I 17 ASP cc_start: 0.9011 (t0) cc_final: 0.8427 (m-30) REVERT: I 139 PHE cc_start: 0.8277 (p90) cc_final: 0.7565 (p90) REVERT: I 148 TRP cc_start: 0.7015 (m100) cc_final: 0.6268 (m100) REVERT: I 155 GLN cc_start: 0.8419 (mm-40) cc_final: 0.8204 (mp10) REVERT: I 173 TYR cc_start: 0.6659 (OUTLIER) cc_final: 0.6035 (p90) REVERT: J 3 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8218 (pm20) REVERT: J 6 GLU cc_start: 0.7674 (mp0) cc_final: 0.6573 (mp0) REVERT: J 22 CYS cc_start: 0.8618 (t) cc_final: 0.8151 (t) REVERT: J 72 ASP cc_start: 0.8593 (t0) cc_final: 0.8122 (t0) REVERT: J 86 ASP cc_start: 0.8996 (m-30) cc_final: 0.8620 (m-30) REVERT: J 105 GLN cc_start: 0.8478 (pm20) cc_final: 0.7982 (pm20) REVERT: J 128 LEU cc_start: 0.7724 (mm) cc_final: 0.6900 (mm) REVERT: J 171 PHE cc_start: 0.7785 (m-80) cc_final: 0.7128 (m-80) REVERT: J 217 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8402 (tm-30) REVERT: K 3 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.8228 (pm20) REVERT: K 6 GLU cc_start: 0.7686 (mp0) cc_final: 0.6609 (mp0) REVERT: K 22 CYS cc_start: 0.8631 (t) cc_final: 0.8214 (t) REVERT: K 72 ASP cc_start: 0.8419 (t0) cc_final: 0.7928 (t0) REVERT: K 86 ASP cc_start: 0.8983 (m-30) cc_final: 0.8611 (m-30) REVERT: K 105 GLN cc_start: 0.8477 (pm20) cc_final: 0.7981 (pm20) REVERT: K 171 PHE cc_start: 0.7708 (m-80) cc_final: 0.7064 (m-80) REVERT: L 17 ASP cc_start: 0.8996 (t0) cc_final: 0.8403 (m-30) REVERT: L 23 CYS cc_start: 0.7179 (t) cc_final: 0.6288 (t) REVERT: L 123 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7470 (tt0) REVERT: L 139 PHE cc_start: 0.8449 (p90) cc_final: 0.8149 (p90) REVERT: L 145 LYS cc_start: 0.8992 (mttp) cc_final: 0.8706 (mmtt) REVERT: L 167 ASP cc_start: 0.7760 (t0) cc_final: 0.7459 (t0) outliers start: 42 outliers final: 17 residues processed: 412 average time/residue: 1.1666 time to fit residues: 549.8986 Evaluate side-chains 394 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 366 time to evaluate : 2.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain D residue 150 ARG Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 108 CYS Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain G residue 88 CYS Chi-restraints excluded: chain G residue 117 ILE Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 173 TYR Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain H residue 156 THR Chi-restraints excluded: chain I residue 88 CYS Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 173 TYR Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 108 CYS Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 11 CYS Chi-restraints excluded: chain K residue 108 CYS Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain L residue 123 GLU Chi-restraints excluded: chain L residue 197 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 191 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 203 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 198 optimal weight: 0.6980 chunk 125 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 GLN G 79 GLN G 138 ASN ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 176 GLN I 137 ASN ** J 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.116321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.065583 restraints weight = 36410.929| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 3.07 r_work: 0.2575 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2440 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21016 Z= 0.166 Angle : 0.736 11.920 28704 Z= 0.374 Chirality : 0.047 0.171 3220 Planarity : 0.006 0.065 3648 Dihedral : 5.423 52.190 2867 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.48 % Allowed : 19.84 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 0.09 (0.17), residues: 2640 helix: -1.10 (0.47), residues: 124 sheet: 1.43 (0.16), residues: 916 loop : -0.71 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 148 HIS 0.003 0.001 HIS L 198 PHE 0.012 0.002 PHE D 153 TYR 0.030 0.002 TYR H 181 ARG 0.009 0.001 ARG G 108 Details of bonding type rmsd hydrogen bonds : bond 0.03254 ( 709) hydrogen bonds : angle 5.52960 ( 1995) SS BOND : bond 0.00763 ( 56) SS BOND : angle 1.87802 ( 112) covalent geometry : bond 0.00390 (20960) covalent geometry : angle 0.72799 (28592) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 379 time to evaluate : 2.