Starting phenix.real_space_refine on Thu Jan 23 17:46:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vgk_43203/01_2025/8vgk_43203.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vgk_43203/01_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_43203/01_2025/8vgk_43203.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vgk_43203/01_2025/8vgk_43203.map" model { file = "/net/cci-nas-00/data/ceres_data/8vgk_43203/01_2025/8vgk_43203.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vgk_43203/01_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-5571/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: 12.70, per 1000 atoms: 0.62 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: 4.74 Conformation dependent library (CDL) restraints added in 2.9 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: 3.85 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: 8.18 Time building geometry restraints manager: 5.52 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: 4.660 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: 0.850 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 48.640 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.160 ------------------------------------------------------------------------------- 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 20960 Z= 0.357 Angle : 1.040 10.021 28592 Z= 0.593 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 *********************** 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 : 2.685 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: 1.5168 time to fit residues: 1069.6188 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 : 2.432 ------------------------------------------------------------------------------- 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 20960 Z= 0.288 Angle : 0.831 12.661 28592 Z= 0.436 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 *********************** 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 : 2.423 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: 1.2380 time to fit residues: 715.0547 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 : 2.670 ------------------------------------------------------------------------------- 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 20960 Z= 0.315 Angle : 0.770 10.784 28592 Z= 0.399 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 *********************** 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 : 2.597 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: 1.2540 time to fit residues: 654.7126 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 : 2.471 ------------------------------------------------------------------------------- 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: 0.5980 chunk 176 optimal weight: 6.9990 chunk 83 optimal weight: 0.0870 chunk 60 optimal weight: 0.9980 chunk 238 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 227 optimal weight: 2.9990 overall best weight: 0.9518 ------------------------------------------------------------------------------- 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 160 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.117486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.066246 restraints weight = 36351.649| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 3.12 r_work: 0.2585 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2451 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20960 Z= 0.236 Angle : 0.731 11.778 28592 Z= 0.377 Chirality : 0.047 0.158 3220 Planarity : 0.006 0.065 3648 Dihedral : 5.805 51.057 2867 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.00 % Allowed : 17.49 % Favored : 80.51 % 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: 0.08 (0.17), residues: 2640 helix: -0.73 (0.48), residues: 124 sheet: 1.18 (0.17), residues: 940 loop : -0.60 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 148 HIS 0.003 0.001 HIS L 198 PHE 0.024 0.002 PHE F 27 TYR 0.025 0.002 TYR H 181 ARG 0.008 0.001 ARG I 142 *********************** 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 442 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 396 time to evaluate : 1.992 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: 0.9148 (tp30) cc_final: 0.8883 (tp30) REVERT: A 134 MET cc_start: 0.9022 (tpp) cc_final: 0.8493 (mpp) REVERT: A 164 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7992 (mm-30) REVERT: B 134 MET cc_start: 0.8817 (tpp) cc_final: 0.8328 (mpp) REVERT: B 147 ASP cc_start: 0.8902 (t0) cc_final: 0.8394 (m-30) REVERT: B 150 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8642 (mmp80) REVERT: B 164 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8020 (mm-30) REVERT: C 109 GLU cc_start: 0.9127 (tp30) cc_final: 0.8872 (tp30) REVERT: C 134 MET cc_start: 0.8966 (tpp) cc_final: 0.8556 (mpp) REVERT: C 149 GLU cc_start: 0.8508 (mp0) cc_final: 0.8125 (mp0) REVERT: C 164 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8070 (mm-30) REVERT: D 134 MET cc_start: 0.8943 (tpp) cc_final: 0.8417 (mpp) REVERT: D 147 ASP cc_start: 0.8902 (t0) cc_final: 0.8415 (m-30) REVERT: D 150 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8527 (mmp80) REVERT: D 164 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8089 (mm-30) REVERT: E 4 MET cc_start: 0.8853 (mtp) cc_final: 0.7982 (mtp) REVERT: E 17 ASP cc_start: 0.8677 (t0) cc_final: 0.8149 (m-30) REVERT: E 78 LEU cc_start: 0.9267 (mt) cc_final: 0.9040 (tm) REVERT: E 82 ASP cc_start: 0.8370 (m-30) cc_final: 0.7935 (m-30) REVERT: E 108 ARG cc_start: 0.6763 (tmm-80) cc_final: 0.5918 (tmm-80) REVERT: E 139 PHE cc_start: 0.8208 (p90) cc_final: 0.7915 (p90) REVERT: E 167 ASP cc_start: 0.7569 (t0) cc_final: 0.7338 (t0) REVERT: E 173 TYR cc_start: 0.6406 (OUTLIER) cc_final: 0.5917 (p90) REVERT: F 3 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8157 (pm20) REVERT: F 6 GLU cc_start: 0.7710 (mp0) cc_final: 0.6736 (mp0) REVERT: F 22 CYS cc_start: 0.8720 (t) cc_final: 0.8305 (t) REVERT: F 26 ARG cc_start: 0.8526 (pmm-80) cc_final: 0.7941 (pmm-80) REVERT: F 72 ASP cc_start: 0.8377 (t0) cc_final: 0.7931 (t0) REVERT: F 86 ASP cc_start: 0.9014 (m-30) cc_final: 0.8679 (m-30) REVERT: F 105 GLN cc_start: 0.8487 (pm20) cc_final: 0.8082 (pm20) REVERT: F 128 LEU cc_start: 0.8938 (mp) cc_final: 0.8570 (mm) REVERT: F 171 PHE cc_start: 0.7801 (m-80) cc_final: 0.7214 (m-80) REVERT: G 4 MET cc_start: 0.8846 (mtp) cc_final: 0.7965 (mtp) REVERT: G 17 ASP cc_start: 0.8696 (t0) cc_final: 0.8140 (m-30) REVERT: G 78 LEU cc_start: 0.9229 (mt) cc_final: 0.8982 (tm) REVERT: G 82 ASP cc_start: 0.8336 (m-30) cc_final: 0.8124 (m-30) REVERT: G 139 PHE cc_start: 0.8120 (p90) cc_final: 0.7533 (p90) REVERT: G 148 TRP cc_start: 0.6961 (m100) cc_final: 0.6142 (m100) REVERT: G 155 GLN cc_start: 0.8376 (mm-40) cc_final: 0.8045 (mp10) REVERT: G 173 TYR cc_start: 