Starting phenix.real_space_refine on Thu Sep 18 22:03:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vgk_43203/09_2025/8vgk_43203.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vgk_43203/09_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_43203/09_2025/8vgk_43203.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vgk_43203/09_2025/8vgk_43203.map" model { file = "/net/cci-nas-00/data/ceres_data/8vgk_43203/09_2025/8vgk_43203.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vgk_43203/09_2025/8vgk_43203.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.008 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.98, per 1000 atoms: 0.19 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: 1.63 Conformation dependent library (CDL) restraints added in 881.2 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 1.02 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: 3.60 Time building geometry restraints manager: 2.22 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.020 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 21016 Z= 0.256 Angle : 1.044 10.021 28704 Z= 0.594 Chirality : 0.060 0.277 3220 Planarity : 0.010 0.096 3648 Dihedral : 13.841 89.332 7480 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.61 % Allowed : 7.05 % Favored : 92.35 % Rotamer: Outliers : 0.65 % Allowed : 3.91 % Favored : 95.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (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 ARG 0.025 0.004 ARG H 97 TYR 0.035 0.008 TYR H 181 PHE 0.022 0.003 PHE G 92 TRP 0.025 0.003 TRP F 159 HIS 0.011 0.003 HIS D 72 Details of bonding type rmsd covalent geometry : bond 0.00544 (20960) covalent geometry : angle 1.03976 (28592) SS BOND : bond 0.01013 ( 56) SS BOND : angle 1.89601 ( 112) hydrogen bonds : bond 0.20065 ( 709) hydrogen bonds : angle 9.17229 ( 1995) *********************** 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 : 0.758 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: 0.7567 (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: 0.7445 (tp) REVERT: K 128 LEU cc_start: 0.7776 (tp) cc_final: 0.7430 (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: 0.6795 time to fit residues: 476.9225 Evaluate side-chains 391 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 388 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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 197 optimal weight: 10.0000 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 8.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.119525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.067761 restraints weight = 36166.615| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 3.12 r_work: 0.2601 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2466 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21016 Z= 0.193 Angle : 0.840 11.856 28704 Z= 0.443 Chirality : 0.050 0.208 3220 Planarity : 0.006 0.074 3648 Dihedral : 6.791 48.455 2872 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.78 % Allowed : 14.15 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.16), residues: 2640 helix: -1.32 (0.45), residues: 148 sheet: 1.04 (0.17), residues: 908 loop : -0.68 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 61 TYR 0.022 0.002 TYR I 140 PHE 0.021 0.002 PHE L 139 TRP 0.020 0.001 TRP B 215 HIS 0.004 0.001 HIS B 173 Details of bonding type rmsd covalent geometry : bond 0.00441 (20960) covalent geometry : angle 0.83642 (28592) SS BOND : bond 0.00979 ( 56) SS BOND : angle 1.53488 ( 112) hydrogen bonds : bond 0.04506 ( 709) hydrogen bonds : angle 6.63610 ( 1995) *********************** 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 506 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 465 time to evaluate : 0.674 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: A 109 GLU cc_start: 0.9120 (tp30) cc_final: 0.8822 (tp30) REVERT: A 164 GLU cc_start: 0.8336 (mm-30) cc_final: 0.8095 (mm-30) REVERT: B 109 GLU cc_start: 0.9135 (tp30) cc_final: 0.8853 (tp30) REVERT: B 164 GLU cc_start: 0.8355 (mm-30) cc_final: 0.7907 (mm-30) REVERT: C 109 GLU cc_start: 0.9095 (tp30) cc_final: 0.8797 (tp30) REVERT: C 145 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7271 (p0) REVERT: C 149 GLU cc_start: 0.8271 (mp0) cc_final: 0.7912 (mp0) REVERT: C 164 GLU cc_start: 0.8423 (mm-30) cc_final: 0.7951 (mm-30) REVERT: D 109 GLU cc_start: 0.9151 (tp30) cc_final: 0.8874 (tp30) REVERT: D 164 GLU cc_start: 0.8387 (mm-30) cc_final: 0.7975 (mm-30) REVERT: E 78 LEU cc_start: 0.9140 (mt) cc_final: 0.8857 (tm) REVERT: E 139 PHE cc_start: 0.8267 (p90) cc_final: 0.7974 (p90) REVERT: E 148 TRP cc_start: 0.6826 (m100) cc_final: 0.6603 (m100) REVERT: E 167 ASP cc_start: 0.7549 (t0) cc_final: 0.7349 (t0) REVERT: E 173 TYR cc_start: 0.5816 (OUTLIER) cc_final: 0.4951 (p90) REVERT: F 3 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8161 (pm20) REVERT: F 6 GLU cc_start: 0.7756 (mp0) cc_final: 0.7308 (mp0) REVERT: F 72 ASP cc_start: 0.8270 (t0) cc_final: 0.8018 (t0) REVERT: F 105 GLN cc_start: 0.8462 (pm20) cc_final: 0.8087 (pm20) REVERT: F 152 GLU cc_start: 0.8379 (pm20) cc_final: 0.7942 (pm20) REVERT: F 160 ASN cc_start: 0.8750 (m-40) cc_final: 0.8362 (m110) REVERT: F 204 ASN cc_start: 0.7723 (p0) cc_final: 0.7495 (p0) REVERT: F 209 ASN cc_start: 0.9203 (m110) cc_final: 0.8975 (m-40) REVERT: G 78 LEU cc_start: 0.9124 (mt) cc_final: 0.8850 (tm) REVERT: G 123 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6652 (tt0) REVERT: G 139 PHE cc_start: 0.8198 (p90) cc_final: 0.7758 (p90) REVERT: G 142 ARG cc_start: 0.8387 (mtm-85) cc_final: 0.8164 (mpt-90) REVERT: G 148 TRP cc_start: 0.6652 (m100) cc_final: 0.5871 (m100) REVERT: G 155 GLN cc_start: 0.8385 (mm-40) cc_final: 0.8049 (mp10) REVERT: G 173 TYR cc_start: 0.5786 (OUTLIER) cc_final: 0.4518 (p90) REVERT: H 3 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8126 (pm20) REVERT: H 6 GLU cc_start: 0.7367 (mp0) cc_final: 0.6547 (mp0) REVERT: H 72 ASP cc_start: 0.8215 (t0) cc_final: 0.7933 (t0) REVERT: H 86 ASP cc_start: 0.9059 (m-30) cc_final: 0.8856 (m-30) REVERT: H 105 GLN cc_start: 0.8225 (pm20) cc_final: 0.7641 (pm20) REVERT: H 152 GLU cc_start: 0.8432 (pm20) cc_final: 0.8108 (pm20) REVERT: I 78 LEU cc_start: 0.9109 (mt) cc_final: 0.8842 (tm) REVERT: I 139 PHE cc_start: 0.8195 (p90) cc_final: 0.7854 (p90) REVERT: I 148 TRP cc_start: 0.6726 (m100) cc_final: 0.5638 (m100) REVERT: I 155 GLN cc_start: 0.8401 (mm-40) cc_final: 0.7990 (mp10) REVERT: I 173 TYR cc_start: 0.5883 (OUTLIER) cc_final: 0.5043 (p90) REVERT: J 3 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8126 (pm20) REVERT: J 6 GLU cc_start: 0.7746 (mp0) cc_final: 0.7328 (mp0) REVERT: J 46 GLU cc_start: 0.8962 (pt0) cc_final: 0.8753 (pt0) REVERT: J 72 ASP cc_start: 0.8364 (t0) cc_final: 0.7999 (t0) REVERT: J 105 GLN cc_start: 0.8502 (pm20) cc_final: 0.8132 (pm20) REVERT: J 117 LYS cc_start: 0.8641 (ttpp) cc_final: 0.8280 (ttpp) REVERT: J 152 GLU cc_start: 0.8433 (pm20) cc_final: 0.7801 (pm20) REVERT: J 160 ASN cc_start: 0.8888 (m-40) cc_final: 0.8374 (m110) REVERT: J 206 LYS cc_start: 0.9189 (mmpt) cc_final: 0.8983 (mmmt) REVERT: J 217 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8452 (tm-30) REVERT: K 3 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8132 (pm20) REVERT: K 6 GLU cc_start: 0.7752 (mp0) cc_final: 0.7330 (mp0) REVERT: K 46 GLU cc_start: 0.8941 (pt0) cc_final: 0.8732 (pt0) REVERT: K 72 ASP cc_start: 0.8344 (t0) cc_final: 0.8100 (t0) REVERT: K 105 GLN cc_start: 0.8490 (pm20) cc_final: 0.8120 (pm20) REVERT: K 152 GLU cc_start: 0.8138 (pm20) cc_final: 0.7872 (pm20) REVERT: K 160 ASN cc_start: 0.8888 (m-40) cc_final: 0.8339 (m110) REVERT: K 171 PHE cc_start: 0.7765 (m-80) cc_final: 0.7559 (m-80) REVERT: L 78 LEU cc_start: 0.9133 (mt) cc_final: 0.8852 (tm) REVERT: L 139 PHE cc_start: 0.8147 (p90) cc_final: 0.7910 (p90) outliers start: 41 outliers final: 8 residues processed: 493 average time/residue: 0.5197 time to fit residues: 291.0930 Evaluate side-chains 413 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 395 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 J residue 217 GLU Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 11 CYS Chi-restraints excluded: chain K residue 156 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 190 optimal weight: 8.9990 chunk 52 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 173 optimal weight: 0.8980 chunk 251 optimal weight: 1.9990 chunk 168 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 152 optimal weight: 3.9990 chunk 186 optimal weight: 6.