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.9068 (tpp) cc_final: 0.8756 (mtt) REVERT: B 134 MET cc_start: 0.8925 (tpp) cc_final: 0.8584 (mtt) REVERT: B 164 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8098 (mm-30) REVERT: C 134 MET cc_start: 0.9096 (tpp) cc_final: 0.8698 (mtt) REVERT: C 149 GLU cc_start: 0.8617 (mp0) cc_final: 0.8093 (mp0) REVERT: C 164 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8102 (mm-30) REVERT: D 134 MET cc_start: 0.8991 (tpp) cc_final: 0.8660 (mtt) REVERT: D 150 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.8550 (mmp80) REVERT: D 164 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8135 (mm-30) REVERT: E 17 ASP cc_start: 0.9072 (t0) cc_final: 0.8483 (m-30) REVERT: E 108 ARG cc_start: 0.6741 (tmm-80) cc_final: 0.6245 (tmm-80) REVERT: E 136 LEU cc_start: 0.8755 (mp) cc_final: 0.8490 (pt) REVERT: E 139 PHE cc_start: 0.8253 (p90) cc_final: 0.7303 (p90) REVERT: E 155 GLN cc_start: 0.8410 (mm-40) cc_final: 0.8139 (mp10) REVERT: E 173 TYR cc_start: 0.6831 (OUTLIER) cc_final: 0.6262 (p90) REVERT: E 211 ARG cc_start: 0.7884 (ttp-170) cc_final: 0.7580 (ptm160) REVERT: F 3 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8160 (pm20) REVERT: F 6 GLU cc_start: 0.7626 (mp0) cc_final: 0.6735 (mp0) REVERT: F 22 CYS cc_start: 0.8651 (t) cc_final: 0.8144 (t) REVERT: F 26 ARG cc_start: 0.8516 (pmm-80) cc_final: 0.8302 (pmm-80) REVERT: F 72 ASP cc_start: 0.8465 (t0) cc_final: 0.7995 (t0) REVERT: F 79 SER cc_start: 0.9342 (m) cc_final: 0.8707 (p) REVERT: F 86 ASP cc_start: 0.8978 (m-30) cc_final: 0.8614 (m-30) REVERT: F 105 GLN cc_start: 0.8530 (pm20) cc_final: 0.8144 (pm20) REVERT: F 128 LEU cc_start: 0.8875 (mp) cc_final: 0.8525 (mm) REVERT: F 171 PHE cc_start: 0.7908 (m-80) cc_final: 0.7260 (m-80) REVERT: G 17 ASP cc_start: 0.9011 (t0) cc_final: 0.8443 (m-30) REVERT: G 23 CYS cc_start: 0.7048 (t) cc_final: 0.6358 (t) REVERT: G 136 LEU cc_start: 0.8851 (mp) cc_final: 0.8491 (pt) REVERT: G 139 PHE cc_start: 0.8143 (p90) cc_final: 0.7220 (p90) REVERT: G 148 TRP cc_start: 0.7047 (m100) cc_final: 0.6295 (m100) REVERT: G 155 GLN cc_start: 0.8417 (mm-40) cc_final: 0.8172 (mp10) REVERT: G 173 TYR cc_start: 0.6088 (OUTLIER) cc_final: 0.5767 (p90) REVERT: H 3 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8407 (pm20) REVERT: H 6 GLU cc_start: 0.7521 (mp0) cc_final: 0.6267 (mp0) REVERT: H 72 ASP cc_start: 0.8468 (t0) cc_final: 0.8003 (t0) REVERT: H 79 SER cc_start: 0.9396 (m) cc_final: 0.8817 (p) REVERT: H 86 ASP cc_start: 0.8959 (m-30) cc_final: 0.8639 (m-30) REVERT: H 105 GLN cc_start: 0.8247 (pm20) cc_final: 0.7495 (pm20) REVERT: H 164 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9134 (mp) REVERT: H 171 PHE cc_start: 0.7408 (m-80) cc_final: 0.6909 (m-80) REVERT: I 17 ASP cc_start: 0.9041 (t0) cc_final: 0.8447 (m-30) REVERT: I 23 CYS cc_start: 0.7202 (t) cc_final: 0.6340 (t) REVERT: I 108 ARG cc_start: 0.7188 (tmm-80) cc_final: 0.6855 (tmm-80) REVERT: I 136 LEU cc_start: 0.8743 (mp) cc_final: 0.8484 (pt) REVERT: I 139 PHE cc_start: 0.8282 (p90) cc_final: 0.7366 (p90) REVERT: I 148 TRP cc_start: 0.7056 (m100) cc_final: 0.6285 (m100) REVERT: I 155 GLN cc_start: 0.8397 (mm-40) cc_final: 0.8178 (mp10) REVERT: I 173 TYR cc_start: 0.6739 (p90) cc_final: 0.6140 (p90) REVERT: J 3 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8186 (pm20) REVERT: J 6 GLU cc_start: 0.7664 (mp0) cc_final: 0.6585 (mp0) REVERT: J 22 CYS cc_start: 0.8643 (t) cc_final: 0.8172 (t) REVERT: J 72 ASP cc_start: 0.8572 (t0) cc_final: 0.7976 (t0) REVERT: J 75 LYS cc_start: 0.9458 (OUTLIER) cc_final: 0.9147 (mttm) REVERT: J 79 SER cc_start: 0.9364 (m) cc_final: 0.8802 (p) REVERT: J 86 ASP cc_start: 0.8967 (m-30) cc_final: 0.8601 (m-30) REVERT: J 105 GLN cc_start: 0.8503 (pm20) cc_final: 0.8008 (pm20) REVERT: J 171 PHE cc_start: 0.7925 (m-80) cc_final: 0.7246 (m-80) REVERT: J 217 GLU cc_start: 0.8777 (tm-30) cc_final: 0.8171 (tm-30) REVERT: K 3 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8481 (pm20) REVERT: K 6 GLU cc_start: 0.7674 (mp0) cc_final: 0.6591 (mp0) REVERT: K 22 CYS cc_start: 0.8600 (t) cc_final: 0.8129 (t) REVERT: K 72 ASP cc_start: 0.8450 (t0) cc_final: 0.7980 (t0) REVERT: