Starting phenix.real_space_refine on Thu Sep 18 22:11:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vgj_43202/09_2025/8vgj_43202.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vgj_43202/09_2025/8vgj_43202.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vgj_43202/09_2025/8vgj_43202.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vgj_43202/09_2025/8vgj_43202.map" model { file = "/net/cci-nas-00/data/ceres_data/8vgj_43202/09_2025/8vgj_43202.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vgj_43202/09_2025/8vgj_43202.cif" } resolution = 2.5 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= -0.009 sd= 0.357 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 116 5.16 5 C 12968 2.51 5 N 3492 2.21 5 O 4003 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 20579 Number of models: 1 Model: "" Number of chains: 21 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: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1621 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 204} Chain: "F" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1580 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Chain: "G" Number of atoms: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1621 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 204} Chain: "H" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1580 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Chain: "I" Number of atoms: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1621 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 204} Chain: "J" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1580 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Chain: "K" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1580 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Chain: "L" Number of atoms: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1621 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 204} Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} 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: "I" 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: 4.98, per 1000 atoms: 0.24 Number of scatterers: 20579 At special positions: 0 Unit cell: (97, 111, 183, 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 116 16.00 O 4003 8.00 N 3492 7.00 C 12968 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 58 " distance=2.05 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=2.05 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 168 " - pdb=" SG CYS B 182 " distance=2.03 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=2.05 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=2.05 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 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=2.05 Simple disulfide: pdb=" SG CYS F 108 " - pdb=" SG CYS F 153 " distance=2.02 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 201 " distance=2.03 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 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=2.05 Simple disulfide: pdb=" SG CYS H 108 " - pdb=" SG CYS H 153 " distance=2.02 Simple disulfide: pdb=" SG CYS H 144 " - pdb=" SG CYS H 201 " distance=2.03 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 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=2.05 Simple disulfide: pdb=" SG CYS J 108 " - pdb=" SG CYS J 153 " distance=2.02 Simple disulfide: pdb=" SG CYS J 144 " - pdb=" SG CYS J 201 " distance=2.03 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=2.05 Simple disulfide: pdb=" SG CYS K 108 " - pdb=" SG CYS K 153 " distance=2.02 Simple disulfide: pdb=" SG CYS K 144 " - pdb=" SG CYS K 201 " distance=2.03 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: 1.81 Conformation dependent library (CDL) restraints added in 908.1 milliseconds Enol-peptide restraints added in 715.3 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: 48 helices and 52 sheets defined 9.3% alpha, 41.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 55 through 59 removed outlier: 3.577A pdb=" N CYS A 58 " --> pdb=" O ALA A 55 " (cutoff:3.500A) 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 removed outlier: 3.517A pdb=" N LEU A 173A" --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 Processing helix chain 'B' and resid 55 through 59 removed outlier: 3.576A pdb=" N CYS B 58 " --> pdb=" O ALA B 55 " (cutoff:3.500A) 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 removed outlier: 3.518A pdb=" N LEU B 173A" --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 239 Processing helix chain 'C' and resid 55 through 59 removed outlier: 3.579A pdb=" N CYS C 58 " --> pdb=" O ALA C 55 " (cutoff:3.500A) 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 removed outlier: 3.518A pdb=" N LEU C 173A" --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 239 Processing helix chain 'D' and resid 55 through 59 removed outlier: 3.576A pdb=" N CYS D 58 " --> pdb=" O ALA D 55 " (cutoff:3.500A) 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 removed outlier: 3.515A pdb=" N LEU D 173A" --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 239 Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'E' and resid 121 through 126 removed outlier: 3.627A pdb=" N LEU E 125 " --> pdb=" O SER E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 187 Processing helix 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 192 through 197 removed outlier: 4.651A pdb=" N THR F 196 " --> pdb=" O SER F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 209 No H-bonds generated for 'chain 'F' and resid 207 through 209' Processing helix chain 'G' and resid 79 through 83 Processing helix chain 'G' and resid 121 through 126 removed outlier: 3.646A pdb=" N LEU G 125 " --> pdb=" O SER G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 187 Processing helix 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 192 through 197 removed outlier: 4.653A pdb=" N THR H 196 " --> pdb=" O SER H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 207 through 209 No H-bonds generated for 'chain 'H' and resid 207 through 209' Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'I' and resid 121 through 126 removed outlier: 3.651A pdb=" N LEU I 125 " --> pdb=" O SER I 121 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 187 Processing helix 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 192 through 197 removed outlier: 4.656A pdb=" N THR J 196 " --> pdb=" O SER J 192 " (cutoff:3.500A) Processing helix chain 'J' and resid 207 through 209 No H-bonds generated for 'chain 'J' and resid 207 through 209' Processing helix 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 192 through 197 removed outlier: 4.669A pdb=" N THR K 196 " --> pdb=" O SER K 192 " (cutoff:3.500A) Processing helix chain 'K' and resid 207 through 209 No H-bonds generated for 'chain 'K' and resid 207 through 209' Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'L' and resid 121 through 126 removed outlier: 3.631A pdb=" N LEU L 125 " --> pdb=" O SER L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 21 removed outlier: 4.177A pdb=" N CYS A 136 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR A 139 " --> pdb=" O PRO A 198 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU A 199 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N VAL A 213 " --> pdb=" O THR A 229 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N THR A 229 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N CYS A 182 " --> pdb=" O MET A 163 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 67 removed outlier: 3.730A pdb=" N CYS A 42 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL A 35 " --> pdb=" O HIS A 40 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N HIS A 40 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TRP A 51 " --> pdb=" O ILE A 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 20 through 21 removed outlier: 4.177A pdb=" N CYS B 136 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR B 139 " --> pdb=" O PRO B 198 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU B 199 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N VAL B 213 " --> pdb=" O THR B 229 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N THR B 229 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 4.541A 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: 3.730A pdb=" N CYS B 42 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL B 35 " --> pdb=" O HIS B 40 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N HIS B 40 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TRP B 51 " --> pdb=" O ILE B 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 20 through 21 removed outlier: 4.178A pdb=" N CYS C 136 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR C 139 " --> pdb=" O PRO C 198 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU C 199 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N VAL C 213 " --> pdb=" O THR C 229 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N THR C 229 " --> pdb=" O VAL C 213 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N CYS C 182 " --> pdb=" O MET C 163 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 64 through 67 removed outlier: 3.727A pdb=" N CYS C 42 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL C 35 " --> pdb=" O HIS C 40 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N HIS C 40 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TRP C 51 " --> pdb=" O ILE C 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 20 through 21 removed outlier: 4.180A pdb=" N CYS D 136 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR D 139 " --> pdb=" O PRO D 198 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU D 199 " --> pdb=" O ALA D 210 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N VAL D 213 " --> pdb=" O THR D 229 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N THR D 229 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N CYS D 182 " --> pdb=" O MET D 163 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 64 through 67 removed outlier: 3.724A pdb=" N CYS D 42 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL D 35 " --> pdb=" O HIS D 40 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N HIS D 40 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TRP D 51 " --> pdb=" O ILE D 47 " (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: 3.844A pdb=" N ALA E 84 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.531A 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: 3.844A 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: 5.228A pdb=" N TYR E 173 " --> pdb=" O ASN E 138 " (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: 3.856A pdb=" N ALA F 33 " --> pdb=" O ASP F 95 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE F 34 " --> pdb=" O GLY F 50 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLY F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.929A 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: 3.554A pdb=" N SER F 124 " --> pdb=" O LYS F 147 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY F 143 " --> pdb=" O LEU F 128 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLY F 143 " --> pdb=" O VAL F 187 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL F 187 " --> pdb=" O GLY F 143 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N LEU F 145 " --> pdb=" O SER F 185 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N SER F 185 " --> pdb=" O LEU F 145 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LYS F 147 " --> pdb=" O LEU F 183 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU F 183 " --> pdb=" O LYS F 147 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 124 through 128 removed outlier: 3.554A pdb=" N SER F 124 " --> pdb=" O LYS F 147 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY F 143 " --> pdb=" O LEU F 128 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLY F 143 " --> pdb=" O VAL F 187 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL F 187 " --> pdb=" O GLY F 143 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N LEU F 145 " --> pdb=" O SER F 185 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N SER F 185 " --> pdb=" O LEU F 145 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LYS F 147 " --> pdb=" O LEU F 183 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU F 183 " --> pdb=" O LYS F 147 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 155 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: 3.843A pdb=" N ALA G 84 " --> pdb=" O VAL G 104 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.530A 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: 3.843A 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: 5.229A pdb=" N TYR G 173 " --> pdb=" O ASN G 138 " (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: 3.857A pdb=" N ALA H 33 " --> pdb=" O ASP H 95 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.930A 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: 3.550A pdb=" N SER H 124 " --> pdb=" O LYS H 147 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY H 143 " --> pdb=" O LEU H 128 " (cutoff:3.500A) removed outlier: 4.900A 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: 3.550A pdb=" N SER H 124 " --> pdb=" O LYS H 147 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY H 143 " --> pdb=" O LEU H 128 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N TYR H 181 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 155 through 159 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: 3.837A pdb=" N ALA I 84 " --> pdb=" O VAL I 104 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.530A 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: 3.837A 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: 5.224A pdb=" N TYR I 173 " --> pdb=" O ASN I 138 " (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: 3.857A pdb=" N ALA J 33 " --> pdb=" O ASP J 95 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE J 34 " --> pdb=" O GLY J 50 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLY J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.931A 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: 3.547A pdb=" N SER J 124 " --> pdb=" O LYS J 147 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY J 143 " --> pdb=" O LEU J 128 " (cutoff:3.500A) removed outlier: 4.900A 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: 3.547A pdb=" N SER J 124 " --> pdb=" O LYS J 147 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY J 143 " --> pdb=" O LEU J 128 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N TYR J 181 " --> pdb=" O ASP J 148 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 155 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: 3.858A pdb=" N ALA K 33 " --> pdb=" O ASP K 95 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE K 34 " --> pdb=" O GLY K 50 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLY K 50 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.930A 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: 3.551A pdb=" N SER K 124 " --> pdb=" O LYS K 147 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY K 143 " --> pdb=" O LEU K 128 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLY K 143 " --> pdb=" O VAL K 187 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL K 187 " --> pdb=" O GLY K 143 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N LEU K 145 " --> pdb=" O SER K 185 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N SER K 185 " --> pdb=" O LEU K 145 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N LYS K 147 " --> pdb=" O LEU K 183 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU K 183 " --> pdb=" O LYS K 147 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 124 through 128 removed outlier: 3.551A pdb=" N SER K 124 " --> pdb=" O LYS K 147 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY K 143 " --> pdb=" O LEU K 128 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLY K 143 " --> pdb=" O VAL K 187 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL K 187 " --> pdb=" O GLY K 143 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N LEU K 145 " --> pdb=" O SER K 185 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N SER K 185 " --> pdb=" O LEU K 145 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N LYS K 147 " --> pdb=" O LEU K 183 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU K 183 " --> pdb=" O LYS K 147 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 155 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: 3.839A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.531A 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: 3.839A 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: 5.228A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 153 through 154 792 hydrogen bonds defined for protein. 2016 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: 4.36 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5303 1.33 - 1.46: 5276 1.46 - 1.58: 10301 1.58 - 1.71: 0 1.71 - 1.84: 136 Bond restraints: 21016 Sorted by residual: bond pdb=" C GLU A 21 " pdb=" N ALA A 22 " ideal model delta sigma weight residual 1.331 1.253 0.078 2.07e-02 2.33e+03 1.41e+01 bond pdb=" C GLU B 21 " pdb=" N ALA B 22 " ideal model delta sigma weight residual 1.335 1.252 0.083 3.04e-02 1.08e+03 7.43e+00 bond pdb=" CB ARG J 38 " pdb=" CG ARG J 38 " ideal model delta sigma weight residual 1.520 1.450 0.070 3.00e-02 1.11e+03 5.52e+00 bond pdb=" CB ARG K 38 " pdb=" CG ARG K 38 " ideal model delta sigma weight residual 1.520 1.450 0.070 3.00e-02 1.11e+03 5.49e+00 bond pdb=" CB ARG H 38 " pdb=" CG ARG H 38 " ideal model delta sigma weight residual 1.520 1.450 0.070 3.00e-02 1.11e+03 5.48e+00 ... (remaining 21011 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 26767 2.29 - 4.58: 1693 4.58 - 6.87: 153 6.87 - 9.16: 41 9.16 - 11.45: 14 Bond angle restraints: 28668 Sorted by residual: angle pdb=" N PRO D 152A" pdb=" CA PRO D 152A" pdb=" C PRO D 152A" ideal model delta sigma weight residual 110.70 122.15 -11.45 1.22e+00 6.72e-01 8.80e+01 angle pdb=" N PRO B 152A" pdb=" CA PRO B 152A" pdb=" C PRO B 152A" ideal model delta sigma weight residual 110.70 122.05 -11.35 1.22e+00 6.72e-01 8.65e+01 angle pdb=" N PRO C 152A" pdb=" CA PRO C 152A" pdb=" C PRO C 152A" ideal model delta sigma weight residual 110.70 122.03 -11.33 1.22e+00 6.72e-01 8.63e+01 angle pdb=" N PRO A 152A" pdb=" CA PRO A 152A" pdb=" C PRO A 152A" ideal model delta sigma weight residual 110.70 121.67 -10.97 1.22e+00 6.72e-01 8.09e+01 angle pdb=" C PRO D 152 " pdb=" N PRO D 152A" pdb=" CA PRO D 152A" ideal model delta sigma weight residual 120.38 127.54 -7.16 1.03e+00 9.43e-01 4.83e+01 ... (remaining 28663 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 11531 17.36 - 34.71: 781 34.71 - 52.07: 148 52.07 - 69.43: 60 69.43 - 86.78: 28 Dihedral angle restraints: 12548 sinusoidal: 4872 harmonic: 7676 Sorted by residual: dihedral pdb=" CA PRO H 123 " pdb=" C PRO H 123 " pdb=" N SER H 124 " pdb=" CA SER H 124 " ideal model delta harmonic sigma weight residual 180.00 153.62 26.38 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA PRO F 123 " pdb=" C PRO F 123 " pdb=" N SER F 124 " pdb=" CA SER F 124 " ideal model delta harmonic sigma weight residual 180.00 153.65 26.35 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA PRO K 123 " pdb=" C PRO K 123 " pdb=" N SER K 124 " pdb=" CA SER K 124 " ideal model delta harmonic sigma weight residual 180.00 153.66 26.34 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 12545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2143 0.071 - 0.141: 869 0.141 - 0.212: 155 0.212 - 0.283: 44 0.283 - 0.353: 9 Chirality restraints: 3220 Sorted by residual: 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 2.37 0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CA PRO C 152A" pdb=" N PRO C 152A" pdb=" C PRO C 152A" pdb=" CB PRO C 152A" both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 3.06e+00 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 2.37 0.35 2.00e-01 2.50e+01 3.02e+00 ... (remaining 3217 not shown) Planarity restraints: 3660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 95 " -0.036 2.00e-02 2.50e+03 2.15e-02 9.23e+00 pdb=" CG TYR B 95 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR B 95 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR B 95 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR B 95 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 95 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 95 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR B 95 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 95 " 0.036 2.00e-02 2.50e+03 2.13e-02 9.07e+00 pdb=" CG TYR A 95 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR A 95 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR A 95 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A 95 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 95 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 95 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 95 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 95 " 0.035 2.00e-02 2.50e+03 2.12e-02 8.95e+00 pdb=" CG TYR D 95 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR D 95 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR D 95 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR D 95 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR D 95 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR D 95 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR D 95 " 0.006 2.00e-02 2.50e+03 ... (remaining 3657 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 555 2.68 - 3.24: 19492 3.24 - 3.79: 32253 3.79 - 4.35: 44840 4.35 - 4.90: 72393 Nonbonded interactions: 169533 Sorted by model distance: nonbonded pdb=" OH TYR E 29 " pdb=" NH1 ARG E 94 " model vdw 2.128 3.120 nonbonded pdb=" OH TYR I 29 " pdb=" NH1 ARG I 94 " model vdw 2.129 3.120 nonbonded pdb=" OH TYR G 29 " pdb=" NH1 ARG G 94 " model vdw 2.129 3.120 nonbonded pdb=" OH TYR L 29 " pdb=" NH1 ARG L 94 " model vdw 2.129 3.120 nonbonded pdb=" ND2 ASN G 158 " pdb=" O THR G 180 " model vdw 2.176 3.120 ... (remaining 169528 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: 4.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.700 Find NCS groups from input model: 0.390 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:6.