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 155 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.118747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.067336 restraints weight = 36311.521| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 3.12 r_work: 0.2601 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2467 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 21016 Z= 0.160 Angle : 0.757 11.530 28704 Z= 0.389 Chirality : 0.048 0.156 3220 Planarity : 0.006 0.066 3648 Dihedral : 6.074 45.741 2867 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.52 % Allowed : 15.89 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.17), residues: 2640 helix: -0.40 (0.51), residues: 124 sheet: 1.29 (0.17), residues: 908 loop : -0.58 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 142 TYR 0.015 0.002 TYR G 140 PHE 0.018 0.002 PHE A 153 TRP 0.014 0.001 TRP B 215 HIS 0.005 0.001 HIS G 189 Details of bonding type rmsd covalent geometry : bond 0.00361 (20960) covalent geometry : angle 0.75462 (28592) SS BOND : bond 0.00788 ( 56) SS BOND : angle 1.19775 ( 112) hydrogen bonds : bond 0.03642 ( 709) hydrogen bonds : angle 6.07794 ( 1995) *********************** 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 483 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 425 time to evaluate : 0.689 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: A 134 MET cc_start: 0.8940 (tpp) cc_final: 0.8440 (mpp) REVERT: B 109 GLU cc_start: 0.9172 (tp30) cc_final: 0.8827 (tp30) REVERT: B 134 MET cc_start: 0.8720 (tpp) cc_final: 0.8119 (mpp) REVERT: B 147 ASP cc_start: 0.8836 (t0) cc_final: 0.8305 (m-30) REVERT: B 164 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7963 (mm-30) REVERT: C 134 MET cc_start: 0.8902 (tpp) cc_final: 0.8380 (mpp) REVERT: C 164 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8082 (mm-30) REVERT: D 109 GLU cc_start: 0.9112 (tp30) cc_final: 0.8734 (tp30) REVERT: D 134 MET cc_start: 0.8908 (tpp) cc_final: 0.8370 (mpp) REVERT: D 147 ASP cc_start: 0.8799 (t0) cc_final: 0.8306 (m-30) REVERT: D 150 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.8605 (mmp80) REVERT: D 164 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8041 (mm-30) REVERT: E 17 ASP cc_start: 0.8517 (t0) cc_final: 0.8055 (m-30) REVERT: E 78 LEU cc_start: 0.9203 (mt) cc_final: 0.8921 (tm) REVERT: E 108 ARG cc_start: 0.6733 (tmm-80) cc_final: 0.5943 (tmm-80) REVERT: E 139 PHE cc_start: 0.8279 (p90) cc_final: 0.7915 (p90) REVERT: E 148 TRP cc_start: 0.6935 (m100) cc_final: 0.6072 (m100) REVERT: E 155 GLN cc_start: 0.8420 (mm-40) cc_final: 0.8148 (mp10) REVERT: E 167 ASP cc_start: 0.7511 (t0) cc_final: 0.7308 (t0) REVERT: E 173 TYR cc_start: 0.5842 (p90) cc_final: 0.5233 (p90) REVERT: F 3 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8237 (pm20) REVERT: F 6 GLU cc_start: 0.7800 (mp0) cc_final: 0.7082 (mp0) REVERT: F 72 ASP cc_start: 0.8329 (t0) cc_final: 0.7748 (t0) REVERT: F 75 LYS cc_start: 0.9369 (OUTLIER) cc_final: 0.9121 (mttm) REVERT: F 86 ASP cc_start: 0.8975 (m-30) cc_final: 0.8761 (m-30) REVERT: F 105 GLN cc_start: 0.8468 (pm20) cc_final: 0.8078 (pm20) REVERT: F 128 LEU cc_start: 0.8986 (mp) cc_final: 0.8527 (mm) REVERT: F 164 LEU cc_start: 0.8469 (mt) cc_final: 0.8253 (mt) REVERT: F 171 PHE cc_start: 0.7726 (m-80) cc_final: 0.7051 (m-80) REVERT: F 209 ASN cc_start: 0.9200 (m110) cc_final: 0.8998 (m-40) REVERT: G 17 ASP cc_start: 0.8571 (t0) cc_final: 0.8078 (m-30) REVERT: G 78 LEU cc_start: 0.9205 (mt) cc_final: 0.8909 (tm) REVERT: G 123 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6721 (tt0) REVERT: G 139 PHE cc_start: 0.8160 (p90) cc_final: 0.7906 (p90) REVERT: G 148 TRP cc_start: 0.6792 (m100) cc_final: 0.6019 (m100) REVERT: G 155 GLN cc_start: 0.8371 (mm-40) cc_final: 0.8036 (mp10) REVERT: G 173 TYR cc_start: 0.5976 (OUTLIER) cc_final: 0.5380 (p90) REVERT: H 3 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8193 (pm20) REVERT: H 6 GLU cc_start: 0.7410 (mp0) cc_final: 0.6297 (mp0) REVERT: H 72 ASP cc_start: 0.8308 (t0) cc_final: 0.7889 (t0) REVERT: H 86 ASP cc_start: 0.9011 (m-30) cc_final: 0.8726 (m-30) REVERT: H 105 GLN cc_start: 0.8246 (pm20) cc_final: 0.7765 (pm20) REVERT: H 128 LEU cc_start: 0.7586 (mm) cc_final: 0.6744 (mm) REVERT: H 171 PHE cc_start: 0.7674 (m-80) cc_final: 0.7044 (m-80) REVERT: I 17 ASP cc_start: 0.8526 (t0) cc_final: 0.8081 (m-30) REVERT: I 78 LEU cc_start: 0.9180 (mt) cc_final: 0.8894 (tm) REVERT: I 82 ASP cc_start: 0.8288 (m-30) cc_final: 0.8034 (m-30) REVERT: I 139 PHE cc_start: 0.8212 (p90) cc_final: 0.7989 (p90) REVERT: I 148 TRP cc_start: 0.6837 (m100) cc_final: 0.5995 (m100) REVERT: I 155 GLN cc_start: 0.8352 (mm-40) cc_final: 0.8014 (mp10) REVERT: I 173 TYR cc_start: 0.5747 (OUTLIER) cc_final: 0.5192 (p90) REVERT: J 3 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8186 (pm20) REVERT: J 6 GLU cc_start: 0.7743 (mp0) cc_final: 0.6940 (mp0) REVERT: J 72 ASP cc_start: 0.8455 (t0) cc_final: 0.8051 (t0) REVERT: J 86 ASP cc_start: 0.8971 (m-30) cc_final: 0.8763 (m-30) REVERT: J 105 GLN cc_start: 0.8485 (pm20) cc_final: 0.8045 (pm20) REVERT: J 171 PHE cc_start: 0.7744 (m-80) cc_final: 0.7150 (m-80) REVERT: J 176 GLN cc_start: 0.5993 (mp10) cc_final: 0.5713 (mp10) REVERT: K 3 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8198 (pm20) REVERT: K 6 GLU cc_start: 0.7743 (mp0) cc_final: 0.6926 (mp0) REVERT: K 72 ASP cc_start: 0.8337 (t0) cc_final: 0.7760 (t0) REVERT: K 75 LYS cc_start: 0.9378 (OUTLIER) cc_final: 0.9136 (mttm) REVERT: K 86 ASP cc_start: 0.8971 (m-30) cc_final: 0.8761 (m-30) REVERT: K 105 GLN cc_start: 0.8470 (pm20) cc_final: 0.8028 (pm20) REVERT: K 171 PHE cc_start: 0.7701 (m-80) cc_final: 0.7086 (m-80) REVERT: L 4 MET cc_start: 0.8982 (mtp) cc_final: 0.8291 (mtp) REVERT: L 17 ASP cc_start: 0.8521 (t0) cc_final: 0.8065 (m-30) REVERT: L 78 LEU cc_start: 0.9202 (mt) cc_final: 0.8911 (tm) REVERT: L 123 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7128 (tt0) REVERT: L 139 PHE cc_start: 0.8273 (p90) cc_final: 0.7961 (p90) outliers start: 58 outliers final: 24 residues processed: 466 average time/residue: 0.5134 time to fit residues: 273.4511 Evaluate side-chains 421 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 386 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 GLN 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 75 LYS 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 G residue 123 GLU Chi-restraints excluded: chain G residue 129 THR 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 164 LEU Chi-restraints excluded: chain H residue 202 ASN 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 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 75 LYS 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 183 LEU 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 176 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 174 optimal weight: 6.9990 chunk 190 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 253 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 184 optimal weight: 4.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 30 ASN E 210 ASN G 30 ASN I 30 ASN ** J 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 209 ASN ** K 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.116164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.064681 restraints weight = 36564.038| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 3.11 r_work: 0.2550 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2413 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 21016 Z= 0.225 Angle : 0.765 11.376 28704 Z= 0.398 Chirality : 0.049 0.168 3220 Planarity : 0.006 0.069 3648 Dihedral : 5.961 48.381 2867 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.13 % Allowed : 17.27 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.17), residues: 2640 helix: -0.78 (0.48), residues: 124 sheet: 1.14 (0.16), residues: 936 loop : -0.65 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 211 TYR 0.023 0.002 TYR H 181 PHE 0.024 0.002 PHE F 27 TRP 0.012 0.001 TRP B 215 HIS 0.004 0.001 HIS G 189 Details of bonding type rmsd covalent geometry : bond 0.00523 (20960) covalent geometry : angle 0.76001 (28592) SS BOND : bond 0.00770 ( 56) SS BOND : angle 1.59271 ( 112) hydrogen bonds : bond 0.03771 ( 709) hydrogen bonds : angle 5.94128 ( 1995) *********************** 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 444 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 395 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 GLU cc_start: 0.9150 (tp30) cc_final: 0.8881 (tp30) REVERT: A 164 GLU cc_start: 0.8281 (mm-30) cc_final: 0.8043 (mm-30) REVERT: B 134 MET cc_start: 0.8844 (tpp) cc_final: 0.8304 (mpp) REVERT: B 164 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8066 (mm-30) REVERT: C 109 GLU cc_start: 0.9131 (tp30) cc_final: 0.8863 (tp30) REVERT: C 134 MET cc_start: 0.9018 (tpp) cc_final: 0.8525 (mpp) REVERT: C 149 GLU cc_start: 0.8449 (mp0) cc_final: 0.8002 (mp0) REVERT: C 164 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8109 (mm-30) REVERT: D 150 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8559 (mmp80) REVERT: D 164 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8114 (mm-30) REVERT: E 4 MET cc_start: 0.8839 (mtp) cc_final: 0.8096 (mtp) REVERT: E 17 ASP cc_start: 0.8692 (t0) cc_final: 0.8176 (m-30) REVERT: E 50 GLU cc_start: 0.9371 (mt-10) cc_final: 0.8755 (pp20) REVERT: E 78 LEU cc_start: 0.9226 (mt) cc_final: 0.9018 (tm) REVERT: E 82 ASP cc_start: 0.8352 (m-30) cc_final: 0.8116 (m-30) REVERT: E 139 PHE cc_start: 0.8200 (p90) cc_final: 0.7888 (p90) REVERT: E 167 ASP cc_start: 0.7625 (t0) cc_final: 0.7378 (t0) REVERT: E 173 TYR cc_start: 0.6354 (OUTLIER) cc_final: 0.5934 (p90) REVERT: E 210 ASN cc_start: 0.8534 (OUTLIER) cc_final: 0.8221 (m-40) REVERT: F 3 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8133 (pm20) REVERT: F 6 GLU cc_start: 0.7721 (mp0) cc_final: 0.6756 (mp0) REVERT: F 22 CYS cc_start: 0.8700 (t) cc_final: 0.8215 (t) REVERT: F 26 ARG cc_start: 0.8513 (pmm-80) cc_final: 0.7849 (pmm-80) REVERT: F 72 ASP cc_start: 0.8390 (t0) cc_final: 0.7950 (t0) REVERT: F 86 ASP cc_start: 0.8979 (m-30) cc_final: 0.8712 (m-30) REVERT: F 105 GLN cc_start: 0.8492 (pm20) cc_final: 0.8105 (pm20) REVERT: F 128 LEU cc_start: 0.9013 (mp) cc_final: 0.8607 (mm) REVERT: F 171 PHE cc_start: 0.7710 (m-80) cc_final: 0.7061 (m-80) REVERT: G 4 MET cc_start: 0.8849 (mtp) cc_final: 0.8114 (mtp) REVERT: G 17 ASP cc_start: 0.8717 (t0) cc_final: 0.8178 (m-30) REVERT: G 50 GLU cc_start: 0.9382 (mt-10) cc_final: 0.8771 (pp20) REVERT: G 78 LEU cc_start: 0.9222 (mt) cc_final: 0.8993 (tm) REVERT: G 82 ASP cc_start: 0.8366 (m-30) cc_final: 0.8129 (m-30) REVERT: G 123 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6906 (tt0) REVERT: G 139 PHE cc_start: 0.8200 (p90) cc_final: 0.7589 (p90) REVERT: G 148 TRP cc_start: 0.6906 (m100) cc_final: 0.6132 (m100) REVERT: G 155 GLN cc_start: 0.8376 (mm-40) cc_final: 0.8057 (mp10) REVERT: G 173 TYR cc_start: 0.6386 (OUTLIER) cc_final: 0.5620 (p90) REVERT: H 3 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8173 (pm20) REVERT: H 6 GLU cc_start: 0.7493 (mp0) cc_final: 0.6364 (mp0) REVERT: H 22 CYS cc_start: 0.8556 (t) cc_final: 0.8181 (t) REVERT: H 26 ARG cc_start: 0.8407 (pmm-80) cc_final: 0.7750 (pmm-80) REVERT: H 72 ASP cc_start: 0.8384 (t0) cc_final: 0.7942 (t0) REVERT: H 86 ASP cc_start: 0.9003 (m-30) cc_final: 0.8691 (m-30) REVERT: H 105 GLN cc_start: 0.8343 (pm20) cc_final: 0.7632 (pm20) REVERT: H 171 PHE cc_start: 0.7734 (m-80) cc_final: 0.7110 (m-80) REVERT: I 4 MET cc_start: 0.8859 (mtp) cc_final: 0.8132 (mtp) REVERT: I 17 ASP cc_start: 0.8701 (t0) cc_final: 0.8181 (m-30) REVERT: I 50 GLU cc_start: 0.9376 (mt-10) cc_final: 0.8772 (pp20) REVERT: I 78 LEU cc_start: 0.9186 (mt) cc_final: 0.8952 (tm) REVERT: I 82 ASP cc_start: 0.8354 (m-30) cc_final: 0.8144 (m-30) REVERT: I 139 PHE cc_start: 0.8173 (p90) cc_final: 0.7524 (p90) REVERT: I 148 TRP cc_start: 0.6874 (m100) cc_final: 0.6124 (m100) REVERT: I 155 GLN cc_start: 0.8340 (mm-40) cc_final: 0.8036 (mp10) REVERT: I 173 TYR cc_start: 0.6401 (OUTLIER) cc_final: 0.5953 (p90) REVERT: J 3 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.8187 (pm20) REVERT: J 6 GLU cc_start: 0.7718 (mp0) cc_final: 0.6787 (mp0) REVERT: J 22 CYS cc_start: 0.8714 (t) cc_final: 0.8269 (t) REVERT: J 72 ASP cc_start: 0.8507 (t0) cc_final: 0.8055 (t0) REVERT: J 86 ASP cc_start: 0.8980 (m-30) cc_final: 0.8711 (m-30) REVERT: J 105 GLN cc_start: 0.8502 (pm20) cc_final: 0.8120 (pm20) REVERT: J 171 PHE cc_start: 0.7685 (m-80) cc_final: 0.7063 (m-80) REVERT: J 202 ASN cc_start: 0.8015 (m-40) cc_final: 0.7538 (t0) REVERT: K 3 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8180 (pm20) REVERT: K 6 GLU cc_start: 0.7721 (mp0) cc_final: 0.6770 (mp0) REVERT: K 22 CYS cc_start: 0.8709 (t) cc_final: 0.8262 (t) REVERT: K 72 ASP cc_start: 0.8382 (t0) cc_final: 0.7941 (t0) REVERT: K 86 ASP cc_start: 0.8976 (m-30) cc_final: 0.8704 (m-30) REVERT: K 105 GLN cc_start: 0.8469 (pm20) cc_final: 0.8083 (pm20) REVERT: K 128 LEU cc_start: 0.7726 (mm) cc_final: 0.6827 (mm) REVERT: K 171 PHE cc_start: 0.7814 (m-80) cc_final: 0.7195 (m-80) REVERT: L 17 ASP cc_start: 0.8693 (t0) cc_final: 0.8176 (m-30) REVERT: L 23 CYS cc_start: 0.7332 (t) cc_final: 0.5092 (t) REVERT: L 50 GLU cc_start: 0.9367 (mt-10) cc_final: 0.8767 (pp20) REVERT: L 78 LEU cc_start: 0.9208 (mt) cc_final: 0.8990 (tm) REVERT: L 82 ASP cc_start: 0.8359 (m-30) cc_final: 0.8124 (m-30) REVERT: L 139 PHE cc_start: 0.8259 (p90) cc_final: 0.7938 (p90) REVERT: L 173 TYR cc_start: 0.5486 (OUTLIER) cc_final: 0.4390 (p90) outliers start: 49 outliers final: 20 residues processed: 426 average time/residue: 0.5692 time to fit residues: 276.4715 Evaluate side-chains 397 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 366 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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 129 THR Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 210 ASN 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 123 GLU 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 183 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 183 LEU Chi-restraints excluded: chain J residue 201 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 183 LEU Chi-restraints excluded: chain L residue 173 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 164 optimal weight: 0.0570 chunk 163 optimal weight: 0.5980 chunk 167 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 243 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 193 optimal weight: 10.0000 chunk 207 optimal weight: 1.9990 chunk 168 optimal weight: 0.8980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 137 ASN E 210 ASN F 176 GLN ** G 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 176 GLN I 137 ASN ** J 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.117724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.066641 restraints weight = 36072.071| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 3.09 r_work: 0.2593 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2458 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21016 Z= 0.134 Angle : 0.712 11.516 28704 Z= 0.365 Chirality : 0.047 0.164 3220 Planarity : 0.006 0.065 3648 Dihedral : 5.673 51.001 2867 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.13 % Allowed : 18.19 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.17), residues: 2640 helix: -0.88 (0.48), residues: 124 sheet: 1.33 (0.16), residues: 936 loop : -0.61 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 108 TYR 0.025 0.002 TYR H 181 PHE 0.013 0.002 PHE A 153 TRP 0.018 0.001 TRP E 148 HIS 0.003 0.001 HIS L 198 Details of bonding type rmsd covalent geometry : bond 0.00305 (20960) covalent geometry : angle 0.70715 (28592) SS BOND : bond 0.00546 ( 56) SS BOND : angle 1.45930 ( 112) hydrogen bonds : bond 0.03319 ( 709) hydrogen bonds : angle 5.72077 ( 1995) *********************** 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 433 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 384 time to evaluate : 0.645 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 134 MET cc_start: 0.9085 (tpp) cc_final: 0.8672 (mpp) REVERT: B 134 MET cc_start: 0.8782 (tpp) cc_final: 0.8340 (mpp) REVERT: B 150 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8672 (mmp80) REVERT: B 164 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8029 (mm-30) REVERT: C 134 MET cc_start: 0.8979 (tpp) cc_final: 0.8525 (mpp) REVERT: C 149 GLU cc_start: 0.8566 (mp0) cc_final: 0.8176 (mp0) REVERT: C 164 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8060 (mm-30) REVERT: D 134 MET cc_start: 0.9012 (tpp) cc_final: 0.8594 (mpp) REVERT: D 150 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8578 (mmp80) REVERT: D 164 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8101 (mm-30) REVERT: E 17 ASP cc_start: 0.8803 (t0) cc_final: 0.8307 (m-30) REVERT: E 23 CYS cc_start: 0.7236 (t) cc_final: 0.6503 (t) REVERT: E 78 LEU cc_start: 0.9218 (mt) cc_final: 0.8992 (tm) REVERT: E 108 ARG cc_start: 0.6583 (tmm-80) cc_final: 0.6370 (tmm-80) REVERT: E 139 PHE cc_start: 0.8227 (p90) cc_final: 0.7513 (p90) REVERT: E 167 ASP cc_start: 0.7529 (t0) cc_final: 0.7274 (t0) REVERT: E 173 TYR cc_start: 0.6677 (OUTLIER) cc_final: 0.6067 (p90) REVERT: E 210 ASN cc_start: 0.8714 (OUTLIER) cc_final: 0.8340 (m-40) REVERT: F 3 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8186 (pm20) REVERT: F 6 GLU cc_start: 0.7715 (mp0) cc_final: 0.6866 (mp0) REVERT: F 22 CYS cc_start: 0.8602 (t) cc_final: 0.8082 (t) REVERT: F 26 ARG cc_start: 0.8492 (pmm-80) cc_final: 0.8113 (pmm-80) REVERT: F 27 PHE cc_start: 0.8405 (m-80) cc_final: 0.8192 (m-80) REVERT: F 72 ASP cc_start: 0.8376 (t0) cc_final: 0.7888 (t0) REVERT: F 86 ASP cc_start: 0.8963 (m-30) cc_final: 0.8668 (m-30) REVERT: F 105 GLN cc_start: 0.8466 (pm20) cc_final: 0.8136 (pm20) REVERT: F 171 PHE