Starting phenix.real_space_refine on Thu Jan 23 18:32:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vgj_43202/01_2025/8vgj_43202.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vgj_43202/01_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_43202/01_2025/8vgj_43202.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vgj_43202/01_2025/8vgj_43202.map" model { file = "/net/cci-nas-00/data/ceres_data/8vgj_43202/01_2025/8vgj_43202.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vgj_43202/01_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-5571/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: 13.00, per 1000 atoms: 0.63 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: 4.61 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: 3.72 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: 8.65 Time building geometry restraints manager: 5.43 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.740 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 48.390 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.130 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:13.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.080 ------------------------------------------------------------------------------- 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 21016 Z= 0.743 Angle : 1.203 11.446 28668 Z= 0.662 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 *********************** 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 : 2.328 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: 1.3123 time to fit residues: 869.5253 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 : 2.395 ------------------------------------------------------------------------------- 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: 0.9990 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: 0.5980 chunk 239 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 158 ASN ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.103247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.061627 restraints weight = 40785.495| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 3.17 r_work: 0.2581 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2453 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 21016 Z= 0.362 Angle : 0.783 9.772 28668 Z= 0.412 Chirality : 0.050 0.140 3220 Planarity : 0.005 0.048 3660 Dihedral : 6.305 102.494 2866 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.35 % Allowed : 14.39 % Favored : 83.26 % 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: -0.28 (0.16), residues: 2640 helix: -1.01 (0.42), residues: 152 sheet: 0.49 (0.16), residues: 932 loop : -0.48 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 148 HIS 0.006 0.001 HIS A 173 PHE 0.031 0.002 PHE D 153 TYR 0.027 0.002 TYR G 140 ARG 0.011 0.001 ARG G 18 *********************** 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 510 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 456 time to evaluate : 2.432 Fit side-chains revert: symmetry clash REVERT: E 50 GLU cc_start: 0.9401 (mt-10) cc_final: 0.8846 (mp0) REVERT: E 105 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8429 (mp0) REVERT: E 117 ILE cc_start: 0.8168 (tt) cc_final: 0.7958 (mt) REVERT: E 167 ASP cc_start: 0.8169 (t70) cc_final: 0.7870 (t0) REVERT: F 3 GLN cc_start: 0.9104 (pt0) cc_final: 0.8527 (pm20) REVERT: F 16 GLU cc_start: 0.8572 (mp0) cc_final: 0.8214 (mp0) REVERT: F 26 ARG cc_start: 0.8171 (pmm-80) cc_final: 0.7473 (pmm-80) REVERT: F 27 PHE cc_start: 0.8557 (m-10) cc_final: 0.8294 (m-10) REVERT: F 72 ASP cc_start: 0.8606 (t0) cc_final: 0.8086 (t0) REVERT: F 105 GLN cc_start: 0.8379 (pm20) cc_final: 0.7833 (pm20) REVERT: F 148 ASP cc_start: 0.9058 (p0) cc_final: 0.8670 (p0) REVERT: F 214 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.7111 (ttpt) REVERT: G 50 GLU cc_start: 0.9399 (mt-10) cc_final: 0.8845 (mp0) REVERT: G 105 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8428 (mp0) REVERT: G 117 ILE cc_start: 0.8161 (tt) cc_final: 0.7958 (mt) REVERT: G 167 ASP cc_start: 0.8162 (t70) cc_final: 0.7866 (t0) REVERT: G 173 TYR cc_start: 0.7280 (p90) cc_final: 0.7069 (p90) REVERT: H 3 GLN cc_start: 0.9101 (pt0) cc_final: 0.8531 (pm20) REVERT: H 16 GLU cc_start: 0.8575 (mp0) cc_final: 0.8215 (mp0) REVERT: H 26 ARG cc_start: 0.8136 (pmm-80) cc_final: 0.7446 (pmm-80) REVERT: H 27 PHE cc_start: 0.8531 (m-10) cc_final: 0.8272 (m-10) REVERT: H 72 ASP cc_start: 0.8663 (t0) cc_final: 0.8458 (t0) REVERT: H 105 GLN cc_start: 0.8377 (pm20) cc_final: 0.7831 (pm20) REVERT: H 148 ASP cc_start: 0.9097 (p0) cc_final: 0.8774 (p0) REVERT: H 152 GLU cc_start: 0.7481 (pm20) cc_final: 0.7280 (pm20) REVERT: H 176 GLN cc_start: 0.8011 (mt0) cc_final: 0.7511 (mt0) REVERT: H 214 LYS cc_start: 0.7679 (OUTLIER) cc_final: 0.7070 (ttpt) REVERT: I 50 GLU cc_start: 0.9320 (mt-10) cc_final: 0.8749 (mp0) REVERT: I 105 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8393 (mp0) REVERT: I 117 ILE cc_start: 0.8175 (tt) cc_final: 0.7967 (mt) REVERT: I 167 ASP cc_start: 0.8171 (t70) cc_final: 0.7874 (t0) REVERT: J 3 GLN cc_start: 0.9091 (pt0) cc_final: 0.8528 (pm20) REVERT: J 16 GLU cc_start: 0.8567 (mp0) cc_final: 0.8206 (mp0) REVERT: J 26 ARG cc_start: 0.8110 (pmm-80) cc_final: 0.7501 (pmm-80) REVERT: J 27 PHE cc_start: 0.8535 (m-10) cc_final: 0.8305 (m-10) REVERT: J 72 ASP cc_start: 0.8658 (t0) cc_final: 0.8452 (t0) REVERT: J 105 GLN cc_start: 0.8348 (pm20) cc_final: 0.7793 (pm20) REVERT: J 148 ASP cc_start: 0.9086 (p0) cc_final: 0.8763 (p0) REVERT: J 214 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7090 (ttpt) REVERT: K 3 GLN cc_start: 0.9100 (pt0) cc_final: 0.8527 (pm20) REVERT: K 16 GLU cc_start: 0.8550 (mp0) cc_final: 0.8192 (mp0) REVERT: K 26 ARG cc_start: 0.8114 (pmm-80) cc_final: 0.7410 (pmm-80) REVERT: K 27 PHE cc_start: 0.8545 (m-10) cc_final: 0.8280 (m-10) REVERT: K 72 ASP cc_start: 0.8665 (t0) cc_final: 0.8460 (t0) REVERT: K 105 GLN cc_start: 0.8377 (pm20) cc_final: 0.7833 (pm20) REVERT: K 148 ASP cc_start: 0.9060 (p0) cc_final: 0.8648 (p0) REVERT: K 214 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7137 (ttpt) REVERT: L 50 GLU cc_start: 0.9405 (mt-10) cc_final: 0.8847 (mp0) REVERT: L 105 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8405 (mp0) REVERT: L 117 ILE cc_start: 0.8169 (tt) cc_final: 0.7966 (mt) REVERT: L 167 ASP cc_start: 0.8168 (t70) cc_final: 0.7880 (t0) REVERT: L 173 TYR cc_start: 0.7285 (p90) cc_final: 0.7077 (p90) outliers start: 54 outliers final: 12 residues processed: 484 average time/residue: 1.1528 time to fit residues: 642.4502 Evaluate side-chains 416 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 400 time to evaluate : 2.448 ------------------------------------------------------------------------------- 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 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: 0.0470 chunk 93 optimal weight: 0.5980 chunk 224 optimal weight: 8.9990 chunk 251 optimal weight: 2.9990 chunk 235 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 238 optimal weight: 0.4980 chunk 144 optimal weight: 10.0000 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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** F 169 HIS ** G 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 169 HIS L 79 GLN ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.105004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.063449 restraints weight = 40056.797| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 3.14 r_work: 0.2612 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21016 Z= 0.210 Angle : 0.685 9.244 28668 Z= 0.357 Chirality : 0.046 0.151 3220 Planarity : 0.005 0.055 3660 Dihedral : 5.416 23.876 2864 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.39 % Allowed : 16.78 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.16), residues: 2640 helix: -0.47 (0.45), residues: 152 sheet: 0.82 (0.16), residues: 924 loop : -0.27 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 148 HIS 0.005 0.001 HIS C 173 PHE 0.019 0.002 PHE L 209 TYR 0.027 0.002 TYR I 140 ARG 0.005 0.000 ARG I 108 *********************** 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 484 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 429 time to evaluate : 2.