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.091 21064 Z= 0.479 Angle : 1.209 11.446 28764 Z= 0.664 Chirality : 0.078 0.353 3220 Planarity : 0.012 0.092 3660 Dihedral : 13.485 86.783 7492 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.21 % Favored : 93.48 % Rotamer: Outliers : 1.57 % Allowed : 4.30 % Favored : 94.13 % 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: -1.25 (0.15), residues: 2640 helix: -2.42 (0.32), residues: 144 sheet: 0.15 (0.17), residues: 892 loop : -1.29 (0.14), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.004 ARG D 69 TYR 0.047 0.006 TYR B 95 PHE 0.027 0.007 PHE I 116 TRP 0.039 0.006 TRP B 141 HIS 0.019 0.005 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.01128 (21016) covalent geometry : angle 1.20307 (28668) SS BOND : bond 0.01136 ( 48) SS BOND : angle 2.45950 ( 96) hydrogen bonds : bond 0.21597 ( 710) hydrogen bonds : angle 9.13738 ( 2016) *********************** 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 596 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 560 time to evaluate : 0.720 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: E 82 ASP cc_start: 0.8406 (m-30) cc_final: 0.8198 (m-30) REVERT: E 117 ILE cc_start: 0.9016 (tt) cc_final: 0.8799 (mt) REVERT: E 181 LEU cc_start: 0.8476 (tp) cc_final: 0.8125 (tp) REVERT: E 186 TYR cc_start: 0.9049 (t80) cc_final: 0.8845 (t80) REVERT: F 148 ASP cc_start: 0.8195 (p0) cc_final: 0.7855 (p0) REVERT: F 160 ASN cc_start: 0.8778 (m-40) cc_final: 0.8407 (m-40) REVERT: G 82 ASP cc_start: 0.8420 (m-30) cc_final: 0.8194 (m-30) REVERT: G 117 ILE cc_start: 0.9003 (tt) cc_final: 0.8784 (mt) REVERT: G 181 LEU cc_start: 0.8471 (tp) cc_final: 0.8127 (tp) REVERT: G 186 TYR cc_start: 0.9059 (t80) cc_final: 0.8857 (t80) REVERT: H 148 ASP cc_start: 0.8198 (p0) cc_final: 0.7802 (p0) REVERT: H 160 ASN cc_start: 0.8760 (m-40) cc_final: 0.8402 (m-40) REVERT: I 82 ASP cc_start: 0.8429 (m-30) cc_final: 0.8207 (m-30) REVERT: I 117 ILE cc_start: 0.9006 (tt) cc_final: 0.8794 (mt) REVERT: I 181 LEU cc_start: 0.8477 (tp) cc_final: 0.8126 (tp) REVERT: I 186 TYR cc_start: 0.9050 (t80) cc_final: 0.8848 (t80) REVERT: J 148 ASP cc_start: 0.8185 (p0) cc_final: 0.7789 (p0) REVERT: J 160 ASN cc_start: 0.8749 (m-40) cc_final: 0.8388 (m-40) REVERT: K 148 ASP cc_start: 0.8183 (p0) cc_final: 0.7769 (p0) REVERT: K 160 ASN cc_start: 0.8754 (m-40) cc_final: 0.8368 (m-40) REVERT: K 176 GLN cc_start: 0.8487 (mt0) cc_final: 0.7941 (mt0) REVERT: L 82 ASP cc_start: 0.8423 (m-30) cc_final: 0.7978 (m-30) REVERT: L 117 ILE cc_start: 0.9002 (tt) cc_final: 0.8781 (mt) REVERT: L 181 LEU cc_start: 0.8477 (tp) cc_final: 0.8122 (tp) outliers start: 36 outliers final: 1 residues processed: 584 average time/residue: 0.6360 time to fit residues: 419.4827 Evaluate side-chains 370 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 369 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 72 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.0970 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 8.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 158 ASN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 HIS G 158 ASN ** G 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 169 HIS I 147 GLN I 158 ASN ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 169 HIS K 169 HIS L 158 ASN ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.105449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.064010 restraints weight = 40505.006| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 3.20 r_work: 0.2624 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21064 Z= 0.161 Angle : 0.764 9.000 28764 Z= 0.400 Chirality : 0.048 0.140 3220 Planarity : 0.005 0.050 3660 Dihedral : 6.212 101.106 2866 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.30 % Allowed : 13.78 % Favored : 83.91 % 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: -0.21 (0.16), residues: 2640 helix: -1.10 (0.41), residues: 152 sheet: 0.60 (0.16), residues: 924 loop : -0.47 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 18 TYR 0.026 0.002 TYR E 140 PHE 0.030 0.002 PHE B 153 TRP 0.016 0.001 TRP L 148 HIS 0.007 0.001 HIS C 173 Details of bonding type rmsd covalent geometry : bond 0.00366 (21016) covalent geometry : angle 0.76050 (28668) SS BOND : bond 0.00397 ( 48) SS BOND : angle 1.43274 ( 96) hydrogen bonds : bond 0.03985 ( 710) hydrogen bonds : angle 6.51310 ( 2016) *********************** 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 513 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 460 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 149 GLU cc_start: 0.8585 (mp0) cc_final: 0.8265 (mp0) REVERT: C 149 GLU cc_start: 0.8594 (mp0) cc_final: 0.8270 (mp0) REVERT: E 50 GLU cc_start: 0.9149 (mt-10) cc_final: 0.8595 (mp0) REVERT: E 61 ARG cc_start: 0.9081 (mtm-85) cc_final: 0.8691 (mtm-85) REVERT: E 82 ASP cc_start: 0.8499 (m-30) cc_final: 0.8228 (m-30) REVERT: E 117 ILE cc_start: 0.8142 (tt) cc_final: 0.7923 (mt) REVERT: E 139 PHE cc_start: 0.8277 (p90) cc_final: 0.8014 (p90) REVERT: E 142 ARG cc_start: 0.8700 (ttm-80) cc_final: 0.7995 (mmt90) REVERT: E 167 ASP cc_start: 0.8033 (t70) cc_final: 0.7764 (t0) REVERT: F 3 GLN cc_start: 0.9030 (pt0) cc_final: 0.8485 (pm20) REVERT: F 16 GLU cc_start: 0.8469 (mp0) cc_final: 0.8132 (mp0) REVERT: F 26 ARG cc_start: 0.7987 (pmm-80) cc_final: 0.7355 (pmm-80) REVERT: F 27 PHE cc_start: 0.8447 (m-10) cc_final: 0.8239 (m-10) REVERT: F 72 ASP cc_start: 0.8503 (t0) cc_final: 0.7967 (t0) REVERT: F 105 GLN cc_start: 0.8237 (pm20) cc_final: 0.7612 (pm20) REVERT: F 148 ASP cc_start: 0.8992 (p0) cc_final: 0.8604 (p0) REVERT: F 183 LEU cc_start: 0.9249 (tt) cc_final: 0.8598 (mt) REVERT: F 214 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7186 (ttpt) REVERT: G 50 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8611 (mp0) REVERT: G 61 ARG cc_start: 0.9086 (mtm-85) cc_final: 0.8697 (mtm-85) REVERT: G 82 ASP cc_start: 0.8507 (m-30) cc_final: 0.8240 (m-30) REVERT: G 117 ILE cc_start: 0.8130 (tt) cc_final: 0.7919 (mt) REVERT: G 139 PHE cc_start: 0.8297 (p90) cc_final: 0.7983 (p90) REVERT: G 167 ASP cc_start: 0.8031 (t70) cc_final: 0.7742 (t0) REVERT: H 3 GLN cc_start: 0.9023 (pt0) cc_final: 0.8480 (pm20) REVERT: H 16 GLU cc_start: 0.8466 (mp0) cc_final: 0.8128 (mp0) REVERT: H 26 ARG cc_start: 0.7990 (pmm-80) cc_final: 0.7369 (pmm-80) REVERT: H 27 PHE cc_start: 0.8452 (m-10) cc_final: 0.8248 (m-10) REVERT: H 72 ASP cc_start: 0.8576 (t0) cc_final: 0.8365 (t0) REVERT: H 101 ASP cc_start: 0.9293 (p0) cc_final: 0.9093 (p0) REVERT: H 105 GLN cc_start: 0.8209 (pm20) cc_final: 0.7580 (pm20) REVERT: H 148 ASP cc_start: 0.8998 (p0) cc_final: 0.8673 (p0) REVERT: H 176 GLN cc_start: 0.7915 (mt0) cc_final: 0.7362 (mt0) REVERT: H 183 LEU cc_start: 0.9235 (tt) cc_final: 0.8696 (mt) REVERT: H 214 LYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7179 (ttpt) REVERT: I 50 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8515 (mp0) REVERT: I 61 ARG cc_start: 0.9071 (mtm-85) cc_final: 0.8681 (mtm-85) REVERT: I 82 ASP cc_start: 0.8488 (m-30) cc_final: 0.8217 (m-30) REVERT: I 117 ILE cc_start: 0.8151 (tt) cc_final: 0.7931 (mt) REVERT: I 139 PHE cc_start: 0.8310 (p90) cc_final: 0.8036 (p90) REVERT: I 142 ARG cc_start: 0.8653 (ttm-80) cc_final: 0.7844 (mmt90) REVERT: I 167 ASP cc_start: 0.8025 (t70) cc_final: 0.7756 (t0) REVERT: J 3 GLN cc_start: 0.9021 (pt0) cc_final: 0.8476 (pm20) REVERT: J 16 GLU cc_start: 0.8460 (mp0) cc_final: 0.8126 (mp0) REVERT: J 26 ARG cc_start: 0.7978 (pmm-80) cc_final: 0.7348 (pmm-80) REVERT: J 27 PHE cc_start: 0.8457 (m-10) cc_final: 0.8245 (m-10) REVERT: J 72 ASP cc_start: 0.8516 (t0) cc_final: 0.8305 (t0) REVERT: J 101 ASP cc_start: 0.9276 (p0) cc_final: 0.9075 (p0) REVERT: J 105 GLN cc_start: 0.8211 (pm20) cc_final: 0.7576 (pm20) REVERT: J 148 ASP cc_start: 0.8988 (p0) cc_final: 0.8681 (p0) REVERT: J 183 LEU cc_start: 0.9249 (tt) cc_final: 0.8706 (mt) REVERT: J 214 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7193 (ttpt) REVERT: K 3 GLN cc_start: 0.9026 (pt0) cc_final: 0.8479 (pm20) REVERT: K 16 GLU cc_start: 0.8447 (mp0) cc_final: 0.8113 (mp0) REVERT: K 26 ARG cc_start: 0.7983 (pmm-80) cc_final: 0.7354 (pmm-80) REVERT: K 27 PHE cc_start: 0.8456 (m-10) cc_final: 0.8246 (m-10) REVERT: K 72 ASP cc_start: 0.8573 (t0) cc_final: 0.8362 (t0) REVERT: K 105 GLN cc_start: 0.8218 (pm20) cc_final: 0.7594 (pm20) REVERT: K 148 ASP cc_start: 0.8987 (p0) cc_final: 0.8582 (p0) REVERT: K 214 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.7081 (ttpt) REVERT: L 50 GLU cc_start: 0.9192 (mt-10) cc_final: 0.8628 (mp0) REVERT: L 117 ILE cc_start: 0.8123 (tt) cc_final: 0.7907 (mt) REVERT: L 139 PHE cc_start: 0.8315 (p90) cc_final: 0.8002 (p90) REVERT: L 167 ASP cc_start: 0.8033 (t70) cc_final: 0.7744 (t0) outliers start: 53 outliers final: 15 residues processed: 482 average time/residue: 0.5827 time to fit residues: 321.7443 Evaluate side-chains 425 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 406 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain D residue 20 GLN Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain F residue 214 LYS Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain H residue 214 LYS Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 173 TYR Chi-restraints excluded: chain J residue 214 LYS Chi-restraints excluded: chain K residue 214 LYS Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 27 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 186 optimal weight: 9.9990 chunk 257 optimal weight: 0.5980 chunk 132 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 189 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 232 optimal weight: 4.9990 chunk 135 optimal weight: 10.0000 chunk 39 optimal weight: 0.9980 chunk 145 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 79 GLN E 158 ASN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 HIS G 79 GLN G 158 ASN ** G 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 169 HIS I 79 GLN I 158 ASN ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 169 HIS K 169 HIS L 158 ASN ** L 166 GLN ** 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 = 0.3622 r_free = 0.3622 target = 0.104494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.062752 restraints weight = 40649.276| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 3.18 r_work: 0.2596 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21064 Z= 0.174 Angle : 0.705 9.284 28764 Z= 0.369 Chirality : 0.047 0.154 3220 Planarity : 0.005 0.055 3660 Dihedral : 5.478 23.350 2864 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.74 % Allowed : 16.26 % Favored : 81.00 % 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: 0.12 (0.16), residues: 2640 helix: -0.50 (0.45), residues: 152 sheet: 0.74 (0.16), residues: 932 loop : -0.22 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 108 TYR 0.023 0.002 TYR I 140 PHE 0.019 0.002 PHE L 209 TRP 0.016 0.001 TRP I 148 HIS 0.004 0.001 HIS C 173 Details of bonding type rmsd covalent geometry : bond 0.00401 (21016) covalent geometry : angle 0.69977 (28668) SS BOND : bond 0.00795 ( 48) SS BOND : angle 1.64418 ( 96) hydrogen bonds : bond 0.03470 ( 710) hydrogen bonds : angle 5.91678 ( 2016) *********************** 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 492 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 429 time to evaluate : 0.857 Fit side-chains revert: symmetry clash REVERT: B 109 GLU cc_start: 0.8974 (tp30) cc_final: 0.8636 (tp30) REVERT: E 50 GLU cc_start: 0.9141 (mt-10) cc_final: 0.8607 (mp0) REVERT: E 61 ARG cc_start: 0.9081 (mtm-85) cc_final: 0.8766 (mtm-85) REVERT: E 82 ASP cc_start: 0.8519 (m-30) cc_final: 0.8261 (m-30) REVERT: E 105 GLU cc_start: 0.6966 (mp0) cc_final: 0.6748 (mp0) REVERT: E 139 PHE cc_start: 0.8327 (p90) cc_final: 0.8090 (p90) REVERT: E 167 ASP cc_start: 0.8128 (t70) cc_final: 0.7861 (t0) REVERT: F 3 GLN cc_start: 0.9060 (pt0) cc_final: 0.8563 (pm20) REVERT: F 6 GLU cc_start: 0.7792 (mp0) cc_final: 0.6991 (pm20) REVERT: F 16 GLU cc_start: 0.8457 (mp0) cc_final: 0.8226 (mp0) REVERT: F 26 ARG cc_start: 0.8060 (pmm-80) cc_final: 0.7535 (pmm-80) REVERT: F 27 PHE cc_start: 0.8464 (m-10) cc_final: 0.8222 (m-10) REVERT: F 72 ASP cc_start: 0.8562 (t0) cc_final: 0.8037 (t0) REVERT: F 148 ASP cc_start: 0.9007 (p0) cc_final: 0.8611 (p0) REVERT: F 152 GLU cc_start: 0.7486 (pm20) cc_final: 0.7284 (pm20) REVERT: F 160 ASN cc_start: 0.8804 (m-40) cc_final: 0.8452 (m-40) REVERT: F 214 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7349 (ttpt) REVERT: G 50 GLU cc_start: 0.9160 (mt-10) cc_final: 0.8623 (mp0) REVERT: G 61 ARG cc_start: 0.9074 (mtm-85) cc_final: 0.8754 (mtm-85) REVERT: G 82 ASP cc_start: 0.8532 (m-30) cc_final: 0.8275 (m-30) REVERT: G 105 GLU cc_start: 0.6968 (mp0) cc_final: 0.6745 (mp0) REVERT: G 139 PHE cc_start: 0.8222 (p90) cc_final: 0.7976 (p90) REVERT: G 167 ASP cc_start: 0.8093 (t70) cc_final: 0.7822 (t0) REVERT: H 3 GLN cc_start: 0.9078 (pt0) cc_final: 0.8581 (pm20) REVERT: H 6 GLU cc_start: 0.7815 (mp0) cc_final: 0.7025 (pm20) REVERT: H 16 GLU cc_start: 0.8452 (mp0) cc_final: 0.8224 (mp0) REVERT: H 26 ARG cc_start: 0.8058 (pmm-80) cc_final: 0.7533 (pmm-80) REVERT: H 27 PHE cc_start: 0.8469 (m-10) cc_final: 0.8230 (m-10) REVERT: H 72 ASP cc_start: 0.8575 (t0) cc_final: 0.8292 (t0) REVERT: H 148 ASP cc_start: 0.9010 (p0) cc_final: 0.8742 (p0) REVERT: H 149 TYR cc_start: 0.8870 (p90) cc_final: 0.8602 (p90) REVERT: H 152 GLU cc_start: 0.7550 (pm20) cc_final: 0.7304 (pm20) REVERT: H 160 ASN cc_start: 0.8826 (m-40) cc_final: 0.8468 (m-40) REVERT: H 183 LEU cc_start: 0.9248 (tt) cc_final: 0.8738 (mt) REVERT: H 214 LYS cc_start: 0.7639 (OUTLIER) cc_final: 0.7109 (ttpt) REVERT: I 50 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8523 (mp0) REVERT: I 61 ARG cc_start: 0.9085 (mtm-85) cc_final: 0.8773 (mtm-85) REVERT: I 82 ASP cc_start: 0.8513 (m-30) cc_final: 0.8261 (m-30) REVERT: I 105 GLU cc_start: 0.7037 (mp0) cc_final: 0.6829 (mp0) REVERT: I 139 PHE cc_start: 0.8324 (p90) cc_final: 0.7956 (p90) REVERT: I 167 ASP cc_start: 0.8087 (t70) cc_final: 0.7801 (t0) REVERT: I 173 TYR cc_start: 0.7155 (OUTLIER) cc_final: 0.6258 (p90) REVERT: J 3 GLN cc_start: 0.9075 (pt0) cc_final: 0.8573 (pm20) REVERT: J 6 GLU cc_start: 0.7791 (mp0) cc_final: 0.6998 (pm20) REVERT: J 16 GLU cc_start: 0.8451 (mp0) cc_final: 0.8225 (mp0) REVERT: J 26 ARG cc_start: 0.8048 (pmm-80) cc_final: 0.7523 (pmm-80) REVERT: J 27 PHE cc_start: 0.8465 (m-10) cc_final: 0.8219 (m-10) REVERT: J 72 ASP cc_start: 0.8578 (t0) cc_final: 0.8296 (t0) REVERT: J 148 ASP cc_start: 0.8998 (p0) cc_final: 0.8720 (p0) REVERT: J 149 TYR cc_start: 0.8837 (p90) cc_final: 0.8546 (p90) REVERT: J 152 GLU cc_start: 0.7567 (pm20) cc_final: 0.7326 (pm20) REVERT: J 160 ASN cc_start: 0.8839 (m-40) cc_final: 0.8491 (m-40) REVERT: J 183 LEU cc_start: 0.9253 (tt) cc_final: 0.8733 (mt) REVERT: J 214 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7222 (ttpt) REVERT: K 3 GLN cc_start: 0.9065 (pt0) cc_final: 0.8569 (pm20) REVERT: K 6 GLU cc_start: 0.7803 (mp0) cc_final: 0.7002 (pm20) REVERT: K 16 GLU cc_start: 0.8444 (mp0) cc_final: 0.8213 (mp0) REVERT: K 26 ARG cc_start: 0.8034 (pmm-80) cc_final: 0.7511 (pmm-80) REVERT: K 27 PHE cc_start: 0.8446 (m-10) cc_final: 0.8208 (m-10) REVERT: K 72 ASP cc_start: 0.8580 (t0) cc_final: 0.8299 (t0) REVERT: K 148 ASP cc_start: 0.8981 (p0) cc_final: 0.8573 (p0) REVERT: K 152 GLU cc_start: 0.7492 (pm20) cc_final: 0.7286 (pm20) REVERT: K 160 ASN cc_start: 0.8834 (m-40) cc_final: 0.8492 (m-40) REVERT: K 214 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7477 (ttpt) REVERT: L 50 GLU cc_start: 0.9167 (mt-10) cc_final: 0.8629 (mp0) REVERT: L 105 GLU cc_start: 0.6976 (mp0) cc_final: 0.6763 (mp0) REVERT: L 139 PHE cc_start: 0.8238 (p90) cc_final: 0.7987 (p90) REVERT: L 167 ASP cc_start: 0.8108 (t70) cc_final: 0.7841 (t0) outliers start: 63 outliers final: 29 residues processed: 460 average time/residue: 0.5760 time to fit residues: 304.4742 Evaluate side-chains 430 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 396 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain D residue 20 GLN Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain F residue 11 CYS Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 214 LYS Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 173 TYR Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 214 LYS Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 173 TYR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain J residue 11 CYS Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 214 LYS Chi-restraints excluded: chain K residue 11 CYS Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 214 LYS Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 173 TYR Chi-restraints excluded: chain L residue 179 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 144 optimal weight: 10.0000 chunk 136 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 196 optimal weight: 3.9990 chunk 235 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 245 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 ASN F 76 ASN ** F 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 ASN F 204 ASN ** G 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 210 ASN H 76 ASN H 169 HIS H 202 ASN H 204 ASN ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 210 ASN J 76 ASN J 202 ASN J 204 ASN K 169 HIS K 197 GLN K 202 ASN K 204 ASN L 79 GLN ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 210 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.102030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.060461 restraints weight = 40857.586| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 3.13 r_work: 0.2554 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2423 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 21064 Z= 0.249 Angle : 0.730 9.305 28764 Z= 0.383 Chirality : 0.048 0.175 3220 Planarity : 0.006 0.061 3660 Dihedral : 5.363 25.068 2864 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.78 % Allowed : 16.39 % Favored : 79.83 % 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: 0.03 (0.16), residues: 2640 helix: 0.04 (0.47), residues: 152 sheet: 0.67 (0.16), residues: 928 loop : -0.34 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG L 142 TYR 0.019 0.002 TYR L 173 PHE 0.026 0.002 PHE L 209 TRP 0.013 0.001 TRP D 215 HIS 0.004 0.001 HIS B 173 Details of bonding type rmsd covalent geometry : bond 0.00585 (21016) covalent geometry : angle 0.71594 (28668) SS BOND : bond 0.00510 ( 48) SS BOND : angle 2.53381 ( 96) hydrogen bonds : bond 0.03520 ( 710) hydrogen bonds : angle 5.76135 ( 2016) *********************** 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 498 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 411 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 GLU cc_start: 0.9274 (OUTLIER) cc_final: 0.9038 (tp30) REVERT: B 109 GLU cc_start: 0.9180 (tp30) cc_final: 0.8852 (tp30) REVERT: C 20 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8636 (pm20) REVERT: D 20 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.8643 (pm20) REVERT: E 33 LEU cc_start: 0.9724 (OUTLIER) cc_final: 0.9459 (tm) REVERT: E 50 GLU cc_start: 0.9370 (mt-10) cc_final: 0.8869 (mp0) REVERT: E 105 GLU cc_start: 0.7378 (mp0) cc_final: 0.7127 (mp0) REVERT: E 117 ILE cc_start: 0.8545 (tt) cc_final: 0.8309 (mm) REVERT: E 139 PHE cc_start: 0.8261 (p90) cc_final: 0.7931 (p90) REVERT: E 142 ARG cc_start: 0.9013 (ttm-80) cc_final: 0.8695 (mmt90) REVERT: E 167 ASP cc_start: 0.8361 (t0) cc_final: 0.7968 (t0) REVERT: E 173 TYR cc_start: 0.7005 (p90) cc_final: 0.6599 (p90) REVERT: E 179 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9071 (tp) REVERT: E 210 ASN cc_start: 0.8500 (t0) cc_final: 0.8148 (p0) REVERT: F 3 GLN cc_start: 0.9152 (pt0) cc_final: 0.8609 (pm20) REVERT: F 6 GLU cc_start: 0.7972 (mp0) cc_final: 0.7420 (pm20) REVERT: F 26 ARG cc_start: 0.8108 (pmm-80) cc_final: 0.7510 (pmm-80) REVERT: F 27 PHE cc_start: 0.8643 (m-10) cc_final: 0.8398 (m-10) REVERT: F 72 ASP cc_start: 0.8820 (t0) cc_final: 0.8308 (t0) REVERT: F 105 GLN cc_start: 0.8430 (pm20) cc_final: 0.7912 (pm20) REVERT: F 148 ASP cc_start: 0.9050 (p0) cc_final: 0.8685 (p0) REVERT: F 152 GLU cc_start: 0.7517 (pm20) cc_final: 0.7266 (pm20) REVERT: G 33 LEU cc_start: 0.9714 (OUTLIER) cc_final: 0.9445 (tm) REVERT: G 50 GLU cc_start: 0.9376 (mt-10) cc_final: 0.8876 (mp0) REVERT: G 105 GLU cc_start: 0.7330 (mp0) cc_final: 0.7065 (mp0) REVERT: G 117 ILE cc_start: 0.8536 (tt) cc_final: 0.8305 (mm) REVERT: G 139 PHE cc_start: 0.8257 (p90) cc_final: 0.7968 (p90) REVERT: G 167 ASP cc_start: 0.8379 (t0) cc_final: 0.7975 (t0) REVERT: G 179 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9073 (tp) REVERT: G 210 ASN cc_start: 0.8505 (t0) cc_final: 0.8202 (p0) REVERT: H 3 GLN cc_start: 0.9142 (pt0) cc_final: 0.8597 (pm20) REVERT: H 6 GLU cc_start: 0.8007 (mp0) cc_final: 0.7278 (pm20) REVERT: H 26 ARG cc_start: 0.8116 (pmm-80) cc_final: 0.7505 (pmm-80) REVERT: H 27 PHE cc_start: 0.8638 (m-10) cc_final: 0.8392 (m-10) REVERT: H 72 ASP cc_start: 0.8690 (t0) cc_final: 0.8390 (t0) REVERT: H 105 GLN cc_start: 0.8429 (pm20) cc_final: 0.8190 (pm20) REVERT: H 148 ASP cc_start: 0.9048 (p0) cc_final: 0.8835 (p0) REVERT: H 149 TYR cc_start: 0.8922 (p90) cc_final: 0.8633 (p90) REVERT: H 152 GLU cc_start: 0.7545 (pm20) cc_final: 0.7246 (pm20) REVERT: H 176 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8217 (mt0) REVERT: H 183 LEU cc_start: 0.9241 (tt) cc_final: 0.8679 (mt) REVERT: H 214 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7085 (ttpt) REVERT: I 33 LEU cc_start: 0.9710 (OUTLIER) cc_final: 0.9443 (tm) REVERT: I 50 GLU cc_start: 0.9274 (mt-10) cc_final: 0.8763 (mp0) REVERT: I 105 GLU cc_start: 0.7322 (mp0) cc_final: 0.7070 (mp0) REVERT: I 117 ILE cc_start: 0.8547 (tt) cc_final: 0.8311 (mm) REVERT: I 142 ARG cc_start: 0.8813 (ttm110) cc_final: 0.8611 (mmt90) REVERT: I 167 ASP cc_start: 0.8369 (t0) cc_final: 0.7985 (t0) REVERT: I 179 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9108 (pp) REVERT: I 210 ASN cc_start: 0.8496 (t0) cc_final: 0.8158 (p0) REVERT: J 3 GLN cc_start: 0.9139 (pt0) cc_final: 0.8592 (pm20) REVERT: J 6 GLU cc_start: 0.7989 (mp0) cc_final: 0.7255 (pm20) REVERT: J 26 ARG cc_start: 0.8088 (pmm-80) cc_final: 0.7472 (pmm-80) REVERT: J 27 PHE cc_start: 0.8636 (m-10) cc_final: 0.8389 (m-10) REVERT: J 72 ASP cc_start: 0.8699 (t0) cc_final: 0.8403 (t0) REVERT: J 105 GLN cc_start: 0.8415 (pm20) cc_final: 0.8175 (pm20) REVERT: J 148 ASP cc_start: 0.9033 (p0) cc_final: 0.8825 (p0) REVERT: J 149 TYR cc_start: 0.8922 (p90) cc_final: 0.8642 (p90) REVERT: J 152 GLU cc_start: 0.7543 (pm20) cc_final: 0.7229 (pm20) REVERT: J 176 GLN cc_start: 0.8500 (mt0) cc_final: 0.8212 (mt0) REVERT: J 183 LEU cc_start: 0.9247 (tt) cc_final: 0.8715 (mt) REVERT: K 3 GLN cc_start: 0.9138 (pt0) cc_final: 0.8591 (pm20) REVERT: K 6 GLU cc_start: 0.7974 (mp0) cc_final: 0.7239 (pm20) REVERT: K 26 ARG cc_start: 0.8076 (pmm-80) cc_final: 0.7456 (pmm-80) REVERT: K 27 PHE cc_start: 0.8648 (m-10) cc_final: 0.8400 (m-10) REVERT: K 72 ASP cc_start: 0.8708 (t0) cc_final: 0.8412 (t0) REVERT: K 105 GLN cc_start: 0.8456 (pm20) cc_final: 0.8218 (pm20) REVERT: K 148 ASP cc_start: 0.9030 (p0) cc_final: 0.8646 (p0) REVERT: K 152 GLU cc_start: 0.7534 (pm20) cc_final: 0.7294 (pm20) REVERT: L 33 LEU cc_start: 0.9716 (OUTLIER) cc_final: 0.9445 (tm) REVERT: L 50 GLU cc_start: 0.9382 (mt-10) cc_final: 0.8882 (mp0) REVERT: L 81 GLU cc_start: 0.9036 (pm20) cc_final: 0.8834 (pm20) REVERT: L 105 GLU cc_start: 0.7345 (mp0) cc_final: 0.7085 (mp0) REVERT: L 117 ILE cc_start: 0.8542 (tt) cc_final: 0.8328 (mm) REVERT: L 139 PHE cc_start: 0.8246 (p90) cc_final: 0.7925 (p90) REVERT: L 167 ASP cc_start: 0.8262 (t0) cc_final: 0.7912 (t0) REVERT: L 179 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9065 (tp) REVERT: L 210 ASN cc_start: 0.8502 (t0) cc_final: 0.8166 (p0) outliers start: 87 outliers final: 27 residues processed: 459 average time/residue: 0.6109 time to fit residues: 320.1239 Evaluate side-chains 421 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 381 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 26 LYS Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain D residue 20 GLN Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain F residue 11 CYS Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain H residue 16 GLU Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 176 GLN Chi-restraints excluded: chain H residue 214 LYS Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain J residue 16 GLU Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain K residue 11 CYS Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 179 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 190 optimal weight: 1.9990 chunk 216 optimal weight: 3.9990 chunk 237 optimal weight: 3.9990 chunk 231 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 218 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 168 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 180 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 221AGLN ** E 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN F 176 GLN F 197 GLN ** G 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN H 197 GLN J 76 ASN J 197 GLN