Starting phenix.real_space_refine on Wed Jun 18 01:15:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vgj_43202/06_2025/8vgj_43202.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vgj_43202/06_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_43202/06_2025/8vgj_43202.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vgj_43202/06_2025/8vgj_43202.map" model { file = "/net/cci-nas-00/data/ceres_data/8vgj_43202/06_2025/8vgj_43202.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vgj_43202/06_2025/8vgj_43202.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.009 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.16, per 1000 atoms: 0.69 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: 5.26 Conformation dependent library (CDL) restraints added in 2.9 seconds 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4912 Finding SS restraints... Secondary structure from input PDB file: 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: 3.97 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: 8.39 Time building geometry restraints manager: 6.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 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: 0.14 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: 6.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.810 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 52.620 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:15.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.160 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (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 TRP 0.039 0.006 TRP B 141 HIS 0.019 0.005 HIS A 173 PHE 0.027 0.007 PHE I 116 TYR 0.047 0.006 TYR B 95 ARG 0.032 0.004 ARG D 69 Details of bonding type rmsd hydrogen bonds : bond 0.21597 ( 710) hydrogen bonds : angle 9.13738 ( 2016) SS BOND : bond 0.01136 ( 48) SS BOND : angle 2.45950 ( 96) covalent geometry : bond 0.01128 (21016) covalent geometry : angle 1.20307 (28668) *********************** 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 : 2.075 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: 0.8798 (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: 1.4871 time to fit residues: 985.0048 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 : 2.729 ------------------------------------------------------------------------------- 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 222 optimal weight: 2.9990 chunk 200 optimal weight: 20.0000 chunk 111 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 206 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 chunk 239 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 147 GLN I 158 ASN ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 169 HIS K 169 HIS L 79 GLN L 158 ASN ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.102266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.060551 restraints weight = 40847.694| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 3.17 r_work: 0.2561 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 21064 Z= 0.284 Angle : 0.803 9.723 28764 Z= 0.425 Chirality : 0.051 0.160 3220 Planarity : 0.005 0.049 3660 Dihedral : 6.345 103.180 2866 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.52 % Allowed : 14.17 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.16), residues: 2640 helix: -1.01 (0.42), residues: 152 sheet: 0.43 (0.16), residues: 932 loop : -0.54 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 148 HIS 0.007 0.001 HIS C 173 PHE 0.030 0.002 PHE D 153 TYR 0.027 0.002 TYR E 140 ARG 0.010 0.001 ARG G 18 Details of bonding type rmsd hydrogen bonds : bond 0.04327 ( 710) hydrogen bonds : angle 6.54381 ( 2016) SS BOND : bond 0.00523 ( 48) SS BOND : angle 1.61045 ( 96) covalent geometry : bond 0.00665 (21016) covalent geometry : angle 0.79898 (28668) *********************** 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 512 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 454 time to evaluate : 3.324 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: E 50 GLU cc_start: 0.9194 (mt-10) cc_final: 0.8639 (mp0) REVERT: E 117 ILE cc_start: 0.8189 (tt) cc_final: 0.7976 (mt) REVERT: E 167 ASP cc_start: 0.8077 (t70) cc_final: 0.7811 (t0) REVERT: F 3 GLN cc_start: 0.9088 (pt0) cc_final: 0.8506 (pm20) REVERT: F 26 ARG cc_start: 0.8046 (pmm-80) cc_final: 0.7366 (pmm-80) REVERT: F 27 PHE cc_start: 0.8501 (m-10) cc_final: 0.8250 (m-10) REVERT: F 72 ASP cc_start: 0.8590 (t0) cc_final: 0.8085 (t0) REVERT: F 105 GLN cc_start: 0.8279 (pm20) cc_final: 0.7736 (pm20) REVERT: F 148 ASP cc_start: 0.9003 (p0) cc_final: 0.8606 (p0) REVERT: F 214 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.7076 (ttpt) REVERT: G 50 GLU cc_start: 0.9188 (mt-10) cc_final: 0.8630 (mp0) REVERT: G 117 ILE cc_start: 0.8176 (tt) cc_final: 0.7969 (mt) REVERT: G 167 ASP cc_start: 0.8081 (t70) cc_final: 0.7816 (t0) REVERT: H 3 GLN cc_start: 0.9078 (pt0) cc_final: 0.8498 (pm20) REVERT: H 26 ARG cc_start: 0.8044 (pmm-80) cc_final: 0.7370 (pmm-80) REVERT: H 27 PHE cc_start: 0.8473 (m-10) cc_final: 0.8232 (m-10) REVERT: H 72 ASP cc_start: 0.8588 (t0) cc_final: 0.8381 (t0) REVERT: H 105 GLN cc_start: 0.8275 (pm20) cc_final: 0.7668 (pm20) REVERT: H 147 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8802 (tppt) REVERT: H 148 ASP cc_start: 0.9007 (p0) cc_final: 0.8653 (p0) REVERT: H 214 LYS cc_start: 0.7634 (OUTLIER) cc_final: 0.7053 (ttpt) REVERT: I 50 GLU cc_start: 0.9111 (mt-10) cc_final: 0.8550 (mp0) REVERT: I 117 ILE cc_start: 0.8185 (tt) cc_final: 0.7972 (mt) REVERT: I 167 ASP cc_start: 0.8086 (t70) cc_final: 0.7796 (t0) REVERT: I 173 TYR cc_start: 0.7270 (p90) cc_final: 0.7048 (p90) REVERT: J 3 GLN cc_start: 0.9074 (pt0) cc_final: 0.8503 (pm20) REVERT: J 26 ARG cc_start: 0.8045 (pmm-80) cc_final: 0.7457 (pmm-80) REVERT: J 27 PHE cc_start: 0.8484 (m-10) cc_final: 0.8275 (m-10) REVERT: J 72 ASP cc_start: 0.8591 (t0) cc_final: 0.8381 (t0) REVERT: J 105 GLN cc_start: 0.8262 (pm20) cc_final: 0.7651 (pm20) REVERT: J 148 ASP cc_start: 0.8996 (p0) cc_final: 0.8669 (p0) REVERT: J 214 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7104 (ttpt) REVERT: K 3 GLN cc_start: 0.9082 (pt0) cc_final: 0.8500 (pm20) REVERT: K 26 ARG cc_start: 0.8034 (pmm-80) cc_final: 0.7353 (pmm-80) REVERT: K 27 PHE cc_start: 0.8496 (m-10) cc_final: 0.8248 (m-10) REVERT: K 72 ASP cc_start: 0.8586 (t0) cc_final: 0.8376 (t0) REVERT: K 105 GLN cc_start: 0.8281 (pm20) cc_final: 0.7673 (pm20) REVERT: K 148 ASP cc_start: 0.9006 (p0) cc_final: 0.8590 (p0) REVERT: K 214 LYS cc_start: 0.7682 (OUTLIER) cc_final: 0.7094 (ttpt) REVERT: L 50 GLU cc_start: 0.9212 (mt-10) cc_final: 0.8649 (mp0) REVERT: L 117 ILE cc_start: 0.8170 (tt) cc_final: 0.7959 (mt) REVERT: L 167 ASP cc_start: 0.8081 (t70) cc_final: 0.7808 (t0) REVERT: L 173 TYR cc_start: 0.7264 (p90) cc_final: 0.6812 (p90) outliers start: 58 outliers final: 12 residues processed: 486 average time/residue: 1.4539 time to fit residues: 811.9231 Evaluate side-chains 416 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 399 time to evaluate : 2.674 ------------------------------------------------------------------------------- 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 F residue 214 LYS Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain H residue 147 LYS 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 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 237 optimal weight: 0.5980 chunk 93 optimal weight: 0.1980 chunk 224 optimal weight: 6.9990 chunk 251 optimal weight: 2.9990 chunk 235 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 238 optimal weight: 2.9990 chunk 144 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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** ** G 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 169 HIS ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 202 ASN ** L 166 GLN ** 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 = 0.103176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.061685 restraints weight = 40195.356| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 3.13 r_work: 0.2576 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2443 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21064 Z= 0.186 Angle : 0.720 9.660 28764 Z= 0.376 Chirality : 0.048 0.176 3220 Planarity : 0.005 0.056 3660 Dihedral : 5.552 24.758 2864 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.26 % Allowed : 17.39 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.16), residues: 2640 helix: -0.42 (0.45), residues: 152 sheet: 0.64 (0.16), residues: 932 loop : -0.32 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 148 HIS 0.005 0.001 HIS B 173 PHE 0.019 0.002 PHE L 209 TYR 0.025 0.002 TYR I 140 ARG 0.010 0.001 ARG L 142 Details of bonding type rmsd hydrogen bonds : bond 0.03592 ( 710) hydrogen bonds : angle 5.83925 ( 2016) SS BOND : bond 0.00466 ( 48) SS BOND : angle 1.66275 ( 96) covalent geometry : bond 0.00435 (21016) covalent geometry : angle 0.71468 (28668) *********************** 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 482 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 430 time to evaluate : 4.