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 50 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8602 (mp0) REVERT: E 139 PHE cc_start: 0.8199 (p90) cc_final: 0.7916 (p90) REVERT: E 148 TRP cc_start: 0.7840 (m100) cc_final: 0.7534 (m100) REVERT: E 167 ASP cc_start: 0.8148 (t70) cc_final: 0.7884 (t0) REVERT: E 179 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9057 (tp) REVERT: F 3 GLN cc_start: 0.9065 (pt0) cc_final: 0.8589 (pm20) REVERT: F 6 GLU cc_start: 0.7779 (mp0) cc_final: 0.7151 (pm20) REVERT: F 16 GLU cc_start: 0.8480 (mp0) cc_final: 0.8220 (mp0) REVERT: F 26 ARG cc_start: 0.8138 (pmm-80) cc_final: 0.7633 (pmm-80) REVERT: F 27 PHE cc_start: 0.8474 (m-10) cc_final: 0.8244 (m-10) REVERT: F 72 ASP cc_start: 0.8571 (t0) cc_final: 0.8045 (t0) REVERT: F 148 ASP cc_start: 0.9002 (p0) cc_final: 0.8605 (p0) REVERT: F 152 GLU cc_start: 0.7444 (pm20) cc_final: 0.7243 (pm20) REVERT: F 160 ASN cc_start: 0.8801 (m-40) cc_final: 0.8452 (m-40) REVERT: F 214 LYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7275 (ttpt) REVERT: G 50 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8604 (mp0) REVERT: G 139 PHE cc_start: 0.8143 (p90) cc_final: 0.7751 (p90) REVERT: G 148 TRP cc_start: 0.7939 (m100) cc_final: 0.7618 (m100) REVERT: G 167 ASP cc_start: 0.8120 (t70) cc_final: 0.7859 (t0) REVERT: G 179 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9130 (pp) REVERT: H 3 GLN cc_start: 0.9068 (pt0) cc_final: 0.8596 (pm20) REVERT: H 6 GLU cc_start: 0.7808 (mp0) cc_final: 0.7180 (pm20) REVERT: H 16 GLU cc_start: 0.8471 (mp0) cc_final: 0.8220 (mp0) REVERT: H 26 ARG cc_start: 0.8132 (pmm-80) cc_final: 0.7635 (pmm-80) REVERT: H 27 PHE cc_start: 0.8458 (m-10) cc_final: 0.8231 (m-10) REVERT: H 72 ASP cc_start: 0.8575 (t0) cc_final: 0.8288 (t0) REVERT: H 148 ASP cc_start: 0.9035 (p0) cc_final: 0.8775 (p0) REVERT: H 149 TYR cc_start: 0.9087 (p90) cc_final: 0.8765 (p90) REVERT: H 160 ASN cc_start: 0.8833 (m-40) cc_final: 0.8490 (m-40) REVERT: H 183 LEU cc_start: 0.9207 (tt) cc_final: 0.8715 (mt) REVERT: H 214 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.7207 (ttpt) REVERT: I 50 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8524 (mp0) REVERT: I 167 ASP cc_start: 0.8112 (t70) cc_final: 0.7844 (t0) REVERT: I 173 TYR cc_start: 0.6545 (p90) cc_final: 0.5740 (p90) REVERT: I 179 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9129 (pp) REVERT: J 3 GLN cc_start: 0.9076 (pt0) cc_final: 0.8615 (pm20) REVERT: J 6 GLU cc_start: 0.7769 (mp0) cc_final: 0.7147 (pm20) REVERT: J 16 GLU cc_start: 0.8471 (mp0) cc_final: 0.8221 (mp0) REVERT: J 26 ARG cc_start: 0.8058 (pmm-80) cc_final: 0.7549 (pmm-80) REVERT: J 27 PHE cc_start: 0.8459 (m-10) cc_final: 0.8237 (m-10) REVERT: J 72 ASP cc_start: 0.8585 (t0) cc_final: 0.8301 (t0) REVERT: J 148 ASP cc_start: 0.8949 (p0) cc_final: 0.8699 (p0) REVERT: J 149 TYR cc_start: 0.8832 (p90) cc_final: 0.8513 (p90) REVERT: J 152 GLU cc_start: 0.7483 (pm20) cc_final: 0.7228 (pm20) REVERT: J 160 ASN cc_start: 0.8848 (m-40) cc_final: 0.8509 (m-40) REVERT: J 183 LEU cc_start: 0.9227 (tt) cc_final: 0.8729 (mt) REVERT: J 214 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7274 (ttpt) REVERT: K 3 GLN cc_start: 0.9066 (pt0) cc_final: 0.8594 (pm20) REVERT: K 6 GLU cc_start: 0.7787 (mp0) cc_final: 0.7161 (pm20) REVERT: K 16 GLU cc_start: 0.8465 (mp0) cc_final: 0.8216 (mp0) REVERT: K 26 ARG cc_start: 0.8118 (pmm-80) cc_final: 0.7615 (pmm-80) REVERT: K 27 PHE cc_start: 0.8479 (m-10) cc_final: 0.8242 (m-10) REVERT: K 72 ASP cc_start: 0.8609 (t0) cc_final: 0.8325 (t0) REVERT: K 148 ASP cc_start: 0.8958 (p0) cc_final: 0.8596 (p0) REVERT: K 160 ASN cc_start: 0.8831 (m-40) cc_final: 0.8493 (m-40) REVERT: K 214 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7550 (ttpt) REVERT: L 50 GLU cc_start: 0.9148 (mt-10) cc_final: 0.8616 (mp0) REVERT: L 139 PHE cc_start: 0.8157 (p90) cc_final: 0.7771 (p90) REVERT: L 148 TRP cc_start: 0.7797 (m100) cc_final: 0.7426 (m100) REVERT: L 167 ASP cc_start: 0.8108 (t70) cc_final: 0.7856 (t0) REVERT: L 179 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9107 (pp) outliers start: 55 outliers final: 18 residues processed: 457 average time/residue: 1.1242 time to fit residues: 595.7311 Evaluate side-chains 422 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 396 time to evaluate : 2.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain D residue 110 GLU 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 F residue 214 LYS Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 214 LYS Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain J residue 11 CYS 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 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 179 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 253 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 242 optimal weight: 6.9990 chunk 217 optimal weight: 0.0970 chunk 37 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 164 optimal weight: 0.0670 chunk 227 optimal weight: 4.9990 chunk 196 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 163 optimal weight: 0.7980 overall best weight: 1.3920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 ASN F 76 ASN ** F 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 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 197 GLN H 202 ASN ** H 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 210 ASN J 76 ASN J 202 ASN J 204 ASN K 76 ASN ** K 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 197 GLN K 202 ASN ** 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.103119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.061545 restraints weight = 40831.827| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 3.14 r_work: 0.2580 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2448 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 21016 Z= 0.310 Angle : 0.699 9.587 28668 Z= 0.367 Chirality : 0.047 0.156 3220 Planarity : 0.005 0.059 3660 Dihedral : 5.262 24.640 2864 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.39 % Allowed : 16.96 % Favored : 79.65 % 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: 0.10 (0.16), residues: 2640 helix: -0.10 (0.46), residues: 152 sheet: 0.74 (0.16), residues: 928 loop : -0.29 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 148 HIS 0.004 0.001 HIS B 173 PHE 0.021 0.002 PHE L 209 TYR 0.017 0.002 TYR H 181 ARG 0.008 0.001 ARG L 142 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 408 time to evaluate : 2.