cc_start: 0.7919 (m-80) cc_final: 0.7291 (m-80) REVERT: G 17 ASP cc_start: 0.8821 (t0) cc_final: 0.8328 (m-30) REVERT: G 23 CYS cc_start: 0.7185 (t) cc_final: 0.6454 (t) REVERT: G 78 LEU cc_start: 0.9234 (mt) cc_final: 0.9009 (tm) REVERT: G 123 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7001 (tt0) REVERT: G 139 PHE cc_start: 0.8138 (p90) cc_final: 0.7508 (p90) REVERT: G 148 TRP cc_start: 0.6935 (m100) cc_final: 0.6159 (m100) REVERT: G 155 GLN cc_start: 0.8398 (mm-40) cc_final: 0.8115 (mp10) REVERT: H 3 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8172 (pm20) REVERT: H 6 GLU cc_start: 0.7442 (mp0) cc_final: 0.6187 (mp0) REVERT: H 22 CYS cc_start: 0.8554 (t) cc_final: 0.8139 (t) REVERT: H 72 ASP cc_start: 0.8360 (t0) cc_final: 0.7868 (t0) REVERT: H 86 ASP cc_start: 0.8971 (m-30) cc_final: 0.8625 (m-30) REVERT: H 105 GLN cc_start: 0.8334 (pm20) cc_final: 0.7550 (pm20) REVERT: H 128 LEU cc_start: 0.7888 (mm) cc_final: 0.7122 (mm) REVERT: H 164 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9189 (mm) REVERT: H 171 PHE cc_start: 0.7803 (m-80) cc_final: 0.7215 (m-80) REVERT: I 17 ASP cc_start: 0.8803 (t0) cc_final: 0.8323 (m-30) REVERT: I 23 CYS cc_start: 0.7206 (t) cc_final: 0.6481 (t) REVERT: I 78 LEU cc_start: 0.9171 (mt) cc_final: 0.8951 (tm) REVERT: I 82 ASP cc_start: 0.8279 (m-30) cc_final: 0.7870 (m-30) REVERT: I 108 ARG cc_start: 0.7147 (tmm-80) cc_final: 0.6563 (tmm-80) REVERT: I 139 PHE cc_start: 0.8168 (p90) cc_final: 0.7486 (p90) REVERT: I 148 TRP cc_start: 0.6888 (m100) cc_final: 0.6133 (m100) REVERT: I 155 GLN cc_start: 0.8399 (mm-40) cc_final: 0.8127 (mp10) REVERT: I 173 TYR cc_start: 0.6613 (OUTLIER) cc_final: 0.6209 (p90) REVERT: I 211 ARG cc_start: 0.8049 (ttp-170) cc_final: 0.7712 (ptm160) REVERT: J 3 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.8200 (pm20) REVERT: J 6 GLU cc_start: 0.7676 (mp0) cc_final: 0.6620 (mp0) REVERT: J 22 CYS cc_start: 0.8612 (t) cc_final: 0.8187 (t) REVERT: J 72 ASP cc_start: 0.8542 (t0) cc_final: 0.8068 (t0) REVERT: J 86 ASP cc_start: 0.8964 (m-30) cc_final: 0.8665 (m-30) REVERT: J 105 GLN cc_start: 0.8465 (pm20) cc_final: 0.8022 (pm20) REVERT: J 171 PHE cc_start: 0.7724 (m-80) cc_final: 0.7019 (m-80) REVERT: K 3 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8195 (pm20) REVERT: K 6 GLU cc_start: 0.7676 (mp0) cc_final: 0.6828 (mp0) REVERT: K 22 CYS cc_start: 0.8665 (t) cc_final: 0.8238 (t) REVERT: K 72 ASP cc_start: 0.8406 (t0) cc_final: 0.7932 (t0) REVERT: K 86 ASP cc_start: 0.8955 (m-30) cc_final: 0.8657 (m-30) REVERT: K 105 GLN cc_start: 0.8455 (pm20) cc_final: 0.8119 (pm20) REVERT: K 171 PHE cc_start: 0.7799 (m-80) cc_final: 0.7138 (m-80) REVERT: L 4 MET cc_start: 0.8597 (ttm) cc_final: 0.8271 (ttm) REVERT: L 17 ASP cc_start: 0.8825 (t0) cc_final: 0.8322 (m-30) REVERT: L 78 LEU cc_start: 0.9225 (mt) cc_final: 0.8988 (tm) REVERT: L 82 ASP cc_start: 0.8322 (m-30) cc_final: 0.8109 (m-30) REVERT: L 108 ARG cc_start: 0.6639 (tmm-80) cc_final: 0.6350 (tmm-80) REVERT: L 139 PHE cc_start: 0.8386 (p90) cc_final: 0.8105 (p90) REVERT: L 173 TYR cc_start: 0.5608 (OUTLIER) cc_final: 0.4451 (p90) outliers start: 49 outliers final: 24 residues processed: 420 average time/residue: 0.5472 time to fit residues: 261.4101 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 : 0.630 ------------------------------------------------------------------------------- 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 88 CYS Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 210 ASN 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 F residue 183 LEU Chi-restraints excluded: chain G residue 88 CYS Chi-restraints excluded: chain G residue 123 GLU 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 164 LEU Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain I residue 88 CYS Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 173 TYR Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 11 CYS Chi-restraints excluded: chain J residue 108 CYS Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 144 CYS 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 108 CYS Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain L residue 173 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 171 optimal weight: 0.4980 chunk 14 optimal weight: 0.0970 chunk 82 optimal weight: 0.6980 chunk 188 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 165 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 78 optimal weight: 0.0970 chunk 53 optimal weight: 3.9990 chunk 177 optimal weight: 0.0170 chunk 86 optimal weight: 0.5980 overall best weight: 0.2614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 137 ASN E 210 ASN F 176 GLN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.118873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.068374 restraints weight = 36011.330| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 3.06 r_work: 0.2627 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2493 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21016 Z= 0.118 Angle : 0.694 11.624 28704 Z= 0.353 Chirality : 0.046 0.155 3220 Planarity : 0.006 0.065 3648 Dihedral : 5.403 53.284 2867 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.39 % Allowed : 18.71 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.17), residues: 2640 helix: -0.85 (0.48), residues: 124 sheet: 1.53 (0.16), residues: 936 loop : -0.60 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 108 TYR 0.026 0.001 TYR H 181 PHE 0.027 0.002 PHE J 27 TRP 0.014 0.001 TRP E 148 HIS 0.003 0.001 HIS L 198 Details of bonding type rmsd covalent geometry : bond 0.00260 (20960) covalent geometry : angle 0.68965 (28592) SS BOND : bond 0.00564 ( 56) SS BOND : angle 1.43064 ( 112) hydrogen bonds : bond 0.03086 ( 709) hydrogen bonds : angle 5.62373 ( 1995) *********************** 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 453 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 398 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 GLU cc_start: 0.9115 (tp30) cc_final: 0.8900 (tp30) REVERT: A 134 MET cc_start: 0.9095 (tpp) cc_final: 0.8806 (mtt) REVERT: B 109 GLU cc_start: 0.9175 (tp30) cc_final: 0.8926 (tp30) REVERT: B 150 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.8705 (mmp80) REVERT: B 164 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8052 (mm-30) REVERT: C 109 GLU cc_start: 0.9108 (tp30) cc_final: 0.8886 (tp30) REVERT: C 149 GLU cc_start: 0.8611 (mp0) cc_final: 0.8210 (mp0) REVERT: C 164 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8083 (mm-30) REVERT: D 109 GLU cc_start: 0.9133 (tp30) cc_final: 0.8910 (tp30) REVERT: D 134 MET cc_start: 0.9028 (tpp) cc_final: 0.8723 (mtt) REVERT: D 164 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8103 (mm-30) REVERT: E 4 MET cc_start: 0.8593 (ttm) cc_final: 0.7958 (ttm) REVERT: E 17 ASP cc_start: 0.8821 (t0) cc_final: 0.8344 (m-30) REVERT: E 78 LEU cc_start: 0.9209 (mt) cc_final: 0.8979 (tm) REVERT: E 108 ARG cc_start: 0.6634 (tmm-80) cc_final: 0.6195 (tmm-80) REVERT: E 136 LEU cc_start: 0.8800 (mp) cc_final: 0.8541 (pt) REVERT: E 139 PHE cc_start: 0.8246 (p90) cc_final: 0.7335 (p90) REVERT: E 167 ASP cc_start: 0.7539 (t0) cc_final: 0.7200 (t0) REVERT: E 173 TYR cc_start: 0.6812 (OUTLIER) cc_final: 0.6020 (p90) REVERT: E 210 ASN cc_start: 0.8761 (OUTLIER) cc_final: 0.8355 (m-40) REVERT: F 3 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.8186 (pm20) REVERT: F 6 GLU cc_start: 0.7663 (mp0) cc_final: 0.6723 (mp0) REVERT: F 22 CYS cc_start: 0.8619 (t) cc_final: 0.8113 (t) REVERT: F 26 ARG cc_start: 0.8474 (pmm-80) cc_final: 0.8104 (pmm-80) REVERT: F 72 ASP cc_start: 0.8379 (t0) cc_final: 0.7873 (t0) REVERT: F 86 ASP cc_start: 0.8941 (m-30) cc_final: 0.8621 (m-30) REVERT: F 105 GLN cc_start: 0.8488 (pm20) cc_final: 0.8116 (pm20) REVERT: F 171 PHE cc_start: 0.7938 (m-80) cc_final: 0.7308 (m-80) REVERT: G 4 MET cc_start: 0.8595 (ttm) cc_final: 0.8014 (ttm) REVERT: G 17 ASP cc_start: 0.8817 (t0) cc_final: 0.8351 (m-30) REVERT: G 123 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7152 (tt0) REVERT: G 139 PHE cc_start: 0.8253 (p90) cc_final: 0.7595 (p90) REVERT: G 142 ARG cc_start: 0.8964 (tpp-160) cc_final: 0.8582 (mpp-170) REVERT: G 148 TRP cc_start: 0.6931 (m100) cc_final: 0.6081 (m100) REVERT: G 155 GLN cc_start: 0.8397 (mm-40) cc_final: 0.8134 (mp10) REVERT: H 3 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8168 (pm20) REVERT: H 6 GLU cc_start: 0.7451 (mp0) cc_final: 0.6039 (mp0) REVERT: H 22 CYS cc_start: 0.8506 (t) cc_final: 0.8106 (t) REVERT: H 72 ASP cc_start: 0.8357 (t0) cc_final: 0.7849 (t0) REVERT: H 86 ASP cc_start: 0.8959 (m-30) cc_final: 0.8602 (m-30) REVERT: H 105 GLN cc_start: 0.8291 (pm20) cc_final: 0.7835 (pm20) REVERT: H 164 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9130 (mp) REVERT: H 171 PHE cc_start: 0.7887 (m-80) cc_final: 