K 79 SER cc_start: 0.9352 (m) cc_final: 0.8721 (p) REVERT: K 86 ASP cc_start: 0.8961 (m-30) cc_final: 0.8593 (m-30) REVERT: K 105 GLN cc_start: 0.8490 (pm20) cc_final: 0.7995 (pm20) REVERT: K 171 PHE cc_start: 0.7695 (m-80) cc_final: 0.7032 (m-80) REVERT: L 17 ASP cc_start: 0.9033 (t0) cc_final: 0.8465 (m-30) REVERT: L 23 CYS cc_start: 0.7221 (t) cc_final: 0.6872 (t) REVERT: L 108 ARG cc_start: 0.6698 (tmm-80) cc_final: 0.6215 (tmm-80) REVERT: L 145 LYS cc_start: 0.9009 (mttp) cc_final: 0.8709 (mmtt) REVERT: L 173 TYR cc_start: 0.5739 (p90) cc_final: 0.5480 (p90) outliers start: 34 outliers final: 17 residues processed: 406 average time/residue: 1.1924 time to fit residues: 553.4136 Evaluate side-chains 388 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 362 time to evaluate : 2.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 150 ARG Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 131 SER Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 11 CYS Chi-restraints excluded: chain F residue 108 CYS Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 173 TYR Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain H residue 144 CYS Chi-restraints excluded: chain H residue 156 THR Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 11 CYS Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 108 CYS Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 108 CYS Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain K residue 197 GLN Chi-restraints excluded: chain L residue 197 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 189 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 245 optimal weight: 0.5980 chunk 238 optimal weight: 6.9990 chunk 136 optimal weight: 20.0000 chunk 174 optimal weight: 8.9990 chunk 201 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 204 optimal weight: 1.9990 chunk 92 optimal weight: 0.4980 chunk 179 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 GLN ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 176 GLN ** J 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.116467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.066227 restraints weight = 36515.072| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 3.04 r_work: 0.2590 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2460 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21016 Z= 0.159 Angle : 0.748 12.191 28704 Z= 0.381 Chirality : 0.047 0.170 3220 Planarity : 0.006 0.064 3648 Dihedral : 5.283 23.051 2864 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.08 % Allowed : 20.57 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.17), residues: 2640 helix: -1.11 (0.47), residues: 124 sheet: 1.51 (0.17), residues: 916 loop : -0.70 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 148 HIS 0.003 0.001 HIS L 198 PHE 0.027 0.001 PHE J 27 TYR 0.028 0.002 TYR H 181 ARG 0.006 0.001 ARG L 18 Details of bonding type rmsd hydrogen bonds : bond 0.03190 ( 709) hydrogen bonds : angle 5.52559 ( 1995) SS BOND : bond 0.00678 ( 56) SS BOND : angle 1.89644 ( 112) covalent geometry : bond 0.00370 (20960) covalent geometry : angle 0.74041 (28592) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 381 time to evaluate : 2.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.9043 (tpp) cc_final: 0.8732 (mtt) REVERT: A 149 GLU cc_start: 0.8545 (mp0) cc_final: 0.8324 (mp0) REVERT: B 134 MET cc_start: 0.8874 (tpp) cc_final: 0.8552 (mtt) REVERT: B 164 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8123 (mm-30) REVERT: C 134 MET cc_start: 0.9054 (tpp) cc_final: 0.8738 (mtt) REVERT: C 149 GLU cc_start: 0.8642 (mp0) cc_final: 0.8108 (mp0) REVERT: C 164 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8123 (mm-30) REVERT: D 134 MET cc_start: 0.8970 (tpp) cc_final: 0.8677 (mtt) REVERT: D 150 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.8558 (mmp80) REVERT: D 164 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8137 (mm-30) REVERT: E 4 MET cc_start: 0.8550 (ttm) cc_final: 0.8114 (ttm) REVERT: E 17 ASP cc_start: 0.9072 (t0) cc_final: 0.8509 (m-30) REVERT: E 50 GLU cc_start: 0.9290 (OUTLIER) cc_final: 0.8911 (mp0) REVERT: E 88 CYS cc_start: 0.7983 (p) cc_final: 0.7608 (p) REVERT: E 136 LEU cc_start: 0.8737 (mp) cc_final: 0.8483 (pt) REVERT: E 139 PHE