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 GLU cc_start: 0.9184 (tp30) cc_final: 0.8900 (tp30) REVERT: E 33 LEU cc_start: 0.9725 (OUTLIER) cc_final: 0.9436 (tm) REVERT: E 50 GLU cc_start: 0.9341 (mt-10) cc_final: 0.8835 (mp0) REVERT: E 117 ILE cc_start: 0.8516 (tt) cc_final: 0.8295 (mm) REVERT: E 139 PHE cc_start: 0.8194 (p90) cc_final: 0.7929 (p90) REVERT: E 167 ASP cc_start: 0.8343 (t0) cc_final: 0.7938 (t0) REVERT: E 210 ASN cc_start: 0.8466 (t0) cc_final: 0.8142 (p0) REVERT: F 3 GLN cc_start: 0.9122 (pt0) cc_final: 0.8583 (pm20) REVERT: F 6 GLU cc_start: 0.7915 (mp0) cc_final: 0.7387 (pm20) REVERT: F 16 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8369 (mp0) REVERT: F 26 ARG cc_start: 0.8215 (pmm-80) cc_final: 0.7640 (pmm-80) REVERT: F 27 PHE cc_start: 0.8628 (m-10) cc_final: 0.8362 (m-10) REVERT: F 72 ASP cc_start: 0.8753 (t0) cc_final: 0.8229 (t0) REVERT: F 105 GLN cc_start: 0.8410 (pm20) cc_final: 0.8192 (pm20) REVERT: F 148 ASP cc_start: 0.9029 (p0) cc_final: 0.8672 (p0) REVERT: F 152 GLU cc_start: 0.7534 (pm20) cc_final: 0.7216 (pm20) REVERT: G 33 LEU cc_start: 0.9711 (OUTLIER) cc_final: 0.9441 (tm) REVERT: G 50 GLU cc_start: 0.9369 (mt-10) cc_final: 0.8865 (mp0) REVERT: G 105 GLU cc_start: 0.7220 (mp0) cc_final: 0.7008 (mp0) REVERT: G 117 ILE cc_start: 0.8508 (tt) cc_final: 0.8291 (mm) REVERT: G 139 PHE cc_start: 0.8152 (p90) cc_final: 0.7914 (p90) REVERT: G 167 ASP cc_start: 0.8362 (t0) cc_final: 0.7948 (t0) REVERT: G 173 TYR cc_start: 0.6955 (p90) cc_final: 0.6391 (p90) REVERT: G 210 ASN cc_start: 0.8490 (t0) cc_final: 0.8229 (p0) REVERT: H 3 GLN cc_start: 0.9130 (pt0) cc_final: 0.8593 (pm20) REVERT: H 6 GLU cc_start: 0.7934 (mp0) cc_final: 0.7426 (pm20) REVERT: H 16 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8365 (mp0) REVERT: H 26 ARG cc_start: 0.8153 (pmm-80) cc_final: 0.7564 (pmm-80) REVERT: H 27 PHE cc_start: 0.8626 (m-10) cc_final: 0.8365 (m-10) REVERT: H 72 ASP cc_start: 0.8704 (t0) cc_final: 0.8389 (t0) REVERT: H 105 GLN cc_start: 0.8401 (pm20) cc_final: 0.8184 (pm20) REVERT: H 148 ASP cc_start: 0.9015 (p0) cc_final: 0.8810 (p0) REVERT: H 149 TYR cc_start: 0.9071 (p90) cc_final: 0.8748 (p90) REVERT: H 160 ASN cc_start: 0.8832 (m-40) cc_final: 0.8596 (m-40) REVERT: H 176 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.8134 (mt0) REVERT: H 183 LEU cc_start: 0.9215 (tt) cc_final: 0.8703 (mt) REVERT: H 214 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7112 (ttpt) REVERT: I 33 LEU cc_start: 0.9732 (OUTLIER) cc_final: 0.9454 (tm) REVERT: I 50 GLU cc_start: 0.9251 (mt-10) cc_final: 0.8747 (mp0) REVERT: I 105 GLU cc_start: 0.7288 (mp0) cc_final: 0.7072 (mp0) REVERT: I 117 ILE cc_start: 0.8455 (tt) cc_final: 0.8218 (mm) REVERT: I 139 PHE cc_start: 0.8201 (p90) cc_final: 0.7920 (p90) REVERT: I 167 ASP cc_start: 0.8340 (t0) cc_final: 0.7940 (t0) REVERT: I 210 ASN cc_start: 0.8482 (t0) cc_final: 0.8168 (p0) REVERT: J 3 GLN cc_start: 0.9123 (pt0) cc_final: 0.8583 (pm20) REVERT: J 6 GLU cc_start: 0.7897 (mp0) cc_final: 0.7389 (pm20) REVERT: J 16 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8367 (mp0) REVERT: J 26 ARG cc_start: 0.8081 (pmm-80) cc_final: 0.7475 (pmm-80) REVERT: J 27 PHE cc_start: 0.8601 (m-10) cc_final: 0.8348 (m-10) REVERT: J 72 ASP cc_start: 0.8717 (t0) cc_final: 0.8410 (t0) REVERT: J 105 GLN cc_start: 0.8386 (pm20) cc_final: 0.8166 (pm20) REVERT: J 148 ASP cc_start: 0.9015 (p0) cc_final: 0.8801 (p0) REVERT: J 149 TYR cc_start: 0.8919 (p90) cc_final: 0.8644 (p90) REVERT: J 152 GLU cc_start: 0.7615 (pm20) cc_final: 0.7219 (pm20) REVERT: J 160 ASN cc_start: 0.8811 (m-40) cc_final: 0.8592 (m-40) REVERT: J 183 LEU cc_start: 0.9225 (tt) cc_final: 0.8718 (mt) REVERT: J 214 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7227 (ttpt) REVERT: K 3 GLN cc_start: 0.9122 (pt0) cc_final: 0.8588 (pm20) REVERT: K 6 GLU cc_start: 0.7929 (mp0) cc_final: 0.7412 (pm20) REVERT: K 16 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8347 (mp0) REVERT: K 26 ARG cc_start: 0.8179 (pmm-80) cc_final: 0.7596 (pmm-80) REVERT: K 27 PHE cc_start: 0.8621 (m-10) cc_final: 0.8358 (m-10) REVERT: K 72 ASP cc_start: 0.8724 (t0) cc_final: 0.8415 (t0) REVERT: K 105 GLN cc_start: 0.8427 (pm20) cc_final: 0.8208 (pm20) REVERT: K 148 ASP cc_start: 0.9026 (p0) cc_final: 0.8646 (p0) REVERT: K 160 ASN cc_start: 0.8790 (m-40) cc_final: 0.8570 (m-40) REVERT: K 214 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7491 (ttpt) REVERT: L 33 LEU cc_start: 0.9709 (OUTLIER) cc_final: 0.9447 (tm) REVERT: L 50 GLU cc_start: 0.9366 (mt-10) cc_final: 0.8861 (mp0) REVERT: L 117 ILE cc_start: 0.8527 (tt) cc_final: 0.8302 (mm) REVERT: L 139 PHE cc_start: 0.8124 (p90) cc_final: 0.7856 (p90) REVERT: L 167 ASP cc_start: 0.8320 (t0) cc_final: 0.7969 (t0) REVERT: L 173 TYR cc_start: 0.6970 (p90) cc_final: 0.6409 (p90) REVERT: L 179 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9097 (pp) REVERT: L 210 ASN cc_start: 0.8483 (t0) cc_final: 0.8172 (p0) outliers start: 78 outliers final: 22 residues processed: 458 average time/residue: 1.1972 time to fit residues: 630.0816 Evaluate side-chains 415 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 380 time to evaluate : 2.301 ------------------------------------------------------------------------------- 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 21 GLU Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 110 GLU 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 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 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 176 GLN 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 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 33 LEU Chi-restraints excluded: chain L residue 179 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 174 optimal weight: 0.0570 chunk 48 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 133 optimal weight: 6.9990 chunk 143 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 135 optimal weight: 0.0570 chunk 173 optimal weight: 1.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN F 176 GLN ** G 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** I 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 ASN J 197 GLN K 76 ASN ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.104668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.063230 restraints weight = 40498.372| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 3.16 r_work: 0.2625 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21016 Z= 0.192 Angle : 0.658 9.208 28668 Z= 0.343 Chirality : 0.045 0.143 3220 Planarity : 0.006 0.060 3660 Dihedral : 4.954 24.658 2864 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.61 % Allowed : 18.35 % Favored : 79.04 % 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: 0.20 (0.16), residues: 2640 helix: -0.06 (0.46), residues: 152 sheet: 0.77 (0.16), residues: 936 loop : -0.20 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 215 HIS 0.003 0.001 HIS B 173 PHE 0.020 0.001 PHE L 209 TYR 0.019 0.001 TYR G 140 ARG 0.011 0.001 ARG E 18 *********************** 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 457 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 397 time to evaluate : 2.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 33 LEU cc_start: 0.9690 (OUTLIER) cc_final: 0.9365 (tm) REVERT: E 50 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8578 (mp0) REVERT: E 117 ILE cc_start: 0.8536 (tt) cc_final: 0.8303 (mm) REVERT: E 139 PHE cc_start: 0.8045 (p90) cc_final: 0.7762 (p90) REVERT: E 167 ASP cc_start: 0.8416 (t0) cc_final: 0.7994 (t0) REVERT: E 179 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9038 (tp) REVERT: E 210 ASN cc_start: 0.8565 (t0) cc_final: 0.8163 (p0) REVERT: F 3 GLN cc_start: 0.9076 (pt0) cc_final: 0.8592 (pm20) REVERT: F 6 GLU cc_start: 0.7575 (mp0) cc_final: 0.6783 (pm20) REVERT: F 26 ARG cc_start: 0.8115 (pmm-80) cc_final: 0.7520 (pmm-80) REVERT: F 27 PHE cc_start: 0.8412 (m-10) cc_final: 0.8201 (m-10) REVERT: F 72 ASP cc_start: 0.8742 (t0) cc_final: 0.8215 (t0) REVERT: F 148 ASP cc_start: 0.8953 (p0) cc_final: 0.8665 (p0) REVERT: F 152 GLU cc_start: 0.7498 (pm20) cc_final: 0.7142 (pm20) REVERT: G 33 LEU cc_start: 0.9674 (OUTLIER) cc_final: 0.9380 (tm) REVERT: G 50 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8597 (mp0) REVERT: G 105 GLU cc_start: 0.7269 (mp0) cc_final: 0.7064 (mp0) REVERT: G 117 ILE cc_start: 0.8530 (tt) cc_final: 0.8298 (mm) REVERT: G 139 PHE cc_start: 0.7903 (p90) cc_final: 0.7566 (p90) REVERT: G 167 ASP cc_start: 0.8436 (t0) cc_final: 0.8021 (t0) REVERT: G 179 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9047 (tp) REVERT: G 210 ASN cc_start: 0.8580 (t0) cc_final: 0.8206 (p0) REVERT: H 3 GLN cc_start: 0.9092 (pt0) cc_final: 0.8605 (pm20) REVERT: H 6 GLU cc_start: 0.7581 (mp0) cc_final: 0.6770 (pm20) REVERT: H 26 ARG cc_start: 0.8110 (pmm-80) cc_final: 0.7505 (pmm-80) REVERT: H 27 PHE cc_start: 0.8414 (m-10) cc_final: 0.8206 (m-10) REVERT: H 72 ASP cc_start: 0.8701 (t0) cc_final: 0.8369 (t0) REVERT: H 149 TYR cc_start: 0.8956 (p90) cc_final: 0.8596 (p90) REVERT: H 164 LEU cc_start: 0.9503 (mp) cc_final: 0.9081 (pt) REVERT: H 183 LEU cc_start: 0.9160 (tt) cc_final: 0.8669 (mt) REVERT: H 214 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7225 (ttpt) REVERT: I 33 LEU cc_start: 0.9699 (OUTLIER) cc_final: 0.9400 (tm) REVERT: I 50 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8485 (mp0) REVERT: I 105 GLU cc_start: 0.7260 (mp0) cc_final: 0.7060 (mp0) REVERT: I 117 ILE cc_start: 0.8463 (tt) cc_final: 0.8253 (mm) REVERT: I 167 ASP cc_start: 0.8437 (t0) cc_final: 0.8013 (t0) REVERT: I 179 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9000 (tp) REVERT: I 210 ASN cc_start: 0.8553 (t0) cc_final: 0.8161 (p0) REVERT: J 3 GLN cc_start: 0.9085 (pt0) cc_final: 0.8618 (pm20) REVERT: J 6 GLU cc_start: 0.7531 (mp0) cc_final: 0.6859 (pm20) REVERT: J 26 ARG cc_start: 0.8053 (pmm-80) cc_final: 0.7456 (pmm-80) REVERT: J 27 PHE cc_start: 0.8402 (m-10) cc_final: 0.8196 (m-10) REVERT: J 72 ASP cc_start: 0.8702 (t0) cc_final: 0.8373 (t0) REVERT: J 105 GLN cc_start: 0.8226 (pm20) cc_final: 0.7612 (pm20) REVERT: J 149 TYR cc_start: 0.8769 (p90) cc_final: 0.8408 (p90) REVERT: J 152 GLU cc_start: 0.7498 (pm20) cc_final: 0.7123 (pm20) REVERT: J 164 LEU cc_start: 0.9497 (mp) cc_final: 0.9079 (pt) REVERT: J 183 LEU cc_start: 0.9163 (tt) cc_final: 0.8681 (mt) REVERT: J 214 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7252 (ttpt) REVERT: K 3 GLN cc_start: 0.9094 (pt0) cc_final: 0.8611 (pm20) REVERT: K 6 GLU cc_start: 0.7524 (mp0) cc_final: 0.6712 (pm20) REVERT: K 26 ARG cc_start: 0.8082 (pmm-80) cc_final: 0.7483 (pmm-80) REVERT: K 27 PHE cc_start: 0.8402 (m-10) cc_final: 0.8189 (m-10) REVERT: K 72 ASP cc_start: 0.8692 (t0) cc_final: 0.8361 (t0) REVERT: K 148 ASP cc_start: 0.8988 (p0) cc_final: 0.8646 (p0) REVERT: K 164 LEU cc_start: 0.9490 (mp) cc_final: 0.9072 (pt) REVERT: K 200 ILE cc_start: 0.9046 (pt) cc_final: 0.8839 (pp) REVERT: K 214 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7637 (ttpt) REVERT: L 33 LEU cc_start: 0.9672 (OUTLIER) cc_final: 0.9382 (tm) REVERT: L 50 GLU cc_start: 0.9119 (mt-10) cc_final: 0.8599 (mp0) REVERT: L 117 ILE cc_start: 0.8535 (tt) cc_final: 0.8302 (mm) REVERT: L 139 PHE cc_start: 0.7913 (p90) cc_final: 0.7577 (p90) REVERT: L 167 ASP cc_start: 0.8440 (t0) cc_final: 0.8010 (t0) REVERT: L 179 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9042 (tp) REVERT: L 210 ASN cc_start: 0.8603 (t0) cc_final: 0.8193 (p0) outliers start: 60 outliers final: 20 residues processed: 422 average time/residue: 1.2007 time to fit residues: 584.5003 Evaluate side-chains 412 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 381 time to evaluate : 2.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 190 SER 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 E residue 19 VAL 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 176 GLN Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 171 CYS Chi-restraints excluded: chain G residue 179 LEU 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 88 CYS Chi-restraints excluded: chain I residue 171 CYS Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain J residue 11 CYS Chi-restraints excluded: chain J residue 214 LYS 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 33 LEU Chi-restraints excluded: chain L residue 88 CYS 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: 3.9990 chunk 131 optimal weight: 1.9990 chunk 186 optimal weight: 0.3980 chunk 207 optimal weight: 5.9990 chunk 11 optimal weight: 0.0980 chunk 78 optimal weight: 0.4980 chunk 3 optimal weight: 0.6980 chunk 165 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 61 optimal weight: 0.0870 chunk 87 optimal weight: 1.9990 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 221AGLN ** E 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN F 176 GLN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.105016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.063707 restraints weight = 40387.998| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 3.16 r_work: 0.2640 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21016 Z= 0.182 Angle : 0.650 9.100 28668 Z= 0.339 Chirality : 0.044 0.145 3220 Planarity : 0.005 0.062 3660 Dihedral : 4.812 23.736 2864 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.30 % Allowed : 19.39 % Favored : 78.30 % 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: 0.36 (0.16), residues: 2640 helix: 0.38 (0.48), residues: 128 sheet: 0.81 (0.16), residues: 948 loop : -0.07 (0.17), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 215 HIS 0.003 0.001 HIS B 173 PHE 0.013 0.001 PHE L 209 TYR 0.022 0.001 TYR I 140 ARG 0.011 0.001 ARG I 18 *********************** 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 443 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 390 time to evaluate : 2.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 149 GLU cc_start: 0.8611 (mp0) cc_final: 0.8404 (mp0) REVERT: E 23 CYS cc_start: 0.5960 (t) cc_final: 0.5696 (t) REVERT: E 33 LEU cc_start: 0.9693 (OUTLIER) cc_final: 0.9329 (tm) REVERT: E 50 GLU cc_start: 0.9057 (mt-10) cc_final: 0.8557 (mp0) REVERT: E 75 ILE cc_start: 0.9455 (mp) cc_final: 0.8843 (tp) REVERT: E 117 ILE cc_start: 0.8550 (tt) cc_final: 0.8323 (mm) REVERT: E 139 PHE cc_start: 0.8001 (p90) cc_final: 0.7727 (p90) REVERT: E 167 ASP cc_start: 0.8467 (t0) cc_final: 0.8066 (t0) REVERT: E 185 ASP cc_start: 0.9290 (m-30) cc_final: 0.8582 (p0) REVERT: E 210 ASN cc_start: 0.8612 (t0) cc_final: 0.8181 (p0) REVERT: F 3 GLN cc_start: 0.9072 (pt0) cc_final: 0.8596 (pm20) REVERT: F 26 ARG cc_start: 0.8131 (pmm-80) cc_final: 0.7505 (pmm-80) REVERT: F 27 PHE cc_start: 0.8397 (m-10) cc_final: 0.8192 (m-10) REVERT: F 72 ASP cc_start: 0.8741 (t0) cc_final: 0.8211 (t0) REVERT: F 148 ASP cc_start: 0.8976 (p0) cc_final: 0.8640 (p0) REVERT: F 152 GLU cc_start: 0.7581 (pm20) cc_final: 0.7167 (pm20) REVERT: F 164 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9079 (pt) REVERT: F 176 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8090 (mp10) REVERT: G 23 CYS cc_start: 0.5984 (t) cc_final: 0.5724 (t) REVERT: G 33 LEU cc_start: 0.9682 (OUTLIER) cc_final: 0.9334 (tm) REVERT: G 50 GLU cc_start: 0.9096 (mt-10) cc_final: 0.8594 (mp0) REVERT: G 75 ILE cc_start: 0.9459 (mp) cc_final: 0.8832 (tp) REVERT: G 105 GLU cc_start: 0.7279 (mp0) cc_final: 0.7055 (mp0) REVERT: G 117 ILE cc_start: 0.8541 (tt) cc_final: 0.8314 (mm) REVERT: G 139 PHE cc_start: 0.7895 (p90) cc_final: 0.7621 (p90) REVERT: G 167 ASP cc_start: 0.8444 (t0) cc_final: 0.8042 (t0) REVERT: G 173 TYR cc_start: 0.6476 (p90) cc_final: 0.5809 (p90) REVERT: G 185 ASP cc_start: 0.9286 (m-30) cc_final: 0.8599 (p0) REVERT: G 210 ASN cc_start: 0.8567 (t0) cc_final: 0.8145 (p0) REVERT: H 3 GLN cc_start: 0.9083 (pt0) cc_final: 0.8610 (pm20) REVERT: H 26 ARG cc_start: 0.8136 (pmm-80) cc_final: 0.7514 (pmm-80) REVERT: H 72 ASP cc_start: 0.8686 (t0) cc_final: 0.8344 (t0) REVERT: H 149 TYR cc_start: 0.8881 (p90) cc_final: 0.8541 (p90) REVERT: H 152 GLU cc_start: 0.7415 (pm20) cc_final: 0.7115 (pm20) REVERT: H 164 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9087 (pt) REVERT: H 183 LEU cc_start: 0.9109 (tt) cc_final: 0.8641 (mt) REVERT: H 214 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7192 (ttpt) REVERT: I 33 LEU cc_start: 0.9704 (OUTLIER) cc_final: 0.9360 (tm) REVERT: I 50 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8451 (mp0) REVERT: I 75 ILE cc_start: 0.9446 (mp) cc_final: 0.8877 (tp) REVERT: I 105 GLU cc_start: 0.7269 (mp0) cc_final: 0.7049 (mp0) REVERT: I 117 ILE cc_start: 0.8552 (tt) cc_final: 0.8328 (mm) REVERT: I 167 ASP cc_start: 0.8454 (t0) cc_final: 0.8046 (t0) REVERT: I 173 TYR cc_start: 0.6194 (p90) cc_final: 0.5368 (p90) REVERT: I 185 ASP cc_start: 0.9278 (m-30) cc_final: 0.8593 (p0) REVERT: I 210 ASN cc_start: 0.8606 (t0) cc_final: 0.8178 (p0) REVERT: J 3 GLN cc_start: 0.9078 (pt0) cc_final: 0.8614 (pm20) REVERT: J 6 GLU cc_start: 0.7493 (mp0) cc_final: 0.6801 (pm20) REVERT: J 26 ARG cc_start: 0.8087 (pmm-80) cc_final: 0.7451 (pmm-80) REVERT: J 72 ASP cc_start: 0.8683 (t0) cc_final: 0.8344 (t0) REVERT: J 105 GLN cc_start: 0.8220 (pm20) cc_final: 0.7891 (pm20) REVERT: J 149 TYR cc_start: 0.8691 (p90) cc_final: 0.8367 (p90) REVERT: J 152 GLU cc_start: 0.7558 (pm20) cc_final: 0.7079 (pm20) REVERT: J 164 LEU cc_start: 0.9477 (OUTLIER) cc_final: 0.9078 (pt) REVERT: J 183 LEU cc_start: 0.9116 (tt) cc_final: 0.8647 (mt) REVERT: J 214 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7222 (ttpt) REVERT: K 3 GLN cc_start: 0.9084 (pt0) cc_final: 0.8611 (pm20) REVERT: K 26 ARG cc_start: 0.8107 (pmm-80) cc_final: 0.7485 (pmm-80) REVERT: K 27 PHE cc_start: 0.8388 (m-10) cc_final: 0.8181 (m-10) REVERT: K 72 ASP cc_start: 0.8687 (t0) cc_final: 0.8353 (t0) REVERT: K 148 ASP cc_start: 0.8957 (p0) cc_final: 0.8597 (p0) REVERT: K 164 LEU cc_start: 0.9468 (mp) cc_final: 0.9077 (pt) REVERT: K 214 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7623 (ttpt) REVERT: L 11 LEU cc_start: 0.8786 (pt) cc_final: 0.8532 (pp) REVERT: L 23 CYS cc_start: 0.6068 (t) cc_final: 0.5771 (t) REVERT: L 33 LEU cc_start: 0.9671 (OUTLIER) cc_final: 0.9320 (tm) REVERT: L 50 GLU cc_start: 0.9108 (mt-10) cc_final: 0.8600 (mp0) REVERT: L 75 ILE cc_start: 0.9454 (mp) cc_final: 0.8746 (tp) REVERT: L 117 ILE cc_start: 0.8550 (tt) cc_final: 0.8324 (mm) REVERT: L 139 PHE cc_start: 0.7908 (p90) cc_final: 0.7633 (p90) REVERT: L 167 ASP cc_start: 0.8430 (t0) cc_final: 0.8013 (t0) REVERT: L 173 TYR cc_start: 0.6464 (p90) cc_final: 0.5802 (p90) REVERT: L 185 ASP cc_start: 0.9304 (m-30) cc_final: 0.8596 (p0) REVERT: L 210 ASN cc_start: 0.8662 (t0) cc_final: 0.8241 (p0) outliers start: 53 outliers final: 19 residues processed: 415 average time/residue: 1.1339 time to fit residues: 544.9706 Evaluate side-chains 402 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 372 time to evaluate : 2.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 171 CYS Chi-restraints excluded: chain F residue 11 CYS Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 176 GLN Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 171 CYS Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain H residue 214 LYS Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 171 CYS Chi-restraints excluded: chain J residue 11 CYS Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 200 ILE Chi-restraints excluded: chain J residue 214 LYS Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain K residue 200 ILE Chi-restraints excluded: chain K residue 214 LYS Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 171 CYS 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: 2.9990 chunk 77 optimal weight: 0.8980 chunk 179 optimal weight: 0.0980 chunk 68 optimal weight: 1.9990 chunk 165 optimal weight: 5.9990 chunk 111 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 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 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 GLN ** G 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3624 r_free = 0.3624 target = 0.103950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.062576 restraints weight = 40363.093| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 3.15 r_work: 0.2614 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21016 Z= 0.232 Angle : 0.668 8.888 28668 Z= 0.348 Chirality : 0.045 0.172 3220 Planarity : 0.005 0.063 3660 Dihedral : 4.780 24.038 2864 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.13 % Allowed : 20.17 % Favored : 77.70 % 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: 0.42 (0.48), residues: 128 sheet: 0.84 (0.16), residues: 944 loop : -0.11 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 148 HIS 0.003 0.001 HIS C 166 PHE 0.022 0.001 PHE J 27 TYR 0.017 0.001 TYR G 140 ARG 0.009 0.001 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 372 time to evaluate : 2.510 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: E 33 LEU cc_start: 0.9703 (OUTLIER) cc_final: 0.9351 (tm) REVERT: E 50 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8569 (mp0) REVERT: E 81 GLU cc_start: 0.8987 (pm20) cc_final: 0.8762 (pm20) REVERT: E 82 ASP cc_start: 0.8532 (m-30) cc_final: 0.8289 (m-30) REVERT: E 117 ILE cc_start: 0.8594 (tt) cc_final: 0.8362 (mm) REVERT: E 139 PHE cc_start: 0.7999 (p90) cc_final: 0.7720 (p90) REVERT: E 167 ASP cc_start: 0.8517 (t0) cc_final: 0.8125 (t0) REVERT: E 185 ASP cc_start: 0.9366 (m-30) cc_final: 0.8645 (p0) REVERT: E 210 ASN cc_start: 0.8635 (t0) cc_final: 0.8204 (p0) REVERT: F 3 GLN cc_start: 0.9104 (pt0) cc_final: 0.8607 (pm20) REVERT: F 26 ARG cc_start: 0.8192 (pmm-80) cc_final: 0.7585 (pmm-80) REVERT: F 72 ASP cc_start: 0.8737 (t0) cc_final: 0.8226 (t0) REVERT: F 148 ASP cc_start: 0.8974 (p0) cc_final: 0.8661 (p0) REVERT: F 152 GLU cc_start: 0.7608 (pm20) cc_final: 0.7098 (pm20) REVERT: F 164 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9061 (pt) REVERT: F 176 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8260 (mp10) REVERT: G 33 LEU cc_start: 0.9687 (OUTLIER) cc_final: 0.9345 (tm) REVERT: G 50 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8600 (mp0) REVERT: G 75 ILE cc_start: 0.9444 (mp) cc_final: 0.8835 (tp) REVERT: G 81 GLU cc_start: 0.8995 (pm20) cc_final: 0.8783 (pm20) REVERT: G 105 GLU cc_start: 0.7292 (mp0) cc_final: 0.7033 (mp0) REVERT: G 117 ILE cc_start: 0.8589 (tt) cc_final: 0.8355 (mm) REVERT: G 139 PHE cc_start: 0.7949 (p90) cc_final: 0.7707 (p90) REVERT: G 167 ASP cc_start: 0.8508 (t0) cc_final: 0.8111 (t0) REVERT: G 185 ASP cc_start: 0.9345 (m-30) cc_final: 0.8630 (p0) REVERT: G 210 ASN cc_start: 0.8632 (t0) cc_final: 0.8242 (p0) REVERT: H 3 GLN cc_start: 0.9047 (pt0) cc_final: 0.8565 (pm20) REVERT: H 26 ARG cc_start: 0.8205 (pmm-80) cc_final: 0.7524 (pmm-80) REVERT: H 27 PHE cc_start: 0.8277 (m-10) cc_final: 0.7948 (m-80) REVERT: H 72 ASP cc_start: 0.8724 (t0) cc_final: 0.8394 (t0) REVERT: H 149 TYR cc_start: 0.8894 (p90) cc_final: 0.8596 (p90) REVERT: H 164 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9079 (pt) REVERT: H 183 LEU cc_start: 0.9066 (tt) cc_final: 0.8567 (mt) REVERT: I 33 LEU cc_start: 0.9718 (OUTLIER) cc_final: 0.9379 (tm) REVERT: I 50 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8488 (mp0) REVERT: I 75 ILE cc_start: 0.9446 (mp) cc_final: 0.8858 (tp) REVERT: I 81 GLU cc_start: 0.8998 (pm20) cc_final: 0.8785 (pm20) REVERT: I 105 GLU cc_start: 0.7265 (mp0) cc_final: 0.7019 (mp0) REVERT: I 117 ILE cc_start: 0.8581 (tt) cc_final: 0.8352 (mm) REVERT: I 167 ASP cc_start: 0.8529 (t0) cc_final: 0.8130 (t0) REVERT: I 173 TYR cc_start: 0.6275 (p90) cc_final: 0.5352 (p90) REVERT: I 185 ASP cc_start: 0.9336 (m-30) cc_final: 0.8633 (p0) REVERT: I 210 ASN cc_start: 0.8634 (t0) cc_final: 0.8205 (p0) REVERT: J 3 GLN cc_start: 0.9029 (pt0) cc_final: 0.8547 (pm20) REVERT: J 6 GLU cc_start: 0.7547 (mp0) cc_final: 0.6779 (pm20) REVERT: J 26 ARG cc_start: 0.8119 (pmm-80) cc_final: 0.7356 (pmm-80) REVERT: J 27 PHE cc_start: 0.8259 (m-10) cc_final: 0.7930 (m-80) REVERT: J 72 ASP cc_start: 0.8692 (t0) cc_final: 0.8354 (t0) REVERT: J 105 GLN cc_start: 0.8212 (pm20) cc_final: 0.7812 (pm20) REVERT: J 149 TYR cc_start: 0.8734 (p90) cc_final: 0.8089 (p90) REVERT: J 152 GLU cc_start: 0.7611 (pm20) cc_final: 