0.7263 (m-80) REVERT: I 4 MET cc_start: 0.8577 (ttm) cc_final: 0.7936 (ttm) REVERT: I 17 ASP cc_start: 0.8794 (t0) cc_final: 0.8351 (m-30) REVERT: I 136 LEU cc_start: 0.8726 (mp) cc_final: 0.8494 (pt) REVERT: I 139 PHE cc_start: 0.8257 (p90) cc_final: 0.7348 (p90) REVERT: I 148 TRP cc_start: 0.6946 (m100) cc_final: 0.6236 (m100) REVERT: I 155 GLN cc_start: 0.8418 (mm-40) cc_final: 0.8195 (mp10) REVERT: I 173 TYR cc_start: 0.6714 (OUTLIER) cc_final: 0.5897 (p90) REVERT: I 211 ARG cc_start: 0.8038 (ttp-170) cc_final: 0.7762 (ptm160) REVERT: J 3 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8154 (pm20) REVERT: J 6 GLU cc_start: 0.7675 (mp0) cc_final: 0.6748 (mp0) REVERT: J 22 CYS cc_start: 0.8621 (t) cc_final: 0.8186 (t) REVERT: J 26 ARG cc_start: 0.8420 (pmm-80) cc_final: 0.7845 (pmm-80) REVERT: J 72 ASP cc_start: 0.8587 (t0) cc_final: 0.8105 (t0) REVERT: J 86 ASP cc_start: 0.8942 (m-30) cc_final: 0.8616 (m-30) REVERT: J 105 GLN cc_start: 0.8467 (pm20) cc_final: 0.8086 (pm20) REVERT: J 171 PHE cc_start: 0.7847 (m-80) cc_final: 0.7194 (m-80) REVERT: K 3 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8166 (pm20) REVERT: K 6 GLU cc_start: 0.7661 (mp0) cc_final: 0.6732 (mp0) REVERT: K 22 CYS cc_start: 0.8643 (t) cc_final: 0.8229 (t) REVERT: K 26 ARG cc_start: 0.8359 (pmm-80) cc_final: 0.7790 (pmm-80) REVERT: K 72 ASP cc_start: 0.8382 (t0) cc_final: 0.7876 (t0) REVERT: K 86 ASP cc_start: 0.8938 (m-30) cc_final: 0.8616 (m-30) REVERT: K 105 GLN cc_start: 0.8482 (pm20) cc_final: 0.8125 (pm20) REVERT: K 128 LEU cc_start: 0.7854 (mm) cc_final: 0.6967 (mm) REVERT: K 171 PHE cc_start: 0.7836 (m-80) cc_final: 0.7112 (m-80) REVERT: L 4 MET cc_start: 0.8728 (ttm) cc_final: 0.8360 (ttm) REVERT: L 17 ASP cc_start: 0.8819 (t0) cc_final: 0.8334 (m-30) REVERT: L 78 LEU cc_start: 0.9197 (mt) cc_final: 0.8958 (tm) REVERT: L 88 CYS cc_start: 0.8203 (p) cc_final: 0.7389 (p) REVERT: L 108 ARG cc_start: 0.6878 (tmm-80) cc_final: 0.6624 (tmm-80) REVERT: L 139 PHE cc_start: 0.8422 (p90) cc_final: 0.7947 (p90) REVERT: L 142 ARG cc_start: 0.8718 (ttm-80) cc_final: 0.8493 (tpp80) REVERT: L 173 TYR cc_start: 0.5743 (p90) cc_final: 0.4089 (p90) outliers start: 55 outliers final: 26 residues processed: 439 average time/residue: 0.5110 time to fit residues: 255.7507 Evaluate side-chains 407 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 371 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 88 CYS Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 210 ASN 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 50 GLU Chi-restraints excluded: chain G residue 88 CYS Chi-restraints excluded: chain G residue 123 GLU 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 164 LEU Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain I residue 50 GLU Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 88 CYS Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 173 TYR Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 108 CYS Chi-restraints excluded: chain J residue 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 108 CYS Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain L residue 50 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 64 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 209 optimal weight: 8.9990 chunk 114 optimal weight: 5.9990 chunk 56 optimal weight: 0.0670 chunk 251 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 30 ASN E 137 ASN E 210 ASN ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 GLN G 30 ASN H 76 ASN H 176 GLN I 30 ASN I 79 GLN ** J 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 GLN L 30 ASN ** L 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.117380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.066795 restraints weight = 36114.289| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 3.07 r_work: 0.2595 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2460 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21016 Z= 0.151 Angle : 0.723 11.674 28704 Z= 0.369 Chirality : 0.047 0.168 3220 Planarity : 0.006 0.065 3648 Dihedral : 5.378 57.447 2867 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.82 % Allowed : 20.18 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.17), residues: 2640 helix: -0.94 (0.47), residues: 124 sheet: 1.62 (0.16), residues: 908 loop : -0.69 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 108 TYR 0.027 0.002 TYR H 181 PHE 0.011 0.001 PHE D 153 TRP 0.014 0.001 TRP E 148 HIS 0.003 0.001 HIS L 198 Details of bonding type rmsd covalent geometry : bond 0.00353 (20960) covalent geometry : angle 0.71573 (28592) SS BOND : bond 0.00624 ( 56) SS BOND : angle 1.74954 ( 112) hydrogen bonds : bond 0.03258 ( 709) hydrogen bonds : angle 5.56298 ( 1995) *********************** 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 421 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 379 time to evaluate : 0.681 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: 0.9122 (tpp) cc_final: 0.8807 (mtt) REVERT: B 109 GLU cc_start: 0.9135 (tp30) cc_final: 0.8897 (tp30) REVERT: B 134 MET cc_start: 0.8897 (tpp) cc_final: 0.8537 (mtt) REVERT: B 164 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8055 (mm-30) REVERT: C 134 MET cc_start: 0.9061 (tpp) cc_final: 0.8723 (mtt) REVERT: C 149 GLU cc_start: 0.8608 (mp0) cc_final: 0.8197 (mp0) REVERT: C 164 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8068 (mm-30) REVERT: D 109 GLU cc_start: 0.9116 (tp30) cc_final: 0.8901 (tp30) REVERT: D 134 MET cc_start: 0.9058 (tpp) cc_final: 0.8732 (mtt) REVERT: D 164 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8106 (mm-30) REVERT: E 17 ASP cc_start: 0.8869 (t0) cc_final: 0.8450 (m-30) REVERT: E 23 CYS cc_start: 0.7297 (t) cc_final: 0.6487 (t) REVERT: E 50 GLU cc_start: 0.9304 (mt-10) cc_final: 0.8692 (pp20) REVERT: E 78 LEU cc_start: 0.9197 (mt) cc_final: 0.8972 (tm) REVERT: E 108 ARG cc_start: 0.6585 (tmm-80) cc_final: 0.5929 (tmm-80) REVERT: E 136 LEU cc_start: 0.8751 (mp) cc_final: 0.8490 (pt) REVERT: E 139 PHE cc_start: 0.8275 (p90) cc_final: 0.7319 (p90) REVERT: E 167 ASP cc_start: 0.7567 (t0) cc_final: 0.7266 (t0) REVERT: E 173 TYR cc_start: 0.6885 (OUTLIER) cc_final: 0.6261 (p90) REVERT: E 210 ASN cc_start: 0.8799 (OUTLIER) cc_final: 0.8380 (m-40) REVERT: F 3 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8183 (pm20) REVERT: F 6 GLU cc_start: 0.7688 (mp0) cc_final: 0.6734 (mp0) REVERT: F 22 CYS cc_start: 0.8655 (t) cc_final: 0.8174 (t) REVERT: F 26 ARG cc_start: 0.8473 (pmm-80) cc_final: 0.8186 (pmm-80) REVERT: F 72 ASP cc_start: 0.8425 (t0) cc_final: 0.7917 (t0) REVERT: F 86 ASP cc_start: 0.8963 (m-30) cc_final: 0.8634 (m-30) REVERT: F 105 GLN cc_start: 0.8541 (pm20) cc_final: 0.8142 (pm20) REVERT: F 171 PHE cc_start: 0.8041 (m-80) cc_final: 0.7370 (m-80) REVERT: G 17 ASP cc_start: 0.8988 (t0) cc_final: 0.8412 (m-30) REVERT: G 23 CYS cc_start: 0.6607 (t) cc_final: 0.5962 (t) REVERT: G 50 GLU cc_start: 0.9302 (mt-10) cc_final: 0.8698 (pp20) REVERT: G 123 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7382 (tt0) REVERT: G 139 PHE cc_start: 0.8261 (p90) cc_final: 0.7562 (p90) REVERT: G 148 TRP cc_start: 0.6972 (m100) cc_final: 0.6159 (m100) REVERT: G 155 GLN cc_start: 0.8430 (mm-40) cc_final: 0.8198 (mp10) REVERT: H 3 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8201 (pm20) REVERT: H 6 GLU cc_start: 0.7468 (mp0) cc_final: 0.6114 (mp0) REVERT: H 22 CYS cc_start: 0.8543 (t) cc_final: 0.8144 (t) REVERT: H 72 ASP cc_start: 0.8419 (t0) cc_final: 0.7927 (t0) REVERT: H 86 ASP cc_start: 0.8961 (m-30) cc_final: 0.8581 (m-30) REVERT: H 105 GLN cc_start: 0.8245 (pm20) cc_final: 0.7444 (pm20) REVERT: H 128 LEU cc_start: 0.8240 (mm) cc_final: 0.7397 (mm) REVERT: H 164 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9187 (mp) REVERT: H 171 PHE cc_start: 0.7987 (m-80) cc_final: 0.7367 (m-80) REVERT: I 17 ASP cc_start: 0.9015 (t0) cc_final: 0.8437 (m-30) REVERT: I 23 CYS cc_start: 0.7388 (t) cc_final: 0.6660 (t) REVERT: I 50 GLU cc_start: 0.9296 (mt-10) cc_final: 0.8695 (pp20) REVERT: I 136 LEU cc_start: 0.8712 (mp) cc_final: 0.8496 (pt) REVERT: I 139 PHE cc_start: 0.8285 (p90) cc_final: 0.7415 (p90) REVERT: I 148 TRP cc_start: 0.7004 (m100) cc_final: 0.6279 (m100) REVERT: I 155 GLN cc_start: 0.8413 (mm-40) cc_final: 0.8180 (mp10) REVERT: I 173 TYR cc_start: 0.6451 (OUTLIER) cc_final: 0.5920 (p90) REVERT: I 211 ARG cc_start: 0.8169 (ttp-170) cc_final: 0.7879 (ptm160) REVERT: J 3 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8206 (pm20) REVERT: J 6 GLU cc_start: 0.7683 (mp0) cc_final: 0.6754 (mp0) REVERT: J 22 CYS cc_start: 0.8650 (t) cc_final: 0.8216 (t) REVERT: J 72 ASP cc_start: 0.8588 (t0) cc_final: 0.8003 (t0) REVERT: J 75 LYS cc_start: 0.9430 (OUTLIER) cc_final: 0.9123 (mttm) REVERT: J 86 ASP cc_start: 0.8964 (m-30) cc_final: 0.8628 (m-30) REVERT: J 105 GLN