cc_start: 0.8296 (p90) cc_final: 0.7302 (p90) REVERT: E 173 TYR cc_start: 0.6956 (OUTLIER) cc_final: 0.6400 (p90) REVERT: E 211 ARG cc_start: 0.7912 (ttp-170) cc_final: 0.7605 (ptm160) REVERT: F 3 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8180 (pm20) REVERT: F 6 GLU cc_start: 0.7606 (mp0) cc_final: 0.6369 (mp0) REVERT: F 22 CYS cc_start: 0.8691 (t) cc_final: 0.8215 (t) REVERT: F 27 PHE cc_start: 0.8408 (m-80) cc_final: 0.8186 (m-80) REVERT: F 72 ASP cc_start: 0.8474 (t0) cc_final: 0.8008 (t0) REVERT: F 79 SER cc_start: 0.9329 (m) cc_final: 0.8685 (p) REVERT: F 86 ASP cc_start: 0.8975 (m-30) cc_final: 0.8589 (m-30) REVERT: F 105 GLN cc_start: 0.8551 (pm20) cc_final: 0.8016 (pm20) REVERT: F 128 LEU cc_start: 0.8895 (mp) cc_final: 0.8547 (mm) REVERT: F 171 PHE cc_start: 0.8066 (m-80) cc_final: 0.7400 (m-80) REVERT: G 17 ASP cc_start: 0.9011 (t0) cc_final: 0.8443 (m-30) REVERT: G 50 GLU cc_start: 0.9273 (OUTLIER) cc_final: 0.8892 (mp0) REVERT: G 139 PHE cc_start: 0.8164 (p90) cc_final: 0.7396 (p90) REVERT: G 148 TRP cc_start: 0.7122 (m100) cc_final: 0.6385 (m100) REVERT: G 155 GLN cc_start: 0.8357 (mm-40) cc_final: 0.8101 (mp10) REVERT: G 173 TYR cc_start: 0.6595 (OUTLIER) cc_final: 0.5951 (p90) REVERT: H 3 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8487 (pm20) REVERT: H 6 GLU cc_start: 0.7499 (mp0) cc_final: 0.6226 (mp0) REVERT: H 72 ASP cc_start: 0.8488 (t0) cc_final: 0.8026 (t0) REVERT: H 79 SER cc_start: 0.9392 (m) cc_final: 0.8814 (p) REVERT: H 86 ASP cc_start: 0.8950 (m-30) cc_final: 0.8602 (m-30) REVERT: H 105 GLN cc_start: 0.8206 (pm20) cc_final: 0.7447 (pm20) REVERT: H 128 LEU cc_start: 0.8055 (mm) cc_final: 0.7292 (mm) REVERT: H 164 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9207 (mp) REVERT: H 171 PHE cc_start: 0.7573 (m-80) cc_final: 0.7102 (m-80) REVERT: I 17 ASP cc_start: 0.9066 (t0) cc_final: 0.8462 (m-30) REVERT: I 50 GLU cc_start: 0.9277 (OUTLIER) cc_final: 0.8882 (mp0) REVERT: I 136 LEU cc_start: 0.8734 (mp) cc_final: 0.8496 (pt) REVERT: I 139 PHE cc_start: 0.8318 (p90) cc_final: 0.7339 (p90) REVERT: I 148 TRP cc_start: 0.7147 (m100) cc_final: 0.6381 (m100) REVERT: I 155 GLN cc_start: 0.8421 (mm-40) cc_final: 0.8201 (mp10) REVERT: I 173 TYR cc_start: 0.6915 (p90) cc_final: 0.6346 (p90) REVERT: J 3 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8182 (pm20) REVERT: J 6 GLU cc_start: 0.7645 (mp0) cc_final: 0.6544 (mp0) REVERT: J 22 CYS cc_start: 0.8680 (t) cc_final: 0.8213 (t) REVERT: J 72 ASP cc_start: 0.8617 (t0) cc_final: 0.8169 (t0) REVERT: J 79 SER cc_start: 0.9341 (m) cc_final: 0.8711 (p) REVERT: J 86 ASP cc_start: 0.8968 (m-30) cc_final: 0.8579 (m-30) REVERT: J 105 GLN cc_start: 0.8525 (pm20) cc_final: 0.7973 (pm20) REVERT: J 128 LEU cc_start: 0.8031 (mm) cc_final: 0.7169 (mm) REVERT: J 171 PHE cc_start: 0.8069 (m-80) cc_final: 0.7379 (m-80) REVERT: J 217 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8182 (tm-30) REVERT: K 3 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8449 (pm20) REVERT: K 6 GLU cc_start: 0.7639 (mp0) cc_final: 0.6551 (mp0) REVERT: K 22 CYS cc_start: 0.8596 (t) cc_final: 0.8091 (t) REVERT: K 26 ARG cc_start: 0.7635 (ppt170) cc_final: 0.7399 (pmt-80) REVERT: K 72 ASP cc_start: 0.8470 (t0) cc_final: 0.7948 (t0) REVERT: K 79 SER cc_start: 0.9345 (m) cc_final: 0.8708 (p) REVERT: K 86 ASP cc_start: 0.8969 (m-30) cc_final: 0.8576 (m-30) REVERT: K 105 GLN cc_start: 0.8515 (pm20) cc_final: 0.8091 (pm20) REVERT: K 171 PHE cc_start: 0.7944 (m-80) cc_final: 0.7282 (m-80) REVERT: L 17 ASP cc_start: 0.9056 (t0) cc_final: 0.8489 (m-30) REVERT: L 23 CYS cc_start: 0.7252 (t) cc_final: 0.6942 (t) REVERT: L 50 GLU cc_start: 0.9263 (OUTLIER) cc_final: 0.8882 (mp0) REVERT: L 108 ARG cc_start: 0.6927 (tmm-80) cc_final: 0.6398 (tmm-80) REVERT: L 139 PHE cc_start: 0.8593 (p90) cc_final: 0.8391 (p90) REVERT: L 145 LYS cc_start: 0.9007 (mttp) cc_final: 0.8699 (mmtt) REVERT: L 173 TYR cc_start: 0.6306 (p90) cc_final: 0.5685 (p90) outliers start: 48 outliers final: 23 residues processed: 416 average time/residue: 1.1866 time to fit residues: 565.6313 Evaluate side-chains 399 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 364 time to evaluate : 2.