K 76 ASN K 176 GLN ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.103542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.062232 restraints weight = 40289.709| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 3.14 r_work: 0.2602 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2471 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21064 Z= 0.145 Angle : 0.669 8.935 28764 Z= 0.348 Chirality : 0.045 0.153 3220 Planarity : 0.006 0.061 3660 Dihedral : 5.026 23.172 2864 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.04 % Allowed : 17.83 % Favored : 79.13 % 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 (0.16), residues: 2640 helix: 0.06 (0.47), residues: 152 sheet: 0.72 (0.16), residues: 928 loop : -0.25 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 18 TYR 0.015 0.002 TYR K 181 PHE 0.017 0.001 PHE G 209 TRP 0.011 0.001 TRP B 215 HIS 0.003 0.001 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00338 (21016) covalent geometry : angle 0.65914 (28668) SS BOND : bond 0.00391 ( 48) SS BOND : angle 2.08305 ( 96) hydrogen bonds : bond 0.03057 ( 710) hydrogen bonds : angle 5.41162 ( 2016) *********************** 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 467 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 397 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 GLU cc_start: 0.9136 (tp30) cc_final: 0.8870 (tp30) REVERT: C 20 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8610 (pm20) REVERT: C 109 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8778 (mm-30) REVERT: D 20 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8635 (pm20) REVERT: D 109 GLU cc_start: 0.9101 (mm-30) cc_final: 0.8832 (mm-30) REVERT: E 33 LEU cc_start: 0.9726 (OUTLIER) cc_final: 0.9419 (tm) REVERT: E 50 GLU cc_start: 0.9318 (mt-10) cc_final: 0.8811 (mp0) REVERT: E 105 GLU cc_start: 0.7402 (mp0) cc_final: 0.7126 (mp0) REVERT: E 117 ILE cc_start: 0.8518 (tt) cc_final: 0.8295 (mm) REVERT: E 139 PHE cc_start: 0.8208 (p90) cc_final: 0.7815 (p90) REVERT: E 142 ARG cc_start: 0.9012 (ttm-80) cc_final: 0.8741 (mmt90) REVERT: E 167 ASP cc_start: 0.8462 (t0) cc_final: 0.8019 (t0) REVERT: E 210 ASN cc_start: 0.8602 (t0) cc_final: 0.8175 (p0) REVERT: F 3 GLN cc_start: 0.9125 (pt0) cc_final: 0.8599 (pm20) REVERT: F 6 GLU cc_start: 0.7841 (mp0) cc_final: 0.7004 (pm20) REVERT: F 26 ARG cc_start: 0.8191 (pmm-80) cc_final: 0.7550 (pmm-80) REVERT: F 27 PHE cc_start: 0.8556 (m-10) cc_final: 0.8312 (m-10) REVERT: F 72 ASP cc_start: 0.8842 (t0) cc_final: 0.8355 (t0) REVERT: F 105 GLN cc_start: 0.8374 (pm20) cc_final: 0.7748 (pm20) REVERT: F 148 ASP cc_start: 0.9049 (p0) cc_final: 0.8668 (p0) REVERT: F 152 GLU cc_start: 0.7523 (pm20) cc_final: 0.7113 (pm20) REVERT: G 33 LEU cc_start: 0.9723 (OUTLIER) cc_final: 0.9427 (tm) REVERT: G 50 GLU cc_start: 0.9338 (mt-10) cc_final: 0.8828 (mp0) REVERT: G 105 GLU cc_start: 0.7403 (mp0) cc_final: 0.7118 (mp0) REVERT: G 117 ILE cc_start: 0.8445 (tt) cc_final: 0.8232 (mm) REVERT: G 139 PHE cc_start: 0.8167 (p90) cc_final: 0.7893 (p90) REVERT: G 167 ASP cc_start: 0.8436 (t0) cc_final: 0.7978 (t0) REVERT: G 210 ASN cc_start: 0.8614 (t0) cc_final: 0.8231 (p0) REVERT: H 3 GLN cc_start: 0.9134 (pt0) cc_final: 0.8611 (pm20) REVERT: H 6 GLU cc_start: 0.7848 (mp0) cc_final: 0.7034 (pm20) REVERT: H 26 ARG cc_start: 0.8191 (pmm-80) cc_final: 0.7550 (pmm-80) REVERT: H 27 PHE cc_start: 0.8543 (m-10) cc_final: 0.8304 (m-10) REVERT: H 72 ASP cc_start: 0.8765 (t0) cc_final: 0.8435 (t0) REVERT: H 105 GLN cc_start: 0.8380 (pm20) cc_final: 0.7755 (pm20) REVERT: H 149 TYR cc_start: 0.8883 (p90) cc_final: 0.8575 (p90) REVERT: H 152 GLU cc_start: 0.7503 (pm20) cc_final: 0.7164 (pm20) REVERT: H 183 LEU cc_start: 0.9199 (tt) cc_final: 0.8671 (mt) REVERT: H 214 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7168 (ttpt) REVERT: I 33 LEU cc_start: 0.9726 (OUTLIER) cc_final: 0.9432 (tm) REVERT: I 50 GLU cc_start: 0.9228 (mt-10) cc_final: 0.8723 (mp0) REVERT: I 105 GLU cc_start: 0.7399 (mp0) cc_final: 0.7130 (mp0) REVERT: I 117 ILE cc_start: 0.8490 (tt) cc_final: 0.8268 (mm) REVERT: I 139 PHE cc_start: 0.8299 (p90) cc_final: 0.7969 (p90) REVERT: I 167 ASP cc_start: 0.8452 (t0) cc_final: 0.8007 (t0) REVERT: I 210 ASN cc_start: 0.8593 (t0) cc_final: 0.8176 (p0) REVERT: J 3 GLN cc_start: 0.9133 (pt0) cc_final: 0.8611 (pm20) REVERT: J 6 GLU cc_start: 0.7830 (mp0) cc_final: 0.7006 (pm20) REVERT: J 26 ARG cc_start: 0.8162 (pmm-80) cc_final: 0.7516 (pmm-80) REVERT: J 27 PHE cc_start: 0.8538 (m-10) cc_final: 0.8302 (m-10) REVERT: J 72 ASP cc_start: 0.8770 (t0) cc_final: 0.8443 (t0) REVERT: J 105 GLN cc_start: 0.8352 (pm20) cc_final: 0.7716 (pm20) REVERT: J 149 TYR cc_start: 0.8888 (p90) cc_final: 0.8541 (p90) REVERT: J 152 GLU cc_start: 0.7505 (pm20) cc_final: 0.7127 (pm20) REVERT: J 176 GLN cc_start: 0.8505 (mt0) cc_final: 0.8226 (mt0) REVERT: J 183 LEU cc_start: 0.9197 (tt) cc_final: 0.8671 (mt) REVERT: K 3 GLN cc_start: 0.9138 (pt0) cc_final: 0.8617 (pm20) REVERT: K 6 GLU cc_start: 0.7819 (mp0) cc_final: 0.6998 (pm20) REVERT: K 26 ARG cc_start: 0.8152 (pmm-80) cc_final: 0.7505 (pmm-80) REVERT: K 27 PHE cc_start: 0.8541 (m-10) cc_final: 0.8301 (m-10) REVERT: K 72 ASP cc_start: 0.8765 (t0) cc_final: 0.8439 (t0) REVERT: K 105 GLN cc_start: 0.8400 (pm20) cc_final: 0.7774 (pm20) REVERT: K 148 ASP cc_start: 0.9036 (p0) cc_final: 0.8686 (p0) REVERT: K 152 GLU cc_start: 0.7544 (pm20) cc_final: 0.7119 (pm20) REVERT: L 33 LEU cc_start: 0.9712 (OUTLIER) cc_final: 0.9416 (tm) REVERT: L 50 GLU cc_start: 0.9340 (mt-10) cc_final: 0.8826 (mp0) REVERT: L 81 GLU cc_start: 0.9031 (pm20) cc_final: 0.8733 (pm20) REVERT: L 105 GLU cc_start: 0.7401 (mp0) cc_final: 0.7113 (mp0) REVERT: L 117 ILE cc_start: 0.8480 (tt) cc_final: 0.8265 (mm) REVERT: L 139 PHE cc_start: 0.8212 (p90) cc_final: 0.7970 (p90) REVERT: L 167 ASP cc_start: 0.8469 (t0) cc_final: 0.8023 (t0) REVERT: L 210 ASN cc_start: 0.8640 (t0) cc_final: 0.8217 (p0) outliers start: 70 outliers final: 20 residues processed: 432 average time/residue: 0.5510 time to fit residues: 272.1712 Evaluate side-chains 402 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 375 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain D residue 20 GLN Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 171 CYS Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 176 GLN Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 171 CYS Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain H residue 214 LYS Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 171 CYS Chi-restraints excluded: chain J residue 11 CYS Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain K residue 176 GLN Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 171 CYS 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 152 optimal weight: 0.0470 chunk 204 optimal weight: 2.9990 chunk 214 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 250 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 219 optimal weight: 0.8980 chunk 259 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 249 optimal weight: 4.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN F 176 GLN ** G 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** I 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 ASN K 76 ASN K 176 GLN ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.103647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.062467 restraints weight = 40234.677| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 3.14 r_work: 0.2611 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2479 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21064 Z= 0.135 Angle : 0.675 9.099 28764 Z= 0.347 Chirality : 0.045 0.155 3220 Planarity : 0.006 0.061 3660 Dihedral : 4.921 22.291 2864 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.87 % Allowed : 18.70 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.21 (0.16), residues: 2640 helix: -0.02 (0.46), residues: 152 sheet: 0.75 (0.16), residues: 940 loop : -0.18 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 142 TYR 0.017 0.001 TYR F 181 PHE 0.013 0.001 PHE G 209 TRP 0.010 0.001 TRP D 215 HIS 0.003 0.001 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00315 (21016) covalent geometry : angle 0.66537 (28668) SS BOND : bond 0.00409 ( 48) SS BOND : angle 2.02696 ( 96) hydrogen bonds : bond 0.02972 ( 710) hydrogen bonds : angle 5.27468 ( 2016) *********************** 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 451 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 385 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 GLU cc_start: 0.9134 (tp30) cc_final: 0.8866 (tp30) REVERT: C 20 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8594 (pm20) REVERT: C 109 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8721 (mm-30) REVERT: D 20 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8604 (pm20) REVERT: D 109 GLU cc_start: 0.9135 (mm-30) cc_final: 0.8877 (mm-30) REVERT: E 33 LEU cc_start: 0.9725 (OUTLIER) cc_final: 0.9377 (tm) REVERT: E 50 GLU cc_start: 0.9316 (mt-10) cc_final: 0.8811 (mp0) REVERT: E 75 ILE cc_start: 0.9477 (mp) cc_final: 0.8853 (tp) REVERT: E 105 GLU cc_start: 0.7400 (mp0) cc_final: 0.7096 (mp0) REVERT: E 117 ILE cc_start: 0.8533 (tt) cc_final: 0.8306 (mm) REVERT: E 139 PHE cc_start: 0.8144 (p90) cc_final: 0.7730 (p90) REVERT: E 142 ARG cc_start: 0.8997 (ttm-80) cc_final: 0.8690 (mmt90) REVERT: E 167 ASP cc_start: 0.8473 (t0) cc_final: 0.8070 (t0) REVERT: E 185 ASP cc_start: 0.9352 (m-30) cc_final: 0.8602 (p0) REVERT: E 210 ASN cc_start: 0.8595 (t0) cc_final: 0.8159 (p0) REVERT: F 3 GLN cc_start: 0.9123 (pt0) cc_final: 0.8596 (pm20) REVERT: F 6 GLU cc_start: 0.7769 (mp0) cc_final: 0.6804 (pm20) REVERT: F 26 ARG cc_start: 0.8232 (pmm-80) cc_final: 0.7523 (pmm-80) REVERT: F 27 PHE cc_start: 0.8484 (m-10) cc_final: 0.8235 (m-10) REVERT: F 72 ASP cc_start: 0.8822 (t0) cc_final: 0.8286 (t0) REVERT: F 105 GLN cc_start: 0.8376 (pm20) cc_final: 0.7703 (pm20) REVERT: F 148 ASP cc_start: 0.9051 (p0) cc_final: 0.8690 (p0) REVERT: F 152 GLU cc_start: 0.7513 (pm20) cc_final: 0.7276 (pm20) REVERT: F 164 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9055 (pt) REVERT: F 176 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8131 (mp10) REVERT: G 23 CYS cc_start: 0.6929 (t) cc_final: 0.6626 (t) REVERT: G 33 LEU cc_start: 0.9728 (OUTLIER) cc_final: 0.9403 (tm) REVERT: G 50 GLU cc_start: 0.9324 (mt-10) cc_final: 0.8822 (mp0) REVERT: G 75 ILE cc_start: 0.9470 (mp) cc_final: 0.8837 (tp) REVERT: G 105 GLU cc_start: 0.7378 (mp0) cc_final: 0.7071 (mp0) REVERT: G 117 ILE cc_start: 0.8480 (tt) cc_final: 0.8258 (mm) REVERT: G 139 PHE cc_start: 0.8018 (p90) cc_final: 0.7698 (p90) REVERT: G 167 ASP cc_start: 0.8447 (t0) cc_final: 0.8026 (t0) REVERT: G 179 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9194 (tp) REVERT: G 185 ASP cc_start: 0.9342 (m-30) cc_final: 0.8651 (p0) REVERT: G 210 ASN cc_start: 0.8606 (t0) cc_final: 0.8184 (p0) REVERT: H 3 GLN cc_start: 0.9138 (pt0) cc_final: 0.8612 (pm20) REVERT: H 6 GLU cc_start: 0.7773 (mp0) cc_final: 0.6827 (pm20) REVERT: H 26 ARG cc_start: 0.8229 (pmm-80) cc_final: 0.7513 (pmm-80) REVERT: H 27 PHE cc_start: 0.8477 (m-10) cc_final: 0.8225 (m-10) REVERT: H 72 ASP cc_start: 0.8751 (t0) cc_final: 0.8409 (t0) REVERT: H 105 GLN cc_start: 0.8365 (pm20) cc_final: 0.7695 (pm20) REVERT: H 149 TYR cc_start: 0.8823 (p90) cc_final: 0.8514 (p90) REVERT: H 152 GLU cc_start: 0.7585 (pm20) cc_final: 0.7216 (pm20) REVERT: H 164 LEU cc_start: 0.9472 (mp) cc_final: 0.9059 (pt) REVERT: H 183 LEU cc_start: 0.9159 (tt) cc_final: 0.8638 (mt) REVERT: I 33 LEU cc_start: 0.9729 (OUTLIER) cc_final: 0.9415 (tm) REVERT: I 50 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8713 (mp0) REVERT: I 75 ILE cc_start: 0.9460 (mp) cc_final: 0.8856 (tp) REVERT: I 105 GLU cc_start: 0.7399 (mp0) cc_final: 0.7087 (mp0) REVERT: I 117 ILE cc_start: 0.8555 (tt) cc_final: 0.8325 (mm) REVERT: I 139 