0.6115 (OUTLIER) cc_final: 0.5910 (p90) REVERT: H 3 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8213 (pm20) REVERT: H 6 GLU cc_start: 0.7405 (mp0) cc_final: 0.6103 (mp0) REVERT: H 22 CYS cc_start: 0.8519 (t) cc_final: 0.8130 (t) REVERT: H 72 ASP cc_start: 0.8373 (t0) cc_final: 0.7923 (t0) REVERT: H 86 ASP cc_start: 0.9017 (m-30) cc_final: 0.8688 (m-30) REVERT: H 105 GLN cc_start: 0.8369 (pm20) cc_final: 0.7880 (pm20) REVERT: H 171 PHE cc_start: 0.7721 (m-80) cc_final: 0.7050 (m-80) REVERT: I 4 MET cc_start: 0.8839 (mtp) cc_final: 0.7930 (mtp) REVERT: I 17 ASP cc_start: 0.8681 (t0) cc_final: 0.8191 (m-30) REVERT: I 78 LEU cc_start: 0.9218 (mt) cc_final: 0.8984 (tm) REVERT: I 82 ASP cc_start: 0.8372 (m-30) cc_final: 0.7935 (m-30) REVERT: I 139 PHE cc_start: 0.8118 (p90) cc_final: 0.7874 (p90) REVERT: I 148 TRP cc_start: 0.6968 (m100) cc_final: 0.6198 (m100) REVERT: I 155 GLN cc_start: 0.8408 (mm-40) cc_final: 0.8129 (mp10) REVERT: I 167 ASP cc_start: 0.7585 (t0) cc_final: 0.7363 (t0) REVERT: I 173 TYR cc_start: 0.6377 (OUTLIER) cc_final: 0.5868 (p90) REVERT: J 3 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.8186 (pm20) REVERT: J 6 GLU cc_start: 0.7734 (mp0) cc_final: 0.6778 (mp0) REVERT: J 22 CYS cc_start: 0.8695 (t) cc_final: 0.8254 (t) REVERT: J 72 ASP cc_start: 0.8521 (t0) cc_final: 0.8072 (t0) REVERT: J 86 ASP cc_start: 0.9022 (m-30) cc_final: 0.8689 (m-30) REVERT: J 105 GLN cc_start: 0.8484 (pm20) cc_final: 0.8081 (pm20) REVERT: J 171 PHE cc_start: 0.7686 (m-80) cc_final: 0.7072 (m-80) REVERT: J 215 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8753 (tmtt) REVERT: J 217 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8167 (tm-30) REVERT: K 3 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8193 (pm20) REVERT: K 6 GLU cc_start: 0.7718 (mp0) cc_final: 0.6739 (mp0) REVERT: K 22 CYS cc_start: 0.8761 (t) cc_final: 0.8333 (t) REVERT: K 72 ASP cc_start: 0.8383 (t0) cc_final: 0.7938 (t0) REVERT: K 86 ASP cc_start: 0.9014 (m-30) cc_final: 0.8675 (m-30) REVERT: K 105 GLN cc_start: 0.8476 (pm20) cc_final: 0.8068 (pm20) REVERT: K 128 LEU cc_start: 0.7140 (tp) cc_final: 0.6807 (tp) REVERT: K 171 PHE cc_start: 0.7571 (m-80) cc_final: 0.7015 (m-80) REVERT: L 4 MET cc_start: 0.9016 (mtp) cc_final: 0.8106 (mtp) REVERT: L 17 ASP cc_start: 0.8669 (t0) cc_final: 0.8143 (m-30) REVERT: L 78 LEU cc_start: 0.9218 (mt) cc_final: 0.8987 (tm) REVERT: L 82 ASP cc_start: 0.8366 (m-30) cc_final: 0.7921 (m-30) REVERT: L 108 ARG cc_start: 0.6683 (tmm-80) cc_final: 0.6401 (tmm-80) REVERT: L 123 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6820 (tt0) REVERT: L 139 PHE cc_start: 0.8373 (p90) cc_final: 0.8062 (p90) REVERT: L 145 LYS cc_start: 0.8872 (mttp) cc_final: 0.8639 (mmtt) REVERT: L 167 ASP cc_start: 0.7659 (t0) cc_final: 0.7430 (t0) outliers start: 46 outliers final: 17 residues processed: 423 average time/residue: 1.2340 time to fit residues: 597.2920 Evaluate side-chains 397 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 369 time to evaluate : 2.348 ------------------------------------------------------------------------------- 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 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 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 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 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 K residue 202 ASN 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: 0.7980 chunk 218 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 195 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 118 optimal weight: 5.9990 chunk 174 optimal weight: 10.0000 chunk 139 optimal weight: 8.9990 chunk 193 optimal weight: 9.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3729 r_free = 0.3729 target = 0.116271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.065223 restraints weight = 36312.150| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 3.10 r_work: 0.2571 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2437 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20960 Z= 0.291 Angle : 0.726 11.198 28592 Z= 0.374 Chirality : 0.048 0.170 3220 Planarity : 0.006 0.066 3648 Dihedral : 5.693 54.297 2867 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.30 % Allowed : 17.19 % Favored : 80.51 % 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: 0.03 (0.17), residues: 2640 helix: -0.89 (0.47), residues: 124 sheet: 1.23 (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 D 173 PHE 0.013 0.002 PHE D 153 TYR 0.026 0.002 TYR H 181 ARG 0.009 0.001 ARG L 142 *********************** 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 437 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 384 time to evaluate : 2.425 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: 0.9087 (tpp) cc_final: 0.8652 (mpp) REVERT: B 134 MET cc_start: 0.8858 (tpp) cc_final: 0.8407 (mpp) REVERT: B 164 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8063 (mm-30) REVERT: C 134 MET cc_start: 0.9015 (tpp) cc_final: 0.8577 (mpp) REVERT: C 149 GLU cc_start: 0.8522 (mp0) cc_final: 0.8038 (mp0) REVERT: C 164 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8109 (mm-30) REVERT: D 134 MET cc_start: 0.9008 (tpp) cc_final: 0.8572 (mpp) REVERT: D 150 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.8537 (mmp80) REVERT: D 164 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8129 (mm-30) REVERT: E 17 ASP cc_start: 0.8841 (t0) cc_final: 0.8365 (m-30) REVERT: E 78 LEU cc_start: 0.9181 (mt) cc_final: 0.8908 (tm) REVERT: E 139 PHE cc_start: 0.8262 (p90) cc_final: 0.7555 (p90) REVERT: E 167 ASP cc_start: 0.7745 (t0) cc_final: 0.7443 (t0) REVERT: E 173 TYR cc_start: 0.6632 (OUTLIER) cc_final: 0.6208 (p90) REVERT: E 211 ARG cc_start: 0.7728 (ttp-170) cc_final: 0.7371 (ptm160) REVERT: F 3 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8191 (pm20) REVERT: F 6 GLU cc_start: 0.7682 (mp0) cc_final: 0.6827 (mp0) REVERT: F 22 CYS cc_start: 0.8665 (t) cc_final: 0.8170 (t) REVERT: F 26 ARG cc_start: 0.8520 (pmm-80) cc_final: 0.8168 (pmm-80) REVERT: F 27 PHE cc_start: 0.8311 (m-80) cc_final: 0.8092 (m-80) REVERT: F 72 ASP cc_start: 0.8406 (t0) cc_final: 0.7924 (t0) REVERT: F 86 ASP cc_start: 0.9002 (m-30) cc_final: 0.8658 (m-30) REVERT: F 105 GLN cc_start: 0.8476 (pm20) cc_final: 0.8141 (pm20) REVERT: F 128 LEU cc_start: 0.8899 (mp) cc_final: 0.8529 (mm) REVERT: F 171 PHE cc_start: 0.7781 (m-80) cc_final: 0.7162 (m-80) REVERT: G 17 ASP cc_start: 0.8852 (t0) cc_final: 0.8351 (m-30) REVERT: G 78 LEU cc_start: 0.9212 (mt) cc_final: 0.8966 (tm) REVERT: G 139 PHE cc_start: 0.8202 (p90) cc_final: 0.7523 (p90) REVERT: G 148 TRP cc_start: 0.7013 (m100) cc_final: 0.6101 (m100) REVERT: G 155 GLN cc_start: 0.8379 (mm-40) cc_final: 0.8084 (mp10) REVERT: G 173 TYR cc_start: 0.6235 (OUTLIER) cc_final: 0.5659 (p90) REVERT: H 3 