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain D residue 150 ARG Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 131 SER Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 11 CYS Chi-restraints excluded: chain F residue 108 CYS Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 173 TYR Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain H residue 144 CYS Chi-restraints excluded: chain H residue 156 THR Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain I residue 50 GLU Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 11 CYS Chi-restraints excluded: chain J residue 108 CYS Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 11 CYS Chi-restraints excluded: chain K residue 108 CYS Chi-restraints excluded: chain K residue 156 THR Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain K residue 197 GLN Chi-restraints excluded: chain L residue 50 GLU Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 197 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 144 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 46 optimal weight: 0.2980 chunk 177 optimal weight: 9.9990 chunk 249 optimal weight: 7.9990 chunk 112 optimal weight: 8.9990 chunk 1 optimal weight: 0.6980 chunk 145 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 218 optimal weight: 10.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 GLN ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.116212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.065873 restraints weight = 36651.365| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 3.06 r_work: 0.2583 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2453 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.4645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21016 Z= 0.162 Angle : 0.763 12.833 28704 Z= 0.389 Chirality : 0.048 0.187 3220 Planarity : 0.006 0.065 3648 Dihedral : 5.268 26.630 2864 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.65 % Allowed : 21.40 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 0.15 (0.17), residues: 2640 helix: -1.12 (0.47), residues: 124 sheet: 1.53 (0.17), residues: 916 loop : -0.71 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 148 HIS 0.003 0.001 HIS L 198 PHE 0.031 0.001 PHE K 27 TYR 0.041 0.002 TYR H 181 ARG 0.010 0.001 ARG H 26 Details of bonding type rmsd hydrogen bonds : bond 0.03142 ( 709) hydrogen bonds : angle 5.49360 ( 1995) SS BOND : bond 0.00654 ( 56) SS BOND : angle 1.78808 ( 112) covalent geometry : bond 0.00379 (20960) covalent geometry : angle 0.75632 (28592) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 367 time to evaluate : 2.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.9048 (tpp) cc_final: 0.8759 (mtt) REVERT: A 149 GLU cc_start: 0.8586 (mp0) cc_final: 0.8345 (mp0) REVERT: B 109 GLU cc_start: 0.9219 (OUTLIER) cc_final: 0.9003 (mm-30) REVERT: B 134 MET cc_start: 0.8909 (tpp) cc_final: 0.8566 (mtt) REVERT: B 164 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8137 (mm-30) REVERT: C 134 MET cc_start: 0.9085 (tpp) cc_final: 0.8771 (mtt) REVERT: C 149 GLU cc_start: 0.8666 (mp0) cc_final: 0.8136 (mp0) REVERT: C 164 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8124 (mm-30) REVERT: D 109 GLU cc_start: 0.9201 (OUTLIER) cc_final: 0.8992 (mm-30) REVERT: D 134 MET cc_start: 0.8987 (tpp) cc_final: 0.8671 (mtt) REVERT: D 150 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.8530 (mmp80) REVERT: D 164 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8136 (mm-30) REVERT: E 17 ASP cc_start: 0.9109 (t0) cc_final: 0.8597 (m-30) REVERT: E 50 GLU cc_start: 0.9260 (mp0) cc_final: 0.8881 (mp0) REVERT: E 136 LEU cc_start: 0.8682 (mp) cc_final: 0.8411 (pt) REVERT: E 139 PHE cc_start: 0.8311 (p90) cc_final: 0.7292 (p90) REVERT: E 173 TYR cc_start: 0.7171 (p90) cc_final: 0.6499 (p90) REVERT: E 211 ARG cc_start: 0.7872 (ttp-170) cc_final: 0.7528 (ptm-80) REVERT: F 3 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8167 (pm20) REVERT: F 6 GLU cc_start: 0.7588 (mp0) cc_final: 0.6326 (mp0) REVERT: F 22 CYS cc_start: 0.8702 (t) cc_final: 0.8239 (t) REVERT: F 72 ASP cc_start: 0.8486 (t0) cc_final: 0.8013 (t0) REVERT: F 79 SER cc_start: 0.9318 (m) cc_final: 0.8666 (p) REVERT: F 86 ASP cc_start: 0.8971 (m-30) cc_final: 0.8598 (m-30) REVERT: F 105 GLN cc_start: 0.8523 (pm20) cc_final: 0.7980 (pm20) REVERT: F 128 LEU cc_start: 