cc_start: 0.8536 (pm20) cc_final: 0.8140 (pm20) REVERT: J 171 PHE cc_start: 0.7902 (m-80) cc_final: 0.7233 (m-80) REVERT: K 3 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8201 (pm20) REVERT: K 6 GLU cc_start: 0.7680 (mp0) cc_final: 0.6581 (mp0) REVERT: K 22 CYS cc_start: 0.8595 (t) cc_final: 0.8093 (t) REVERT: K 72 ASP cc_start: 0.8408 (t0) cc_final: 0.7922 (t0) REVERT: K 86 ASP cc_start: 0.8947 (m-30) cc_final: 0.8613 (m-30) REVERT: K 105 GLN cc_start: 0.8517 (pm20) cc_final: 0.8016 (pm20) REVERT: K 128 LEU cc_start: 0.7931 (mm) cc_final: 0.7040 (mm) REVERT: K 171 PHE cc_start: 0.7951 (m-80) cc_final: 0.7207 (m-80) REVERT: L 4 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8422 (ttm) REVERT: L 17 ASP cc_start: 0.8875 (t0) cc_final: 0.8462 (m-30) REVERT: L 78 LEU cc_start: 0.9201 (mt) cc_final: 0.8986 (tm) REVERT: L 88 CYS cc_start: 0.8357 (p) cc_final: 0.7647 (p) REVERT: L 108 ARG cc_start: 0.6865 (tmm-80) cc_final: 0.6526 (tmm-80) REVERT: L 139 PHE cc_start: 0.8546 (p90) cc_final: 0.8038 (p90) REVERT: L 173 TYR cc_start: 0.5804 (p90) cc_final: 0.4513 (p90) outliers start: 42 outliers final: 20 residues processed: 412 average time/residue: 0.5096 time to fit residues: 239.4216 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 : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain F residue 3 GLN 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 88 CYS Chi-restraints excluded: chain G residue 123 GLU 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 164 LEU Chi-restraints excluded: chain H residue 183 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 75 LYS Chi-restraints excluded: chain J residue 108 CYS Chi-restraints excluded: chain J residue 144 CYS 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 108 CYS Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 156 THR Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain L residue 4 MET 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 63 optimal weight: 0.0670 chunk 134 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 212 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 231 optimal weight: 0.8980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 79 GLN E 210 ASN ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 GLN H 176 GLN ** J 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 GLN L 79 GLN L 137 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.117772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.067469 restraints weight = 36261.735| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 3.06 r_work: 0.2615 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2483 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21016 Z= 0.137 Angle : 0.725 12.046 28704 Z= 0.369 Chirality : 0.047 0.168 3220 Planarity : 0.006 0.065 3648 Dihedral : 5.300 58.255 2867 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.91 % Allowed : 20.79 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.17), residues: 2640 helix: -0.97 (0.48), residues: 124 sheet: 1.68 (0.17), residues: 916 loop : -0.64 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 108 TYR 0.027 0.002 TYR J 181 PHE 0.027 0.002 PHE F 27 TRP 0.016 0.001 TRP L 148 HIS 0.003 0.001 HIS L 198 Details of bonding type rmsd covalent geometry : bond 0.00315 (20960) covalent geometry : angle 0.71866 (28592) SS BOND : bond 0.00631 ( 56) SS BOND : angle 1.71155 ( 112) hydrogen bonds : bond 0.03129 ( 709) hydrogen bonds : angle 5.50261 ( 1995) *********************** 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 425 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 381 time to evaluate : 0.757 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: 0.9089 (tpp) cc_final: 0.8838 (mtt) REVERT: A 164 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7949 (tm-30) REVERT: B 134 MET cc_start: 0.8880 (tpp) cc_final: 0.8500 (mtt) REVERT: B 164 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8048 (mm-30) REVERT: C 109 GLU cc_start: 0.9145 (mm-30) cc_final: 0.8934 (mm-30) REVERT: C 134 MET cc_start: 0.9038 (tpp) cc_final: 0.8685 (mtt) REVERT: C 149 GLU cc_start: 0.8629 (mp0) cc_final: 0.8212 (mp0) REVERT: C 164 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8121 (mm-30) REVERT: D 134 MET cc_start: 0.9019 (tpp) cc_final: 0.8753 (mtt) REVERT: D 164 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8098 (mm-30) REVERT: E 17 ASP cc_start: 0.8894 (t0) cc_final: 0.8481 (m-30) REVERT: E 108 ARG cc_start: 0.6609 (tmm-80) cc_final: 0.5813 (tmm-80) REVERT: E 136 LEU cc_start: 0.8758 (mp) cc_final: 0.8500 (pt) REVERT: E 139 PHE cc_start: 0.8304 (p90) cc_final: 0.7362 (p90) REVERT: E 155 GLN cc_start: 0.8407 (mm-40) cc_final: 0.8152 (mp10) REVERT: E 167 ASP cc_start: 0.7684 (t0) cc_final: 0.7381 (t0) REVERT: E 173 TYR cc_start: 0.6914 (OUTLIER) cc_final: 0.6126 (p90) REVERT: E 210 ASN cc_start: 0.8753 (OUTLIER) cc_final: 0.8339 (m-40) REVERT: F 3 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8159 (pm20) REVERT: F 6 GLU cc_start: 0.7672 (mp0) cc_final: 0.6664 (mp0) REVERT: F 22 CYS cc_start: 0.8677 (t) cc_final: 0.8203 (t) REVERT: F 26 ARG cc_start: 0.8439 (pmm-80) cc_final: 0.8219 (pmm-80) REVERT: F 27 PHE cc_start: 0.8398 (m-80) cc_final: 0.8134 (m-80) REVERT: F 72 ASP cc_start: 0.8437 (t0) cc_final: 0.7950 (t0) REVERT: F 79 SER cc_start: 0.9259 (OUTLIER) cc_final: 0.8629 (p) REVERT: F 86 ASP cc_start: 0.8964 (m-30) cc_final: 0.8626 (m-30) REVERT: F 105 GLN cc_start: 0.8501 (pm20) cc_final: 0.8062 (pm20) REVERT: F 171 PHE cc_start: 0.8091 (m-80) cc_final: 0.7439 (m-80) REVERT: G 17 ASP cc_start: 0.9011 (t0) cc_final: 0.8451 (m-30) REVERT: G 117 ILE cc_start: 0.7437 (OUTLIER) cc_final: 0.7231 (mt) REVERT: G 123 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7733 (tt0) REVERT: G 139 PHE cc_start: 0.8250 (p90) cc_final: 0.7521 (p90) REVERT: G 148 TRP cc_start: 0.7073 (m100) cc_final: 0.6276 (m100) REVERT: G 155 GLN cc_start: 0.8446 (mm-40) cc_final: 0.8209 (mp10) REVERT: H 3 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8207 (pm20) REVERT: H 6 GLU cc_start: 0.7471 (mp0) cc_final: 0.6094 (mp0) REVERT: H 22 CYS cc_start: 0.8561 (t) cc_final: 0.8171 (t) REVERT: H 72 ASP cc_start: 0.8413 (t0) cc_final: 0.7920 (t0) REVERT: H 79 SER cc_start: 0.9266 (OUTLIER) cc_final: 0.8711 (p) REVERT: H 86 ASP cc_start: 0.8966 (m-30) cc_final: 0.8584 (m-30) REVERT: H 105 GLN cc_start: 0.8236 (pm20) cc_final: 0.7408 (pm20) REVERT: H 128 LEU cc_start: 0.8371 (mm) cc_final: 0.7614 (mm) REVERT: H 164 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9286 (mp) REVERT: H 171 PHE cc_start: 0.8098 (m-80) cc_final: 0.7461 (m-80) REVERT: I 17 ASP cc_start: 0.9072 (t0) cc_final: 0.8521 (m-30) REVERT: I 136 LEU cc_start: 0.8738 (mp) cc_final: 0.8479 (pt) REVERT: I 139 PHE cc_start: 0.8262 (p90) cc_final: 0.7273 (p90) REVERT: I 148 TRP cc_start: 0.7135 (m100) cc_final: 0.6410 (m100) REVERT: I 155 GLN cc_start: 0.8435 (mm-40) cc_final: 0.8210 (mp10) REVERT: I 173 TYR cc_start: 0.6624 (p90) cc_final: 0.6154 (p90) REVERT: I 211 ARG cc_start: 0.8197 (ttp-170) cc_final: 0.7963 (ptm160) REVERT: J 3 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8215 (pm20) REVERT: J 6 GLU cc_start: 0.7652 (mp0) cc_final: 0.6520 (mp0) REVERT: J 22 CYS cc_start: 0.8664 (t) cc_final: 0.8263 (t) REVERT: J 72 ASP cc_start: 0.8590 (t0) cc_final: 0.8014 (t0) REVERT: J 75 LYS cc_start: 0.9450 (OUTLIER) cc_final: 0.9151 (mttm) REVERT: J 79 SER cc_start: 0.9263 (OUTLIER) cc_final: 0.8640 (p) REVERT: J 86 ASP cc_start: 0.8965 (m-30) cc_final: 0.8623 (m-30) REVERT: J 105 GLN cc_start: 0.8514 (pm20) cc_final: 0.7998 (pm20) REVERT: J 171 PHE cc_start: 0.8058 (m-80) cc_final: 0.7374 (m-80) REVERT: K 3 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8205 (pm20) REVERT: K 6 GLU cc_start: 0.7650 (mp0) cc_final: 0.6509 (mp0) REVERT: K 22 CYS cc_start: 0.8628 (t) cc_final: 0.8138 (t) REVERT: K 72 ASP cc_start: 0.8432 (t0) cc_final: 0.7946 (t0) REVERT: K 79 SER cc_start: 0.9269 (OUTLIER) cc_final: 0.8646 (p) REVERT: K 86 ASP cc_start: 0.8953 (m-30) cc_final: 0.8612 (m-30) REVERT: K 105 GLN cc_start: 0.8517 (pm20) cc_final: 0.7996 (pm20) REVERT: K 128 LEU cc_start: 0.8126 (mm) cc_final: 0.7281 (mm) REVERT: K 171 PHE cc_start: 0.7993 (m-80) cc_final: 0.7237 (m-80) REVERT: L 4 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8416 (ttm) REVERT: L 17 ASP cc_start: 0.8891 (t0) cc_final: 0.8491 (m-30) REVERT: L 88 CYS cc_start: 0.8244 (p) cc_final: 0.7688 (p) REVERT: L 136 LEU cc_start: 0.8969 (tp) cc_final: 0.8715 (tp) REVERT: L 139 PHE cc_start: 0.8537 (p90) cc_final: 0.7634 (p90) REVERT: L 142 ARG cc_start: 0.8662 (ttm-80) cc_final: 0.8443 (tpp80) REVERT: L 173 TYR cc_start: 0.5977 (p90) cc_final: 0.4927 (p90) outliers start: 44 outliers final: 23 residues processed: 418 average time/residue: 0.5073 time to fit residues: 241.4173 Evaluate