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8212 (pm20) REVERT: H 6 GLU cc_start: 0.7533 (mp0) cc_final: 0.6226 (mp0) REVERT: H 72 ASP cc_start: 0.8390 (t0) cc_final: 0.7908 (t0) REVERT: H 86 ASP cc_start: 0.8989 (m-30) cc_final: 0.8654 (m-30) REVERT: H 105 GLN cc_start: 0.8344 (pm20) cc_final: 0.7521 (pm20) REVERT: H 171 PHE cc_start: 0.7678 (m-80) cc_final: 0.7019 (m-80) REVERT: I 17 ASP cc_start: 0.8834 (t0) cc_final: 0.8369 (m-30) REVERT: I 78 LEU cc_start: 0.9135 (mt) cc_final: 0.8870 (tm) REVERT: I 139 PHE cc_start: 0.8282 (p90) cc_final: 0.7591 (p90) REVERT: I 148 TRP cc_start: 0.6980 (m100) cc_final: 0.6187 (m100) REVERT: I 155 GLN cc_start: 0.8413 (mm-40) cc_final: 0.8157 (mp10) REVERT: I 167 ASP cc_start: 0.7715 (t0) cc_final: 0.7446 (t0) REVERT: I 173 TYR cc_start: 0.6515 (OUTLIER) cc_final: 0.6175 (p90) REVERT: J 3 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8191 (pm20) REVERT: J 6 GLU cc_start: 0.7735 (mp0) cc_final: 0.6863 (mp0) REVERT: J 22 CYS cc_start: 0.8700 (t) cc_final: 0.8282 (t) REVERT: J 72 ASP cc_start: 0.8555 (t0) cc_final: 0.8087 (t0) REVERT: J 86 ASP cc_start: 0.8999 (m-30) cc_final: 0.8652 (m-30) REVERT: J 105 GLN cc_start: 0.8480 (pm20) cc_final: 0.8128 (pm20) REVERT: J 128 LEU cc_start: 0.7763 (mm) cc_final: 0.6914 (mm) REVERT: J 171 PHE cc_start: 0.7635 (m-80) cc_final: 0.6995 (m-80) REVERT: J 217 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8252 (tm-30) REVERT: K 3 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8198 (pm20) REVERT: K 6 GLU cc_start: 0.7673 (mp0) cc_final: 0.6804 (mp0) REVERT: K 22 CYS cc_start: 0.8671 (t) cc_final: 0.8212 (t) REVERT: K 72 ASP cc_start: 0.8439 (t0) cc_final: 0.7972 (t0) REVERT: K 86 ASP cc_start: 0.8996 (m-30) cc_final: 0.8648 (m-30) REVERT: K 105 GLN cc_start: 0.8470 (pm20) cc_final: 0.8127 (pm20) REVERT: K 171 PHE cc_start: 0.7543 (m-80) cc_final: 0.6933 (m-80) REVERT: L 17 ASP cc_start: 0.8837 (t0) cc_final: 0.8358 (m-30) REVERT: L 78 LEU cc_start: 0.9168 (mt) cc_final: 0.8895 (tm) REVERT: L 108 ARG cc_start: 0.6711 (tmm-80) cc_final: 0.5800 (tmm-80) REVERT: L 123 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7101 (tt0) REVERT: L 139 PHE cc_start: 0.8356 (p90) cc_final: 0.8122 (p90) REVERT: L 145 LYS cc_start: 0.8982 (mttp) cc_final: 0.8706 (mmtt) REVERT: L 167 ASP cc_start: 0.7758 (t0) cc_final: 0.7498 (t0) outliers start: 53 outliers final: 22 residues processed: 424 average time/residue: 1.1861 time to fit residues: 576.7687 Evaluate side-chains 391 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 360 time to evaluate : 2.684 ------------------------------------------------------------------------------- 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 173 TYR Chi-restraints excluded: chain E residue 198 HIS 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 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 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 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 110 THR 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: 0.0010 chunk 232 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 255 optimal weight: 2.9990 chunk 179 optimal weight: 9.9990 chunk 187 optimal weight: 5.9990 chunk 208 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 overall best weight: 0.8988 ------------------------------------------------------------------------------- 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 ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 176 GLN I 79 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 L 79 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.116902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.065976 restraints weight = 36197.644| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 3.08 r_work: 0.2585 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2448 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20960 Z= 0.228 Angle : 0.705 12.072 28592 Z= 0.362 Chirality : 0.047 0.163 3220 Planarity : 0.006 0.065 3648 Dihedral : 5.530 59.038 2867 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.74 % Allowed : 18.32 % Favored : 79.95 % 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: 0.12 (0.17), residues: 2640 helix: -1.06 (0.47), residues: 124 sheet: 1.39 (0.16), residues: 936 loop : -0.66 (0.16), residues: 1580 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 0.024 0.002 PHE K 27 TYR 0.028 0.002 TYR H 181 ARG 0.009 0.001 ARG G 211 *********************** 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 426 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 386 time to evaluate : 2.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.9056 (tpp) cc_final: 0.8759 (mtt) REVERT: B 109 GLU cc_start: 0.9154 (tp30) cc_final: 0.8915 (tp30) REVERT: B 150 ARG cc_start: 0.9095 (OUTLIER) cc_final: 0.8657 (mmp80) REVERT: B 164 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8076 (mm-30) REVERT: C 149 GLU cc_start: 0.8577 (mp0) cc_final: 0.8087 (mp0) REVERT: C 164 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8095 (mm-30) REVERT: D 134 MET cc_start: 0.8976 (tpp) cc_final: 0.8632 (mpp) REVERT: D 150 ARG cc_start: 0.9087 (OUTLIER) cc_final: 0.8592 (mmp80) REVERT: D 164 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8110 (mm-30) REVERT: E 4 MET cc_start: 0.8712 (mtp) cc_final: 0.8046 (ttm) REVERT: E 17 ASP cc_start: 0.8890 (t0) cc_final: 0.8471 (m-30) REVERT: E 88 CYS cc_start: 0.8271 (p) cc_final: 0.7439 (p) REVERT: E 108 ARG cc_start: 0.6554 (tmm-80) cc_final: 0.6215 (tmm-80) REVERT: E 136 LEU cc_start: 0.8782 (mp) cc_final: 0.8532 (pt) REVERT: E 139 PHE cc_start: 0.8289 (p90) cc_final: 0.7374 (p90) REVERT: E 155 GLN cc_start: 0.8430 (mm-40) cc_final: 0.8147 (mp10) REVERT: E 173 TYR cc_start: 0.6722 (OUTLIER) cc_final: 0.6080 (p90) REVERT: E 211 ARG cc_start: 0.7878 (ttp-170) cc_final: 0.7580 (ptm160) REVERT: F 3 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8207 (pm20) REVERT: F 6 GLU cc_start: 0.7642 (mp0) cc_final: 0.6770 (mp0) REVERT: F 22 CYS cc_start: 0.8637 (t) cc_final: 0.8164 (t) REVERT: F 26 ARG cc_start: 0.8499 (pmm-80) cc_final: 0.8130 (pmm-80) REVERT: F 27 PHE cc_start: 0.8405 (m-80) cc_final: 0.8191 (m-80) REVERT: F 72 ASP cc_start: 0.8446 (t0) cc_final: 0.7958 (t0) REVERT: F 86 ASP cc_start: 0.8989 (m-30) cc_final: 0.8619 (m-30) REVERT: F 105 GLN cc_start: 0.8494 (pm20) cc_final: 0.8116 (pm20) REVERT: F 128 LEU cc_start: 0.8897 (mp) cc_final: 0.8551 (mm) REVERT: F 171 PHE cc_start: 0.7776 (m-80) cc_final: 0.7144 (m-80) REVERT: G 4 MET cc_start: 0.8569 (ttm) cc_final: 0.7864 (ttm) REVERT: G 17 ASP cc_start: 0.8877 (t0) cc_final: 0.8422 (m-30) REVERT: G 88 CYS cc_start: 0.8011 (p) cc_final: 0.7548 (p) REVERT: G 117 ILE cc_start: 0.7632 (OUTLIER) cc_final: 0.7422 (mt) REVERT: G 139 PHE cc_start: 0.8234 (p90) cc_final: 0.7613 (p90) REVERT: G 148 