0.8902 (mp) cc_final: 0.8584 (mm) REVERT: F 171 PHE cc_start: 0.8166 (m-80) cc_final: 0.7501 (m-80) REVERT: G 17 ASP cc_start: 0.9039 (t0) cc_final: 0.8451 (m-30) REVERT: G 50 GLU cc_start: 0.9248 (mp0) cc_final: 0.8857 (mp0) REVERT: G 108 ARG cc_start: 0.6725 (tmm-80) cc_final: 0.6477 (tmm-80) REVERT: G 136 LEU cc_start: 0.8860 (mp) cc_final: 0.8482 (pt) REVERT: G 139 PHE cc_start: 0.8113 (p90) cc_final: 0.7035 (p90) REVERT: G 148 TRP cc_start: 0.7173 (m100) cc_final: 0.6432 (m100) REVERT: G 155 GLN cc_start: 0.8436 (mm-40) cc_final: 0.8196 (mp10) REVERT: H 3 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8378 (pm20) REVERT: H 6 GLU cc_start: 0.7446 (mp0) cc_final: 0.6192 (mp0) REVERT: H 26 ARG cc_start: 0.7582 (pmt-80) cc_final: 0.7330 (pmt-80) REVERT: H 72 ASP cc_start: 0.8483 (t0) cc_final: 0.8016 (t0) REVERT: H 79 SER cc_start: 0.9368 (m) cc_final: 0.8809 (p) REVERT: H 86 ASP cc_start: 0.8931 (m-30) cc_final: 0.8560 (m-30) REVERT: H 105 GLN cc_start: 0.8208 (pm20) cc_final: 0.7431 (pm20) REVERT: H 128 LEU cc_start: 0.8147 (mm) cc_final: 0.7382 (mm) REVERT: H 164 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9236 (mp) REVERT: H 171 PHE cc_start: 0.7875 (m-80) cc_final: 0.7309 (m-80) REVERT: I 17 ASP cc_start: 0.9092 (t0) cc_final: 0.8547 (m-30) REVERT: I 50 GLU cc_start: 0.9252 (mp0) cc_final: 0.8874 (mp0) REVERT: I 136 LEU cc_start: 0.8697 (mp) cc_final: 0.8458 (pt) REVERT: I 139 PHE cc_start: 0.8311 (p90) cc_final: 0.7329 (p90) REVERT: I 148 TRP cc_start: 0.7155 (m100) cc_final: 0.6379 (m100) REVERT: I 155 GLN cc_start: 0.8432 (mm-40) cc_final: 0.8211 (mp10) REVERT: I 173 TYR cc_start: 0.7061 (p90) cc_final: 0.6372 (p90) REVERT: J 3 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8182 (pm20) REVERT: J 6 GLU cc_start: 0.7616 (mp0) cc_final: 0.6454 (mp0) REVERT: J 22 CYS cc_start: 0.8677 (t) cc_final: 0.8225 (t) REVERT: J 26 ARG cc_start: 0.8442 (pmm-80) cc_final: 0.8157 (pmm-80) REVERT: J 27 PHE cc_start: 0.8434 (m-80) cc_final: 0.8225 (m-80) REVERT: J 72 ASP cc_start: 0.8586 (t0) cc_final: 0.8110 (OUTLIER) REVERT: J 79 SER cc_start: 0.9325 (m) cc_final: 0.8682 (p) REVERT: J 86 ASP cc_start: 0.8962 (m-30) cc_final: 0.8586 (m-30) REVERT: J 105 GLN cc_start: 0.8504 (pm20) cc_final: 0.7953 (pm20) REVERT: J 128 LEU cc_start: 0.8043 (mm) cc_final: 0.7178 (mm) REVERT: J 171 PHE cc_start: 0.8193 (m-80) cc_final: 0.7511 (m-80) REVERT: J 217 GLU cc_start: 0.8828 (tm-30) cc_final: 0.8234 (tm-30) REVERT: K 3 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8363 (pm20) REVERT: K 6 GLU cc_start: 0.7607 (mp0) cc_final: 0.6539 (mp0) REVERT: K 22 CYS cc_start: 0.8615 (t) cc_final: 0.8103 (t) REVERT: K 72 ASP cc_start: 0.8542 (t0) cc_final: 0.8095 (t0) REVERT: K 79 SER cc_start: 0.9339 (m) cc_final: 0.8698 (p) REVERT: K 86 ASP cc_start: 0.8967 (m-30) cc_final: 0.8594 (m-30) REVERT: K 105 GLN cc_start: 0.8488 (pm20) cc_final: 0.8066 (pm20) REVERT: K 171 PHE cc_start: 0.8118 (m-80) cc_final: 0.7474 (m-80) REVERT: L 17 ASP cc_start: 0.9089 (t0) cc_final: 0.8585 (m-30) REVERT: L 23 CYS cc_start: 0.7338 (t) cc_final: 0.7020 (t) REVERT: L 50 GLU cc_start: 0.9240 (mp0) cc_final: 0.8858 (mp0) REVERT: L 108 ARG cc_start: 0.6989 (tmm-80) cc_final: 0.6430 (tmm-80) REVERT: L 139 PHE cc_start: 0.8715 (p90) cc_final: 0.8507 (p90) REVERT: L 145 LYS cc_start: 0.9010 (mttp) cc_final: 0.8702 (mmtt) REVERT: L 167 ASP cc_start: 0.7966 (t0) cc_final: 0.7717 (p0) outliers start: 38 outliers final: 17 residues processed: 395 average time/residue: 1.1600 time to fit residues: 524.5566 Evaluate side-chains 385 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 361 time to evaluate : 2.