PHE cc_start: 0.8088 (p90) cc_final: 0.7803 (p90) REVERT: I 167 ASP cc_start: 0.8485 (t0) cc_final: 0.8076 (t0) REVERT: I 185 ASP cc_start: 0.9367 (m-30) cc_final: 0.8612 (p0) REVERT: I 210 ASN cc_start: 0.8588 (t0) cc_final: 0.8161 (p0) REVERT: J 3 GLN cc_start: 0.9118 (pt0) cc_final: 0.8592 (pm20) REVERT: J 6 GLU cc_start: 0.7756 (mp0) cc_final: 0.6803 (pm20) REVERT: J 26 ARG cc_start: 0.8197 (pmm-80) cc_final: 0.7479 (pmm-80) REVERT: J 27 PHE cc_start: 0.8464 (m-10) cc_final: 0.8215 (m-10) REVERT: J 72 ASP cc_start: 0.8753 (t0) cc_final: 0.8414 (t0) REVERT: J 105 GLN cc_start: 0.8361 (pm20) cc_final: 0.7690 (pm20) REVERT: J 149 TYR cc_start: 0.8836 (p90) cc_final: 0.8536 (p90) REVERT: J 152 GLU cc_start: 0.7594 (pm20) cc_final: 0.7232 (pm20) REVERT: J 164 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9057 (pt) REVERT: J 183 LEU cc_start: 0.9160 (tt) cc_final: 0.8651 (mt) REVERT: K 3 GLN cc_start: 0.9139 (pt0) cc_final: 0.8616 (pm20) REVERT: K 6 GLU cc_start: 0.7738 (mp0) cc_final: 0.6789 (pm20) REVERT: K 26 ARG cc_start: 0.8194 (pmm-80) cc_final: 0.7474 (pmm-80) REVERT: K 27 PHE cc_start: 0.8487 (m-10) cc_final: 0.8235 (m-10) REVERT: K 72 ASP cc_start: 0.8735 (t0) cc_final: 0.8391 (t0) REVERT: K 105 GLN cc_start: 0.8397 (pm20) cc_final: 0.7726 (pm20) REVERT: K 148 ASP cc_start: 0.9036 (p0) cc_final: 0.8650 (p0) REVERT: K 152 GLU cc_start: 0.7515 (pm20) cc_final: 0.7211 (pm20) REVERT: K 164 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9063 (pt) REVERT: L 23 CYS cc_start: 0.6993 (t) cc_final: 0.6726 (t) REVERT: L 33 LEU cc_start: 0.9718 (OUTLIER) cc_final: 0.9417 (tm) REVERT: L 50 GLU cc_start: 0.9334 (mt-10) cc_final: 0.8824 (mp0) REVERT: L 75 ILE cc_start: 0.9479 (mp) cc_final: 0.8760 (tp) REVERT: L 81 GLU cc_start: 0.9046 (pm20) cc_final: 0.8754 (pm20) REVERT: L 105 GLU cc_start: 0.7392 (mp0) cc_final: 0.7081 (mp0) REVERT: L 117 ILE cc_start: 0.8547 (tt) cc_final: 0.8321 (mm) REVERT: L 139 PHE cc_start: 0.8012 (p90) cc_final: 0.7704 (p90) REVERT: L 167 ASP cc_start: 0.8458 (t0) cc_final: 0.8010 (t0) REVERT: L 179 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9160 (tp) REVERT: L 185 ASP cc_start: 0.9350 (m-30) cc_final: 0.8637 (p0) REVERT: L 210 ASN cc_start: 0.8584 (t0) cc_final: 0.8257 (p0) outliers start: 66 outliers final: 32 residues processed: 418 average time/residue: 0.5611 time to fit residues: 268.7687 Evaluate side-chains 407 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 363 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 26 LYS Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain D residue 20 GLN Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 171 CYS Chi-restraints excluded: chain F residue 11 CYS Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 176 GLN Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 171 CYS Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 171 CYS Chi-restraints excluded: chain J residue 11 CYS Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain K residue 11 CYS Chi-restraints excluded: chain K residue 164 LEU Chi-restraints excluded: chain K residue 176 GLN Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 171 CYS Chi-restraints excluded: chain L residue 179 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 50 optimal weight: 0.9990 chunk 175 optimal weight: 0.7980 chunk 256 optimal weight: 5.9990 chunk 257 optimal weight: 0.6980 chunk 114 optimal weight: 9.9990 chunk 103 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 189 optimal weight: 4.9990 chunk 237 optimal weight: 0.2980 chunk 209 optimal weight: 5.9990 chunk 123 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 GLN ** G 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** I 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 ASN ** J 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 ASN ** K 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 GLN ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.103749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.062518 restraints weight = 40382.023| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 3.14 r_work: 0.2615 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21064 Z= 0.133 Angle : 0.672 11.780 28764 Z= 0.345 Chirality : 0.046 0.281 3220 Planarity : 0.005 0.062 3660 Dihedral : 4.834 21.368 2864 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.74 % Allowed : 19.04 % Favored : 78.22 % 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: 0.26 (0.16), residues: 2640 helix: -0.04 (0.45), residues: 152 sheet: 0.81 (0.16), residues: 948 loop : -0.15 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 18 TYR 0.015 0.001 TYR L 173 PHE 0.011 0.001 PHE I 139 TRP 0.009 0.001 TRP C 215 HIS 0.003 0.001 HIS B 173 Details of bonding type rmsd covalent geometry : bond 0.00309 (21016) covalent geometry : angle 0.66461 (28668) SS BOND : bond 0.00317 ( 48) SS BOND : angle 1.79210 ( 96) hydrogen bonds : bond 0.02913 ( 710) hydrogen bonds : angle 5.13953 ( 2016) *********************** 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 433 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 370 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 GLU cc_start: 0.8924 (tp30) cc_final: 0.8645 (tp30) REVERT: C 20 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8407 (pm20) REVERT: D 20 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8403 (pm20) REVERT: D 109 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8654 (mm-30) REVERT: E 23 CYS cc_start: 0.5956 (t) cc_final: 0.5687 (t) REVERT: E 33 LEU cc_start: 0.9705 (OUTLIER) cc_final: 0.9333 (tm) REVERT: E 50 GLU cc_start: 0.9098 (mt-10) cc_final: 0.8613 (mp0) REVERT: E 75 ILE cc_start: 0.9459 (mp) cc_final: 0.8857 (tp) REVERT: E 105 GLU cc_start: 0.7222 (mp0) cc_final: 0.6918 (mp0) REVERT: E 117 ILE cc_start: 0.8555 (tt) cc_final: 0.8324 (mm) REVERT: E 139 PHE cc_start: 0.8000 (p90) cc_final: 0.7764 (p90) REVERT: E 167 ASP cc_start: 0.8515 (t0) cc_final: 0.8136 (t0) REVERT: E 185 ASP cc_start: 0.9385 (m-30) cc_final: 0.8579 (p0) REVERT: E 210 ASN cc_start: 0.8639 (t0) cc_final: 0.8215 (p0) REVERT: F 3 GLN cc_start: 0.9099 (pt0) cc_final: 0.8599 (pm20) REVERT: F 6 GLU cc_start: 0.7537 (mp0) cc_final: 0.6517 (pm20) REVERT: F 26 ARG cc_start: 0.8202 (pmm-80) cc_final: 0.7581 (pmm-80) REVERT: F 72 ASP cc_start: 0.8794 (t0) cc_final: 0.8254 (t0) REVERT: F 105 GLN cc_start: 0.8219 (pm20) cc_final: 0.7676 (pm20) REVERT: F 148 ASP cc_start: 0.8980 (p0) cc_final: 0.8646 (p0) REVERT: F 152 GLU cc_start: 0.7584 (pm20) cc_final: 0.7235 (pm20) REVERT: F 164 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9064 (pt) REVERT: F 176 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8237 (mp10) REVERT: G 33 LEU cc_start: 0.9707 (OUTLIER) cc_final: 0.9356 (tm) REVERT: G 50 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8590 (mp0) REVERT: G 75 ILE cc_start: 0.9451 (mp) cc_final: 0.8849 (tp) REVERT: G 81 GLU cc_start: 0.8977 (pm20) cc_final: 0.8753 (pm20) REVERT: G 82 ASP cc_start: 0.8426 (m-30) cc_final: 0.8211 (m-30) REVERT: G 105 GLU cc_start: 0.7215 (mp0) cc_final: 0.6911 (mp0) REVERT: G 117 ILE cc_start: 0.8515 (tt) cc_final: 0.8291 (mm) REVERT: G 139 PHE cc_start: 0.7964 (p90) cc_final: 0.7715 (p90) REVERT: G 167 ASP cc_start: 0.8485 (t0) cc_final: 0.8112 (t0) REVERT: G 185 ASP cc_start: 0.9414 (m-30) cc_final: 0.8601 (p0) REVERT: G 186 TYR cc_start: 0.8835 (t80) cc_final: 0.8628 (t80) REVERT: G 210 ASN cc_start: 0.8625 (t0) cc_final: 0.8206 (p0) REVERT: H 3 GLN cc_start: 0.9104 (pt0) cc_final: 0.8577 (pm20) REVERT: H 6 GLU cc_start: 0.7577 (mp0) cc_final: 0.6563 (pm20) REVERT: H 26 ARG cc_start: 0.8212 (pmm-80) cc_final: 0.7395 (pmm-80) REVERT: H 72 ASP cc_start: 0.8701 (t0) cc_final: 0.8360 (t0) REVERT: H 105 GLN cc_start: 0.8208 (pm20) cc_final: 0.7670 (pm20) REVERT: H 149 TYR cc_start: 0.8727 (p90) cc_final: 0.8447 (p90) REVERT: H 152 GLU cc_start: 0.7549 (pm20) cc_final: 0.7127 (pm20) REVERT: H 164 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9072 (pt) REVERT: H 183 LEU cc_start: 0.9112 (tt) cc_final: 0.8624 (mt) REVERT: I 23 CYS cc_start: 0.6063 (t) cc_final: 0.5795 (t) REVERT: I 33 LEU cc_start: 0.9709 (OUTLIER) cc_final: 0.9366 (tm) REVERT: I 50 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8488 (mp0) REVERT: I 75 ILE cc_start: 0.9451 (mp) cc_final: 0.8863 (tp) REVERT: I 81 GLU cc_start: 0.9002 (pm20) cc_final: 0.8774 (pm20) REVERT: I 82 ASP cc_start: 0.8416 (m-30) cc_final: 0.8198 (m-30) REVERT: I 105 GLU cc_start: 0.7224 (mp0) cc_final: 0.6920 (mp0) REVERT: I 117 ILE cc_start: 0.8569 (tt) cc_final: 0.8339 (mm) REVERT: I 139 PHE cc_start: 0.7881 (p90) cc_final: 0.7634 (p90) REVERT: I 167 ASP cc_start: 0.8528 (t0) cc_final: 0.8138 (t0) REVERT: I 185 ASP cc_start: 0.9399 (m-30) cc_final: 0.8589 (p0) REVERT: I 186 TYR cc_start: 0.8847 (t80) cc_final: 0.8621 (t80) REVERT: I 210 ASN cc_start: 0.8576 (t0) cc_final: 0.8143 (p0) REVERT: J 3 GLN cc_start: 0.9107 (pt0) cc_final: 0.8602 (pm20) REVERT: J 6 GLU cc_start: 0.7527 (mp0) cc_final: 0.6517 (pm20) REVERT: J 26 ARG cc_start: 0.8178 (pmm-80) cc_final: 0.7552 (pmm-80) REVERT: J 72 ASP cc_start: 0.8698 (t0) cc_final: 0.8357 (t0) REVERT: J 105 GLN cc_start: 0.8207 (pm20) cc_final: 0.7664 (pm20) REVERT: J 149 TYR cc_start: 0.8721 (p90) cc_final: 0.8011 (p90) REVERT: J 152 GLU cc_start: 0.7546 (pm20) cc_final: 0.7117 (pm20) REVERT: J 164 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9067 (pt) REVERT: J 183 LEU cc_start: 0.9096 (tt) cc_final: 0.8712 (mt) REVERT: K 3 GLN cc_start: 0.9112 (pt0) cc_final: 0.8615 (pm20) REVERT: K 6 GLU cc_start: 0.7530 (mp0) cc_final: 0.6598 (pm20) REVERT: K 26 ARG cc_start: 0.8182 (pmm-80) cc_final: 0.7562 (pmm-80) REVERT: K 72 ASP cc_start: 0.8687 (t0) cc_final: 0.8344 (t0) REVERT: K 105 GLN cc_start: 0.8244 (pm20) cc_final: 0.7836 (pm20) REVERT: K 148 ASP cc_start: 0.8965 (p0) cc_final: 0.8574 (p0) REVERT: K 152 GLU cc_start: 0.7559 (pm20) cc_final: 0.7222 (pm20) REVERT: K 164 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9065 (pt) REVERT: K 176 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8069 (mp10) REVERT: L 23 CYS cc_start: 0.6044 (t) cc_final: 0.5731 (t) REVERT: L 33 LEU cc_start: 0.9693 (OUTLIER) cc_final: 0.9359 (tm) REVERT: L 50 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8609 (mp0) REVERT: L 81 GLU cc_start: 0.9044 (pm20) cc_final: 0.8728 (pm20) REVERT: L 105 GLU cc_start: 0.7216 (mp0) cc_final: 0.6913 (mp0) REVERT: L 117 ILE cc_start: 0.8564 (tt) cc_final: 0.8331 (mm) REVERT: L 139 PHE cc_start: 0.7981 (p90) cc_final: 0.7776 (p90) REVERT: L 167 ASP cc_start: 0.8520 (t0) cc_final: 0.8130 (t0) REVERT: L 185 ASP cc_start: 0.9417 (m-30) cc_final: 0.8642 (p0) REVERT: L 210 ASN cc_start: 0.8659 (t0) cc_final: 0.8219 (p0) outliers start: 63 outliers final: 25 residues processed: 404 average time/residue: 0.6136 time to fit residues: 281.6689 Evaluate side-chains 390 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 353 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain D residue 20 GLN Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 171 CYS Chi-restraints excluded: chain F residue 11 CYS Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 176 GLN Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 171 CYS Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 171 CYS Chi-restraints excluded: chain J residue 11 CYS Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain K residue 11 CYS Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 164 LEU Chi-restraints excluded: chain K residue 176 GLN Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 171 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 115 optimal weight: 1.9990 chunk 258 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 126 optimal weight: 3.9990 chunk 8 optimal weight: 0.0170 chunk 101 optimal weight: 0.0980 chunk 152 optimal weight: 0.7980 chunk 187 optimal weight: 0.7980 chunk 151 optimal weight: 6.