TRP cc_start: 0.7036 (m100) cc_final: 0.6213 (m100) REVERT: G 155 GLN cc_start: 0.8411 (mm-40) cc_final: 0.8142 (mp10) REVERT: G 173 TYR cc_start: 0.6011 (OUTLIER) cc_final: 0.5773 (p90) REVERT: H 3 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8138 (pm20) REVERT: H 6 GLU cc_start: 0.7487 (mp0) cc_final: 0.6190 (mp0) REVERT: H 26 ARG cc_start: 0.8421 (pmm-80) cc_final: 0.7806 (pmm-80) REVERT: H 72 ASP cc_start: 0.8412 (t0) cc_final: 0.7921 (t0) REVERT: H 79 SER cc_start: 0.9408 (m) cc_final: 0.8836 (p) REVERT: H 86 ASP cc_start: 0.8964 (m-30) cc_final: 0.8600 (m-30) REVERT: H 105 GLN cc_start: 0.8302 (pm20) cc_final: 0.7551 (pm20) REVERT: H 128 LEU cc_start: 0.7603 (mm) cc_final: 0.6838 (mm) REVERT: H 164 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9227 (mm) REVERT: H 171 PHE cc_start: 0.7749 (m-80) cc_final: 0.7169 (m-80) REVERT: I 4 MET cc_start: 0.8664 (mtp) cc_final: 0.7973 (ttm) REVERT: I 17 ASP cc_start: 0.8908 (t0) cc_final: 0.8497 (m-30) REVERT: I 78 LEU cc_start: 0.9179 (mt) cc_final: 0.8914 (tm) REVERT: I 88 CYS cc_start: 0.8191 (p) cc_final: 0.7321 (p) REVERT: I 139 PHE cc_start: 0.8257 (p90) cc_final: 0.7533 (p90) REVERT: I 148 TRP cc_start: 0.7024 (m100) cc_final: 0.6242 (m100) REVERT: I 155 GLN cc_start: 0.8427 (mm-40) cc_final: 0.8214 (mp10) REVERT: I 167 ASP cc_start: 0.7699 (t0) cc_final: 0.7407 (t0) REVERT: I 173 TYR cc_start: 0.6764 (OUTLIER) cc_final: 0.6115 (p90) REVERT: J 3 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8199 (pm20) REVERT: J 6 GLU cc_start: 0.7656 (mp0) cc_final: 0.6728 (mp0) REVERT: J 22 CYS cc_start: 0.8608 (t) cc_final: 0.8130 (t) REVERT: J 72 ASP cc_start: 0.8586 (t0) cc_final: 0.8017 (t0) REVERT: J 75 LYS cc_start: 0.9440 (OUTLIER) cc_final: 0.9133 (mttm) REVERT: J 86 ASP cc_start: 0.8987 (m-30) cc_final: 0.8605 (m-30) REVERT: J 105 GLN cc_start: 0.8522 (pm20) cc_final: 0.8137 (pm20) REVERT: J 128 LEU cc_start: 0.7727 (mm) cc_final: 0.6904 (mm) REVERT: J 171 PHE cc_start: 0.7797 (m-80) cc_final: 0.7130 (m-80) REVERT: J 215 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8892 (tmtt) REVERT: J 217 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8426 (tm-30) REVERT: K 3 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8188 (pm20) REVERT: K 6 GLU cc_start: 0.7660 (mp0) cc_final: 0.6586 (mp0) REVERT: K 22 CYS cc_start: 0.8631 (t) cc_final: 0.8138 (t) REVERT: K 72 ASP cc_start: 0.8412 (t0) cc_final: 0.7918 (t0) REVERT: K 86 ASP cc_start: 0.8980 (m-30) cc_final: 0.8604 (m-30) REVERT: K 105 GLN cc_start: 0.8474 (pm20) cc_final: 0.7985 (pm20) REVERT: K 171 PHE cc_start: 0.7704 (m-80) cc_final: 0.7069 (m-80) REVERT: L 4 MET cc_start: 0.8888 (mtp) cc_final: 0.8077 (ttm) REVERT: L 17 ASP cc_start: 0.8900 (t0) cc_final: 0.8461 (m-30) REVERT: L 78 LEU cc_start: 0.9168 (mt) cc_final: 0.8865 (tm) REVERT: L 88 CYS cc_start: 0.8155 (p) cc_final: 0.7281 (p) REVERT: L 123 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7485 (tt0) REVERT: L 139 PHE cc_start: 0.8529 (p90) cc_final: 0.8242 (p90) REVERT: L 145 LYS cc_start: 0.8993 (mttp) cc_final: 0.8708 (mmtt) REVERT: L 167 ASP cc_start: 0.7716 (t0) cc_final: 0.7416 (t0) REVERT: L 173 TYR cc_start: 0.5217 (p90) cc_final: 0.4647 (p90) outliers start: 40 outliers final: 16 residues processed: 416 average time/residue: 1.2652 time to fit residues: 600.0504 Evaluate side-chains 401 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 371 time to evaluate : 2.742 ------------------------------------------------------------------------------- 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 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 H residue 164 LEU 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 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 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: 0.7980 chunk 181 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 203 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 68 optimal weight: 0.0050 chunk 198 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 chunk 173 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 176 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.117318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.066868 restraints weight = 36342.894| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 3.08 r_work: 0.2605 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2473 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20960 Z= 0.208 Angle : 0.714 13.285 28592 Z= 0.362 Chirality : 0.047 0.164 3220 Planarity : 0.005 0.064 3648 Dihedral : 5.368 52.463 2867 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.69 % Allowed : 19.31 % Favored : 78.99 % 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: 0.18 (0.17), residues: 2640 helix: -1.04 (0.48), residues: 124 sheet: 1.49 (0.16), residues: 924 loop : -0.65 (0.16), residues: 1592 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 0.001 PHE C 153 TYR 0.028 0.001 TYR H 181 ARG 0.008 0.001 ARG G 108 *********************** 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 430 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 391 time to evaluate : 2.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 GLU cc_start: 0.9159 (mm-30) cc_final: 0.8903 (mm-30) REVERT: A 134 MET cc_start: 0.9045 (tpp) cc_final: 0.8723 (mtt) REVERT: A 149 GLU cc_start: 0.8569 (mp0) cc_final: 0.8351 (mp0) REVERT: B 134 MET cc_start: 0.8850 (tpp) cc_final: 0.8497 (mtt) REVERT: B 164 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8062 (mm-30) REVERT: C 109 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8906 (mm-30) REVERT: C 134 MET cc_start: 0.9030 (tpp) cc_final: 0.8688 (mtt) REVERT: C 149 GLU cc_start: 0.8672 (mp0) cc_final: 0.8238 (mp0) REVERT: C 164 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8096 (mm-30) REVERT: D 109 GLU cc_start: 0.9178 (mm-30) cc_final: 0.8932 (mm-30) REVERT: D 134 MET cc_start: 0.8957 (tpp) cc_final: 0.8634 (mtt) REVERT: D 150 ARG cc_start: 0.9087 (OUTLIER) cc_final: 0.8594 (mmp80) REVERT: D 164 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8107 (mm-30) REVERT: E 4 MET cc_start: 0.8753 (mtp) cc_final: 0.8365 (mtp) REVERT: E 17 ASP cc_start: 0.9057 (t0) cc_final: 0.8498 (m-30) REVERT: E 88 CYS cc_start: 0.8091 (p) cc_final: 0.7804 (p) REVERT: E 108 ARG cc_start: 0.6791 (tmm-80) cc_final: 0.6284 (tmm-80) REVERT: E 136 LEU cc_start: 0.8769 (mp) cc_final: 0.8522 (pt) REVERT: E 139 PHE cc_start: 0.8268 (p90) cc_final: 0.7307 (p90) REVERT: E 155 GLN cc_start: 0.8400 (mm-40) cc_final: 0.8112 (mp10) REVERT: E 173 TYR cc_start: 0.6901 (OUTLIER) cc_final: 0.6316 (p90) REVERT: E 211 ARG cc_start: 0.7885 (ttp-170) cc_final: 0.7591 (ptm160) REVERT: F 3 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8218 (pm20) REVERT: F 6 GLU cc_start: 0.7641 (mp0) cc_final: 0.6689 (mp0) REVERT: F 22 CYS cc_start: 0.8675 (t) cc_final: 