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 ASP cc_start: 0.9123 (t70) cc_final: 0.8891 (t0) REVERT: C 109 GLU cc_start: 0.9147 (tp30) cc_final: 0.8815 (tp30) REVERT: C 169 ASP cc_start: 0.9108 (t70) cc_final: 0.8877 (t0) REVERT: D 169 ASP cc_start: 0.9117 (t70) cc_final: 0.8884 (t0) REVERT: E 50 GLU cc_start: 0.9355 (mt-10) cc_final: 0.8822 (mp0) REVERT: E 81 GLU cc_start: 0.9008 (pm20) cc_final: 0.8803 (pm20) REVERT: E 105 GLU cc_start: 0.7261 (mp0) cc_final: 0.7045 (mp0) REVERT: E 139 PHE cc_start: 0.8264 (p90) cc_final: 0.7998 (p90) REVERT: E 148 TRP cc_start: 0.7958 (m100) cc_final: 0.7679 (m100) REVERT: E 167 ASP cc_start: 0.8217 (t70) cc_final: 0.7925 (t0) REVERT: E 179 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9033 (tp) REVERT: F 3 GLN cc_start: 0.9121 (pt0) cc_final: 0.8567 (pm20) REVERT: F 6 GLU cc_start: 0.7969 (mp0) cc_final: 0.7269 (pm20) REVERT: F 16 GLU cc_start: 0.8635 (mp0) cc_final: 0.8372 (mp0) REVERT: F 26 ARG cc_start: 0.8194 (pmm-80) cc_final: 0.7652 (pmm-80) REVERT: F 27 PHE cc_start: 0.8617 (m-10) cc_final: 0.8357 (m-10) REVERT: F 72 ASP cc_start: 0.8726 (t0) cc_final: 0.8194 (t0) REVERT: F 148 ASP cc_start: 0.9068 (p0) cc_final: 0.8656 (p0) REVERT: F 152 GLU cc_start: 0.7484 (pm20) cc_final: 0.7255 (pm20) REVERT: F 160 ASN cc_start: 0.8794 (m-40) cc_final: 0.8412 (m-40) REVERT: G 50 GLU cc_start: 0.9371 (mt-10) cc_final: 0.8840 (mp0) REVERT: G 81 GLU cc_start: 0.9007 (pm20) cc_final: 0.8805 (pm20) REVERT: G 142 ARG cc_start: 0.8914 (ttm-80) cc_final: 0.8705 (mmt90) REVERT: G 148 TRP cc_start: 0.7941 (m100) cc_final: 0.7658 (m100) REVERT: G 167 ASP cc_start: 0.8222 (t70) cc_final: 0.7928 (t0) REVERT: G 179 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9034 (tp) REVERT: H 3 GLN cc_start: 0.9151 (pt0) cc_final: 0.8600 (pm20) REVERT: H 6 GLU cc_start: 0.7994 (mp0) cc_final: 0.7210 (pm20) REVERT: H 16 GLU cc_start: 0.8629 (mp0) cc_final: 0.8370 (mp0) REVERT: H 26 ARG cc_start: 0.8206 (pmm-80) cc_final: 0.7673 (pmm-80) REVERT: H 27 PHE cc_start: 0.8608 (m-10) cc_final: 0.8351 (m-10) REVERT: H 72 ASP cc_start: 0.8699 (t0) cc_final: 0.8428 (t0) REVERT: H 105 GLN cc_start: 0.8624 (pm20) cc_final: 0.7912 (pm20) REVERT: H 147 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8766 (tppt) REVERT: H 148 ASP cc_start: 0.9085 (p0) cc_final: 0.8770 (p0) REVERT: H 160 ASN cc_start: 0.8808 (m-40) cc_final: 0.8442 (m-40) REVERT: H 214 LYS cc_start: 0.7593 (OUTLIER) cc_final: 0.7067 (ttpt) REVERT: I 50 GLU cc_start: 0.9276 (mt-10) cc_final: 0.8746 (mp0) REVERT: I 81 GLU cc_start: 0.9010 (pm20) cc_final: 0.8809 (pm20) REVERT: I 105 GLU cc_start: 0.7265 (mp0) cc_final: 0.6992 (mp0) REVERT: I 117 ILE cc_start: 0.8376 (tt) cc_final: 0.8173 (mt) REVERT: I 148 TRP cc_start: 0.7535 (m100) cc_final: 0.7310 (m100) REVERT: I 167 ASP cc_start: 0.8220 (t70) cc_final: 0.7925 (t0) REVERT: I 179 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9025 (tp) REVERT: J 3 GLN cc_start: 0.9145 (pt0) cc_final: 0.8593 (pm20) REVERT: J 6 GLU cc_start: 0.7978 (mp0) cc_final: 0.7194 (pm20) REVERT: J 16 GLU cc_start: 0.8622 (mp0) cc_final: 0.8363 (mp0) REVERT: J 26 ARG cc_start: 0.8161 (pmm-80) cc_final: 0.7604 (pmm-80) REVERT: J 27 PHE cc_start: 0.8627 (m-10) cc_final: 0.8361 (m-10) REVERT: J 72 ASP cc_start: 0.8711 (t0) cc_final: 0.8443 (t0) REVERT: J 105 GLN cc_start: 0.8610 (pm20) cc_final: 0.7890 (pm20) REVERT: J 148 ASP cc_start: 0.9095 (p0) cc_final: 0.8818 (p0) REVERT: J 160 ASN cc_start: 0.8862 (m-40) cc_final: 0.8473 (m-40) REVERT: J 164 LEU cc_start: 0.9659 (mm) cc_final: 0.9454 (mp) REVERT: J 214 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7083 (ttpt) REVERT: K 3 GLN cc_start: 0.9136 (pt0) cc_final: 0.8585 (pm20) REVERT: K 6 GLU cc_start: 0.7989 (mp0) cc_final: 0.7192 (pm20) REVERT: K 16 GLU cc_start: 0.8612 (mp0) cc_final: 0.8348 (mp0) REVERT: K 26 ARG cc_start: 0.8175 (pmm-80) cc_final: 0.7641 (pmm-80) REVERT: K 27 PHE cc_start: 0.8602 (m-10) cc_final: 0.8346 (m-10) REVERT: K 72 ASP cc_start: 0.8722 (t0) cc_final: 0.8455 (t0) REVERT: K 105 GLN cc_start: 0.8624 (pm20) cc_final: 0.7912 (pm20) REVERT: K 148 ASP cc_start: 0.9067 (p0) cc_final: 0.8649 (p0) REVERT: K 152 GLU cc_start: 0.7519 (pm20) cc_final: 0.7318 (pm20) REVERT: K 160 ASN cc_start: 0.8844 (m-40) cc_final: 0.8487 (m-40) REVERT: K 214 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7363 (ttpt) REVERT: L 50 GLU cc_start: 0.9361 (mt-10) cc_final: 0.8823 (mp0) REVERT: L 105 GLU cc_start: 0.7188 (mp0) cc_final: 0.6943 (mp0) REVERT: L 139 PHE cc_start: 0.8438 (p90) cc_final: 0.8127 (p90) REVERT: L 142 ARG cc_start: 0.8856 (ttm110) cc_final: 0.8548 (mtt-85) REVERT: L 148 TRP cc_start: 0.7869 (m100) cc_final: 0.7580 (m100) REVERT: L 167 ASP cc_start: 0.8213 (t70) cc_final: 0.7923 (t0) outliers start: 52 outliers final: 32 residues processed: 451 average time/residue: 1.8104 time to fit residues: 943.9817 Evaluate side-chains 447 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 408 time to evaluate : 3.147 ------------------------------------------------------------------------------- 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 60 LYS Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 60 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 60 LYS 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 60 LYS 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 179 LEU Chi-restraints excluded: chain F residue 11 CYS 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 179 LEU Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 147 LYS Chi-restraints excluded: chain H residue 214 LYS Chi-restraints excluded: chain I residue 19 VAL 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 183 LEU Chi-restraints excluded: chain K residue 214 LYS Chi-restraints excluded: chain L residue 19 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 253 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 242 optimal weight: 0.9990 chunk 217 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 153 optimal weight: 0.0050 chunk 164 optimal weight: 2.9990 chunk 227 optimal weight: 0.9990 chunk 196 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- 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 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 ASN F 76 ASN F 197 GLN F 202 ASN F 204 ASN ** G 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 210 ASN H 76 ASN ** H 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 202 ASN ** H 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 210 ASN J 76 ASN ** J 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 197 GLN J 202 ASN J 204 ASN K 76 ASN K 197 GLN ** K 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 210 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.102830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.061493 restraints weight = 40900.461| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 3.14 r_work: 0.2574 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3293 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= 0.177 Angle : 0.701 9.169 28764 Z= 0.367 Chirality : 0.046 0.172 3220 Planarity : 0.006 0.059 3660 Dihedral : 5.290 24.813 2864 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.87 % Allowed : 17.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.16), residues: 2640 helix: -0.07 (0.46), residues: 152 sheet: 0.72 (0.16), residues: 928 loop : -0.33 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 215 HIS 0.004 0.001 HIS C 173 PHE 0.022 0.002 PHE L 209 TYR 0.015 0.002 TYR I 140 ARG 0.011 0.001 ARG E 142 Details of bonding type rmsd hydrogen bonds : bond 0.03324 ( 710) hydrogen bonds : angle 5.61882 ( 2016) SS BOND : bond 0.00406 ( 48) SS BOND : angle 2.58352 ( 96) covalent geometry : bond 0.00416 (21016) covalent geometry : angle 0.68589 (28668) *********************** 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 509 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 420 time to evaluate : 2.