0.7145 (pm20) REVERT: J 164 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9071 (pt) REVERT: J 183 LEU cc_start: 0.9081 (tt) cc_final: 0.8706 (mt) REVERT: K 3 GLN cc_start: 0.9111 (pt0) cc_final: 0.8619 (pm20) REVERT: K 26 ARG cc_start: 0.8166 (pmm-80) cc_final: 0.7560 (pmm-80) REVERT: K 72 ASP cc_start: 0.8722 (t0) cc_final: 0.8392 (t0) REVERT: K 148 ASP cc_start: 0.8944 (p0) cc_final: 0.8582 (p0) REVERT: K 152 GLU cc_start: 0.7496 (pm20) cc_final: 0.7157 (pm20) REVERT: K 164 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9042 (pt) REVERT: K 214 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7517 (ttpt) REVERT: L 33 LEU cc_start: 0.9686 (OUTLIER) cc_final: 0.9332 (tm) REVERT: L 50 GLU cc_start: 0.9101 (mt-10) cc_final: 0.8601 (mp0) REVERT: L 117 ILE cc_start: 0.8592 (tt) cc_final: 0.8358 (mm) REVERT: L 139 PHE cc_start: 0.7950 (p90) cc_final: 0.7710 (p90) REVERT: L 167 ASP cc_start: 0.8525 (t0) cc_final: 0.8124 (t0) REVERT: L 185 ASP cc_start: 0.9359 (m-30) cc_final: 0.8653 (p0) REVERT: L 210 ASN cc_start: 0.8661 (t0) cc_final: 0.8252 (p0) outliers start: 49 outliers final: 20 residues processed: 396 average time/residue: 1.2262 time to fit residues: 555.7334 Evaluate side-chains 385 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 355 time to evaluate : 2.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain C residue 110 GLU 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 104 VAL Chi-restraints excluded: chain E residue 171 CYS Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 176 GLN Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 171 CYS Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 171 CYS Chi-restraints excluded: chain J residue 11 CYS Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 200 ILE 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 K residue 214 LYS 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: 4.9990 chunk 0 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 260 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 151 optimal weight: 6.9990 chunk 125 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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** F 76 ASN ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 GLN G 124 GLN ** G 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 124 GLN ** I 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 124 GLN ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.099792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.058205 restraints weight = 40948.448| |-----------------------------------------------------------------------------| r_work (start): 0.2684 rms_B_bonded: 3.12 r_work: 0.2526 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2397 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.073 21016 Z= 0.645 Angle : 0.805 12.445 28668 Z= 0.422 Chirality : 0.052 0.294 3220 Planarity : 0.007 0.068 3660 Dihedral : 5.219 24.855 2864 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.70 % Allowed : 20.13 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.16), residues: 2640 helix: -0.28 (0.45), residues: 152 sheet: 0.53 (0.16), residues: 968 loop : -0.38 (0.16), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 141 HIS 0.005 0.001 HIS C 173 PHE 0.025 0.002 PHE F 27 TYR 0.023 0.002 TYR E 173 ARG 0.014 0.001 ARG L 18 *********************** 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 420 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 358 time to evaluate : 2.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7958 (tm-30) REVERT: B 164 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7953 (tm-30) REVERT: E 23 CYS cc_start: 0.7135 (t) cc_final: 0.6759 (t) REVERT: E 33 LEU cc_start: 0.9777 (OUTLIER) cc_final: 0.9475 (tm) REVERT: E 50 GLU cc_start: 0.9365 (mt-10) cc_final: 0.8885 (mp0) REVERT: E 81 GLU cc_start: 0.9043 (pm20) cc_final: 0.8802 (pm20) REVERT: E 117 ILE cc_start: 0.8634 (tt) cc_final: 0.8391 (mm) REVERT: E 139 PHE cc_start: 0.8244 (p90) cc_final: 0.8027 (p90) REVERT: E 167 ASP cc_start: 0.8547 (t0) cc_final: 0.8144 (t0) REVERT: E 185 ASP cc_start: 0.9410 (m-30) cc_final: 0.8585 (p0) REVERT: E 186 TYR cc_start: 0.8903 (t80) cc_final: 0.8694 (t80) REVERT: E 210 ASN cc_start: 0.8617 (t0) cc_final: 0.8282 (p0) REVERT: F 3 GLN cc_start: 0.9169 (pt0) cc_final: 0.8588 (pm20) REVERT: F 26 ARG cc_start: 0.8332 (pmm-80) cc_final: 0.7698 (pmm-80) REVERT: F 27 PHE cc_start: 0.8421 (m-10) cc_final: 0.8083 (m-10) REVERT: F 72 ASP cc_start: 0.8882 (t0) cc_final: 0.8382 (t0) REVERT: F 148 ASP cc_start: 0.9073 (p0) cc_final: 0.8729 (p0) REVERT: F 152 GLU cc_start: 0.7653 (pm20) cc_final: 0.7138 (pm20) REVERT: F 176 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8343 (mp10) REVERT: G 33 LEU cc_start: 0.9750 (OUTLIER) cc_final: 0.9471 (tm) REVERT: G 50 GLU cc_start: 0.9361 (mt-10) cc_final: 0.8881 (mp0) REVERT: G 81 GLU cc_start: 0.9057 (pm20) cc_final: 0.8832 (pm20) REVERT: G 82 ASP cc_start: 0.8803 (m-30) cc_final: 0.8584 (m-30) REVERT: G 105 GLU cc_start: 0.7496 (mp0) cc_final: 0.7256 (mp0) REVERT: G 117 ILE cc_start: 0.8631 (tt) cc_final: 0.8385 (mm) REVERT: G 167 ASP cc_start: 0.8511 (t0) cc_final: 0.8095 (t0) REVERT: G 185 ASP cc_start: 0.9404 (m-30) cc_final: 0.8578 (p0) REVERT: G 186 TYR cc_start: 0.8853 (t80) cc_final: 0.8650 (t80) REVERT: G 210 ASN cc_start: 0.8609 (t0) cc_final: 0.8304 (p0) REVERT: H 3 GLN cc_start: 0.9165 (pt0) cc_final: 0.8541 (pm20) REVERT: H 26 ARG cc_start: 0.8306 (pmm-80) cc_final: 0.7454 (pmm-80) REVERT: H 27 PHE cc_start: 0.8368 (m-10) cc_final: 0.8107 (m-80) REVERT: H 72 ASP cc_start: 0.8768 (t0) cc_final: 0.8437 (t0) REVERT: H 152 GLU cc_start: 0.7615 (pm20) cc_final: 0.7394 (pm20) REVERT: I 23 CYS cc_start: 0.7288 (t) cc_final: 0.7008 (t) REVERT: I 33 LEU cc_start: 0.9772 (OUTLIER) cc_final: 0.9468 (tm) REVERT: I 50 GLU cc_start: 0.9277 (mt-10) cc_final: 0.8820 (mp0) REVERT: I 81 GLU cc_start: 0.9076 (pm20) cc_final: 0.8851 (pm20) REVERT: I 82 ASP cc_start: 0.8791 (m-30) cc_final: 0.8548 (m-30) REVERT: I 105 GLU cc_start: 0.7498 (mp0) cc_final: 0.7254 (mp0) REVERT: I 117 ILE cc_start: 0.8594 (tt) cc_final: 0.8351 (mm) REVERT: I 167 ASP cc_start: 0.8549 (t0) cc_final: 0.8137 (t0) REVERT: I 173 TYR cc_start: 0.6790 (p90) cc_final: 0.6063 (p90) REVERT: I 185 ASP cc_start: 0.9382 (m-30) cc_final: 0.8546 (p0) REVERT: I 186 TYR cc_start: 0.8909 (t80) cc_final: 0.8667 (t80) REVERT: I 210 ASN cc_start: 0.8619 (t0) cc_final: 0.8288 (p0) REVERT: J 3 GLN cc_start: 0.9142 (pt0) cc_final: 0.8516 (pm20) REVERT: J 6 GLU cc_start: 0.7681 (mp0) cc_final: 0.6724 (mp0) REVERT: J 26 ARG cc_start: 0.8219 (pmm-80) cc_final: 0.7316 (pmm-80) REVERT: J 27 PHE cc_start: 0.8405 (m-10) cc_final: 0.8151 (m-80) REVERT: J 72 ASP cc_start: 0.8765 (t0) cc_final: 0.8425 (t0) REVERT: J 105 GLN cc_start: 0.8361 (pm20) cc_final: 0.7854 (pm20) REVERT: J 152 GLU cc_start: 0.7644 (pm20) cc_final: 0.7195 (pm20) REVERT: K 3 GLN cc_start: 0.9175 (pt0) cc_final: 0.8609 (pm20) REVERT: K 26 ARG cc_start: 0.8304 (pmm-80) cc_final: 0.7643 (pmm-80) REVERT: K 27 PHE cc_start: 0.8411 (m-10) cc_final: 0.8070 (m-10) REVERT: K 72 ASP cc_start: 0.8780 (t0) cc_final: 0.8453 (t0) REVERT: K 148 ASP cc_start: 0.9080 (p0) cc_final: 0.8685 (p0) REVERT: L 23 CYS cc_start: 0.7208 (t) cc_final: 0.6839 (t) REVERT: L 33 LEU cc_start: 0.9748 (OUTLIER) cc_final: 0.9464 (tm) REVERT: L 50 GLU cc_start: 0.9377 (mt-10) cc_final: 0.8898 (mp0) REVERT: L 117 ILE cc_start: 0.8614 (tt) cc_final: 0.8345 (mm) REVERT: L 167 ASP cc_start: 0.8540 (t0) cc_final: 0.8127 (t0) REVERT: L 185 ASP cc_start: 0.9419 (m-30) cc_final: 0.8612 (p0) REVERT: L 186 TYR cc_start: 0.8916 (t80) cc_final: 0.8714 (t80) REVERT: L 210 ASN cc_start: 0.8634 (t0) cc_final: 0.8313 (p0) outliers start: 62 outliers final: 39 residues processed: 395 average time/residue: 