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 150 ARG Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 131 SER Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 108 CYS Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain H residue 144 CYS Chi-restraints excluded: chain H residue 156 THR Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 108 CYS Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 108 CYS Chi-restraints excluded: chain K residue 156 THR Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain K residue 197 GLN Chi-restraints excluded: chain L residue 197 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 88 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 chunk 147 optimal weight: 0.9980 chunk 166 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 GLN ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.115444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.065026 restraints weight = 36693.370| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 3.06 r_work: 0.2566 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2436 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.4732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 21016 Z= 0.198 Angle : 0.772 12.949 28704 Z= 0.397 Chirality : 0.048 0.186 3220 Planarity : 0.006 0.066 3648 Dihedral : 5.327 27.036 2864 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.30 % Allowed : 21.66 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 2640 helix: -1.21 (0.46), residues: 124 sheet: 1.51 (0.17), residues: 912 loop : -0.72 (0.16), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 148 HIS 0.003 0.001 HIS L 198 PHE 0.033 0.001 PHE F 27 TYR 0.034 0.002 TYR G 173 ARG 0.006 0.001 ARG I 108 Details of bonding type rmsd hydrogen bonds : bond 0.03282 ( 709) hydrogen bonds : angle 5.54033 ( 1995) SS BOND : bond 0.00657 ( 56) SS BOND : angle 1.89302 ( 112) covalent geometry : bond 0.00466 (20960) covalent geometry : angle 0.76389 (28592) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 368 time to evaluate : 2.382 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: A 134 MET cc_start: 0.9059 (tpp) cc_final: 0.8740 (mtt) REVERT: A 149 GLU cc_start: 0.8578 (mp0) cc_final: 0.8323 (mp0) REVERT: B 134 MET cc_start: 0.8904 (tpp) cc_final: 0.8583 (mtt) REVERT: B 164 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8118 (mm-30) REVERT: C 134 MET cc_start: 0.9099 (tpp) cc_final: 0.8781 (mtt) REVERT: C 149 GLU cc_start: 0.8650 (mp0) cc_final: 0.8128 (mp0) REVERT: C 164 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8086 (mm-30) REVERT: D 134 MET cc_start: 0.9002 (tpp) cc_final: 0.8681 (mtt) REVERT: D 150 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.8737 (mmt-90) REVERT: D 164 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8128 (mm-30) REVERT: E 17 ASP cc_start: 0.9096 (t0) cc_final: 0.8578 (m-30) REVERT: E 50 GLU cc_start: 0.9280 (mp0) cc_final: 0.8887 (mp0) REVERT: E 136 LEU cc_start: 0.8609 (mp) cc_final: 0.8335 (pt) REVERT: E 139 PHE cc_start: 0.8310 (p90) cc_final: 0.7260 (p90) REVERT: E 173 TYR cc_start: 0.7217 (p90) cc_final: 0.6800 (p90) REVERT: E 211 ARG cc_start: 0.7913 (ttp-170) cc_final: 0.7547 (ptm-80) REVERT: F 3 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.8162 (pm20) REVERT: F 6 GLU cc_start: 0.7597 (mp0) cc_final: 0.6344 (mp0) REVERT: F 22 CYS cc_start: 0.8712 (t) cc_final: 0.8251 (t) REVERT: F 72 ASP cc_start: 0.8493 (t0) cc_final: 0.8037 (t0) REVERT: F 79 SER cc_start: 0.9334 (m) cc_final: 0.8679 (p) REVERT: F 86 ASP cc_start: 0.8972 (m-30) cc_final: 0.8595 (m-30) REVERT: F 105 GLN cc_start: 0.8509 (pm20) cc_final: 0.7970 (pm20) REVERT: F 128 LEU cc_start: 0.8930 (mp) cc_final: 0.8618 (mm) REVERT: F 171 PHE cc_start: 0.8194 (m-80) cc_final: 0.7530 (m-80) REVERT: G 17 ASP cc_start: 0.9063 (t0) cc_final: 0.8528 (m-30) REVERT: G 50 GLU cc_start: 0.9270 (mp0) cc_final: 0.8869 (mp0) REVERT: G 139 PHE cc_start: 0.8265 (p90) cc_final: 0.7372 (p90) REVERT: G 148 TRP cc_start: 0.7228 (m100) cc_final: 0.6502 (m100) REVERT: G 155 GLN cc_start: 0.8401 (mm-40) cc_final: 0.8157 (mp10) REVERT: H 3 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8431 (pm20) REVERT: H 6 GLU cc_start: 0.7479 (mp0) cc_final: 0.6250 (mp0) REVERT: H 26 ARG cc_start: 0.7762 (pmt-80) cc_final: 0.7518 (pmt-80) REVERT: H 72 ASP cc_start: 0.8506 (t0) cc_final: 0.8046 (t0) REVERT: H 79 SER cc_start: 0.9404 (m) cc_final: 0.8831 (p) REVERT: H 86 ASP cc_start: 0.8946 (m-30) cc_final: 0.8570 (m-30) REVERT: H 105 GLN cc_start: 0.8199 (pm20) cc_final: 0.7422 (pm20) REVERT: H 128 LEU cc_start: 0.8197 (mm) cc_final: 0.7484 (mm) REVERT: H 164 LEU cc_start: 0.9483 (OUTLIER) cc_final: 0.9257 (mp) REVERT: H 171 PHE cc_start: 0.7843 (m-80) cc_final: 0.7306 (m-80) REVERT: I 17 ASP cc_start: 0.9093 (t0) cc_final: 0.8576 (m-30) REVERT: I 50 GLU cc_start: 0.9268 (mp0) cc_final: 0.8873 (mp0) REVERT: I 136 LEU