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 GLU cc_start: 0.8999 (tp30) cc_final: 0.8798 (tp30) REVERT: A 169 ASP cc_start: 0.8977 (t70) cc_final: 0.8766 (t0) REVERT: B 109 GLU cc_start: 0.8983 (tp30) cc_final: 0.8768 (tp30) REVERT: C 20 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8460 (pm20) REVERT: C 109 GLU cc_start: 0.8931 (tp30) cc_final: 0.8589 (tp30) REVERT: C 169 ASP cc_start: 0.8969 (t70) cc_final: 0.8756 (t0) REVERT: D 169 ASP cc_start: 0.8973 (t70) cc_final: 0.8759 (t0) REVERT: E 33 LEU cc_start: 0.9700 (OUTLIER) cc_final: 0.9405 (tm) REVERT: E 50 GLU cc_start: 0.9148 (mt-10) cc_final: 0.8651 (mp0) REVERT: E 81 GLU cc_start: 0.9027 (pm20) cc_final: 0.8701 (pm20) REVERT: E 117 ILE cc_start: 0.8551 (tt) cc_final: 0.8303 (mm) REVERT: E 167 ASP cc_start: 0.8335 (t0) cc_final: 0.7944 (t0) REVERT: E 210 ASN cc_start: 0.8496 (t0) cc_final: 0.8105 (p0) REVERT: E 211 ARG cc_start: 0.8001 (ttp80) cc_final: 0.7793 (ttp-110) REVERT: F 3 GLN cc_start: 0.9084 (pt0) cc_final: 0.8551 (pm20) REVERT: F 6 GLU cc_start: 0.7695 (mp0) cc_final: 0.7274 (pm20) REVERT: F 16 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8325 (mp0) REVERT: F 26 ARG cc_start: 0.8155 (pmm-80) cc_final: 0.7628 (pmm-80) REVERT: F 27 PHE cc_start: 0.8471 (m-10) cc_final: 0.8259 (m-10) REVERT: F 72 ASP cc_start: 0.8766 (t0) cc_final: 0.8268 (t0) REVERT: F 105 GLN cc_start: 0.8294 (pm20) cc_final: 0.7879 (pm20) REVERT: F 148 ASP cc_start: 0.9024 (p0) cc_final: 0.8635 (p0) REVERT: F 152 GLU cc_start: 0.7537 (pm20) cc_final: 0.7249 (pm20) REVERT: F 160 ASN cc_start: 0.8763 (m-40) cc_final: 0.8535 (m-40) REVERT: G 33 LEU cc_start: 0.9699 (OUTLIER) cc_final: 0.9403 (tm) REVERT: G 50 GLU cc_start: 0.9147 (mt-10) cc_final: 0.8664 (mp0) REVERT: G 81 GLU cc_start: 0.9024 (pm20) cc_final: 0.8687 (pm20) REVERT: G 117 ILE cc_start: 0.8545 (tt) cc_final: 0.8313 (mm) REVERT: G 139 PHE cc_start: 0.7885 (p90) cc_final: 0.7512 (p90) REVERT: G 142 ARG cc_start: 0.8913 (ttm-80) cc_final: 0.8632 (mmt90) REVERT: G 167 ASP cc_start: 0.8348 (t0) cc_final: 0.7970 (t0) REVERT: G 210 ASN cc_start: 0.8493 (t0) cc_final: 0.8075 (p0) REVERT: H 3 GLN cc_start: 0.9103 (pt0) cc_final: 0.8564 (pm20) REVERT: H 6 GLU cc_start: 0.7715 (mp0) cc_final: 0.6916 (pm20) REVERT: H 16 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8325 (mp0) REVERT: H 26 ARG cc_start: 0.8105 (pmm-80) cc_final: 0.7568 (pmm-80) REVERT: H 27 PHE cc_start: 0.8485 (m-10) cc_final: 0.8274 (m-10) REVERT: H 72 ASP cc_start: 0.8696 (t0) cc_final: 0.8388 (t0) REVERT: H 105 GLN cc_start: 0.8367 (pm20) cc_final: 0.7868 (pm20) REVERT: H 147 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8706 (tppt) REVERT: H 148 ASP cc_start: 0.9022 (p0) cc_final: 0.8740 (p0) REVERT: H 160 ASN cc_start: 0.8808 (m-40) cc_final: 0.8592 (m-40) REVERT: H 176 GLN cc_start: 0.7986 (mt0) cc_final: 0.7509 (mt0) REVERT: H 214 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7145 (ttpt) REVERT: I 33 LEU cc_start: 0.9704 (OUTLIER) cc_final: 0.9407 (tm) REVERT: I 50 GLU cc_start: 0.9026 (mt-10) cc_final: 0.8546 (mp0) REVERT: I 81 GLU cc_start: 0.9027 (pm20) cc_final: 0.8691 (pm20) REVERT: I 139 PHE cc_start: 0.7978 (p90) cc_final: 0.7724 (p90) REVERT: I 167 ASP cc_start: 0.8365 (t0) cc_final: 0.7967 (t0) REVERT: I 210 ASN cc_start: 0.8508 (t0) cc_final: 0.8142 (p0) REVERT: I 211 ARG cc_start: 0.7976 (ttp80) cc_final: 0.7772 (ttp-110) REVERT: J 3 GLN cc_start: 0.9100 (pt0) cc_final: 0.8564 (pm20) REVERT: J 6 GLU cc_start: 0.7658 (mp0) cc_final: 0.6869 (pm20) REVERT: J 16 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8323 (mp0) REVERT: J 26 ARG cc_start: 0.8025 (pmm-80) cc_final: 0.7471 (pmm-80) REVERT: J 27 PHE cc_start: 0.8501 (m-10) cc_final: 0.8293 (m-10) REVERT: J 72 ASP cc_start: 0.8695 (t0) cc_final: 0.8392 (t0) REVERT: J 105 GLN cc_start: 0.8362 (pm20) cc_final: 0.7859 (pm20) REVERT: J 148 ASP cc_start: 0.9015 (p0) cc_final: 0.8764 (p0) REVERT: J 214 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7151 (ttpt) REVERT: K 3 GLN cc_start: 0.9098 (pt0) cc_final: 0.8566 (pm20) REVERT: K 6 GLU cc_start: 0.7676 (mp0) cc_final: 0.6848 (pm20) REVERT: K 16 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8311 (mp0) REVERT: K 26 ARG cc_start: 0.8073 (pmm-80) cc_final: 0.7533 (pmm-80) REVERT: K 27 PHE cc_start: 0.8489 (m-10) cc_final: 0.8276 (m-10) REVERT: K 72 ASP cc_start: 0.8694 (t0) cc_final: 0.8391 (t0) REVERT: K 148 ASP cc_start: 0.8960 (p0) cc_final: 0.8583 (p0) REVERT: K 152 GLU cc_start: 0.7510 (pm20) cc_final: 0.7208 (pm20) REVERT: K 160 ASN cc_start: 0.8786 (m-40) cc_final: 0.8569 (m-40) REVERT: K 214 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7467 (ttpt) REVERT: L 33 LEU cc_start: 0.9695 (OUTLIER) cc_final: 0.9407 (tm) REVERT: L 50 GLU cc_start: 0.9155 (mt-10) cc_final: 0.8668 (mp0) REVERT: L 117 ILE cc_start: 0.8555 (tt) cc_final: 0.8321 (mm) REVERT: L 139 PHE cc_start: 0.8306 (p90) cc_final: 0.8005 (p90) REVERT: L 167 ASP cc_start: 0.8290 (t0) cc_final: 0.7947 (t0) REVERT: L 210 ASN cc_start: 0.8496 (t0) cc_final: 0.8067 (p0) outliers start: 89 outliers final: 28 residues processed: 467 average time/residue: 1.3011 time to fit residues: 702.2158 Evaluate side-chains 432 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 391 time to evaluate : 2.537 ------------------------------------------------------------------------------- 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 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 C residue 190 SER 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 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 H residue 11 CYS Chi-restraints excluded: chain H residue 16 GLU Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 147 LYS 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 J residue 11 CYS Chi-restraints excluded: chain J residue 16 GLU 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 16 GLU Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain K residue 214 LYS Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 33 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 174 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 143 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 135 optimal weight: 0.4980 chunk 173 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 ** G 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN H 197 GLN ** I 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 ASN K 76 ASN K 176 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.102663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.061342 restraints weight = 40718.459| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 3.14 r_work: 0.2577 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2445 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.3479 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= 0.177 Angle : 0.691 9.076 28764 Z= 0.361 Chirality : 0.046 0.174 3220 Planarity : 0.005 0.060 3660 Dihedral : 5.106 25.374 2864 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.61 % Allowed : 17.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.16), residues: 2640 helix: 0.01 (0.46), residues: 152 sheet: 0.71 (0.16), residues: 928 loop : -0.31 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 215 HIS 0.003 0.001 HIS B 173 PHE 0.014 0.001 PHE E 209 TYR 0.020 0.002 TYR I 140 ARG 0.014 0.001 ARG E 142 Details of bonding type rmsd hydrogen bonds : bond 0.03204 ( 710) hydrogen bonds : angle 5.43506 ( 2016) SS BOND : bond 0.00428 ( 48) SS BOND : angle 2.49812 ( 96) covalent geometry : bond 0.00417 (21016) covalent geometry : angle 0.67653 (28668) *********************** 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 477 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 394 time to evaluate : 4.