1.1946 time to fit residues: 541.1957 Evaluate side-chains 384 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 340 time to evaluate : 2.754 ------------------------------------------------------------------------------- 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 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 26 ILE Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 171 CYS Chi-restraints excluded: chain F residue 11 CYS Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 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 19 VAL Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 171 CYS Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 26 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 125 VAL 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 200 ILE Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 132 VAL 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: 5.9990 chunk 238 optimal weight: 0.7980 chunk 186 optimal weight: 4.9990 chunk 192 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 214 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 207 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 GLN ** G 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3594 r_free = 0.3594 target = 0.102199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.060756 restraints weight = 40287.554| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 3.13 r_work: 0.2587 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2458 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21016 Z= 0.259 Angle : 0.728 10.798 28668 Z= 0.375 Chirality : 0.047 0.211 3220 Planarity : 0.006 0.063 3660 Dihedral : 5.038 24.214 2864 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.09 % Allowed : 21.57 % 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: 0.06 (0.16), residues: 2640 helix: -0.25 (0.45), residues: 152 sheet: 0.81 (0.16), residues: 932 loop : -0.38 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 159 HIS 0.003 0.001 HIS B 173 PHE 0.020 0.001 PHE F 27 TYR 0.021 0.002 TYR L 140 ARG 0.014 0.001 ARG I 18 *********************** 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 401 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 353 time to evaluate : 2.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 164 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7978 (tm-30) REVERT: C 164 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7927 (tm-30) REVERT: D 164 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7940 (tm-30) REVERT: E 33 LEU cc_start: 0.9744 (OUTLIER) cc_final: 0.9403 (tm) REVERT: E 50 GLU cc_start: 0.9342 (mt-10) cc_final: 0.8857 (mp0) REVERT: E 81 GLU cc_start: 0.9004 (pm20) cc_final: 0.8702 (pm20) REVERT: E 82 ASP cc_start: 0.8538 (m-30) cc_final: 0.8336 (m-30) REVERT: E 117 ILE cc_start: 0.8648 (tt) cc_final: 0.8435 (mm) REVERT: E 139 PHE cc_start: 0.8143 (p90) cc_final: 0.7849 (p90) REVERT: E 167 ASP cc_start: 0.8603 (t0) cc_final: 0.8213 (t0) REVERT: E 185 ASP cc_start: 0.9400 (m-30) cc_final: 0.8580 (p0) REVERT: E 186 TYR cc_start: 0.8879 (t80) cc_final: 0.8661 (t80) REVERT: E 210 ASN cc_start: 0.8658 (t0) cc_final: 0.8268 (p0) REVERT: F 3 GLN cc_start: 0.9181 (pt0) cc_final: 0.8651 (pm20) REVERT: F 26 ARG cc_start: 0.8309 (pmm-80) cc_final: 0.7643 (pmm-80) REVERT: F 27 PHE cc_start: 0.8368 (m-10) cc_final: 0.8004 (m-10) REVERT: F 72 ASP cc_start: 0.8832 (t0) cc_final: 0.8319 (t0) REVERT: F 148 ASP cc_start: 0.9050 (p0) cc_final: 0.8767 (p0) REVERT: F 152 GLU cc_start: 0.7581 (pm20) cc_final: 0.7038 (pm20) REVERT: F 176 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8353 (mp10) REVERT: G 33 LEU cc_start: 0.9742 (OUTLIER) cc_final: 0.9448 (tm) REVERT: G 50 GLU cc_start: 0.9344 (mt-10) cc_final: 0.8878 (mp0) REVERT: G 75 ILE cc_start: 0.9502 (mp) cc_final: 0.8912 (tp) REVERT: G 81 GLU cc_start: 0.8996 (pm20) cc_final: 0.8754 (pm20) REVERT: G 82 ASP cc_start: 0.8749 (m-30) cc_final: 0.8470 (m-30) REVERT: G 105 GLU cc_start: 0.7424 (mp0) cc_final: 0.7183 (mp0) REVERT: G 117 ILE cc_start: 0.8633 (tt) cc_final: 0.8400 (mm) REVERT: G 167 ASP cc_start: 0.8614 (t0) cc_final: 0.8237 (t0) REVERT: G 185 ASP cc_start: 0.9392 (m-30) cc_final: 0.8612 (p0) REVERT: G 210 ASN cc_start: 0.8625 (t0) cc_final: 0.8263 (p0) REVERT: H 3 GLN cc_start: 0.9170 (pt0) cc_final: 0.8651 (pm20) REVERT: H 26 ARG cc_start: 0.8332 (pmm-80) cc_final: 0.7560 (pmm-80) REVERT: H 27 PHE cc_start: 0.8355 (m-10) cc_final: 0.8030 (m-80) REVERT: H 72 ASP cc_start: 0.8789 (t0) cc_final: 0.8458 (t0) REVERT: H 152 GLU cc_start: 0.7654 (pm20) cc_final: 0.7409 (pm20) REVERT: I 33 LEU cc_start: 0.9756 (OUTLIER) cc_final: 0.9421 (tm) REVERT: I 50 GLU cc_start: 0.9263 (mt-10) cc_final: 0.8776 (mp0) REVERT: I 75 ILE cc_start: 0.9490 (mp) cc_final: 0.8928 (tp) REVERT: I 81 GLU cc_start: 0.9006 (pm20) cc_final: 0.8766 (pm20) REVERT: I 82 ASP cc_start: 0.8714 (m-30) cc_final: 0.8432 (m-30) REVERT: I 105 GLU cc_start: 0.7445 (mp0) cc_final: 0.7206 (mp0) REVERT: I 117 ILE cc_start: 0.8608 (tt) cc_final: 0.8387 (mm) REVERT: I 142 ARG cc_start: 0.8774 (ttm-80) cc_final: 0.8523 (mmt90) REVERT: I 167 ASP cc_start: 0.8621 (t0) cc_final: 0.8236 (t0) REVERT: I 210 ASN cc_start: 0.8666 (t0) cc_final: 0.8282 (p0) REVERT: J 3 GLN cc_start: 0.9165 (pt0) cc_final: 0.8630 (pm20) REVERT: J 6 GLU cc_start: 0.7608 (mp0) cc_final: 0.6797 (pm20) REVERT: J 26 ARG cc_start: 0.8258 (pmm-80) cc_final: 0.7550 (pmm-80) REVERT: J 27 PHE cc_start: 0.8336 (m-10) cc_final: 0.7997 (m-10) REVERT: J 72 ASP cc_start: 0.8780 (t0) cc_final: 0.8436 (t0) REVERT: J 105 GLN cc_start: 0.8361 (pm20) cc_final: 0.7809 (pm20) REVERT: J 152 GLU cc_start: 0.7465 (pm20) cc_final: 0.7145 (pm20) REVERT: K 3 GLN cc_start: 0.9173 (pt0) cc_final: 0.8642 (pm20) REVERT: K 26 ARG cc_start: 0.8290 (pmm-80) cc_final: 0.7621 (pmm-80) REVERT: K 27 PHE cc_start: 0.8354 (m-10) cc_final: 0.7984 (m-10) REVERT: K 72 ASP cc_start: 0.8789 (t0) cc_final: 0.8462 (t0) REVERT: K 148 ASP cc_start: 0.9036 (p0) cc_final: 0.8653 (p0) REVERT: K 152 GLU cc_start: 0.7614 (pm20) cc_final: 0.7397 (pm20) REVERT: L 33 LEU cc_start: 0.9742 (OUTLIER) cc_final: 0.9460 (tm) REVERT: L 50 GLU cc_start: 0.9355 (mt-10) cc_final: 0.8882 (mp0) REVERT: L 117 ILE cc_start: 0.8598 (tt) cc_final: 0.8384 (mm) REVERT: L 167 ASP cc_start: 0.8631 (t0) cc_final: 0.8248 (t0) REVERT: L 173 TYR cc_start: 0.6780 (p90) cc_final: 0.6480 (p90) REVERT: L 185 ASP cc_start: 0.9401 (m-30) cc_final: 0.8591 (p0) REVERT: L 186 TYR cc_start: 0.8899 (t80) cc_final: 0.8683 (t80) REVERT: L 210 ASN cc_start: 0.8673 (t0) cc_final: 0.8300 (p0) outliers start: 48 outliers final: 24 residues processed: 379 average time/residue: 1.1856 time to fit residues: 515.9445 Evaluate side-chains 380 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 351 time to evaluate : 2.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain C residue 26 LYS Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 171 CYS Chi-restraints excluded: chain F residue 176 GLN Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 132 VAL 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 H residue 200 ILE Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 171 CYS Chi-restraints excluded: chain J residue 11 CYS Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 200 ILE Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 200 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 171 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 21 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 261 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 94 optimal weight: 0.1980 chunk 251 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 184 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 GLN ** G 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3600 r_free = 0.3600 target = 0.102909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.061938 restraints weight = 39948.458| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 3.12 r_work: 0.2601 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2472 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21016 Z= 0.224 Angle : 0.719 10.266 28668 Z= 0.369 Chirality : 0.046 0.186 3220 Planarity : 0.006 0.065 3660 Dihedral : 4.906 24.189 2864 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.43 % Allowed : 22.39 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.16), residues: 2640 helix: -0.30 (0.45), residues: 152 sheet: 0.89 (0.16), residues: 936 loop : -0.32 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 159 HIS 0.003 0.001 HIS B 173 PHE 0.020 0.001 PHE F 27 TYR 0.021 0.001 TYR L 140 ARG 0.015 0.001 ARG G 18 ********************** 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 395 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 362 time to evaluate : 2.