cc_start: 0.8684 (mp) cc_final: 0.8422 (pt) REVERT: I 139 PHE cc_start: 0.8331 (p90) cc_final: 0.7325 (p90) REVERT: I 148 TRP cc_start: 0.7205 (m100) cc_final: 0.6423 (m100) REVERT: I 155 GLN cc_start: 0.8368 (mm-40) cc_final: 0.8135 (mp10) REVERT: I 173 TYR cc_start: 0.6997 (p90) cc_final: 0.6510 (p90) REVERT: J 3 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.8474 (pm20) REVERT: J 6 GLU cc_start: 0.7613 (mp0) cc_final: 0.6397 (mp0) REVERT: J 22 CYS cc_start: 0.8719 (t) cc_final: 0.8261 (t) REVERT: J 72 ASP cc_start: 0.8569 (t0) cc_final: 0.8079 (OUTLIER) REVERT: J 79 SER cc_start: 0.9341 (m) cc_final: 0.8691 (p) REVERT: J 86 ASP cc_start: 0.8968 (m-30) cc_final: 0.8662 (m-30) REVERT: J 105 GLN cc_start: 0.8493 (pm20) cc_final: 0.7954 (pm20) REVERT: J 128 LEU cc_start: 0.8098 (mm) cc_final: 0.7239 (mm) REVERT: J 171 PHE cc_start: 0.8249 (m-80) cc_final: 0.7568 (m-80) REVERT: J 217 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8251 (tm-30) REVERT: K 3 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.8323 (pm20) REVERT: K 6 GLU cc_start: 0.7640 (mp0) cc_final: 0.6586 (mp0) REVERT: K 22 CYS cc_start: 0.8693 (t) cc_final: 0.8222 (t) REVERT: K 27 PHE cc_start: 0.8286 (m-80) cc_final: 0.8054 (m-80) REVERT: K 72 ASP cc_start: 0.8544 (t0) cc_final: 0.8100 (t0) REVERT: K 79 SER cc_start: 0.9356 (m) cc_final: 0.8713 (p) REVERT: K 86 ASP cc_start: 0.8982 (m-30) cc_final: 0.8675 (m-30) REVERT: K 105 GLN cc_start: 0.8466 (pm20) cc_final: 0.8042 (pm20) REVERT: K 171 PHE cc_start: 0.8167 (m-80) cc_final: 0.7525 (m-80) REVERT: L 17 ASP cc_start: 0.9109 (t0) cc_final: 0.8564 (m-30) REVERT: L 23 CYS cc_start: 0.7292 (t) cc_final: 0.6956 (t) REVERT: L 50 GLU cc_start: 0.9259 (mp0) cc_final: 0.8863 (mp0) REVERT: L 145 LYS cc_start: 0.9021 (mttp) cc_final: 0.8715 (mmtt) outliers start: 30 outliers final: 19 residues processed: 388 average time/residue: 1.1776 time to fit residues: 521.6103 Evaluate side-chains 386 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 362 time to evaluate : 2.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain D residue 150 ARG Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 108 CYS Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain H residue 144 CYS Chi-restraints excluded: chain H residue 156 THR Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 108 CYS Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 108 CYS Chi-restraints excluded: chain K residue 156 THR Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain L residue 197 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 55 optimal weight: 0.3980 chunk 249 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 156 optimal weight: 8.9990 chunk 234 optimal weight: 4.9990 chunk 202 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 176 optimal weight: 5.9990 chunk 260 optimal weight: 7.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.115758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.065307 restraints weight = 36729.054| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 3.07 r_work: 0.2565 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2431 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.4806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21016 Z= 0.177 Angle : 0.783 14.302 28704 Z= 0.399 Chirality : 0.048 0.238 3220 Planarity : 0.006 0.065 3648 Dihedral : 5.325 26.993 2864 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.68 % Favored : 94.28 % Rotamer: Outliers : 1.43 % Allowed : 21.83 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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 (0.17), residues: 2640 helix: -0.24 (0.53), residues: 100 sheet: 1.52 (0.17), residues: 916 loop : -0.70 (0.16), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 148 HIS 0.003 0.001 HIS L 198 PHE 0.027 0.001 PHE L 139 TYR 0.041 0.002 TYR G 173 ARG 0.008 0.001 ARG G 142 Details of bonding type rmsd hydrogen bonds : bond 0.03176 ( 709) hydrogen bonds : angle 5.47932 ( 1995) SS BOND : bond 0.00623 ( 56) SS BOND : angle 1.77804 ( 112) covalent geometry : bond 0.00417 (20960) covalent geometry : angle 0.77682 (28592) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23555.87 seconds wall clock time: 403 minutes 41.64 seconds (24221.64 seconds total)