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 GLU cc_start: 0.9146 (tp30) cc_final: 0.8923 (tp30) REVERT: C 20 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8643 (pm20) REVERT: C 109 GLU cc_start: 0.9097 (tp30) cc_final: 0.8826 (tp30) REVERT: E 33 LEU cc_start: 0.9729 (OUTLIER) cc_final: 0.9411 (tm) REVERT: E 50 GLU cc_start: 0.9345 (mt-10) cc_final: 0.8862 (mp0) REVERT: E 81 GLU cc_start: 0.9061 (pm20) cc_final: 0.8764 (pm20) REVERT: E 117 ILE cc_start: 0.8480 (tt) cc_final: 0.8264 (mm) REVERT: E 167 ASP cc_start: 0.8412 (t0) cc_final: 0.7967 (t0) REVERT: E 173 TYR cc_start: 0.6953 (p90) cc_final: 0.6688 (p90) REVERT: E 179 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9069 (tp) REVERT: E 210 ASN cc_start: 0.8541 (t0) cc_final: 0.8228 (p0) REVERT: F 3 GLN cc_start: 0.9149 (pt0) cc_final: 0.8612 (pm20) REVERT: F 6 GLU cc_start: 0.7826 (mp0) cc_final: 0.7199 (mp0) REVERT: F 26 ARG cc_start: 0.8218 (pmm-80) cc_final: 0.7598 (pmm-80) REVERT: F 27 PHE cc_start: 0.8600 (m-10) cc_final: 0.8351 (m-10) REVERT: F 72 ASP cc_start: 0.8847 (t0) cc_final: 0.8342 (t0) REVERT: F 148 ASP cc_start: 0.9059 (p0) cc_final: 0.8707 (p0) REVERT: F 152 GLU cc_start: 0.7578 (pm20) cc_final: 0.7218 (pm20) REVERT: F 164 LEU cc_start: 0.9494 (mp) cc_final: 0.9052 (pt) REVERT: G 33 LEU cc_start: 0.9736 (OUTLIER) cc_final: 0.9435 (tm) REVERT: G 50 GLU cc_start: 0.9366 (mt-10) cc_final: 0.8885 (mp0) REVERT: G 81 GLU cc_start: 0.9060 (pm20) cc_final: 0.8768 (pm20) REVERT: G 117 ILE cc_start: 0.8472 (tt) cc_final: 0.8259 (mm) REVERT: G 167 ASP cc_start: 0.8437 (t0) cc_final: 0.7999 (t0) REVERT: G 179 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9068 (tp) REVERT: G 210 ASN cc_start: 0.8592 (t0) cc_final: 0.8194 (p0) REVERT: H 3 GLN cc_start: 0.9160 (pt0) cc_final: 0.8623 (pm20) REVERT: H 6 GLU cc_start: 0.7694 (mp0) cc_final: 0.6869 (pm20) REVERT: H 16 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8399 (mp0) REVERT: H 26 ARG cc_start: 0.8178 (pmm-80) cc_final: 0.7556 (pmm-80) REVERT: H 27 PHE cc_start: 0.8580 (m-10) cc_final: 0.8339 (m-10) REVERT: H 72 ASP cc_start: 0.8783 (t0) cc_final: 0.8457 (t0) REVERT: H 105 GLN cc_start: 0.8441 (pm20) cc_final: 0.8038 (pm20) REVERT: H 147 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8707 (tppt) REVERT: H 148 ASP cc_start: 0.9116 (p0) cc_final: 0.8895 (p0) REVERT: H 164 LEU cc_start: 0.9500 (mp) cc_final: 0.9055 (pt) REVERT: H 214 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7194 (ttpt) REVERT: I 33 LEU cc_start: 0.9738 (OUTLIER) cc_final: 0.9436 (tm) REVERT: I 50 GLU cc_start: 0.9253 (mt-10) cc_final: 0.8784 (mp0) REVERT: I 117 ILE cc_start: 0.8584 (tt) cc_final: 0.8379 (mm) REVERT: I 167 ASP cc_start: 0.8447 (t0) cc_final: 0.8016 (t0) REVERT: I 173 TYR cc_start: 0.6965 (p90) cc_final: 0.6712 (p90) REVERT: I 179 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9036 (tp) REVERT: I 210 ASN cc_start: 0.8511 (t0) cc_final: 0.8214 (p0) REVERT: J 3 GLN cc_start: 0.9147 (pt0) cc_final: 0.8609 (pm20) REVERT: J 6 GLU cc_start: 0.7661 (mp0) cc_final: 0.6835 (pm20) REVERT: J 16 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8378 (mp0) REVERT: J 26 ARG cc_start: 0.8170 (pmm-80) cc_final: 0.7531 (pmm-80) REVERT: J 27 PHE cc_start: 0.8579 (m-10) cc_final: 0.8342 (m-10) REVERT: J 72 ASP cc_start: 0.8782 (t0) cc_final: 0.8463 (t0) REVERT: J 105 GLN cc_start: 0.8410 (pm20) cc_final: 0.8004 (pm20) REVERT: J 152 GLU cc_start: 0.7530 (pm20) cc_final: 0.7180 (pm20) REVERT: J 176 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8128 (mp10) REVERT: J 214 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7194 (ttpt) REVERT: K 3 GLN cc_start: 0.9162 (pt0) cc_final: 0.8627 (pm20) REVERT: K 6 GLU cc_start: 0.7919 (mp0) cc_final: 0.7319 (pm20) REVERT: K 16 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8370 (mp0) REVERT: K 26 ARG cc_start: 0.8140 (pmm-80) cc_final: 0.7512 (pmm-80) REVERT: K 27 PHE cc_start: 0.8561 (m-10) cc_final: 0.8319 (m-10) REVERT: K 72 ASP cc_start: 0.8776 (t0) cc_final: 0.8456 (t0) REVERT: K 148 ASP cc_start: 0.9059 (p0) cc_final: 0.8690 (p0) REVERT: K 152 GLU cc_start: 0.7579 (pm20) cc_final: 0.7175 (pm20) REVERT: K 164 LEU cc_start: 0.9477 (mp) cc_final: 0.9038 (pt) REVERT: K 200 ILE cc_start: 0.9054 (pt) cc_final: 0.8830 (pp) REVERT: K 214 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7634 (ttpt) REVERT: L 33 LEU cc_start: 0.9734 (OUTLIER) cc_final: 0.9443 (tm) REVERT: L 50 GLU cc_start: 0.9362 (mt-10) cc_final: 0.8876 (mp0) REVERT: L 108 ARG cc_start: 0.8521 (ppp80) cc_final: 0.8211 (ppp80) REVERT: L 117 ILE cc_start: 0.8488 (tt) cc_final: 0.8273 (mm) REVERT: L 139 PHE cc_start: 0.8149 (p90) cc_final: 0.7845 (p90) REVERT: L 167 ASP cc_start: 0.8491 (t0) cc_final: 0.8050 (t0) REVERT: L 179 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9096 (tp) REVERT: L 210 ASN cc_start: 0.8674 (t0) cc_final: 0.8305 (p0) outliers start: 83 outliers final: 30 residues processed: 440 average time/residue: 1.2654 time to fit residues: 639.2912 Evaluate side-chains 419 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 372 time to evaluate : 2.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 190 SER 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 110 GLU Chi-restraints excluded: chain C residue 190 SER 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 88 CYS Chi-restraints excluded: chain E residue 171 CYS Chi-restraints excluded: chain E residue 179 LEU 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 27 SER Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 88 CYS Chi-restraints excluded: chain G residue 171 CYS 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 147 LYS 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 171 CYS 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 J residue 176 GLN Chi-restraints excluded: chain J residue 214 LYS Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 176 GLN Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain K residue 214 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 186 optimal weight: 7.9990 chunk 207 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 165 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 87 optimal weight: 0.3980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.103408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.062080 restraints weight = 40289.107| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 3.14 r_work: 0.2601 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.3686 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= 0.136 Angle : 0.666 9.101 28764 Z= 0.346 Chirality : 0.045 0.151 3220 Planarity : 0.006 0.062 3660 Dihedral : 4.939 24.158 2864 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.83 % Allowed : 19.13 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.16), residues: 2640 helix: -0.27 (0.45), residues: 152 sheet: 0.76 (0.16), residues: 936 loop : -0.21 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 215 HIS 0.003 0.001 HIS A 166 PHE 0.011 0.001 PHE E 139 TYR 0.020 0.001 TYR I 140 ARG 0.019 0.001 ARG I 211 Details of bonding type rmsd hydrogen bonds : bond 0.02994 ( 710) hydrogen bonds : angle 5.26609 ( 2016) SS BOND : bond 0.00391 ( 48) SS BOND : angle 1.80808 ( 96) covalent geometry : bond 0.00317 (21016) covalent geometry : angle 0.65866 (28668) *********************** 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 454 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 389 time to evaluate : 2.595 Fit side-chains revert: symmetry clash REVERT: B 109 GLU cc_start: 0.8919 (tp30) cc_final: 0.8702 (tp30) REVERT: B 169 ASP cc_start: 0.8872 (t70) cc_final: 0.8668 (t0) REVERT: C 20 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8438 (pm20) REVERT: C 109 GLU cc_start: 0.8869 (tp30) cc_final: 0.8589 (tp30) REVERT: E 23 CYS cc_start: 0.6180 (t) cc_final: 0.5868 (t) REVERT: E 33 LEU cc_start: 0.9708 (OUTLIER) cc_final: 0.9370 (tm) REVERT: E 50 GLU cc_start: 0.9113 (mt-10) cc_final: 0.8648 (mp0) REVERT: E 75 ILE cc_start: 0.9479 (mp) cc_final: 0.8860 (tp) REVERT: E 108 ARG cc_start: 0.8373 (ppp80) cc_final: 0.8056 (ppp80) REVERT: E 117 ILE cc_start: 0.8581 (tt) cc_final: 0.8358 (mm) REVERT: E 139 PHE cc_start: 0.7909 (p90) cc_final: 0.7570 (p90) REVERT: E 167 ASP cc_start: 0.8429 (t0) cc_final: 0.7996 (t0) REVERT: E 173 TYR cc_start: 0.6800 (p90) cc_final: 0.6179 (p90) REVERT: E 179 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9105 (tp) REVERT: E 185 ASP cc_start: 0.9312 (m-30) cc_final: 0.8577 (p0) REVERT: E 210 ASN cc_start: 0.8703 (t0) cc_final: 0.8177 (p0) REVERT: F 3 GLN cc_start: 0.9096 (pt0) cc_final: 0.8584 (pm20) REVERT: F 6 GLU cc_start: 0.7518 (mp0) cc_final: 0.7309 (pm20) REVERT: F 26 ARG cc_start: 0.8178 (pmm-80) cc_final: 0.7592 (pmm-80) REVERT: F 27 PHE cc_start: 0.8341 (m-10) cc_final: 0.8136 (m-10) REVERT: F 72 ASP cc_start: 0.8778 (t0) cc_final: 0.8270 (t0) REVERT: F 148 ASP cc_start: 0.9006 (p0) cc_final: 0.8653 (p0) REVERT: F 152 GLU cc_start: 0.7521 (pm20) cc_final: 0.7044 (pm20) REVERT: F 164 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9084 (pt) REVERT: F 176 GLN cc_start: 0.8648 (mt0) cc_final: 0.7490 (mp10) REVERT: G 23 CYS cc_start: 0.6080 (t) cc_final: 0.5780 (t) REVERT: G 33 LEU cc_start: 0.9710 (OUTLIER) cc_final: 0.9368 (tm) REVERT: G 50 GLU cc_start: 0.9123 (mt-10) cc_final: 0.8655 (mp0) REVERT: G 75 ILE cc_start: 0.9464 (mp) cc_final: 0.8850 (tp) REVERT: G 117 ILE cc_start: 0.8592 (tt) cc_final: 0.8371 (mm) REVERT: G 167 ASP cc_start: 0.8461 (t0) cc_final: 0.8044 (t0) REVERT: G 179 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9107 (tp) REVERT: G 185 ASP cc_start: 0.9291 (m-30) cc_final: 0.8585 (p0) REVERT: G 210 ASN cc_start: 0.8588 (t0) cc_final: 0.8182 (p0) REVERT: H 3 GLN cc_start: 0.9109 (pt0) cc_final: 0.8596 (pm20) REVERT: H 6 GLU cc_start: 0.7445 (mp0) cc_final: 0.6588 (pm20) REVERT: H 16 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8359 (mp0) REVERT: H 26 ARG cc_start: 0.8174 (pmm-80) cc_final: 0.7590 (pmm-80) REVERT: H 72 ASP cc_start: 0.8744 (t0) cc_final: 0.8416 (t0) REVERT: H 105 GLN cc_start: 0.8332 (pm20) cc_final: 0.7911 (pm20) REVERT: H 147 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8731 (tppt) REVERT: H 164 LEU cc_start: 0.9497 (mp) cc_final: 0.9089 (pt) REVERT: H 176 GLN cc_start: 0.7773 (mt0) cc_final: 0.7177 (mt0) REVERT: H 214 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7165 (ttpt) REVERT: I 23 CYS cc_start: 0.6162 (t) cc_final: 0.5867 (t) REVERT: I 33 LEU cc_start: 0.9718 (OUTLIER) cc_final: 0.9384 (tm) REVERT: I 50 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8555 (mp0) REVERT: I 75 ILE cc_start: 0.9470 (mp) cc_final: 0.8863 (tp) REVERT: I 117 ILE cc_start: 0.8543 (tt) cc_final: 0.8317 (mm) REVERT: I 139 PHE cc_start: 0.7991 (p90) cc_final: 0.7763 (p90) REVERT: I 167 ASP cc_start: 0.8456 (t0) cc_final: 0.8065 (t0) REVERT: I 185 ASP cc_start: 0.9298 (m-30) cc_final: 0.8572 (p0) REVERT: I 210 ASN cc_start: 0.8692 (t0) cc_final: 0.8172 (p0) REVERT: J 3 GLN cc_start: 0.9092 (pt0) cc_final: 0.8576 (pm20) REVERT: J 6 GLU cc_start: 0.7381 (mp0) cc_final: 0.6297 (mp0) REVERT: J 16 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8361 (mp0) REVERT: J 26 ARG cc_start: 0.8116 (pmm-80) cc_final: 0.7459 (pmm-80) REVERT: J 72 ASP cc_start: 0.8744 (t0) cc_final: 0.8418 (t0) REVERT: J 105 GLN cc_start: 0.8332 (pm20) cc_final: 0.7896 (pm20) REVERT: J 176 GLN cc_start: 0.8515 (mt0) cc_final: 0.8078 (mt0) REVERT: J 214 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7184 (ttpt) REVERT: K 3 GLN cc_start: 0.9111 (pt0) cc_final: 0.8599 (pm20) REVERT: K 6 GLU cc_start: 0.7464 (mp0) cc_final: 0.7195 (pm20) REVERT: K 16 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8348 (mp0) REVERT: K 26 ARG cc_start: 0.8169 (pmm-80) cc_final: 0.7587 (pmm-80) REVERT: K 27 PHE cc_start: 0.8325 (m-10) cc_final: 0.8124 (m-10) REVERT: K 72 ASP cc_start: 0.8744 (t0) cc_final: 0.8421 (t0) REVERT: K 148 ASP cc_start: 0.8973 (p0) cc_final: 0.8576 (p0) REVERT: K 152 GLU cc_start: 0.7508 (pm20) cc_final: 0.7193 (pm20) REVERT: K 164 LEU cc_start: 0.9483 (mp) cc_final: 0.9071 (pt) REVERT: K 214 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7629 (ttpt) REVERT: L 23 CYS cc_start: 0.6156 (t) cc_final: 0.5843 (t) REVERT: L 33 LEU cc_start: 0.9711 (OUTLIER) cc_final: 0.9370 (tm) REVERT: L 50 GLU cc_start: 0.9132 (mt-10) cc_final: 0.8656 (mp0) REVERT: L 117 ILE cc_start: 0.8607 (tt) cc_final: 0.8382 (mm) REVERT: L 139 PHE cc_start: 0.8057 (p90) cc_final: 0.7812 (p90) REVERT: L 167 ASP cc_start: 0.8499 (t0) cc_final: 0.8066 (t0) REVERT: L 179 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9149 (tp) REVERT: L 185 ASP cc_start: 0.9355 (m-30) cc_final: 0.8627 (p0) REVERT: L 210 ASN cc_start: 0.8631 (t0) cc_final: 0.8192 (p0) outliers start: 65 outliers final: 27 residues processed: 421 average time/residue: 1.1702 time to fit residues: 565.6555 Evaluate side-chains 409 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 366 time to evaluate : 2.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 110 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 26 LYS Chi-restraints excluded: chain C residue 110 GLU 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 33 LEU Chi-restraints excluded: chain E residue 171 CYS 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 157 VAL Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 200 ILE 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 G residue 179 LEU Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain H residue 16 GLU Chi-restraints excluded: chain H residue 147 LYS 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 16 GLU Chi-restraints excluded: chain J residue 214 LYS Chi-restraints excluded: chain K residue 11 CYS Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 176 GLN Chi-restraints excluded: chain K residue 200 ILE Chi-restraints excluded: chain K residue 214 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 201 optimal weight: 4.9990 chunk 231 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 179 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 111 optimal weight: 0.0570 chunk 13 optimal weight: 0.4980 chunk 120 optimal weight: 1.9990 chunk 155 optimal weight: 7.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.1102 ------------------------------------------------------------------------------- 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 ** 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 ** 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 = 0.3611 r_free = 0.3611 target = 0.102896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.061583 restraints weight = 40435.151| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 3.14 r_work: 0.2589 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2457 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.3732 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= 0.167 Angle : 0.679 10.764 28764 Z= 0.354 Chirality : 0.046 0.232 3220 Planarity : 0.006 0.062 3660 Dihedral : 4.904 24.166 2864 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.39 % Allowed : 19.57 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.16), residues: 2640 helix: -0.39 (0.44), residues: 152 sheet: 0.74 (0.16), residues: 948 loop : -0.19 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 159 HIS 0.003 0.001 HIS B 166 PHE 0.021 0.001 PHE H 27 TYR 0.019 0.001 TYR I 140 ARG 0.013 0.001 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.03145 ( 710) hydrogen bonds : angle 5.22150 ( 2016) SS BOND : bond 0.00364 ( 48) SS BOND : angle 1.74741 ( 96) covalent geometry : bond 0.00393 (21016) covalent geometry : angle 0.67293 (28668) *********************** 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 464 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 386 time to evaluate : 2.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 GLU cc_start: 0.9132 (tp30) cc_final: 0.8912 (tp30) REVERT: C 20 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8640 (pm20) REVERT: C 109 GLU cc_start: 0.9076 (tp30) cc_final: 0.8799 (tp30) REVERT: E 23 CYS cc_start: 0.7078 (t) cc_final: 0.6727 (t) REVERT: E 33 LEU cc_start: 0.9742 (OUTLIER) cc_final: 0.9377 (tm) REVERT: E 50 GLU cc_start: 0.9332 (mt-10) cc_final: 0.8872 (mp0) REVERT: E 81 GLU cc_start: 0.9036 (pm20) cc_final: 0.8713 (pm20) REVERT: E 82 ASP cc_start: 0.8552 (m-30) cc_final: 0.8344 (m-30) REVERT: E 117 ILE cc_start: 0.8589 (tt) cc_final: 0.8356 (mm) REVERT: E 139 PHE cc_start: 0.8070 (p90) cc_final: 0.7714 (p90) REVERT: E 167 ASP cc_start: 0.8553 (t0) cc_final: 0.8135 (t0) REVERT: E 173 TYR cc_start: 0.6998 (p90) cc_final: 0.6259 (p90) REVERT: E 179 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9138 (tp) REVERT: E 185 ASP cc_start: 0.9347 (m-30) cc_final: 0.8598 (p0) REVERT: E 210 ASN cc_start: 0.8753 (t0) cc_final: 0.8225 (p0) REVERT: F 3 GLN cc_start: 0.9155 (pt0) cc_final: 0.8593 (pm20) REVERT: F 26 ARG cc_start: 0.8313 (pmm-80) cc_final: 0.7521 (pmm-80) REVERT: F 72 ASP cc_start: 0.8832 (t0) cc_final: 0.8315 (t0) REVERT: F 148 ASP cc_start: 0.9065 (p0) cc_final: 0.8669 (p0) REVERT: F 152 GLU cc_start: 0.7508 (pm20) cc_final: 0.7002 (pm20) REVERT: F 164 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9054 (pt) REVERT: G 11 LEU cc_start: 0.8985 (pt) cc_final: 0.8756 (pp) REVERT: G 33 LEU cc_start: 0.9745 (OUTLIER) cc_final: 0.9407 (tm) REVERT: G 50 GLU cc_start: 0.9346 (mt-10) cc_final: 0.8870 (mp0) REVERT: G 81 GLU cc_start: 0.9062 (pm20) cc_final: 0.8745 (pm20) REVERT: G 82 ASP cc_start: 0.8558 (m-30) cc_final: 0.8349 (m-30) REVERT: G 117 ILE cc_start: 0.8545 (tt) cc_final: 0.8315 (mm) REVERT: G 139 PHE cc_start: 0.7926 (p90) cc_final: 0.7662 (p90) REVERT: G 142 ARG cc_start: 0.9002 (ttm-80) cc_final: 0.8686 (mmt90) REVERT: G 167 ASP cc_start: 0.8502 (t0) cc_final: 0.8122 (t0) REVERT: G 179 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9146 (tp) REVERT: G 185 ASP cc_start: 0.9341 (m-30) cc_final: 0.8614 (p0) REVERT: G 210 ASN cc_start: 0.8609 (t0) cc_final: 0.8199 (p0) REVERT: H 3 GLN cc_start: 0.9120 (pt0) cc_final: 0.8597 (pm20) REVERT: H 6 GLU cc_start: 0.7650 (mp0) cc_final: 0.6522 (mp0) REVERT: H 16 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8401 (mp0) REVERT: H 26 ARG cc_start: 0.8318 (pmm-80) cc_final: 0.7607 (pmm-80) REVERT: H 27 PHE cc_start: 0.8458 (m-10) cc_final: 0.8112 (m-80) REVERT: H 72 ASP cc_start: 0.8786 (t0) cc_final: 