0.8216 (t) REVERT: F 26 ARG cc_start: 0.8462 (pmm-80) cc_final: 0.8087 (pmm-80) REVERT: F 72 ASP cc_start: 0.8453 (t0) cc_final: 0.7983 (t0) REVERT: F 79 SER cc_start: 0.9338 (m) cc_final: 0.8702 (p) REVERT: F 86 ASP cc_start: 0.9009 (m-30) cc_final: 0.8634 (m-30) REVERT: F 105 GLN cc_start: 0.8518 (pm20) cc_final: 0.8120 (pm20) REVERT: F 128 LEU cc_start: 0.8876 (mp) cc_final: 0.8526 (mm) REVERT: F 171 PHE cc_start: 0.7981 (m-80) cc_final: 0.7329 (m-80) REVERT: G 4 MET cc_start: 0.8693 (ttm) cc_final: 0.8271 (ttm) REVERT: G 17 ASP cc_start: 0.9006 (t0) cc_final: 0.8451 (m-30) REVERT: G 88 CYS cc_start: 0.8346 (p) cc_final: 0.7617 (p) REVERT: G 139 PHE cc_start: 0.8236 (p90) cc_final: 0.7598 (p90) REVERT: G 148 TRP cc_start: 0.7141 (m100) cc_final: 0.6379 (m100) REVERT: G 155 GLN cc_start: 0.8401 (mm-40) cc_final: 0.8138 (mp10) REVERT: G 173 TYR cc_start: 0.6242 (OUTLIER) cc_final: 0.5770 (p90) REVERT: H 3 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8208 (pm20) REVERT: H 6 GLU cc_start: 0.7485 (mp0) cc_final: 0.6176 (mp0) REVERT: H 72 ASP cc_start: 0.8443 (t0) cc_final: 0.7970 (t0) REVERT: H 79 SER cc_start: 0.9392 (m) cc_final: 0.8811 (p) REVERT: H 86 ASP cc_start: 0.8978 (m-30) cc_final: 0.8618 (m-30) REVERT: H 105 GLN cc_start: 0.8259 (pm20) cc_final: 0.7505 (pm20) REVERT: H 164 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9189 (mp) REVERT: H 171 PHE cc_start: 0.7930 (m-80) cc_final: 0.7307 (m-80) REVERT: I 4 MET cc_start: 0.8710 (mtp) cc_final: 0.8312 (mtp) REVERT: I 17 ASP cc_start: 0.8954 (t0) cc_final: 0.8534 (m-30) REVERT: I 78 LEU cc_start: 0.9201 (mt) cc_final: 0.8933 (tm) REVERT: I 88 CYS cc_start: 0.8063 (p) cc_final: 0.7773 (p) REVERT: I 108 ARG cc_start: 0.7073 (tmm-80) cc_final: 0.6630 (tmm-80) REVERT: I 136 LEU cc_start: 0.8738 (mp) cc_final: 0.8510 (pt) REVERT: I 139 PHE cc_start: 0.8310 (p90) cc_final: 0.7389 (p90) REVERT: I 148 TRP cc_start: 0.7131 (m100) cc_final: 0.6367 (m100) REVERT: I 155 GLN cc_start: 0.8426 (mm-40) cc_final: 0.8208 (mp10) REVERT: I 167 ASP cc_start: 0.7756 (t0) cc_final: 0.7447 (t0) REVERT: I 173 TYR cc_start: 0.6737 (OUTLIER) cc_final: 0.6111 (p90) REVERT: J 3 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8483 (pm20) REVERT: J 6 GLU cc_start: 0.7656 (mp0) cc_final: 0.6565 (mp0) REVERT: J 22 CYS cc_start: 0.8631 (t) cc_final: 0.8189 (t) REVERT: J 72 ASP cc_start: 0.8609 (t0) cc_final: 0.8025 (t0) REVERT: J 75 LYS cc_start: 0.9454 (OUTLIER) cc_final: 0.9136 (mttm) REVERT: J 79 SER cc_start: 0.9352 (m) cc_final: 0.8724 (p) REVERT: J 86 ASP cc_start: 0.8986 (m-30) cc_final: 0.8605 (m-30) REVERT: J 105 GLN cc_start: 0.8512 (pm20) cc_final: 0.8012 (pm20) REVERT: J 171 PHE cc_start: 0.7893 (m-80) cc_final: 0.7278 (m-80) REVERT: J 215 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8943 (tmtt) REVERT: J 217 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8388 (tm-30) REVERT: K 3 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8498 (pm20) REVERT: K 6 GLU cc_start: 0.7657 (mp0) cc_final: 0.6586 (mp0) REVERT: K 22 CYS cc_start: 0.8614 (t) cc_final: 0.8155 (t) REVERT: K 72 ASP cc_start: 0.8443 (t0) cc_final: 0.7921 (t0) REVERT: K 79 SER cc_start: 0.9339 (m) cc_final: 0.8702 (p) REVERT: K 86 ASP cc_start: 0.8986 (m-30) cc_final: 0.8607 (m-30) REVERT: K 105 GLN cc_start: 0.8498 (pm20) cc_final: 0.7999 (pm20) REVERT: K 171 PHE cc_start: 0.7739 (m-80) cc_final: 0.7074 (m-80) REVERT: L 4 MET cc_start: 0.8869 (mtp) cc_final: 0.8437 (mtp) REVERT: L 17 ASP cc_start: 0.8950 (t0) cc_final: 0.8532 (m-30) REVERT: L 88 CYS cc_start: 0.7971 (p) cc_final: 0.7689 (p) REVERT: L 139 PHE cc_start: 0.8591 (p90) cc_final: 0.8316 (p90) REVERT: L 145 LYS cc_start: 0.9000 (mttp) cc_final: 0.8704 (mmtt) REVERT: L 173 TYR cc_start: 0.5327 (p90) cc_final: 0.5044 (p90) outliers start: 39 outliers final: 16 residues processed: 422 average time/residue: 1.2566 time to fit residues: 609.0460 Evaluate side-chains 395 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 368 time to evaluate : 2.304 ------------------------------------------------------------------------------- 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 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 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 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 J residue 215 LYS 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 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: 2.9990 chunk 22 optimal weight: 0.3980 chunk 245 optimal weight: 1.9990 chunk 238 optimal weight: 6.9990 chunk 136 optimal weight: 8.9990 chunk 174 optimal weight: 6.9990 chunk 201 optimal weight: 6.9990 chunk 115 optimal weight: 8.9990 chunk 204 optimal weight: 0.9990 chunk 92 optimal weight: 0.5980 chunk 179 optimal weight: 5.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 GLN G 138 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.115855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.065297 restraints weight = 36625.787| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 3.06 r_work: 0.2570 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2440 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 20960 Z= 0.306 Angle : 0.750 12.807 28592 Z= 0.386 Chirality : 0.048 0.174 3220 Planarity : 0.006 0.065 3648 Dihedral : 5.304 23.466 2864 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.65 % Allowed : 20.62 % Favored : 77.73 % 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: -1.18 (0.46), residues: 124 sheet: 1.48 (0.16), residues: 920 loop : -0.74 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 148 HIS 0.003 0.001 HIS C 173 PHE 0.029 0.002 PHE F 27 TYR 0.027 0.002 TYR H 181 ARG 0.006 0.001 ARG L 142 *********************** 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 414 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 376 time to evaluate : 2.