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 164 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7917 (tm-30) REVERT: D 164 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7919 (tm-30) REVERT: E 33 LEU cc_start: 0.9741 (OUTLIER) cc_final: 0.9389 (tm) REVERT: E 50 GLU cc_start: 0.9324 (mt-10) cc_final: 0.8852 (mp0) REVERT: E 81 GLU cc_start: 0.9012 (pm20) cc_final: 0.8657 (pm20) REVERT: E 82 ASP cc_start: 0.8600 (m-30) cc_final: 0.8329 (m-30) REVERT: E 117 ILE cc_start: 0.8611 (tt) cc_final: 0.8394 (mm) REVERT: E 139 PHE cc_start: 0.8129 (p90) cc_final: 0.7839 (p90) REVERT: E 167 ASP cc_start: 0.8610 (t0) cc_final: 0.8337 (t0) REVERT: E 185 ASP cc_start: 0.9400 (m-30) cc_final: 0.8612 (p0) REVERT: E 186 TYR cc_start: 0.8865 (t80) cc_final: 0.8639 (t80) REVERT: E 210 ASN cc_start: 0.8723 (t0) cc_final: 0.8309 (p0) REVERT: F 3 GLN cc_start: 0.9182 (pt0) cc_final: 0.8661 (pm20) REVERT: F 26 ARG cc_start: 0.8313 (pmm-80) cc_final: 0.7607 (pmm-80) REVERT: F 27 PHE cc_start: 0.8345 (m-10) cc_final: 0.8025 (m-80) REVERT: F 72 ASP cc_start: 0.8851 (t0) cc_final: 0.8314 (t0) REVERT: F 148 ASP cc_start: 0.9014 (p0) cc_final: 0.8683 (p0) REVERT: F 152 GLU cc_start: 0.7575 (pm20) cc_final: 0.7105 (pm20) REVERT: F 176 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8451 (mp10) REVERT: G 17 ASP cc_start: 0.8174 (t0) cc_final: 0.7927 (t0) REVERT: G 33 LEU cc_start: 0.9737 (OUTLIER) cc_final: 0.9416 (tm) REVERT: G 50 GLU cc_start: 0.9322 (mt-10) cc_final: 0.8847 (mp0) REVERT: G 75 ILE cc_start: 0.9491 (mp) cc_final: 0.8916 (tp) REVERT: G 81 GLU cc_start: 0.8991 (pm20) cc_final: 0.8699 (pm20) REVERT: G 82 ASP cc_start: 0.8724 (m-30) cc_final: 0.8435 (m-30) REVERT: G 105 GLU cc_start: 0.7438 (mp0) cc_final: 0.7200 (mp0) REVERT: G 117 ILE cc_start: 0.8648 (tt) cc_final: 0.8433 (mm) REVERT: G 167 ASP cc_start: 0.8623 (t0) cc_final: 0.8365 (t0) REVERT: G 185 ASP cc_start: 0.9409 (m-30) cc_final: 0.8652 (p0) REVERT: G 186 TYR cc_start: 0.8844 (t80) cc_final: 0.8613 (t80) REVERT: G 210 ASN cc_start: 0.8727 (t0) cc_final: 0.8329 (p0) REVERT: H 3 GLN cc_start: 0.9146 (pt0) cc_final: 0.8612 (pm20) REVERT: H 26 ARG cc_start: 0.8355 (pmm-80) cc_final: 0.7624 (pmm-80) REVERT: H 27 PHE cc_start: 0.8350 (m-10) cc_final: 0.8004 (m-10) REVERT: H 72 ASP cc_start: 0.8805 (t0) cc_final: 0.8478 (t0) REVERT: H 152 GLU cc_start: 0.7755 (pm20) cc_final: 0.7438 (pm20) REVERT: H 176 GLN cc_start: 0.8545 (mt0) cc_final: 0.7831 (mp10) REVERT: I 17 ASP cc_start: 0.8266 (t0) cc_final: 0.8042 (t0) REVERT: I 33 LEU cc_start: 0.9754 (OUTLIER) cc_final: 0.9421 (tm) REVERT: I 50 GLU cc_start: 0.9248 (mt-10) cc_final: 0.8753 (mp0) REVERT: I 75 ILE cc_start: 0.9487 (mp) cc_final: 0.8931 (tp) REVERT: I 81 GLU cc_start: 0.8993 (pm20) cc_final: 0.8701 (pm20) REVERT: I 82 ASP cc_start: 0.8692 (m-30) cc_final: 0.8399 (m-30) REVERT: I 105 GLU cc_start: 0.7412 (mp0) cc_final: 0.7163 (mp0) REVERT: I 142 ARG cc_start: 0.8770 (ttm-80) cc_final: 0.8511 (mmt90) REVERT: I 167 ASP cc_start: 0.8607 (t0) cc_final: 0.8346 (t0) REVERT: I 181 LEU cc_start: 0.9262 (mm) cc_final: 0.9058 (mm) REVERT: I 185 ASP cc_start: 0.9371 (m-30) cc_final: 0.8967 (p0) REVERT: I 210 ASN cc_start: 0.8706 (t0) cc_final: 0.8265 (p0) REVERT: J 3 GLN cc_start: 0.9161 (pt0) cc_final: 0.8645 (pm20) REVERT: J 6 GLU cc_start: 0.7568 (mp0) cc_final: 0.6789 (pm20) REVERT: J 26 ARG cc_start: 0.8246 (pmm-80) cc_final: 0.7482 (pmm-80) REVERT: J 27 PHE cc_start: 0.8360 (m-10) cc_final: 0.8035 (m-80) REVERT: J 72 ASP cc_start: 0.8735 (t0) cc_final: 0.8385 (t0) REVERT: J 105 GLN cc_start: 0.8378 (pm20) cc_final: 0.7850 (pm20) REVERT: J 152 GLU cc_start: 0.7530 (pm20) cc_final: 0.7138 (pm20) REVERT: J 176 GLN cc_start: 0.8637 (mt0) cc_final: 0.7920 (mp10) REVERT: K 3 GLN cc_start: 0.9165 (pt0) cc_final: 0.8640 (pm20) REVERT: K 26 ARG cc_start: 0.8313 (pmm-80) cc_final: 0.7591 (pmm-80) REVERT: K 27 PHE cc_start: 0.8327 (m-10) cc_final: 0.8014 (m-80) REVERT: K 72 ASP cc_start: 0.8800 (t0) cc_final: 0.8476 (t0) REVERT: K 148 ASP cc_start: 0.9028 (p0) cc_final: 0.8627 (p0) REVERT: K 152 GLU cc_start: 0.7709 (pm20) cc_final: 0.7388 (pm20) REVERT: K 176 GLN cc_start: 0.8307 (mp10) cc_final: 0.8017 (mp10) REVERT: L 33 LEU cc_start: 0.9743 (OUTLIER) cc_final: 0.9429 (tm) REVERT: L 50 GLU cc_start: 0.9343 (mt-10) cc_final: 0.8865 (mp0) REVERT: L 117 ILE cc_start: 0.8626 (tt) cc_final: 0.8422 (mm) REVERT: L 167 ASP cc_start: 0.8613 (t0) cc_final: 0.8338 (t0) REVERT: L 185 ASP cc_start: 0.9406 (m-30) cc_final: 0.8622 (p0) REVERT: L 186 TYR cc_start: 0.8890 (t80) cc_final: 0.8675 (t80) REVERT: L 210 ASN cc_start: 0.8750 (t0) cc_final: 0.8323 (p0) outliers start: 33 outliers final: 22 residues processed: 384 average time/residue: 1.1805 time to fit residues: 520.7595 Evaluate side-chains 379 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 352 time to evaluate : 2.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain C residue 26 LYS Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 171 CYS Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 176 GLN Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 132 VAL 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 H residue 200 ILE 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 I residue 179 LEU Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 200 ILE Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 200 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 171 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 94 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 245 optimal weight: 0.2980 chunk 88 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 198 optimal weight: 9.9990 chunk 156 optimal weight: 2.9990 chunk 223 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 GLN G 158 ASN ** 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 ** J 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.103519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.062203 restraints weight = 40326.668| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 3.15 r_work: 0.2615 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2487 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21016 Z= 0.217 Angle : 0.730 10.123 28668 Z= 0.374 Chirality : 0.046 0.184 3220 Planarity : 0.006 0.064 3660 Dihedral : 4.895 23.855 2864 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.70 % Allowed : 22.13 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.16), residues: 2640 helix: -0.40 (0.44), residues: 152 sheet: 0.96 (0.16), residues: 936 loop : -0.29 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 159 HIS 0.003 0.001 HIS A 166 PHE 0.019 0.001 PHE F 27 TYR 0.021 0.001 TYR G 140 ARG 0.015 0.001 ARG G 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19536.83 seconds wall clock time: 344 minutes 29.17 seconds (20669.17 seconds total)