0.8443 (t0) REVERT: H 105 GLN cc_start: 0.8428 (pm20) cc_final: 0.7940 (pm20) REVERT: H 149 TYR cc_start: 0.9005 (p90) cc_final: 0.8716 (p90) REVERT: H 152 GLU cc_start: 0.7476 (pm20) cc_final: 0.7184 (pm20) REVERT: H 164 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9060 (pt) REVERT: H 183 LEU cc_start: 0.9249 (tt) cc_final: 0.8642 (mt) REVERT: I 33 LEU cc_start: 0.9754 (OUTLIER) cc_final: 0.9413 (tm) REVERT: I 50 GLU cc_start: 0.9257 (mt-10) cc_final: 0.8791 (mp0) REVERT: I 81 GLU cc_start: 0.9060 (pm20) cc_final: 0.8738 (pm20) REVERT: I 82 ASP cc_start: 0.8554 (m-30) cc_final: 0.8341 (m-30) REVERT: I 117 ILE cc_start: 0.8554 (tt) cc_final: 0.8338 (mm) REVERT: I 167 ASP cc_start: 0.8554 (t0) cc_final: 0.8168 (t0) REVERT: I 185 ASP cc_start: 0.9353 (m-30) cc_final: 0.8503 (p0) REVERT: I 186 TYR cc_start: 0.8902 (t80) cc_final: 0.8646 (t80) REVERT: I 210 ASN cc_start: 0.8752 (t0) cc_final: 0.8234 (p0) REVERT: J 3 GLN cc_start: 0.9106 (pt0) cc_final: 0.8585 (pm20) REVERT: J 6 GLU cc_start: 0.7622 (mp0) cc_final: 0.6488 (mp0) REVERT: J 16 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8408 (mp0) REVERT: J 26 ARG cc_start: 0.8268 (pmm-80) cc_final: 0.7486 (pmm-80) REVERT: J 27 PHE cc_start: 0.8438 (m-10) cc_final: 0.8109 (m-80) REVERT: J 72 ASP cc_start: 0.8798 (t0) cc_final: 0.8463 (t0) REVERT: J 105 GLN cc_start: 0.8407 (pm20) cc_final: 0.7920 (pm20) REVERT: J 152 GLU cc_start: 0.7518 (pm20) cc_final: 0.7233 (pm20) REVERT: J 164 LEU cc_start: 0.9562 (mp) cc_final: 0.9273 (pt) REVERT: J 176 GLN cc_start: 0.8555 (mt0) cc_final: 0.8078 (mp10) REVERT: J 214 LYS cc_start: 0.7783 (OUTLIER) cc_final: 0.7063 (ttpt) REVERT: K 3 GLN cc_start: 0.9167 (pt0) cc_final: 0.8606 (pm20) REVERT: K 16 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8390 (mp0) REVERT: K 26 ARG cc_start: 0.8233 (pmm-80) cc_final: 0.7436 (pmm-80) REVERT: K 72 ASP cc_start: 0.8777 (t0) cc_final: 0.8438 (t0) REVERT: K 148 ASP cc_start: 0.9044 (p0) cc_final: 0.8643 (p0) REVERT: K 152 GLU cc_start: 0.7604 (pm20) cc_final: 0.7027 (pm20) REVERT: K 164 LEU cc_start: 0.9465 (mp) cc_final: 0.9027 (pt) REVERT: K 176 GLN cc_start: 0.8515 (mp10) cc_final: 0.8109 (mp10) REVERT: L 33 LEU cc_start: 0.9749 (OUTLIER) cc_final: 0.9409 (tm) REVERT: L 50 GLU cc_start: 0.9364 (mt-10) cc_final: 0.8882 (mp0) REVERT: L 75 ILE cc_start: 0.9504 (mp) cc_final: 0.8834 (tp) REVERT: L 117 ILE cc_start: 0.8540 (tt) cc_final: 0.8311 (mm) REVERT: L 139 PHE cc_start: 0.8225 (p90) cc_final: 0.7984 (p90) REVERT: L 167 ASP cc_start: 0.8556 (t0) cc_final: 0.8119 (t0) REVERT: L 210 ASN cc_start: 0.8639 (t0) cc_final: 0.8206 (p0) outliers start: 78 outliers final: 38 residues processed: 430 average time/residue: 1.1267 time to fit residues: 557.4215 Evaluate side-chains 414 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 363 time to evaluate : 2.234 ------------------------------------------------------------------------------- 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 110 GLU Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain D residue 31 VAL 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 11 CYS Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 157 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 F residue 200 ILE 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 16 GLU Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 164 LEU 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 11 CYS Chi-restraints excluded: chain J residue 16 GLU Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 200 ILE Chi-restraints excluded: chain J residue 214 LYS Chi-restraints excluded: chain K residue 11 CYS Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 200 ILE 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 176 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 123 optimal weight: 0.5980 chunk 134 optimal weight: 1.9990 chunk 260 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 chunk 119 optimal weight: 0.4980 chunk 138 optimal weight: 0.8980 chunk 151 optimal weight: 7.9990 chunk 125 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ** 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 ** 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 = 0.3615 r_free = 0.3615 target = 0.103360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.061818 restraints weight = 40318.284| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 3.16 r_work: 0.2594 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21064 Z= 0.142 Angle : 0.701 11.065 28764 Z= 0.358 Chirality : 0.046 0.228 3220 Planarity : 0.006 0.065 3660 Dihedral : 4.854 22.891 2864 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.52 % Allowed : 21.00 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.16), residues: 2640 helix: -0.37 (0.44), residues: 152 sheet: 0.84 (0.16), residues: 948 loop : -0.18 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 159 HIS 0.002 0.001 HIS B 173 PHE 0.025 0.001 PHE F 27 TYR 0.023 0.001 TYR I 140 ARG 0.016 0.001 ARG G 18 Details of bonding type rmsd hydrogen bonds : bond 0.03031 ( 710) hydrogen bonds : angle 5.12112 ( 2016) SS BOND : bond 0.00355 ( 48) SS BOND : angle 1.57080 ( 96) covalent geometry : bond 0.00330 (21016) covalent geometry : angle 0.69640 (28668) *********************** 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 432 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 374 time to evaluate : 2.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 GLU cc_start: 0.8926 (tp30) cc_final: 0.8705 (tp30) REVERT: C 20 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8457 (pm20) REVERT: C 109 GLU cc_start: 0.8877 (tp30) cc_final: 0.8594 (tp30) REVERT: E 23 CYS cc_start: 0.6073 (t) cc_final: 0.5762 (t) REVERT: E 33 LEU cc_start: 0.9718 (OUTLIER) cc_final: 0.9349 (tm) REVERT: E 50 GLU cc_start: 0.9110 (mt-10) cc_final: 0.8659 (mp0) REVERT: E 81 GLU cc_start: 0.9021 (pm20) cc_final: 0.8630 (pm20) REVERT: E 82 ASP cc_start: 0.8610 (m-30) cc_final: 0.8377 (m-30) REVERT: E 117 ILE cc_start: 0.8621 (tt) cc_final: 0.8398 (mm) REVERT: E 167 ASP cc_start: 0.8593 (t0) cc_final: 0.8343 (t0) REVERT: E 173 TYR cc_start: 0.6844 (p90) cc_final: 0.6184 (p90) REVERT: E 185 ASP cc_start: 0.9377 (m-30) cc_final: 0.8569 (p0) REVERT: E 210 ASN cc_start: 0.8734 (t0) cc_final: 0.8206 (p0) REVERT: F 3 GLN cc_start: 0.9084 (pt0) cc_final: 0.8550 (pm20) REVERT: F 26 ARG cc_start: 0.8242 (pmm-80) cc_final: 0.7639 (pmm-80) REVERT: F 27 PHE cc_start: 0.8274 (m-10) cc_final: 0.7952 (m-10) REVERT: F 72 ASP cc_start: 0.8784 (t0) cc_final: 0.8283 (t0) REVERT: F 148 ASP cc_start: 0.8999 (p0) cc_final: 0.8595 (p0) REVERT: F 152 GLU cc_start: 0.7608 (pm20) cc_final: 0.7147 (pm20) REVERT: F 164 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9071 (pt) REVERT: F 176 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8367 (mp10) REVERT: G 33 LEU cc_start: 0.9719 (OUTLIER) cc_final: 0.9381 (tm) REVERT: G 50 GLU cc_start: 0.9131 (mt-10) cc_final: 0.8672 (mp0) REVERT: G 81 GLU cc_start: 0.9036 (pm20) cc_final: 0.8686 (pm20) REVERT: G 82 ASP cc_start: 0.8590 (m-30) cc_final: 0.8356 (m-30) REVERT: G 117 ILE cc_start: 0.8619 (tt) cc_final: 0.8401 (mm) REVERT: G 167 ASP cc_start: 0.8589 (t0) cc_final: 0.8208 (t0) REVERT: G 210 ASN cc_start: 0.8646 (t0) cc_final: 0.8250 (p0) REVERT: H 3 GLN cc_start: 0.9107 (pt0) cc_final: 0.8605 (pm20) REVERT: H 6 GLU cc_start: 0.7449 (mp0) cc_final: 0.6306 (mp0) REVERT: H 26 ARG cc_start: 0.8223 (pmm-80) cc_final: 0.7558 (pmm-80) REVERT: H 27 PHE cc_start: 0.8260 (m-10) cc_final: 0.7965 (m-10) REVERT: H 72 ASP cc_start: 0.8703 (t0) cc_final: 0.8367 (t0) REVERT: H 164 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9075 (pt) REVERT: H 176 GLN cc_start: 0.8378 (mt0) cc_final: 0.8094 (mt0) REVERT: I 33 LEU cc_start: 0.9722 (OUTLIER) cc_final: 0.9392 (tm) REVERT: I 50 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8592 (mp0) REVERT: I 81 GLU cc_start: 0.9036 (pm20) cc_final: 0.8708 (pm20) REVERT: I 82 ASP cc_start: 0.8586 (m-30) cc_final: 0.8328 (m-30) REVERT: I 167 ASP cc_start: 0.8592 (t0) cc_final: 0.8198 (t0) REVERT: I 185 ASP cc_start: 0.9357 (m-30) cc_final: 0.8526 (p0) REVERT: I 186 TYR cc_start: 0.8917 (t80) cc_final: 0.8656 (t80) REVERT: I 210 ASN cc_start: 0.8760 (t0) cc_final: 0.8240 (p0) REVERT: J 3 GLN cc_start: 0.9057 (pt0) cc_final: 0.8555 (pm20) REVERT: J 6 GLU cc_start: 0.7393 (mp0) cc_final: 0.6255 (mp0) REVERT: J 26 ARG cc_start: 0.8180 (pmm-80) cc_final: 0.7451 (pmm-80) REVERT: J 27 PHE cc_start: 0.8276 (m-10) cc_final: 0.7988 (m-80) REVERT: J 72 ASP cc_start: 0.8711 (t0) cc_final: 0.8377 (t0) REVERT: J 164 LEU cc_start: 0.9566 (mp) cc_final: 0.9315 (pt) REVERT: J 176 