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.9084 (tpp) cc_final: 0.8788 (mtt) REVERT: B 134 MET cc_start: 0.8933 (tpp) cc_final: 0.8572 (mtt) REVERT: B 164 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8079 (mm-30) REVERT: C 134 MET cc_start: 0.9112 (tpp) cc_final: 0.8752 (mtt) REVERT: C 149 GLU cc_start: 0.8661 (mp0) cc_final: 0.8121 (mp0) REVERT: C 164 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8098 (mm-30) REVERT: D 134 MET cc_start: 0.8990 (tpp) cc_final: 0.8660 (mtt) REVERT: D 150 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8515 (mmp80) REVERT: D 164 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8141 (mm-30) REVERT: E 4 MET cc_start: 0.8828 (mtp) cc_final: 0.8350 (mtp) REVERT: E 17 ASP cc_start: 0.9076 (t0) cc_final: 0.8480 (m-30) REVERT: E 88 CYS cc_start: 0.8258 (p) cc_final: 0.8037 (p) REVERT: E 136 LEU cc_start: 0.8738 (mp) cc_final: 0.8511 (pt) REVERT: E 139 PHE cc_start: 0.8310 (p90) cc_final: 0.7307 (p90) REVERT: E 173 TYR cc_start: 0.6979 (OUTLIER) cc_final: 0.6422 (p90) REVERT: E 211 ARG cc_start: 0.7912 (ttp-170) cc_final: 0.7522 (ptm-80) REVERT: F 3 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8114 (pm20) REVERT: F 6 GLU cc_start: 0.7614 (mp0) cc_final: 0.6425 (mp0) REVERT: F 22 CYS cc_start: 0.8686 (t) cc_final: 0.8209 (t) REVERT: F 26 ARG cc_start: 0.8489 (pmm-80) cc_final: 0.8237 (pmm-80) REVERT: F 72 ASP cc_start: 0.8488 (t0) cc_final: 0.8015 (t0) REVERT: F 79 SER cc_start: 0.9351 (m) cc_final: 0.8718 (p) REVERT: F 86 ASP cc_start: 0.8979 (m-30) cc_final: 0.8607 (m-30) REVERT: F 105 GLN cc_start: 0.8492 (pm20) cc_final: 0.7985 (pm20) REVERT: F 128 LEU cc_start: 0.8910 (mp) cc_final: 0.8566 (mm) REVERT: F 171 PHE cc_start: 0.8123 (m-80) cc_final: 0.7466 (m-80) REVERT: G 4 MET cc_start: 0.8803 (ttm) cc_final: 0.8409 (ttm) REVERT: G 17 ASP cc_start: 0.9037 (t0) cc_final: 0.8478 (m-30) REVERT: G 88 CYS cc_start: 0.8314 (p) cc_final: 0.7671 (p) REVERT: G 139 PHE cc_start: 0.8189 (p90) cc_final: 0.7408 (p90) REVERT: G 148 TRP cc_start: 0.7171 (m100) cc_final: 0.6441 (m100) REVERT: G 155 GLN cc_start: 0.8370 (mm-40) cc_final: 0.8109 (mp10) REVERT: G 173 TYR cc_start: 0.6903 (p90) cc_final: 0.6516 (p90) REVERT: H 3 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8465 (pm20) REVERT: H 6 GLU cc_start: 0.7460 (mp0) cc_final: 0.6195 (mp0) REVERT: H 72 ASP cc_start: 0.8486 (t0) cc_final: 0.8022 (t0) REVERT: H 79 SER cc_start: 0.9405 (m) cc_final: 0.8832 (p) REVERT: H 86 ASP cc_start: 0.8964 (m-30) cc_final: 0.8595 (m-30) REVERT: H 105 GLN cc_start: 0.8257 (pm20) cc_final: 0.7485 (pm20) REVERT: H 128 LEU cc_start: 0.8036 (mm) cc_final: 0.7234 (mm) REVERT: H 164 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.9244 (mp) REVERT: H 171 PHE cc_start: 0.8079 (m-80) cc_final: 0.7430 (m-80) REVERT: I 4 MET cc_start: 0.8800 (mtp) cc_final: 0.8323 (mtp) REVERT: I 17 ASP cc_start: 0.8980 (t0) cc_final: 0.8569 (m-30) REVERT: I 78 LEU cc_start: 0.9190 (mt) cc_final: 0.8947 (tm) REVERT: I 88 CYS cc_start: 0.8258 (p) cc_final: 0.8033 (p) REVERT: I 136 LEU cc_start: 0.8752 (mp) cc_final: 0.8492 (pt) REVERT: I 139 PHE cc_start: 0.8350 (p90) cc_final: 0.7372 (p90) REVERT: I 148 TRP cc_start: 0.7155 (m100) cc_final: 0.6373 (m100) REVERT: I 155 GLN cc_start: 0.8416 (mm-40) cc_final: 0.8184 (mp10) REVERT: I 167 ASP cc_start: 0.7892 (t0) cc_final: 0.7571 (t0) REVERT: I 173 TYR cc_start: 0.6974 (p90) cc_final: 0.6300 (p90) REVERT: J 3 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8374 (pm20) REVERT: J 6 GLU cc_start: 0.7655 (mp0) cc_final: 0.6717 (mp0) REVERT: J 22 CYS cc_start: 0.8656 (t) cc_final: 0.8149 (t) REVERT: J 72 ASP cc_start: 0.8620 (t0) cc_final: 0.8040 (t0) REVERT: J 75 LYS cc_start: 0.9455 (OUTLIER) cc_final: 0.9138 (mttm) REVERT: J 79 SER cc_start: 0.9365 (m) cc_final: 0.8745 (p) REVERT: J 86 ASP cc_start: 0.8985 (m-30) cc_final: 0.8646 (m-30) REVERT: J 105 GLN cc_start: 0.8519 (pm20) cc_final: 0.8095 (pm20) REVERT: J 128 LEU cc_start: 0.8050 (mm) cc_final: 0.7172 (mm) REVERT: J 171 PHE cc_start: 0.8077 (m-80) cc_final: 0.7383 (m-80) REVERT: J 215 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8940 (tmtt) REVERT: J 217 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8448 (tm-30) REVERT: K 3 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8373 (pm20) REVERT: K 6 GLU cc_start: 0.7644 (mp0) cc_final: 0.6636 (mp0) REVERT: K 22 CYS cc_start: 0.8648 (t) cc_final: 0.8169 (t) REVERT: K 72 ASP cc_start: 0.8529 (t0) cc_final: 0.8058 (t0) REVERT: K 79 SER cc_start: 0.9349 (m) cc_final: 0.8712 (p) REVERT: K 86 ASP cc_start: 0.8979 (m-30) cc_final: 0.8639 (m-30) REVERT: K 105 GLN cc_start: 0.8461 (pm20) cc_final: 0.8062 (pm20) REVERT: K 171 PHE cc_start: 0.7957 (m-80) cc_final: 0.7286 (m-80) REVERT: L 4 MET cc_start: 0.8942 (mtp) cc_final: 0.8419 (mtp) REVERT: L 17 ASP cc_start: 0.9084 (t0) cc_final: 0.8493 (m-30) REVERT: L 88 CYS cc_start: 0.8209 (p) cc_final: 0.7989 (p) REVERT: L 139 PHE cc_start: 0.8555 (p90) cc_final: 0.8322 (p90) REVERT: L 145 LYS cc_start: 0.9001 (mttp) cc_final: 0.8695 (mmtt) outliers start: 38 outliers final: 16 residues processed: 403 average time/residue: 1.2522 time to fit residues: 575.1333 Evaluate side-chains 392 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 367 time to evaluate : 2.525 ------------------------------------------------------------------------------- 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 173 TYR Chi-restraints excluded: chain E residue 198 HIS 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 129 THR 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 75 LYS Chi-restraints excluded: chain J residue 108 CYS 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 156 THR 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: 2.9990 chunk 46 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 chunk 249 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 chunk 1 optimal weight: 0.6980 chunk 145 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 152 optimal weight: 8.9990 chunk 218 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 176 GLN ** H 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 = 0.3723 r_free = 0.3723 target = 0.115663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.065186 restraints weight = 36784.739| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 3.06 r_work: 0.2568 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2439 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 20960 Z= 0.299 Angle : 0.752 12.901 28592 Z= 0.387 Chirality : 0.048 0.202 3220 Planarity : 0.006 0.076 3648 Dihedral : 5.325 24.970 2864 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.56 % Allowed : 21.01 % Favored : 77.43 % 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: 0.08 (0.16), residues: 2640 helix: -1.21 (0.46), residues: 124 sheet: 1.51 (0.16), residues: 920 loop : -0.77 (0.16), residues: 1596 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 0.040 0.002 PHE H 27 TYR 0.036 0.002 TYR H 181 ARG 0.008 0.001 ARG I 108 *********************** 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 406 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 370 time to evaluate : 2.417 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: 0.9053 (tpp) cc_final: 0.8731 (mtt) REVERT: A 164 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7931 (tm-30) REVERT: B 134 MET cc_start: 0.8889 (tpp) cc_final: 0.8590 (mtt) REVERT: B 164 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8129 (mm-30) REVERT: C 134 MET cc_start: 0.9080 (tpp) cc_final: 0.8781 (mtt) REVERT: C 149 GLU cc_start: 0.8655 (mp0) cc_final: 0.8122 (mp0) REVERT: C 164 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8113 (mm-30) REVERT: D 134 MET cc_start: 0.8985 (tpp) cc_final: 0.8644 (mtt) REVERT: D 150 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8474 (mmp80) REVERT: D 164 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8152 (mm-30) REVERT: E 4 MET cc_start: 0.8824 (mtp) cc_final: 0.8372 (mtp) REVERT: E 17 ASP cc_start: 0.9104 (t0) cc_final: 0.8563 (m-30) REVERT: E 50 GLU cc_start: 0.9293 (mp0) cc_final: 0.8909 (mp0) REVERT: E 88 CYS cc_start: 0.8240 (p) cc_final: 0.8029 (p) REVERT: E 136 LEU cc_start: 0.8732 (mp) cc_final: 0.8482 (pt) REVERT: E 139 PHE cc_start: 0.8355 (p90) cc_final: 0.7318 (p90) REVERT: E 173 TYR cc_start: 0.7221 (p90) cc_final: 0.6545 (p90) REVERT: E 211 ARG cc_start: 0.7899 (ttp-170) cc_final: 0.7610 (ptm160) REVERT: F 3 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8128 (pm20) REVERT: F 6 GLU cc_start: 0.7585 (mp0) cc_final: 0.6388 (mp0) REVERT: F 22 CYS cc_start: 0.8682 (t) cc_final: 0.8234 (t) REVERT: F 26 ARG cc_start: 0.8485 (pmm-80) cc_final: 0.8252 (pmm-80) REVERT: F 72 ASP cc_start: 0.8493 (t0) cc_final: 0.8025 (t0) REVERT: F 79 SER cc_start: 0.9335 (m) cc_final: 0.8695 (p) REVERT: F 86 ASP cc_start: 0.8977 (m-30) cc_final: 0.8598 (m-30) REVERT: F 105 GLN cc_start: 0.8529 (pm20) cc_final: 0.7989 (pm20) REVERT: F 128 LEU cc_start: 0.8924 (mp) cc_final: 0.8603 (mm) REVERT: F 171 PHE cc_start: 0.8181 (m-80) cc_final: 0.7518 (m-80) REVERT: G 4 MET cc_start: 0.8805 (ttm) cc_final: 0.8271 (ttm) REVERT: G 17 ASP cc_start: 0.9051 (t0) cc_final: 0.8451 (m-30) REVERT: G 50 GLU cc_start: 0.9289 (mp0) cc_final: 0.8905 (mp0) REVERT: G 88 CYS cc_start: 0.8154 (p) cc_final: 0.7537 (p) REVERT: G 139 PHE cc_start: 0.8210 (p90) cc_final: 0.7349 (p90) REVERT: G 148 TRP cc_start: 0.7229 (m100) cc_final: 0.6483 (m100) REVERT: G 155 GLN cc_start: 0.8446 (mm-40) cc_final: 0.8206 (mp10) REVERT: G 173 TYR cc_start: 0.6898 (p90) cc_final: 0.6461 (p90) REVERT: H 3 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8419 (pm20) REVERT: H 6 GLU cc_start: 0.7509 (mp0) cc_final: 0.6260 (mp0) REVERT: H 72 ASP cc_start: 0.8517 (t0) cc_final: 0.8052 (t0) REVERT: H 79 SER cc_start: 0.9403 (m) cc_final: 0.8829 (p) REVERT: H 86 ASP cc_start: 0.8953 (m-30) cc_final: 0.8622 (m-30) REVERT: H 105 GLN cc_start: 0.8238 (pm20) cc_final: 0.7463 (pm20) REVERT: H 128 LEU cc_start: 0.8124 (mm) cc_final: 0.7357 (mm) REVERT: H 171 PHE cc_start: 0.8199 (m-80) cc_final: 0.7539 (m-80) REVERT: I 4 MET cc_start: 0.8834 (mtp) cc_final: 0.8362 (mtp) REVERT: I 17 ASP cc_start: 0.9013 (t0) cc_final: 0.8641 (m-30) REVERT: I 50 GLU cc_start: 0.9286 (mp0) cc_final: 0.8907 (mp0) REVERT: I 78 LEU cc_start: 0.9170 (mt) cc_final: 0.8945 (tm) REVERT: I 88 CYS cc_start: 0.8220 (p) cc_final: 0.7996 (p) REVERT: I 136 LEU cc_start: 0.8704 (mp) cc_final: 0.8426 (pt) REVERT: I 139 PHE cc_start: 0.8328 (p90) cc_final: 0.7387 (p90) REVERT: I 148 TRP cc_start: 0.7171 (m100) cc_final: 0.6422 (m100) REVERT: I 155 GLN cc_start: 0.8410 (mm-40) cc_final: 0.8181 (mp10) REVERT: I 173 TYR cc_start: 0.6666 (p90) cc_final: 0.6183 (p90) REVERT: J 6 GLU cc_start: 0.7626 (mp0) cc_final: 0.6567 (mp0) REVERT: J 22 CYS cc_start: 0.8647 (t) cc_final: 0.8136 (t) REVERT: J 27 PHE cc_start: 0.8382 (m-80) cc_final: 0.8013 (m-80) REVERT: J 72 ASP cc_start: 0.8627 (t0) cc_final: 0.8180 (t0) REVERT: J 79 SER cc_start: 0.9342 (m) cc_final: 0.8712 (p) REVERT: J 86 ASP cc_start: 0.8977 (m-30) cc_final: 0.8673 (m-30) REVERT: J 105 GLN cc_start: 0.8507 (pm20) cc_final: 0.8082 (pm20) REVERT: J 128 LEU cc_start: 0.8077 (mm) cc_final: 0.7189 (mm) REVERT: J 171 PHE cc_start: 0.8110 (m-80) cc_final: 0.7409 (m-80) REVERT: J 215 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8992 (tmtt) REVERT: J 217 GLU cc_start: 0.8885 (tm-30) cc_final: 0.8490 (tm-30) REVERT: K 6 GLU cc_start: 0.7660 (mp0) cc_final: 0.6643 (mp0) REVERT: K 22 CYS cc_start: 0.8667 (t) cc_final: 0.8161 (t) REVERT: K 27 PHE cc_start: 0.8376 (m-80) cc_final: 0.8009 (m-80) REVERT: K 72 ASP cc_start: 0.8540 (t0) cc_final: 0.8097 (t0) REVERT: K 79 SER cc_start: 0.9343 (m) cc_final: 0.8705 (p) REVERT: K 86 ASP cc_start: 0.8979 (m-30) cc_final: 0.8675 (m-30) REVERT: K 105 GLN cc_start: 0.8509 (pm20) cc_final: 0.8099 (pm20) REVERT: K 171 PHE cc_start: 0.8072 (m-80) cc_final: 0.7390 (m-80) REVERT: L 4 MET cc_start: 0.8946 (mtp) cc_final: 0.8457 (mtp) REVERT: L 17 ASP cc_start: 0.9102 (t0) cc_final: 0.8571 (m-30) REVERT: L 50 GLU cc_start: 0.9260 (mp0) cc_final: 0.8877 (mp0) REVERT: L 108 ARG cc_start: 0.6873 (tmm-80) cc_final: 0.6465 (tmm-80) REVERT: L 139 PHE cc_start: 0.8644 (p90) cc_final: 0.8432 (p90) REVERT: L 145 LYS cc_start: 0.9005 (mttp) cc_final: 0.8697 (mmtt) REVERT: L 173 TYR cc_start: 0.5593 (p90) cc_final: 0.5235 (p90) outliers start: 36 outliers final: 20 residues processed: 394 average time/residue: 1.2231 time to fit residues: 550.5411 Evaluate side-chains 388 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 364 time to evaluate : 2.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 E residue 198 HIS 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 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 I residue 129 THR 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 J residue 215 LYS 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 33 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 88 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 35 optimal weight: 0.5980 chunk 5 optimal weight: 0.2980 chunk 43 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 129 optimal weight: 8.9990 chunk 147 optimal weight: 3.9990 chunk 166 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3724 r_free = 0.3724 target = 0.115691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.065221 restraints weight = 36827.239| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 3.07 r_work: 0.2572 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2442 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.4737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20960 Z= 0.277 Angle : 0.768 13.846 28592 Z= 0.393 Chirality : 0.048 0.198 3220 Planarity : 0.006 0.064 3648 Dihedral : 5.298 26.941 2864 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.30 % Allowed : 21.53 % Favored : 77.17 % 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: 0.23 (0.17), residues: 2640 helix: -0.22 (0.54), residues: 100 sheet: 1.55 (0.16), residues: 920 loop : -0.70 (0.16), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 148 HIS 0.003 0.001 HIS L 198 PHE 0.027 0.001 PHE F 27 TYR 0.032 0.002 TYR K 181 ARG 0.011 0.001 ARG H 26 ********************** 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 407 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 377 time to evaluate : 2.408 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: 0.9047 (tpp) cc_final: 0.8754 (mtt) REVERT: B 134 MET cc_start: 0.8906 (tpp) cc_final: 0.8597 (mtt) REVERT: B 164 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8132 (mm-30) REVERT: C 134 MET cc_start: 