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 GLN ** G 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 ASN ** K 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 GLN ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.104326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.063176 restraints weight = 40088.011| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 3.14 r_work: 0.2631 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21064 Z= 0.120 Angle : 0.663 11.621 28764 Z= 0.340 Chirality : 0.045 0.236 3220 Planarity : 0.005 0.062 3660 Dihedral : 4.739 20.658 2864 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.04 % Allowed : 20.39 % Favored : 77.57 % 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: 0.39 (0.16), residues: 2640 helix: 0.49 (0.48), residues: 128 sheet: 0.88 (0.16), residues: 948 loop : -0.10 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 18 TYR 0.017 0.001 TYR G 173 PHE 0.026 0.001 PHE J 27 TRP 0.009 0.001 TRP C 215 HIS 0.003 0.001 HIS B 173 Details of bonding type rmsd covalent geometry : bond 0.00277 (21016) covalent geometry : angle 0.65766 (28668) SS BOND : bond 0.00312 ( 48) SS BOND : angle 1.56870 ( 96) hydrogen bonds : bond 0.02775 ( 710) hydrogen bonds : angle 5.03212 ( 2016) *********************** 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 413 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 366 time to evaluate : 0.841 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: B 109 GLU cc_start: 0.8912 (tp30) cc_final: 0.8633 (tp30) REVERT: C 20 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8394 (pm20) REVERT: D 20 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8404 (pm20) REVERT: D 109 GLU cc_start: 0.8911 (mm-30) cc_final: 0.8652 (mm-30) REVERT: E 33 LEU cc_start: 0.9706 (OUTLIER) cc_final: 0.9343 (tm) REVERT: E 50 GLU cc_start: 0.9112 (mt-10) cc_final: 0.8628 (mp0) REVERT: E 75 ILE cc_start: 0.9447 (mp) cc_final: 0.8849 (tp) REVERT: E 81 GLU cc_start: 0.8976 (pm20) cc_final: 0.8742 (pm20) REVERT: E 82 ASP cc_start: 0.8399 (m-30) cc_final: 0.8150 (m-30) REVERT: E 105 GLU cc_start: 0.7229 (mp0) cc_final: 0.6927 (mp0) REVERT: E 139 PHE cc_start: 0.7947 (p90) cc_final: 0.7747 (p90) REVERT: E 167 ASP cc_start: 0.8565 (t0) cc_final: 0.8186 (t0) REVERT: E 210 ASN cc_start: 0.8627 (t0) cc_final: 0.8186 (p0) REVERT: F 3 GLN cc_start: 0.9069 (pt0) cc_final: 0.8572 (pm20) REVERT: F 6 GLU cc_start: 0.7543 (mp0) cc_final: 0.6495 (pm20) REVERT: F 26 ARG cc_start: 0.8227 (pmm-80) cc_final: 0.7572 (pmm-80) REVERT: F 27 PHE cc_start: 0.8295 (m-10) cc_final: 0.8017 (m-80) REVERT: F 72 ASP cc_start: 0.8790 (t0) cc_final: 0.8248 (t0) REVERT: F 105 GLN cc_start: 0.8180 (pm20) cc_final: 0.7736 (pm20) REVERT: F 148 ASP cc_start: 0.8976 (p0) cc_final: 0.8642 (p0) REVERT: F 152 GLU cc_start: 0.7560 (pm20) cc_final: 0.6997 (pm20) REVERT: F 176 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8415 (mp10) REVERT: G 33 LEU cc_start: 0.9710 (OUTLIER) cc_final: 0.9346 (tm) REVERT: G 50 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8614 (mp0) REVERT: G 75 ILE cc_start: 0.9439 (mp) cc_final: 0.8841 (tp) REVERT: G 81 GLU cc_start: 0.8967 (pm20) cc_final: 0.8736 (pm20) REVERT: G 82 ASP cc_start: 0.8539 (m-30) cc_final: 0.8290 (m-30) REVERT: G 105 GLU cc_start: 0.7227 (mp0) cc_final: 0.6925 (mp0) REVERT: G 117 ILE cc_start: 0.8557 (tt) cc_final: 0.8353 (mm) REVERT: G 139 PHE cc_start: 0.7906 (p90) cc_final: 0.7701 (p90) REVERT: G 167 ASP cc_start: 0.8574 (t0) cc_final: 0.8184 (t0) REVERT: G 210 ASN cc_start: 0.8661 (t0) cc_final: 0.8240 (p0) REVERT: H 3 GLN cc_start: 0.9030 (pt0) cc_final: 0.8548 (pm20) REVERT: H 6 GLU cc_start: 0.7578 (mp0) cc_final: 0.6580 (pm20) REVERT: H 26 ARG cc_start: 0.8222 (pmm-80) cc_final: 0.7566 (pmm-80) REVERT: H 27 PHE cc_start: 0.8264 (m-10) cc_final: 0.7986 (m-80) REVERT: H 72 ASP cc_start: 0.8684 (t0) cc_final: 0.8339 (t0) REVERT: H 105 GLN cc_start: 0.8173 (pm20) cc_final: 0.7728 (pm20) REVERT: H 149 TYR cc_start: 0.8714 (p90) cc_final: 0.8083 (p90) REVERT: H 152 GLU cc_start: 0.7451 (pm20) cc_final: 0.7045 (pm20) REVERT: H 183 LEU cc_start: 0.9031 (tt) cc_final: 0.8646 (mt) REVERT: I 33 LEU cc_start: 0.9710 (OUTLIER) cc_final: 0.9363 (tm) REVERT: I 50 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8514 (mp0) REVERT: I 75 ILE cc_start: 0.9440 (mp) cc_final: 0.8861 (tp) REVERT: I 81 GLU cc_start: 0.8971 (pm20) cc_final: 0.8734 (pm20) REVERT: I 82 ASP cc_start: 0.8530 (m-30) cc_final: 0.8277 (m-30) REVERT: I 105 GLU cc_start: 0.7242 (mp0) cc_final: 0.6936 (mp0) REVERT: I 117 ILE cc_start: 0.8598 (tt) cc_final: 0.8387 (mm) REVERT: I 139 PHE cc_start: 0.7867 (p90) cc_final: 0.7617 (p90) REVERT: I 167 ASP cc_start: 0.8604 (t0) cc_final: 0.8217 (t0) REVERT: I 210 ASN cc_start: 0.8635 (t0) cc_final: 0.8206 (p0) REVERT: J 3 GLN cc_start: 0.9061 (pt0) cc_final: 0.8574 (pm20) REVERT: J 6 GLU cc_start: 0.7534 (mp0) cc_final: 0.6501 (pm20) REVERT: J 26 ARG cc_start: 0.8194 (pmm-80) cc_final: 0.7535 (pmm-80) REVERT: J 27 PHE cc_start: 0.8267 (m-10) cc_final: 0.7989 (m-80) REVERT: J 72 ASP cc_start: 0.8681 (t0) cc_final: 0.8336 (t0) REVERT: J 105 GLN cc_start: 0.8185 (pm20) cc_final: 0.7739 (pm20) REVERT: J 149 TYR cc_start: 0.8720 (p90) cc_final: 0.8056 (p90) REVERT: J 152 GLU cc_start: 0.7449 (pm20) cc_final: 0.7039 (pm20) REVERT: J 176 GLN cc_start: 0.8538 (mt0) cc_final: 0.8241 (mp10) REVERT: J 183 LEU cc_start: 0.9035 (tt) cc_final: 0.8660 (mt) REVERT: K 3 GLN cc_start: 0.9038 (pt0) cc_final: 0.8556 (pm20) REVERT: K 6 GLU cc_start: 0.7541 (mp0) cc_final: 0.6510 (pm20) REVERT: K 26 ARG cc_start: 0.8205 (pmm-80) cc_final: 0.7558 (pmm-80) REVERT: K 27 PHE cc_start: 0.8279 (m-10) cc_final: 0.8006 (m-80) REVERT: K 72 ASP cc_start: 0.8678 (t0) cc_final: 0.8332 (t0) REVERT: K 105 GLN cc_start: 0.8215 (pm20) cc_final: 0.7771 (pm20) REVERT: K 148 ASP cc_start: 0.8978 (p0) cc_final: 0.8586 (p0) REVERT: K 152 GLU cc_start: 0.7512 (pm20) cc_final: 0.6968 (pm20) REVERT: K 176 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8157 (mp10) REVERT: L 33 LEU cc_start: 0.9698 (OUTLIER) cc_final: 0.9362 (tm) REVERT: L 50 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8631 (mp0) REVERT: L 75 ILE cc_start: 0.9488 (mp) cc_final: 0.8905 (tp) REVERT: L 81 GLU cc_start: 0.9045 (pm20) cc_final: 0.8726 (pm20) REVERT: L 105 GLU cc_start: 0.7230 (mp0) cc_final: 0.6924 (mp0) REVERT: L 117 ILE cc_start: 0.8605 (tt) cc_final: 0.8382 (mm) REVERT: L 139 PHE cc_start: 0.7984 (p90) cc_final: 0.7783 (p90) REVERT: L 167 ASP cc_start: 0.8582 (t0) cc_final: 0.8196 (t0) REVERT: L 185 ASP cc_start: 0.9414 (m-30) cc_final: 0.8636 (p0) REVERT: L 210 ASN cc_start: 0.8679 (t0) cc_final: 0.8239 (p0) outliers start: 47 outliers final: 17 residues processed: 394 average time/residue: 0.5682 time to fit residues: 255.9207 Evaluate side-chains 384 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 359 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain D residue 20 GLN Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 171 CYS Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 176 GLN Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 171 CYS Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 171 CYS Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 176 GLN Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 171 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 217 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 137 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 248 optimal weight: 0.0670 chunk 225 optimal weight: 0.4980 chunk 199 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 GLN ** G 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** I 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 ASN ** J 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 GLN ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.104310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.063260 restraints weight = 39982.659| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 3.13 r_work: 0.2634 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21064 Z= 0.126 Angle : 0.664 9.828 28764 Z= 0.343 Chirality : 0.045 0.211 3220 Planarity : 0.005 0.062 3660 Dihedral : 4.671 20.310 2864 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.96 % Allowed : 20.74 % 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: 0.38 (0.16), residues: 2640 helix: 0.47 (0.49), residues: 128 sheet: 0.91 (0.16), residues: 944 loop : -0.13 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 18 TYR 0.024 0.001 TYR E 173 PHE 0.021 0.001 PHE K 27 TRP 0.011 0.001 TRP F 159 HIS 0.003 0.001 HIS B 173 Details of bonding type rmsd covalent geometry : bond 0.00292 (21016) covalent geometry : angle 0.65968 (28668) SS BOND : bond 0.00326 ( 48) SS BOND : angle 1.50443 ( 96) hydrogen bonds : bond 0.02775 ( 710) hydrogen bonds : angle 4.98282 ( 2016) *********************** 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 426 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 381 time to evaluate : 0.791 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: B 109 GLU cc_start: 0.8911 (tp30) cc_final: 0.8639 (tp30) REVERT: C 20 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8426 (pm20) REVERT: D 20 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8400 (pm20) REVERT: D 109 GLU cc_start: 0.8922 (mm-30) cc_final: 0.8673 (mm-30) REVERT: E 17 ASP cc_start: 0.8234 (t0) cc_final: 0.8017 (t0) REVERT: E 33 LEU cc_start: 0.9706 (OUTLIER) cc_final: 0.9346 (tm) REVERT: E 50 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8665 (mp0) REVERT: E 81 GLU cc_start: 0.8974 (pm20) cc_final: 0.8736 (pm20) REVERT: E 82 ASP cc_start: 0.8540 (m-30) cc_final: 0.8275 (m-30) REVERT: E 105 GLU cc_start: 0.7269 (mp0) cc_final: 0.6956 (mp0) REVERT: E 167 ASP cc_start: 0.8576 (t0) cc_final: 0.8190 (t0) REVERT: E 185 ASP cc_start: 0.9370 (m-30) cc_final: 0.8975 (p0) REVERT: E 210 ASN cc_start: 0.8697 (t0) cc_final: 0.8210 (p0) REVERT: F 3 GLN cc_start: 0.9073 (pt0) cc_final: 0.8572 (pm20) REVERT: F 6 GLU cc_start: 0.7522 (mp0) cc_final: 0.6493 (pm20) REVERT: F 26 ARG cc_start: 0.8176 (pmm-80) cc_final: 0.7489 (pmm-80) REVERT: F 27 PHE cc_start: 0.8262 (m-10) cc_final: 0.7967 (m-80) REVERT: F 72 ASP cc_start: 0.8778 (t0) cc_final: 0.8238 (t0) REVERT: F 105 GLN cc_start: 0.8154 (pm20) cc_final: 0.7702 (pm20) REVERT: F 148 ASP cc_start: 0.8983 (p0) cc_final: 0.8651 (p0) REVERT: F 176 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8435 (mp10) REVERT: G 33 LEU cc_start: 0.9714 (OUTLIER) cc_final: 0.9342 (tm) REVERT: G 50 GLU cc_start: 0.9120 (mt-10) cc_final: 0.8661 (mp0) REVERT: G 75 ILE cc_start: 0.9442 (mp) cc_final: 0.8822 (tp) REVERT: G 81 GLU cc_start: 0.8968 (pm20) cc_final: 0.8731 (pm20) REVERT: G 82 ASP cc_start: 0.8573 (m-30) cc_final: 0.8301 (m-30) REVERT: G 105 GLU cc_start: 0.7264 (mp0) cc_final: 0.6951 (mp0) REVERT: G 139 PHE cc_start: 0.7924 (p90) cc_final: 0.7714 (p90) REVERT: G 167 ASP cc_start: 0.8589 (t0) cc_final: 0.8187 (t0) REVERT: G 210 ASN cc_start: 0.8708 (t0) cc_final: 0.8249 (p0) REVERT: H 3 GLN cc_start: 0.9078 (pt0) cc_final: 0.8587 (pm20) REVERT: H 6 GLU cc_start: 0.7569 (mp0) cc_final: 0.6543 (pm20) REVERT: H 26 ARG cc_start: 0.8190 (pmm-80) cc_final: 0.7512 (pmm-80) REVERT: H 27 PHE cc_start: 0.8216 (m-10) cc_final: 0.7919 (m-80) REVERT: H 72 ASP cc_start: 0.8692 (t0) cc_final: 0.8348 (t0) REVERT: H 105 GLN cc_start: 0.8157 (pm20) cc_final: 0.7711 (pm20) REVERT: H 149 TYR cc_start: 0.8741 (p90) cc_final: 0.8103 (p90) REVERT: H 152 GLU cc_start: 0.7510 (pm20) cc_final: 0.7065 (pm20) REVERT: H 183 LEU cc_start: 0.9026 (tt) cc_final: 0.8640 (mt) REVERT: I 17 ASP cc_start: 0.8239 (t0) cc_final: 0.8023 (t0) REVERT: I 33 LEU cc_start: 0.9710 (OUTLIER) cc_final: 0.9359 (tm) REVERT: I 50 GLU cc_start: 0.9000 (mt-10) cc_final: 0.8560 (mp0) REVERT: I 75 ILE cc_start: 0.9441 (mp) cc_final: 0.8858 (tp) REVERT: I 81 GLU cc_start: 