side-chains 403 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 365 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 11 CYS Chi-restraints excluded: chain F residue 79 SER 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 117 ILE Chi-restraints excluded: chain G residue 123 GLU 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 79 SER Chi-restraints excluded: chain H residue 144 CYS Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 201 CYS 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 79 SER Chi-restraints excluded: chain J residue 108 CYS Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 144 CYS Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain J residue 201 CYS Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 11 CYS Chi-restraints excluded: chain K residue 79 SER 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 L residue 4 MET 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 82 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 227 optimal weight: 0.9990 chunk 196 optimal weight: 7.9990 chunk 246 optimal weight: 0.7980 chunk 135 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 193 optimal weight: 8.9990 chunk 221 optimal weight: 10.0000 chunk 156 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 30 ASN ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 GLN G 30 ASN G 79 GLN I 30 ASN ** J 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 GLN L 30 ASN L 166 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.113989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.063010 restraints weight = 36638.024| |-----------------------------------------------------------------------------| r_work (start): 0.2690 rms_B_bonded: 3.04 r_work: 0.2520 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2387 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 21016 Z= 0.303 Angle : 0.829 14.075 28704 Z= 0.427 Chirality : 0.051 0.173 3220 Planarity : 0.006 0.070 3648 Dihedral : 5.640 47.317 2867 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.08 % Allowed : 21.05 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.16), residues: 2640 helix: -1.32 (0.45), residues: 124 sheet: 1.51 (0.16), residues: 904 loop : -0.82 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 108 TYR 0.039 0.002 TYR H 181 PHE 0.027 0.002 PHE F 27 TRP 0.015 0.002 TRP L 148 HIS 0.005 0.001 HIS C 173 Details of bonding type rmsd covalent geometry : bond 0.00717 (20960) covalent geometry : angle 0.81975 (28592) SS BOND : bond 0.00788 ( 56) SS BOND : angle 2.13379 ( 112) hydrogen bonds : bond 0.03939 ( 709) hydrogen bonds : angle 5.69521 ( 1995) *********************** 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 412 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 364 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.9184 (tpp) cc_final: 0.8831 (mtt) REVERT: A 164 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8079 (tm-30) REVERT: B 134 MET cc_start: 0.8948 (tpp) cc_final: 0.8563 (mtt) REVERT: B 164 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8127 (mm-30) REVERT: C 134 MET cc_start: 0.9112 (tpp) cc_final: 0.8722 (mtt) REVERT: C 149 GLU cc_start: 0.8596 (mp0) cc_final: 0.8056 (mp0) REVERT: C 164 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8172 (mm-30) REVERT: D 134 MET cc_start: 0.9122 (tpp) cc_final: 0.8752 (mtt) REVERT: D 164 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8179 (mm-30) REVERT: E 17 ASP cc_start: 0.9069 (t0) cc_final: 0.8428 (m-30) REVERT: E 23 CYS cc_start: 0.7566 (t) cc_final: 0.7353 (t) REVERT: E 108 ARG cc_start: 0.6657 (tmm-80) cc_final: 0.6198 (tmm-80) REVERT: E 136 LEU cc_start: 0.8701 (mp) cc_final: 0.8450 (pt) REVERT: E 139 PHE cc_start: 0.8360 (p90) cc_final: 0.7344 (p90) REVERT: E 167 ASP cc_start: 0.7883 (t0) cc_final: 0.7484 (t0) REVERT: E 173 TYR cc_start: 0.7052 (p90) cc_final: 0.6418 (p90) REVERT: F 3 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8121 (pm20) REVERT: F 6 GLU cc_start: 0.7625 (mp0) cc_final: 0.6527 (mp0) REVERT: F 22 CYS cc_start: 0.8697 (t) cc_final: 0.8197 (t) REVERT: F 26 ARG cc_start: 0.8534 (pmm-80) cc_final: 0.8249 (pmm-80) REVERT: F 27 PHE cc_start: 0.8482 (m-80) cc_final: 0.8278 (m-80) REVERT: F 72 ASP cc_start: 0.8516 (t0) cc_final: 0.8038 (t0) REVERT: F 79 SER cc_start: 0.9326 (OUTLIER) cc_final: 0.8698 (p) REVERT: F 86 ASP cc_start: 0.8967 (m-30) cc_final: 0.8635 (m-30) REVERT: F 105 GLN cc_start: 0.8429 (pm20) cc_final: 0.8036 (pm20) REVERT: F 171 PHE cc_start: 0.8216 (m-80) cc_final: 0.7592 (m-80) REVERT: G 17 ASP cc_start: 0.9071 (t0) cc_final: 0.8454 (m-30) REVERT: G 23 CYS cc_start: 0.7487 (t) cc_final: 0.7245 (t) REVERT: G 50 GLU cc_start: 0.9286 (mt-10) cc_final: 0.8661 (pp20) REVERT: G 108 ARG cc_start: 0.6879 (tmm-80) cc_final: 0.6439 (tmm-80) REVERT: G 139 PHE cc_start: 0.8315 (p90) cc_final: 0.7476 (p90) REVERT: G 142 ARG cc_start: 0.9030 (tpp-160) cc_final: 0.8663 (mpp-170) REVERT: G 148 TRP cc_start: 0.7118 (m100) cc_final: 0.6293 (m100) REVERT: G 155 GLN cc_start: 0.8381 (mm-40) cc_final: 0.8132 (mp10) REVERT: G 211 ARG cc_start: 0.7392 (ptm160) cc_final: 0.7178 (ptm160) REVERT: H 3 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8193 (pm20) REVERT: H 6 GLU cc_start: 0.7554 (mp0) cc_final: 0.6225 (mp0) REVERT: H 22 CYS cc_start: 0.8617 (t) cc_final: 0.8202 (t) REVERT: H 26 ARG cc_start: 0.8441 (pmm-80) cc_final: 0.8084 (pmm-80) REVERT: H 27 PHE cc_start: 0.8405 (m-80) cc_final: 0.8198 (m-80) REVERT: H 72 ASP cc_start: 0.8492 (t0) cc_final: 0.8005 (t0) REVERT: H 79 SER cc_start: 0.9312 (OUTLIER) cc_final: 0.8724 (p) REVERT: H 86 ASP cc_start: 0.8955 (m-30) cc_final: 0.8633 (m-30) REVERT: H 105 GLN cc_start: 0.8228 (pm20) cc_final: 0.7519 (pm20) REVERT: H 128 LEU cc_start: 0.8379 (mm) cc_final: 0.8023 (tt) REVERT: H 164 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9233 (mp) REVERT: H 171 PHE cc_start: 0.8225 (m-80) cc_final: 0.7569 (m-80) REVERT: I 17 ASP cc_start: 0.9097 (t0) cc_final: 0.8481 (m-30) REVERT: I 136 LEU cc_start: 0.8706 (mp) cc_final: 0.8428 (pt) REVERT: I 139 PHE cc_start: 0.8279 (p90) cc_final: 0.7308 (p90) REVERT: I 148 TRP cc_start: 0.7067 (m100) cc_final: 0.6291 (m100) REVERT: I 155 GLN cc_start: 0.8281 (mm-40) cc_final: 0.8037 (mp10) REVERT: I 173 TYR cc_start: 0.6523 (p90) cc_final: 0.6018 (p90) REVERT: J 3 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8185 (pm20) REVERT: J 6 GLU cc_start: 0.7614 (mp0) cc_final: 0.6540 (mp0) REVERT: J 22 CYS cc_start: 0.8665 (t) cc_final: 0.8148 (t) REVERT: J 26 ARG cc_start: 0.8506 (pmm-80) cc_final: 0.8185 (pmm-80) REVERT: J 72 ASP cc_start: 0.8596 (t0) cc_final: 0.7994 (t0) REVERT: J 75 LYS cc_start: 0.9438 (OUTLIER) cc_final: 0.9093 (mttm) REVERT: J 79 SER cc_start: 0.9326 (OUTLIER) cc_final: 0.8725 (p) REVERT: J 86 ASP cc_start: 0.8950 (m-30) cc_final: 0.8644 (m-30) REVERT: J 105 GLN cc_start: 0.8429 (pm20) cc_final: 0.8037 (pm20) REVERT: J 171 PHE cc_start: 0.8163 (m-80) cc_final: 0.7494 (m-80) REVERT: K 3 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8182 (pm20) REVERT: K 6 GLU cc_start: 0.7604 (mp0) cc_final: 0.6521 (mp0) REVERT: K 22 CYS cc_start: 0.8673 (t) cc_final: 0.8179 (t) REVERT: K 26 ARG cc_start: 0.8439 (pmm-80) cc_final: 0.8131 (pmm-80) REVERT: K 27 PHE cc_start: 0.8411 (m-80) cc_final: 0.8209 (m-80) REVERT: K 72 ASP cc_start: 0.8514 (t0) cc_final: 0.8040 (t0) REVERT: K 79 SER cc_start: 0.9329 (OUTLIER) cc_final: 0.8703 (p) REVERT: K 86 ASP cc_start: 0.8963 (m-30) cc_final: 0.8658 (m-30) REVERT: K 105 GLN cc_start: 0.8433 (pm20) cc_final: 0.8042 (pm20) REVERT: K 128 LEU cc_start: 0.8189 (mm) cc_final: 0.7412 (mm) REVERT: K 171 PHE cc_start: 0.8175 (m-80) cc_final: 0.7444 (m-80) REVERT: L 4 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8566 (ttm) REVERT: L 17 ASP cc_start: 0.9071 (t0) cc_final: 0.8474 (m-30) REVERT: L 88 CYS cc_start: 0.8483 (p) cc_final: 0.7988 (p) REVERT: L 136 LEU cc_start: 0.8882 (tp) cc_final: 0.8662 (tp) REVERT: L 139 PHE cc_start: 0.8441 (p90) cc_final: 0.7534 (p90) REVERT: L 142 ARG cc_start: 0.8681 (ttm-80) cc_final: 0.8429 (tpp80) REVERT: L 173 TYR cc_start: 0.5704 (p90) cc_final: 0.4789 (p90) outliers start: 48 outliers final: 23 residues processed: 398 average time/residue: 0.5130 time to fit residues: 233.2210 Evaluate side-chains 379 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 345 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 79 SER Chi-restraints excluded: chain F residue 108 CYS Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain G residue 33 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 79 SER Chi-restraints excluded: chain H residue 144 CYS Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 201 CYS Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain J residue 108 CYS Chi-restraints excluded: chain J residue 144 