GLN cc_start: 0.8535 (mt0) cc_final: 0.8152 (mp10) REVERT: J 214 LYS cc_start: 0.7810 (OUTLIER) cc_final: 0.7163 (ttpt) REVERT: K 3 GLN cc_start: 0.9082 (pt0) cc_final: 0.8560 (pm20) REVERT: K 26 ARG cc_start: 0.8225 (pmm-80) cc_final: 0.7622 (pmm-80) REVERT: K 27 PHE cc_start: 0.8258 (m-10) cc_final: 0.7938 (m-10) REVERT: K 72 ASP cc_start: 0.8709 (t0) cc_final: 0.8380 (t0) REVERT: K 148 ASP cc_start: 0.8965 (p0) cc_final: 0.8558 (p0) REVERT: K 152 GLU cc_start: 0.7587 (pm20) cc_final: 0.7071 (pm20) REVERT: K 164 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9045 (pt) REVERT: K 176 GLN cc_start: 0.8426 (mp10) cc_final: 0.8030 (mp10) REVERT: L 33 LEU cc_start: 0.9716 (OUTLIER) cc_final: 0.9361 (tm) REVERT: L 50 GLU cc_start: 0.9142 (mt-10) cc_final: 0.8671 (mp0) REVERT: L 75 ILE cc_start: 0.9496 (mp) cc_final: 0.8836 (tp) REVERT: L 82 ASP cc_start: 0.8358 (m-30) cc_final: 0.8156 (m-30) REVERT: L 108 ARG cc_start: 0.8454 (ppp80) cc_final: 0.8173 (ppp80) REVERT: L 117 ILE cc_start: 0.8624 (tt) cc_final: 0.8401 (mm) REVERT: L 139 PHE cc_start: 0.8032 (p90) cc_final: 0.7766 (p90) REVERT: L 167 ASP cc_start: 0.8589 (t0) cc_final: 0.8321 (t0) REVERT: L 185 ASP cc_start: 0.9350 (m-30) cc_final: 0.8567 (p0) REVERT: L 210 ASN cc_start: 0.8648 (t0) cc_final: 0.8221 (p0) outliers start: 58 outliers final: 28 residues processed: 408 average time/residue: 1.1685 time to fit residues: 547.4161 Evaluate side-chains 399 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 361 time to evaluate : 2.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 31 VAL 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 31 VAL Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 31 VAL 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 164 LEU Chi-restraints excluded: chain F residue 176 GLN Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 200 ILE 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 164 LEU 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 157 VAL Chi-restraints excluded: chain J residue 200 ILE Chi-restraints excluded: chain J residue 214 LYS Chi-restraints excluded: chain K residue 11 CYS Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 164 LEU Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain K residue 200 ILE 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 146 optimal weight: 4.9990 chunk 238 optimal weight: 0.3980 chunk 186 optimal weight: 2.9990 chunk 192 optimal weight: 10.0000 chunk 147 optimal weight: 0.1980 chunk 214 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 124 GLN ** E 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.103049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.061979 restraints weight = 40046.385| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 3.14 r_work: 0.2605 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2476 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.3949 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= 0.154 Angle : 0.720 9.851 28764 Z= 0.371 Chirality : 0.046 0.206 3220 Planarity : 0.006 0.070 3660 Dihedral : 4.901 23.373 2864 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.39 % Allowed : 21.35 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.16), residues: 2640 helix: 0.18 (0.47), residues: 128 sheet: 0.84 (0.16), residues: 940 loop : -0.19 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 159 HIS 0.003 0.001 HIS B 166 PHE 0.021 0.001 PHE F 27 TYR 0.022 0.001 TYR G 173 ARG 0.015 0.001 ARG L 18 Details of bonding type rmsd hydrogen bonds : bond 0.03027 ( 710) hydrogen bonds : angle 5.14015 ( 2016) SS BOND : bond 0.00374 ( 48) SS BOND : angle 1.52054 ( 96) covalent geometry : bond 0.00362 (21016) covalent geometry : angle 0.71572 (28668) *********************** 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 424 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 369 time to evaluate : 2.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 GLU cc_start: 0.9157 (tp30) cc_final: 0.8932 (tp30) REVERT: B 164 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7892 (tm-30) REVERT: C 20 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8613 (pm20) REVERT: C 109 GLU cc_start: 0.9102 (tp30) cc_final: 0.8826 (tp30) REVERT: E 33 LEU cc_start: 0.9734 (OUTLIER) cc_final: 0.9385 (tm) REVERT: E 50 GLU cc_start: 0.9315 (mt-10) cc_final: 0.8852 (mp0) REVERT: E 82 ASP cc_start: 0.8788 (m-30) cc_final: 0.8559 (m-30) REVERT: E 108 ARG cc_start: 0.8354 (ppp80) cc_final: 0.8066 (ppp80) REVERT: E 139 PHE cc_start: 0.7993 (p90) cc_final: 0.7638 (p90) REVERT: E 167 ASP cc_start: 0.8715 (t0) cc_final: 0.8323 (t0) REVERT: E 173 TYR cc_start: 0.6855 (p90) cc_final: 0.6255 (p90) REVERT: E 185 ASP cc_start: 0.9371 (m-30) cc_final: 0.8580 (p0) REVERT: E 186 TYR cc_start: 0.8972 (t80) cc_final: 0.8759 (t80) REVERT: E 210 ASN cc_start: 0.8714 (t0) cc_final: 0.8222 (p0) REVERT: F 3 GLN cc_start: 0.9182 (pt0) cc_final: 0.8671 (pm20) REVERT: F 26 ARG cc_start: 0.8332 (pmm-80) cc_final: 0.7665 (pmm-80) REVERT: F 27 PHE cc_start: 0.8334 (m-10) cc_final: 0.8013 (m-80) REVERT: F 72 ASP cc_start: 0.8853 (t0) cc_final: 0.8327 (t0) REVERT: F 148 ASP cc_start: 0.9033 (p0) cc_final: 0.8660 (p0) REVERT: F 152 GLU cc_start: 0.7679 (pm20) cc_final: 0.7178 (pm20) REVERT: F 176 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8362 (mp10) REVERT: G 33 LEU cc_start: 0.9744 (OUTLIER) cc_final: 0.9371 (tm) REVERT: G 50 GLU cc_start: 0.9348 (mt-10) cc_final: 0.8872 (mp0) REVERT: G 81 GLU cc_start: 0.9036 (pm20) cc_final: 0.8689 (pm20) REVERT: G 82 ASP cc_start: 0.8713 (m-30) cc_final: 0.8403 (m-30) REVERT: G 108 ARG cc_start: 0.8260 (ppp80) cc_final: 0.7990 (ppp80) REVERT: G 117 ILE cc_start: 0.8602 (tt) cc_final: 0.8397 (mm) REVERT: G 167 ASP cc_start: 0.8626 (t0) cc_final: 0.8354 (t0) REVERT: G 185 ASP cc_start: 0.9359 (m-30) cc_final: 0.8569 (p0) REVERT: G 210 ASN cc_start: 0.8660 (t0) cc_final: 0.8223 (p0) REVERT: H 3 GLN cc_start: 0.9145 (pt0) cc_final: 0.8627 (pm20) REVERT: H 6 GLU cc_start: 0.7879 (mp0) cc_final: 0.7623 (pm20) REVERT: H 26 ARG cc_start: 0.8332 (pmm-80) cc_final: 0.7644 (pmm-80) REVERT: H 27 PHE cc_start: 0.8363 (m-10) cc_final: 0.8033 (m-10) REVERT: H 72 ASP cc_start: 0.8744 (t0) cc_final: 0.8392 (t0) REVERT: H 152 GLU cc_start: 0.7527 (pm20) cc_final: 0.7301 (pm20) REVERT: H 176 GLN cc_start: 0.8495 (mt0) cc_final: 0.8074 (mp10) REVERT: I 33 LEU cc_start: 0.9752 (OUTLIER) cc_final: 0.9410 (tm) REVERT: I 50 GLU cc_start: 0.9241 (mt-10) cc_final: 0.8779 (mp0) REVERT: I 81 GLU cc_start: 0.9041 (pm20) cc_final: 0.8750 (pm20) REVERT: I 82 ASP cc_start: 0.8686 (m-30) cc_final: 0.8373 (m-30) REVERT: I 105 GLU cc_start: 0.8328 (mp0) cc_final: 0.8095 (pm20) REVERT: I 167 ASP cc_start: 0.8639 (t0) cc_final: 0.8240 (t0) REVERT: I 179 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9061 (tp) REVERT: I 185 ASP cc_start: 0.9345 (m-30) cc_final: 0.8621 (p0) REVERT: I 186 TYR cc_start: 0.8940 (t80) cc_final: 0.8732 (t80) REVERT: I 210 ASN cc_start: 0.8725 (t0) cc_final: 0.8233 (p0) REVERT: J 3 GLN cc_start: 0.9147 (pt0) cc_final: 0.8624 (pm20) REVERT: J 6 GLU cc_start: 0.7860 (mp0) cc_final: 0.7613 (pm20) REVERT: J 26 ARG cc_start: 0.8256 (pmm-80) cc_final: 0.7476 (pmm-80) REVERT: J 27 PHE cc_start: 0.8376 (m-10) cc_final: 0.8059 (m-80) REVERT: J 72 ASP cc_start: 0.8750 (t0) cc_final: 0.8403 (t0) REVERT: J 152 GLU cc_start: 0.7577 (pm20) cc_final: 0.7367 (pm20) REVERT: J 164 LEU cc_start: 0.9563 (mp) cc_final: 0.9335 (pt) REVERT: J 176 GLN cc_start: 0.8707 (mt0) cc_final: 0.8306 (mp10) REVERT: K 3 GLN cc_start: 0.9164 (pt0) cc_final: 0.8636 (pm20) REVERT: K 26 ARG cc_start: 0.8305 (pmm-80) cc_final: 0.7633 (pmm-80) REVERT: K 27 PHE cc_start: 0.8306 (m-10) cc_final: 0.7986 (m-80) REVERT: K 72 ASP cc_start: 0.8725 (t0) cc_final: 0.8384 (t0) REVERT: K 148 ASP cc_start: 0.9016 (p0) cc_final: 0.8611 (p0) REVERT: K 152 GLU cc_start: 0.7636 (pm20) cc_final: 0.7103 (pm20) REVERT: K 176 GLN cc_start: 0.8485 (mp10) cc_final: 0.8092 (mp10) REVERT: L 33 LEU cc_start: 0.9735 (OUTLIER) cc_final: 0.9384 (tm) REVERT: L 50 GLU cc_start: 0.9357 (mt-10) cc_final: 0.8873 (mp0) REVERT: L 108 ARG cc_start: 0.8486 (ppp80) cc_final: 0.8154 (ppp80) REVERT: L 117 ILE cc_start: 0.8612 (tt) cc_final: 0.8406 (mm) REVERT: L 139 PHE cc_start: 0.8142 (p90) cc_final: 0.7857 (p90) REVERT: L 167 ASP cc_start: 0.8756 (t0) cc_final: 0.8378 (t0) REVERT: L 185 ASP cc_start: 0.9350 (m-30) cc_final: 0.8551 (p0) REVERT: L 210 ASN cc_start: 0.8679 (t0) cc_final: 0.8253 (p0) outliers start: 55 outliers final: 31 residues processed: 404 average time/residue: 1.1631 time to fit residues: 542.4342 Evaluate side-chains 403 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 365 time to evaluate : 2.