0.8975 (pm20) cc_final: 0.8733 (pm20) REVERT: I 82 ASP cc_start: 0.8551 (m-30) cc_final: 0.8253 (m-30) REVERT: I 105 GLU cc_start: 0.7257 (mp0) cc_final: 0.6956 (mp0) REVERT: I 139 PHE cc_start: 0.7922 (p90) cc_final: 0.7645 (p90) REVERT: I 167 ASP cc_start: 0.8625 (t0) cc_final: 0.8222 (t0) REVERT: I 185 ASP cc_start: 0.9359 (m-30) cc_final: 0.8941 (p0) REVERT: I 210 ASN cc_start: 0.8698 (t0) cc_final: 0.8228 (p0) REVERT: J 3 GLN cc_start: 0.9078 (pt0) cc_final: 0.8584 (pm20) REVERT: J 6 GLU cc_start: 0.7521 (mp0) cc_final: 0.6509 (pm20) REVERT: J 26 ARG cc_start: 0.8155 (pmm-80) cc_final: 0.7480 (pmm-80) REVERT: J 27 PHE cc_start: 0.8246 (m-10) cc_final: 0.7952 (m-80) REVERT: J 72 ASP cc_start: 0.8679 (t0) cc_final: 0.8331 (t0) REVERT: J 105 GLN cc_start: 0.8174 (pm20) cc_final: 0.7722 (pm20) REVERT: J 149 TYR cc_start: 0.8742 (p90) cc_final: 0.8105 (p90) REVERT: J 152 GLU cc_start: 0.7510 (pm20) cc_final: 0.7066 (pm20) REVERT: J 183 LEU cc_start: 0.9029 (tt) cc_final: 0.8642 (mt) REVERT: K 3 GLN cc_start: 0.9083 (pt0) cc_final: 0.8593 (pm20) REVERT: K 6 GLU cc_start: 0.7516 (mp0) cc_final: 0.6507 (pm20) REVERT: K 26 ARG cc_start: 0.8160 (pmm-80) cc_final: 0.7485 (pmm-80) REVERT: K 27 PHE cc_start: 0.8216 (m-10) cc_final: 0.7921 (m-80) REVERT: K 72 ASP cc_start: 0.8663 (t0) cc_final: 0.8313 (t0) REVERT: K 105 GLN cc_start: 0.8189 (pm20) cc_final: 0.7741 (pm20) REVERT: K 148 ASP cc_start: 0.8958 (p0) cc_final: 0.8564 (p0) REVERT: K 176 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8144 (mp10) REVERT: L 33 LEU cc_start: 0.9695 (OUTLIER) cc_final: 0.9351 (tm) REVERT: L 50 GLU cc_start: 0.9137 (mt-10) cc_final: 0.8678 (mp0) REVERT: L 75 ILE cc_start: 0.9484 (mp) cc_final: 0.8868 (tp) REVERT: L 81 GLU cc_start: 0.9056 (pm20) cc_final: 0.8736 (pm20) REVERT: L 105 GLU cc_start: 0.7214 (mp0) cc_final: 0.6922 (mp0) REVERT: L 117 ILE cc_start: 0.8616 (tt) cc_final: 0.8416 (mm) REVERT: L 139 PHE cc_start: 0.7988 (p90) cc_final: 0.7785 (p90) REVERT: L 167 ASP cc_start: 0.8610 (t0) cc_final: 0.8212 (t0) REVERT: L 210 ASN cc_start: 0.8718 (t0) cc_final: 0.8234 (p0) outliers start: 45 outliers final: 22 residues processed: 408 average time/residue: 0.5532 time to fit residues: 258.9924 Evaluate side-chains 397 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 367 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain D residue 20 GLN Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 171 CYS Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 176 GLN Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 171 CYS Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 171 CYS Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 176 GLN Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 171 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 37 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 256 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 224 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 64 optimal weight: 0.0970 chunk 27 optimal weight: 0.2980 chunk 255 optimal weight: 3.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 GLN ** G 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 ASN ** K 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 GLN ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.104431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.063200 restraints weight = 40344.703| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 3.16 r_work: 0.2639 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21064 Z= 0.133 Angle : 0.689 10.751 28764 Z= 0.353 Chirality : 0.045 0.170 3220 Planarity : 0.005 0.063 3660 Dihedral : 4.695 22.050 2864 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.57 % Allowed : 22.04 % Favored : 76.39 % 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: 0.34 (0.16), residues: 2640 helix: 0.40 (0.48), residues: 128 sheet: 0.90 (0.16), residues: 944 loop : -0.16 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG E 142 TYR 0.019 0.001 TYR G 173 PHE 0.020 0.001 PHE F 27 TRP 0.012 0.001 TRP F 159 HIS 0.002 0.000 HIS B 173 Details of bonding type rmsd covalent geometry : bond 0.00308 (21016) covalent geometry : angle 0.68321 (28668) SS BOND : bond 0.00341 ( 48) SS BOND : angle 1.63019 ( 96) hydrogen bonds : bond 0.02791 ( 710) hydrogen bonds : angle 4.96059 ( 2016) ********************** 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 415 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 379 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 GLU cc_start: 0.8928 (tp30) cc_final: 0.8652 (tp30) REVERT: C 20 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8450 (pm20) REVERT: D 20 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8420 (pm20) REVERT: D 109 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8679 (mm-30) REVERT: E 33 LEU cc_start: 0.9710 (OUTLIER) cc_final: 0.9344 (tm) REVERT: E 50 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8672 (mp0) REVERT: E 75 ILE cc_start: 0.9490 (mp) cc_final: 0.8964 (tp) REVERT: E 81 GLU cc_start: 0.8967 (pm20) cc_final: 0.8677 (pm20) REVERT: E 82 ASP cc_start: 0.8566 (m-30) cc_final: 0.8290 (m-30) REVERT: E 105 GLU cc_start: 0.7308 (mp0) cc_final: 0.7002 (mp0) REVERT: E 167 ASP cc_start: 0.8628 (t0) cc_final: 0.8362 (t0) REVERT: E 173 TYR cc_start: 0.6607 (p90) cc_final: 0.6019 (p90) REVERT: E 210 ASN cc_start: 0.8708 (t0) cc_final: 0.8222 (p0) REVERT: F 3 GLN cc_start: 0.9090 (pt0) cc_final: 0.8586 (pm20) REVERT: F 6 GLU cc_start: 0.7511 (mp0) cc_final: 0.6503 (pm20) REVERT: F 26 ARG cc_start: 0.8188 (pmm-80) cc_final: 0.7494 (pmm-80) REVERT: F 27 PHE cc_start: 0.8207 (m-10) cc_final: 0.7918 (m-80) REVERT: F 72 ASP cc_start: 0.8796 (t0) cc_final: 0.8260 (t0) REVERT: F 105 GLN cc_start: 0.8144 (pm20) cc_final: 0.7690 (pm20) REVERT: F 148 ASP cc_start: 0.8931 (p0) cc_final: 0.8617 (p0) REVERT: F 152 GLU cc_start: 0.7758 (pm20) cc_final: 0.7375 (pm20) REVERT: F 176 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8468 (mp10) REVERT: G 33 LEU cc_start: 0.9714 (OUTLIER) cc_final: 0.9344 (tm) REVERT: G 50 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8646 (mp0) REVERT: G 81 GLU cc_start: 0.8964 (pm20) cc_final: 0.8672 (pm20) REVERT: G 82 ASP cc_start: 0.8572 (m-30) cc_final: 0.8269 (m-30) REVERT: G 105 GLU cc_start: 0.7320 (mp0) cc_final: 0.7010 (mp0) REVERT: G 167 ASP cc_start: 0.8625 (t0) cc_final: 0.8360 (t0) REVERT: G 185 ASP cc_start: 0.9352 (m-30) cc_final: 0.8982 (p0) REVERT: G 210 ASN cc_start: 0.8725 (t0) cc_final: 0.8281 (p0) REVERT: H 3 GLN cc_start: 0.9089 (pt0) cc_final: 0.8598 (pm20) REVERT: H 6 GLU cc_start: 0.7575 (mp0) cc_final: 0.6536 (pm20) REVERT: H 26 ARG cc_start: 0.8176 (pmm-80) cc_final: 0.7484 (pmm-80) REVERT: H 27 PHE cc_start: 0.8139 (m-10) cc_final: 0.7830 (m-80) REVERT: H 72 ASP cc_start: 0.8680 (t0) cc_final: 0.8333 (t0) REVERT: H 105 GLN cc_start: 0.8142 (pm20) cc_final: 0.7693 (pm20) REVERT: H 149 TYR cc_start: 0.8714 (p90) cc_final: 0.8068 (p90) REVERT: H 152 GLU cc_start: 0.7513 (pm20) cc_final: 0.7024 (pm20) REVERT: H 183 LEU cc_start: 0.9027 (tt) cc_final: 0.8617 (mt) REVERT: I 33 LEU cc_start: 0.9715 (OUTLIER) cc_final: 0.9351 (tm) REVERT: I 50 GLU cc_start: 0.8992 (mt-10) cc_final: 0.8556 (mp0) REVERT: I 75 ILE cc_start: 0.9438 (mp) cc_final: 0.8829 (tp) REVERT: I 81 GLU cc_start: 0.8973 (pm20) cc_final: 0.8676 (pm20) REVERT: I 82 ASP cc_start: 0.8560 (m-30) cc_final: 0.8252 (m-30) REVERT: I 105 GLU cc_start: 0.7311 (mp0) cc_final: 0.7010 (mp0) REVERT: I 139 PHE cc_start: 0.7904 (p90) cc_final: 0.7659 (p90) REVERT: I 167 ASP cc_start: 0.8685 (t0) cc_final: 0.8418 (t0) REVERT: I 210 ASN cc_start: 0.8717 (t0) cc_final: 0.8262 (p0) REVERT: J 3 GLN cc_start: 0.9089 (pt0) cc_final: 0.8613 (pm20) REVERT: J 6 GLU cc_start: 0.7522 (mp0) cc_final: 0.6529 (pm20) REVERT: J 26 ARG cc_start: 0.8170 (pmm-80) cc_final: 0.7476 (pmm-80) REVERT: J 27 PHE cc_start: 0.8184 (m-10) cc_final: 0.7888 (m-80) REVERT: J 72 ASP cc_start: 0.8670 (t0) cc_final: 0.8093 (t0) REVERT: J 75 LYS cc_start: 0.9452 (mttt) cc_final: 0.9246 (mttt) REVERT: J 105 GLN cc_start: 0.8157 (pm20) cc_final: 0.7699 (pm20) REVERT: J 148 ASP cc_start: 0.9106 (m-30) cc_final: 0.8844 (p0) REVERT: J 152 GLU cc_start: 0.7505 (pm20) cc_final: 0.7036 (pm20) REVERT: J 206 LYS cc_start: 0.9314 (mmpt) cc_final: 0.9009 (mmmm) REVERT: K 3 GLN cc_start: 0.9105 (pt0) cc_final: 0.8612 (pm20) REVERT: K 6 GLU cc_start: 0.7521 (mp0) cc_final: 0.6498 (pm20) REVERT: K 26 ARG cc_start: 0.8135 (pmm-80) cc_final: 0.7444 (pmm-80) REVERT: K 27 PHE cc_start: 0.8168 (m-10) cc_final: 0.7859 (m-80) REVERT: K 72 ASP cc_start: 0.8687 (t0) cc_final: 0.8340 (t0) REVERT: K 105 GLN cc_start: 0.8178 (pm20) cc_final: 0.7728 (pm20) REVERT: K 148 ASP cc_start: 0.8938 (p0) cc_final: 0.8570 (p0) REVERT: K 152 GLU cc_start: 0.7776 (pm20) cc_final: 0.7383 (pm20) REVERT: K 176 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8423 (mp10) REVERT: L 33 LEU cc_start: 0.9698 (OUTLIER) cc_final: 0.9350 (tm) REVERT: L 50 GLU cc_start: 0.9126 (mt-10) cc_final: 0.8667 (mp0) REVERT: L 75 ILE cc_start: 0.9471 (mp) cc_final: 0.8855 (tp) REVERT: L 81 GLU cc_start: 0.9055 (pm20) cc_final: 0.8698 (pm20) REVERT: L 105 GLU cc_start: 0.7274 (mp0) cc_final: 0.6982 (mp0) REVERT: L 117 ILE cc_start: 0.8611 (tt) cc_final: 0.8410 (mm) REVERT: L 139 PHE cc_start: 0.7993 (p90) cc_final: 0.7759 (p90) REVERT: L 167 ASP cc_start: 0.8643 (t0) cc_final: 0.8364 (t0) REVERT: L 185 ASP cc_start: 0.9350 (m-30) cc_final: 0.8950 (p0) REVERT: L 210 ASN cc_start: 0.8741 (t0) cc_final: 0.8272 (p0) outliers start: 36 outliers final: 20 residues processed: 405 average time/residue: 0.6207 time to fit residues: 286.6639 Evaluate side-chains 396 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 368 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain D residue 20 GLN Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 171 CYS Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 176 GLN Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 171 CYS Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 171 CYS Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 176 GLN Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 171 CYS Chi-restraints excluded: chain L residue 179 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 3.9990 chunk 214 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 142 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 250 optimal weight: 4.9990 chunk 146 optimal weight: 0.9990 chunk 164 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 259 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 GLN ** G 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 GLN ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.103169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.062091 restraints weight = 40333.024| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 3.13 r_work: 0.2616 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2488 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21064 Z= 0.160 Angle : 0.708 10.269 28764 Z= 0.364 Chirality : 0.046 0.152 3220 Planarity : 0.006 0.063 3660 Dihedral : 4.824 22.601 2864 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.74 % Allowed : 21.87 % Favored : 76.39 % 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 (0.16), residues: 2640 helix: 0.23 (0.49), residues: 128 sheet: 0.85 (0.16), residues: 948 loop : -0.17 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 18 TYR 0.019 0.001 TYR G 173 PHE 0.019 0.001 PHE F 27 TRP 0.013 0.001 TRP K 159 HIS 0.003 0.001 HIS B 173 Details of bonding type rmsd covalent geometry : bond 0.00380 (21016) covalent geometry : angle 0.70291 (28668) SS BOND : bond 0.00366 ( 48) SS BOND : angle 1.63183 ( 96) hydrogen bonds : bond 0.02841 ( 710) hydrogen bonds : angle 5.00216 ( 2016) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9744.02 seconds wall clock time: 166 minutes 17.60 seconds (9977.60 seconds total)