0.9098 (tpp) cc_final: 0.8795 (mtt) REVERT: C 149 GLU cc_start: 0.8663 (mp0) cc_final: 0.8143 (mp0) REVERT: C 164 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8112 (mm-30) REVERT: D 134 MET cc_start: 0.8992 (tpp) cc_final: 0.8681 (mtt) REVERT: D 150 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.8745 (mmt-90) REVERT: D 164 GLU cc_start: 0.8409 (mm-30) cc_final: 0.8148 (mm-30) REVERT: E 4 MET cc_start: 0.8811 (mtp) cc_final: 0.8438 (mtp) REVERT: E 17 ASP cc_start: 0.9073 (t0) cc_final: 0.8554 (m-30) REVERT: E 50 GLU cc_start: 0.9270 (OUTLIER) cc_final: 0.8877 (mp0) REVERT: E 136 LEU cc_start: 0.8668 (mp) cc_final: 0.8427 (pt) REVERT: E 139 PHE cc_start: 0.8326 (p90) cc_final: 0.7274 (p90) REVERT: E 173 TYR cc_start: 0.7241 (p90) cc_final: 0.6702 (p90) REVERT: E 211 ARG cc_start: 0.7837 (ttp-170) cc_final: 0.7510 (ptm160) REVERT: F 3 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8190 (pm20) REVERT: F 6 GLU cc_start: 0.7606 (mp0) cc_final: 0.6345 (mp0) REVERT: F 22 CYS cc_start: 0.8696 (t) cc_final: 0.8232 (t) REVERT: F 27 PHE cc_start: 0.8498 (m-80) cc_final: 0.8223 (m-80) REVERT: F 72 ASP cc_start: 0.8505 (t0) cc_final: 0.8053 (t0) REVERT: F 79 SER cc_start: 0.9323 (m) cc_final: 0.8675 (p) REVERT: F 86 ASP cc_start: 0.8969 (m-30) cc_final: 0.8664 (m-30) REVERT: F 105 GLN cc_start: 0.8520 (pm20) cc_final: 0.7978 (pm20) REVERT: F 128 LEU cc_start: 0.8909 (mp) cc_final: 0.8622 (mm) REVERT: F 171 PHE cc_start: 0.8168 (m-80) cc_final: 0.7498 (m-80) REVERT: G 4 MET cc_start: 0.8837 (ttm) cc_final: 0.8304 (ttt) REVERT: G 17 ASP cc_start: 0.9075 (t0) cc_final: 0.8546 (m-30) REVERT: G 50 GLU cc_start: 0.9269 (mp0) cc_final: 0.8876 (mp0) REVERT: G 108 ARG cc_start: 0.6306 (tmm-80) cc_final: 0.5787 (tmm-80) REVERT: G 139 PHE cc_start: 0.8127 (p90) cc_final: 0.7286 (p90) REVERT: G 148 TRP cc_start: 0.7204 (m100) cc_final: 0.6468 (m100) REVERT: G 155 GLN cc_start: 0.8335 (mm-40) cc_final: 0.8099 (mp10) REVERT: G 173 TYR cc_start: 0.6818 (p90) cc_final: 0.6552 (p90) REVERT: H 3 GLN cc_start: 0.8642 (pm20) cc_final: 0.8377 (pm20) REVERT: H 6 GLU cc_start: 0.7420 (mp0) cc_final: 0.6179 (mp0) REVERT: H 72 ASP cc_start: 0.8536 (t0) cc_final: 0.8088 (t0) REVERT: H 79 SER cc_start: 0.9383 (m) cc_final: 0.8805 (p) REVERT: H 86 ASP cc_start: 0.8963 (m-30) cc_final: 0.8627 (m-30) REVERT: H 105 GLN cc_start: 0.8205 (pm20) cc_final: 0.7425 (pm20) REVERT: H 128 LEU cc_start: 0.8154 (mm) cc_final: 0.7377 (mm) REVERT: H 171 PHE cc_start: 0.8119 (m-80) cc_final: 0.7528 (m-80) REVERT: I 4 MET cc_start: 0.8813 (mtp) cc_final: 0.8429 (mtp) REVERT: I 17 ASP cc_start: 0.9016 (t0) cc_final: 0.8656 (m-30) REVERT: I 50 GLU cc_start: 0.9260 (OUTLIER) cc_final: 0.8876 (mp0) REVERT: I 78 LEU cc_start: 0.9260 (mt) cc_final: 0.8931 (tm) REVERT: I 136 LEU cc_start: 0.8675 (mp) cc_final: 0.8421 (pt) REVERT: I 139 PHE cc_start: 0.8300 (p90) cc_final: 0.7342 (p90) REVERT: I 148 TRP cc_start: 0.7135 (m100) cc_final: 0.6402 (m100) REVERT: I 155 GLN cc_start: 0.8361 (mm-40) cc_final: 0.8134 (mp10) REVERT: I 167 ASP cc_start: 0.8042 (t0) cc_final: 0.7796 (p0) REVERT: I 173 TYR cc_start: 0.7166 (p90) cc_final: 0.6640 (p90) REVERT: J 6 GLU cc_start: 0.7598 (mp0) cc_final: 0.6521 (mp0) REVERT: J 22 CYS cc_start: 0.8625 (t) cc_final: 0.8144 (t) REVERT: J 72 ASP cc_start: 0.8598 (t0) cc_final: 0.8138 (OUTLIER) REVERT: J 79 SER cc_start: 0.9331 (m) cc_final: 0.8695 (p) REVERT: J 86 ASP cc_start: 0.8978 (m-30) cc_final: 0.8673 (m-30) REVERT: J 105 GLN cc_start: 0.8492 (pm20) cc_final: 0.8072 (pm20) REVERT: J 128 LEU cc_start: 0.8089 (mm) cc_final: 0.7237 (mm) REVERT: J 149 TYR cc_start: 0.8405 (p90) cc_final: 0.8097 (p90) REVERT: J 171 PHE cc_start: 0.8249 (m-80) cc_final: 0.7560 (m-80) REVERT: J 215 LYS cc_start: 0.9218 (OUTLIER) cc_final: 0.9002 (tmtt) REVERT: J 217 GLU cc_start: 0.8899 (tm-30) cc_final: 0.8508 (tm-30) REVERT: K 6 GLU cc_start: 0.7624 (mp0) cc_final: 0.6561 (mp0) REVERT: K 22 CYS cc_start: 0.8675 (t) cc_final: 0.8201 (t) REVERT: K 72 ASP cc_start: 0.8540 (t0) cc_final: 0.8099 (t0) REVERT: K 79 SER cc_start: 0.9334 (m) cc_final: 0.8693 (p) REVERT: K 86 ASP cc_start: 0.8974 (m-30) cc_final: 0.8668 (m-30) REVERT: K 105 GLN cc_start: 0.8496 (pm20) cc_final: 0.8080 (pm20) REVERT: K 171 PHE cc_start: 0.8128 (m-80) cc_final: 0.7457 (m-80) REVERT: L 17 ASP cc_start: 0.9088 (t0) cc_final: 0.8551 (m-30) REVERT: L 50 GLU cc_start: 0.9243 (mp0) cc_final: 0.8857 (mp0) REVERT: L 139 PHE cc_start: 0.8654 (p90) cc_final: 0.8367 (p90) REVERT: L 145 LYS cc_start: 0.9002 (mttp) cc_final: 0.8694 (mmtt) REVERT: L 173 TYR cc_start: 0.5830 (p90) cc_final: 0.5281 (p90) outliers start: 30 outliers final: 16 residues processed: 397 average time/residue: 1.2450 time to fit residues: 565.5987 Evaluate side-chains 387 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 367 time to evaluate : 2.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 150 ARG Chi-restraints excluded: chain E residue 50 GLU 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 183 LEU 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 I residue 50 GLU Chi-restraints excluded: chain I residue 129 THR 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 J residue 215 LYS 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 88 CYS 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: 0.9990 chunk 249 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 chunk 156 optimal weight: 7.9990 chunk 234 optimal weight: 5.9990 chunk 202 optimal weight: 7.9990 chunk 21 optimal weight: 0.0000 chunk 1 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 chunk 260 optimal weight: 9.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- 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** ** J 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 = 0.3739 r_free = 0.3739 target = 0.116717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.066480 restraints weight = 36888.606| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 3.10 r_work: 0.2602 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2472 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.4839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20960 Z= 0.214 Angle : 0.754 14.384 28592 Z= 0.384 Chirality : 0.047 0.238 3220 Planarity : 0.006 0.063 3648 Dihedral : 5.234 26.437 2864 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.04 % Allowed : 21.88 % Favored : 77.08 % 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: 0.32 (0.17), residues: 2640 helix: -0.14 (0.54), residues: 100 sheet: 1.58 (0.17), residues: 924 loop : -0.62 (0.16), residues: 1616 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 0.029 0.001 PHE F 27 TYR 0.029 0.002 TYR J 181 ARG 0.007 0.001 ARG L 142 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23419.73 seconds wall clock time: 411 minutes 56.08 seconds (24716.08 seconds total)