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 31 VAL 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 31 VAL Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 31 VAL 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 F residue 183 LEU Chi-restraints excluded: chain F residue 200 ILE 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 157 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 I residue 179 LEU Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 200 ILE Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain K residue 200 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 21 optimal weight: 0.6980 chunk 130 optimal weight: 0.2980 chunk 95 optimal weight: 0.9980 chunk 261 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 94 optimal weight: 0.0370 chunk 251 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 184 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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** ** G 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.103535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.062485 restraints weight = 40085.986| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 3.14 r_work: 0.2624 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21064 Z= 0.134 Angle : 0.720 10.197 28764 Z= 0.370 Chirality : 0.046 0.212 3220 Planarity : 0.006 0.062 3660 Dihedral : 4.896 23.262 2864 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.78 % Allowed : 21.74 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.16), residues: 2640 helix: -0.04 (0.47), residues: 128 sheet: 0.91 (0.16), residues: 940 loop : -0.20 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 159 HIS 0.005 0.001 HIS C 166 PHE 0.020 0.001 PHE F 27 TYR 0.022 0.001 TYR I 140 ARG 0.013 0.001 ARG L 18 Details of bonding type rmsd hydrogen bonds : bond 0.02878 ( 710) hydrogen bonds : angle 5.09571 ( 2016) SS BOND : bond 0.00319 ( 48) SS BOND : angle 1.57598 ( 96) covalent geometry : bond 0.00312 (21016) covalent geometry : angle 0.71559 (28668) ********************** 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 418 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 377 time to evaluate : 2.419 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: 0.8932 (tp30) cc_final: 0.8698 (tp30) REVERT: C 109 GLU cc_start: 0.8878 (tp30) cc_final: 0.8605 (tp30) REVERT: C 164 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7548 (pp20) REVERT: E 33 LEU cc_start: 0.9709 (OUTLIER) cc_final: 0.9373 (tm) REVERT: E 50 GLU cc_start: 0.9067 (mt-10) cc_final: 0.8599 (mp0) REVERT: E 82 ASP cc_start: 0.8795 (m-30) cc_final: 0.8546 (m-30) REVERT: E 108 ARG cc_start: 0.8299 (ppp80) cc_final: 0.7998 (ppp80) REVERT: E 139 PHE cc_start: 0.7821 (p90) cc_final: 0.7392 (p90) REVERT: E 167 ASP cc_start: 0.8752 (t0) cc_final: 0.8358 (t0) REVERT: E 173 TYR cc_start: 0.6748 (p90) cc_final: 0.6030 (p90) REVERT: E 185 ASP cc_start: 0.9399 (m-30) cc_final: 0.8661 (p0) REVERT: E 186 TYR cc_start: 0.8970 (t80) cc_final: 0.8721 (t80) REVERT: E 210 ASN cc_start: 0.8719 (t0) cc_final: 0.8228 (p0) REVERT: F 3 GLN cc_start: 0.9135 (pt0) cc_final: 0.8635 (pm20) REVERT: F 26 ARG cc_start: 0.8232 (pmm-80) cc_final: 0.7588 (pmm-80) REVERT: F 27 PHE cc_start: 0.8140 (m-10) cc_final: 0.7857 (m-80) REVERT: F 72 ASP cc_start: 0.8777 (t0) cc_final: 0.8274 (t0) REVERT: F 148 ASP cc_start: 0.8963 (p0) cc_final: 0.8587 (p0) REVERT: F 176 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8264 (mp10) REVERT: G 33 LEU cc_start: 0.9713 (OUTLIER) cc_final: 0.9353 (tm) REVERT: G 50 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8647 (mp0) REVERT: G 81 GLU cc_start: 0.8855 (pm20) cc_final: 0.8615 (pm20) REVERT: G 82 ASP cc_start: 0.8709 (m-30) cc_final: 0.8283 (m-30) REVERT: G 167 ASP cc_start: 0.8735 (t0) cc_final: 0.8362 (t0) REVERT: G 185 ASP cc_start: 0.9358 (m-30) cc_final: 0.8595 (p0) REVERT: G 186 TYR cc_start: 0.8880 (t80) cc_final: 0.8671 (t80) REVERT: G 210 ASN cc_start: 0.8713 (t0) cc_final: 0.8265 (p0) REVERT: H 3 GLN cc_start: 0.9117 (pt0) cc_final: 0.8608 (pm20) REVERT: H 6 GLU cc_start: 0.7569 (mp0) cc_final: 0.7271 (mp0) REVERT: H 26 ARG cc_start: 0.8206 (pmm-80) cc_final: 0.7467 (pmm-80) REVERT: H 27 PHE cc_start: 0.8199 (m-10) cc_final: 0.7923 (m-80) REVERT: H 72 ASP cc_start: 0.8714 (t0) cc_final: 0.8387 (t0) REVERT: H 152 GLU cc_start: 0.7567 (pm20) cc_final: 0.7319 (pm20) REVERT: H 176 GLN cc_start: 0.8657 (mt0) cc_final: 0.8279 (mp10) REVERT: I 33 LEU cc_start: 0.9726 (OUTLIER) cc_final: 0.9378 (tm) REVERT: I 50 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8580 (mp0) REVERT: I 81 GLU cc_start: 0.9010 (pm20) cc_final: 0.8656 (pm20) REVERT: I 82 ASP cc_start: 0.8597 (m-30) cc_final: 0.8245 (m-30) REVERT: I 105 GLU cc_start: 0.8111 (mp0) cc_final: 0.7894 (pm20) REVERT: I 167 ASP cc_start: 0.8648 (t0) cc_final: 0.8379 (t0) REVERT: I 210 ASN cc_start: 0.8729 (t0) cc_final: 0.8233 (p0) REVERT: J 3 GLN cc_start: 0.9094 (pt0) cc_final: 0.8589 (pm20) REVERT: J 6 GLU cc_start: 0.7565 (mp0) cc_final: 0.7266 (mp0) REVERT: J 26 ARG cc_start: 0.8164 (pmm-80) cc_final: 0.7396 (pmm-80) REVERT: J 27 PHE cc_start: 0.8154 (m-10) cc_final: 0.7860 (m-80) REVERT: J 72 ASP cc_start: 0.8698 (t0) cc_final: 0.8368 (t0) REVERT: J 152 GLU cc_start: 0.7614 (pm20) cc_final: 0.7379 (pm20) REVERT: J 176 GLN cc_start: 0.8689 (mt0) cc_final: 0.8072 (mp10) REVERT: J 182 SER cc_start: 0.9283 (t) cc_final: 0.8945 (p) REVERT: K 3 GLN cc_start: 0.9125 (pt0) cc_final: 0.8614 (pm20) REVERT: K 26 ARG cc_start: 0.8212 (pmm-80) cc_final: 0.7548 (pmm-80) REVERT: K 27 PHE cc_start: 0.8115 (m-10) cc_final: 0.7829 (m-80) REVERT: K 72 ASP cc_start: 0.8684 (t0) cc_final: 0.8353 (t0) REVERT: K 148 ASP cc_start: 0.8925 (p0) cc_final: 0.8524 (p0) REVERT: K 176 GLN cc_start: 0.8417 (mp10) cc_final: 0.8036 (mp10) REVERT: L 33 LEU cc_start: 0.9710 (OUTLIER) cc_final: 0.9353 (tm) REVERT: L 50 GLU cc_start: 0.9124 (mt-10) cc_final: 0.8654 (mp0) REVERT: L 139 PHE cc_start: 0.8019 (p90) cc_final: 0.7762 (p90) REVERT: L 167 ASP cc_start: 0.8775 (t0) cc_final: 0.8379 (t0) REVERT: L 185 ASP cc_start: 0.9367 (m-30) cc_final: 0.8603 (p0) REVERT: L 186 TYR cc_start: 0.8927 (t80) cc_final: 0.8680 (t80) REVERT: L 210 ASN cc_start: 0.8744 (t0) cc_final: 0.8279 (p0) outliers start: 41 outliers final: 26 residues processed: 405 average time/residue: 1.1812 time to fit residues: 550.8534 Evaluate side-chains 401 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 370 time to evaluate : 2.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain C residue 26 LYS Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 31 VAL 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 F residue 183 LEU Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 171 CYS Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 200 ILE Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain K residue 200 ILE 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 94 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 75 optimal weight: 0.5980 chunk 245 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 198 optimal weight: 5.9990 chunk 156 optimal weight: 6.9990 chunk 223 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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** ** G 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 ASN K 76 ASN ** K 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3608 r_free = 0.3608 target = 0.103137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.061811 restraints weight = 40159.854| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 3.15 r_work: 0.2613 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2483 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21064 Z= 0.155 Angle : 0.746 10.479 28764 Z= 0.385 Chirality : 0.047 0.235 3220 Planarity : 0.006 0.066 3660 Dihedral : 4.952 25.376 2864 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.74 % Allowed : 21.91 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.16), residues: 2640 helix: 0.02 (0.47), residues: 128 sheet: 0.87 (0.16), residues: 940 loop : -0.23 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 159 HIS 0.002 0.001 HIS C 166 PHE 0.022 0.001 PHE G 139 TYR 0.024 0.001 TYR G 173 ARG 0.015 0.001 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.02978 ( 710) hydrogen bonds : angle 5.16415 ( 2016) SS BOND : bond 0.00371 ( 48) SS BOND : angle 1.86633 ( 96) covalent geometry : bond 0.00364 (21016) covalent geometry : angle 0.73947 (28668) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22038.71 seconds wall clock time: 386 minutes 39.20 seconds (23199.20 seconds total)