CYS Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain J residue 169 HIS Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 79 SER 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 4 MET 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 254 optimal weight: 0.9990 chunk 246 optimal weight: 0.6980 chunk 207 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 192 optimal weight: 0.8980 chunk 184 optimal weight: 0.5980 chunk 180 optimal weight: 1.9990 chunk 221 optimal weight: 7.9990 chunk 198 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 187 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 GLN ** J 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 166 GLN ** 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 = 0.3728 r_free = 0.3728 target = 0.116079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.065682 restraints weight = 36549.362| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 3.06 r_work: 0.2583 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2452 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21016 Z= 0.149 Angle : 0.758 13.391 28704 Z= 0.389 Chirality : 0.047 0.204 3220 Planarity : 0.006 0.066 3648 Dihedral : 5.336 28.652 2864 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.43 % Allowed : 21.79 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.16), residues: 2640 helix: -1.13 (0.47), residues: 124 sheet: 1.60 (0.17), residues: 916 loop : -0.72 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 108 TYR 0.040 0.002 TYR K 181 PHE 0.026 0.001 PHE J 27 TRP 0.017 0.001 TRP L 148 HIS 0.003 0.001 HIS L 198 Details of bonding type rmsd covalent geometry : bond 0.00346 (20960) covalent geometry : angle 0.74759 (28592) SS BOND : bond 0.00622 ( 56) SS BOND : angle 2.13324 ( 112) hydrogen bonds : bond 0.03220 ( 709) hydrogen bonds : angle 5.50923 ( 1995) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 365 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.9105 (tpp) cc_final: 0.8801 (mtt) REVERT: B 134 MET cc_start: 0.8883 (tpp) cc_final: 0.8570 (mtt) REVERT: B 149 GLU cc_start: 0.8495 (mp0) cc_final: 0.8203 (pm20) REVERT: B 164 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8112 (mm-30) REVERT: C 134 MET cc_start: 0.9073 (tpp) cc_final: 0.8764 (mtt) REVERT: C 149 GLU cc_start: 0.8612 (mp0) cc_final: 0.8085 (mp0) REVERT: C 164 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8143 (mm-30) REVERT: D 134 MET cc_start: 0.9046 (tpp) cc_final: 0.8727 (mtt) REVERT: D 163 MET cc_start: 0.9222 (ttm) cc_final: 0.8980 (ttm) REVERT: D 164 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8052 (mm-30) REVERT: E 17 ASP cc_start: 0.9044 (t0) cc_final: 0.8444 (m-30) REVERT: E 108 ARG cc_start: 0.6706 (tmm-80) cc_final: 0.5954 (tmm-80) REVERT: E 136 LEU cc_start: 0.8683 (mp) cc_final: 0.8443 (pt) REVERT: E 139 PHE cc_start: 0.8339 (p90) cc_final: 0.7386 (p90) REVERT: E 173 TYR cc_start: 0.6911 (OUTLIER) cc_final: 0.6364 (p90) REVERT: F 3 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8174 (pm20) REVERT: F 6 GLU cc_start: 0.7624 (mp0) cc_final: 0.6504 (mp0) REVERT: F 22 CYS cc_start: 0.8666 (t) cc_final: 0.8173 (t) REVERT: F 27 PHE cc_start: 0.8390 (m-80) cc_final: 0.8151 (m-80) REVERT: F 72 ASP cc_start: 0.8525 (t0) cc_final: 0.8066 (t0) REVERT: F 86 ASP cc_start: 0.8965 (m-30) cc_final: 0.8612 (m-30) REVERT: F 105 GLN cc_start: 0.8494 (pm20) cc_final: 0.8066 (pm20) REVERT: F 171 PHE cc_start: 0.8307 (m-80) cc_final: 0.7646 (m-80) REVERT: G 17 ASP cc_start: 0.9031 (t0) cc_final: 0.8443 (m-30) REVERT: G 23 CYS cc_start: 0.7304 (t) cc_final: 0.7077 (t) REVERT: G 108 ARG cc_start: 0.7030 (tmm-80) cc_final: 0.6816 (tmm-80) REVERT: G 139 PHE cc_start: 0.8280 (p90) cc_final: 0.7494 (p90) REVERT: G 148 TRP cc_start: 0.7209 (m100) cc_final: 0.6362 (m100) REVERT: G 155 GLN cc_start: 0.8463 (mm-40) cc_final: 0.8217 (mp10) REVERT: H 3 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8189 (pm20) REVERT: H 6 GLU cc_start: 0.7522 (mp0) cc_final: 0.6217 (mp0) REVERT: H 22 CYS cc_start: 0.8563 (t) cc_final: 0.8145 (t) REVERT: H 26 ARG cc_start: 0.8393 (pmm-80) cc_final: 0.8084 (pmm-80) REVERT: H 72 ASP cc_start: 0.8500 (t0) cc_final: 0.8016 (t0) REVERT: H 86 ASP cc_start: 0.8955 (m-30) cc_final: 0.8554 (m-30) REVERT: H 105 GLN cc_start: 0.8216 (pm20) cc_final: 0.7491 (pm20) REVERT: H 128 LEU cc_start: 0.8472 (mm) cc_final: 0.8089 (tt) REVERT: H 171 PHE cc_start: 0.8330 (m-80) cc_final: 0.7677 (m-80) REVERT: I 17 ASP cc_start: 0.9094 (t0) cc_final: 0.8604 (m-30) REVERT: I 136 LEU cc_start: 0.8679 (mp) cc_final: 0.8405 (pt) REVERT: I 139 PHE cc_start: 0.8334 (p90) cc_final: 0.7320 (p90) REVERT: I 148 TRP cc_start: 0.7150 (m100) cc_final: 0.6387 (m100) REVERT: I 155 GLN cc_start: 0.8341 (mm-40) cc_final: 0.8108 (mp10) REVERT: I 173 TYR cc_start: 0.6890 (p90) cc_final: 0.6635 (p90) REVERT: J 3 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8198 (pm20) REVERT: J 6 GLU cc_start: 0.7571 (mp0) cc_final: 0.6504 (mp0) REVERT: J 22 CYS cc_start: 0.8650 (t) cc_final: 0.8163 (t) REVERT: J 26 ARG cc_start: 0.8477 (pmm-80) cc_final: 0.8205 (pmm-80) REVERT: J 27 PHE cc_start: 0.8373 (m-80) cc_final: 0.8120 (m-80) REVERT: J 72 ASP cc_start: 0.8605 (t0) cc_final: 0.8032 (t0) REVERT: J 75 LYS cc_start: 0.9457 (OUTLIER) cc_final: 0.9138 (mttm) REVERT: J 79 SER cc_start: 0.9261 (OUTLIER) cc_final: 0.8693 (p) REVERT: J 86 ASP cc_start: 0.8961 (m-30) cc_final: 0.8604 (m-30) REVERT: J 105 GLN cc_start: 0.8488 (pm20) cc_final: 0.8059 (pm20) REVERT: J 171 PHE cc_start: 0.8274 (m-80) cc_final: 0.7604 (m-80) REVERT: J 202 ASN cc_start: 0.8028 (m-40) cc_final: 0.7519 (t0) REVERT: K 3 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8188 (pm20) REVERT: K 6 GLU cc_start: 0.7612 (mp0) cc_final: 0.6499 (mp0) REVERT: K 22 CYS cc_start: 0.8678 (t) cc_final: 0.8194 (t) REVERT: K 26 ARG cc_start: 0.8405 (pmm-80) cc_final: 0.8142 (pmm-80) REVERT: K 72 ASP cc_start: 0.8524 (t0) cc_final: 0.8070 (t0) REVERT: K 86 ASP cc_start: 0.8956 (m-30) cc_final: 0.8591 (m-30) REVERT: K 105 GLN cc_start: 0.8487 (pm20) cc_final: 0.8063 (pm20) REVERT: K 171 PHE cc_start: 0.8219 (m-80) cc_final: 0.7452 (m-80) REVERT: L 4 MET cc_start: 0.8878 (ttm) cc_final: 0.8374 (ttm) REVERT: L 17 ASP cc_start: 0.9025 (t0) cc_final: 0.8436 (m-30) REVERT: L 50 GLU cc_start: 0.9243 (mp0) cc_final: 0.8867 (mp0) REVERT: L 88 CYS cc_start: 0.7919 (p) cc_final: 0.7689 (p) REVERT: L 139 PHE cc_start: 0.8507 (p90) cc_final: 0.7524 (p90) REVERT: L 142 ARG cc_start: 0.8773 (ttm-80) cc_final: 0.8525 (tpp80) REVERT: L 173 TYR cc_start: 0.6441 (p90) cc_final: 0.5249 (p90) outliers start: 33 outliers final: 17 residues processed: 383 average time/residue: 0.5063 time to fit residues: 221.5109 Evaluate side-chains 379 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 355 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 183 LEU Chi-restraints excluded: chain H residue 201 CYS 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 79 SER Chi-restraints excluded: chain J residue 108 CYS Chi-restraints excluded: chain J residue 144 CYS Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 108 CYS Chi-restraints excluded: chain K residue 156 THR Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain L residue 197 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 20 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 chunk 76 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 140 optimal weight: 0.8980 chunk 150 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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** ** 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 = 0.3732 r_free = 0.3732 target = 0.116276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.066007 restraints weight = 36363.039| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 3.05 r_work: 0.2583 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2449 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21016 Z= 0.151 Angle : 0.766 14.511 28704 Z= 0.389 Chirality : 0.047 0.263 3220 Planarity : 0.006 0.066 3648 Dihedral : 5.253 27.721 2864 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.48 % Allowed : 21.96 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.16), residues: 2640 helix: -0.12 (0.54), residues: 100 sheet: 1.69 (0.17), residues: 908 loop : -0.68 (0.16), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 142 TYR 0.038 0.002 TYR F 181 PHE 0.027 0.001 PHE F 27 TRP 0.016 0.001 TRP L 148 HIS 0.003 0.001 HIS E 198 Details of bonding type rmsd covalent geometry : bond 0.00352 (20960) covalent geometry : angle 0.75630 (28592) SS BOND : bond 0.00683 ( 56) SS BOND : angle 2.05920 ( 112) hydrogen bonds : bond 0.03115 ( 709) hydrogen bonds : angle 5.46961 ( 1995) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11115.19 seconds wall clock time: 188 minutes 53.47 seconds (11333.47 seconds total)