Starting phenix.real_space_refine on Mon Oct 26 05:53:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/25rg_80320/10_2026/25rg_80320.cif Found real_map, /net/cci-nas-00/data/ceres_data/25rg_80320/10_2026/25rg_80320.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 { model { file = "/net/cci-nas-00/data/ceres_data/25rg_80320/10_2026/25rg_80320.cif" } default_model = "/net/cci-nas-00/data/ceres_data/25rg_80320/10_2026/25rg_80320.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/25rg_80320/10_2026/25rg_80320.map" default_real_map = "/net/cci-nas-00/data/ceres_data/25rg_80320/10_2026/25rg_80320.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.624 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 90 5.16 5 C 12140 2.51 5 N 3265 2.21 5 O 3870 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19365 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 561 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "B" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1650 Classifications: {'peptide': 220} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 206} Chain: "C" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1662 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 203} Chain: "D" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 561 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "H" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1650 Classifications: {'peptide': 220} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 206} Chain: "L" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1662 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 203} Chain: "E" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 561 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "I" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1650 Classifications: {'peptide': 220} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 206} Chain: "M" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1662 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 203} Chain: "F" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 561 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "J" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1650 Classifications: {'peptide': 220} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 206} Chain: "N" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1662 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 203} Chain: "G" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 561 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "K" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1650 Classifications: {'peptide': 220} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 206} Chain: "O" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1662 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 203} Time building chain proxies: 4.41, per 1000 atoms: 0.23 Number of scatterers: 19365 At special positions: 0 Unit cell: (191.142, 191.88, 70.848, 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 90 16.00 O 3870 8.00 N 3265 7.00 C 12140 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=25, symmetry=0 Simple disulfide: pdb=" SG CYS A 5 " - pdb=" SG CYS A 58 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.04 Simple disulfide: pdb=" SG CYS B 147 " - pdb=" SG CYS B 203 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 5 " - pdb=" SG CYS D 58 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 203 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 5 " - pdb=" SG CYS E 58 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.04 Simple disulfide: pdb=" SG CYS I 147 " - pdb=" SG CYS I 203 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 136 " - pdb=" SG CYS M 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 5 " - pdb=" SG CYS F 58 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.04 Simple disulfide: pdb=" SG CYS J 147 " - pdb=" SG CYS J 203 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS N 136 " - pdb=" SG CYS N 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 5 " - pdb=" SG CYS G 58 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.04 Simple disulfide: pdb=" SG CYS K 147 " - pdb=" SG CYS K 203 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.04 Simple disulfide: pdb=" SG CYS O 136 " - pdb=" SG CYS O 196 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.63 Conformation dependent library (CDL) restraints added in 790.5 milliseconds 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4680 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 60 sheets defined 9.6% alpha, 49.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 36 through 48 removed outlier: 4.183A pdb=" N LEU A 40 " --> pdb=" O ASN A 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.763A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 65 removed outlier: 3.699A pdb=" N GLN B 65 " --> pdb=" O HIS B 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 62 through 65' Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 163 through 165 No H-bonds generated for 'chain 'B' and resid 163 through 165' Processing helix chain 'B' and resid 208 through 211 Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'C' and resid 123 through 130 removed outlier: 3.525A pdb=" N SER C 129 " --> pdb=" O GLU C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 189 Processing helix chain 'D' and resid 36 through 48 removed outlier: 4.030A pdb=" N LEU D 40 " --> pdb=" O ASN D 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.734A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.682A pdb=" N GLN H 65 " --> pdb=" O HIS H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 163 through 165 No H-bonds generated for 'chain 'H' and resid 163 through 165' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.524A pdb=" N VAL L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 130 Processing helix chain 'L' and resid 185 through 189 Processing helix chain 'E' and resid 36 through 48 removed outlier: 4.137A pdb=" N LEU E 40 " --> pdb=" O ASN E 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.744A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 65 removed outlier: 3.671A pdb=" N GLN I 65 " --> pdb=" O HIS I 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 62 through 65' Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'I' and resid 163 through 165 No H-bonds generated for 'chain 'I' and resid 163 through 165' Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'M' and resid 123 through 130 Processing helix chain 'M' and resid 185 through 189 Processing helix chain 'F' and resid 36 through 48 removed outlier: 4.091A pdb=" N LEU F 40 " --> pdb=" O ASN F 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.724A pdb=" N TYR J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 65 removed outlier: 3.762A pdb=" N GLN J 65 " --> pdb=" O HIS J 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 62 through 65' Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'J' and resid 163 through 165 No H-bonds generated for 'chain 'J' and resid 163 through 165' Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'N' and resid 123 through 130 removed outlier: 3.509A pdb=" N SER N 129 " --> pdb=" O GLU N 125 " (cutoff:3.500A) Processing helix chain 'N' and resid 185 through 189 Processing helix chain 'G' and resid 36 through 48 removed outlier: 4.077A pdb=" N LEU G 40 " --> pdb=" O ASN G 36 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.789A pdb=" N TYR K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 65 removed outlier: 3.712A pdb=" N GLN K 65 " --> pdb=" O HIS K 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 62 through 65' Processing helix chain 'K' and resid 87 through 91 Processing helix chain 'K' and resid 163 through 165 No H-bonds generated for 'chain 'K' and resid 163 through 165' Processing helix chain 'O' and resid 79 through 83 removed outlier: 3.516A pdb=" N VAL O 83 " --> pdb=" O PRO O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 123 through 130 Processing helix chain 'O' and resid 185 through 189 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.805A pdb=" N ILE A 53 " --> pdb=" O CYS A 5 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N THR A 7 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL A 51 " --> pdb=" O THR A 7 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU A 66 " --> pdb=" O LYS A 54 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TYR D 12 " --> pdb=" O LYS D 24 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY D 62 " --> pdb=" O GLU D 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 63 removed outlier: 4.063A pdb=" N GLY A 62 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR A 12 " --> pdb=" O LYS A 24 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU G 66 " --> pdb=" O LYS G 54 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL G 51 " --> pdb=" O THR G 7 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N THR G 7 " --> pdb=" O VAL G 51 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE G 53 " --> pdb=" O CYS G 5 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.733A pdb=" N ILE B 34 " --> pdb=" O TRP B 50 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N TRP B 50 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TRP B 36 " --> pdb=" O MET B 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12 Processing sheet with id=AA6, first strand: chain 'B' and resid 127 through 131 removed outlier: 6.374A pdb=" N TYR B 183 " --> pdb=" O ASP B 151 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 127 through 131 removed outlier: 6.374A pdb=" N TYR B 183 " --> pdb=" O ASP B 151 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER B 184 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL B 176 " --> pdb=" O SER B 184 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 158 through 161 removed outlier: 4.523A pdb=" N TYR B 201 " --> pdb=" O VAL B 218 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.662A pdb=" N LEU C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N TYR C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 13 removed outlier: 3.761A pdb=" N MET C 97 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 116 through 120 removed outlier: 5.831A pdb=" N TYR C 175 " --> pdb=" O ASN C 140 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 156 through 157 removed outlier: 4.768A pdb=" N TRP C 150 " --> pdb=" O GLN C 157 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N CYS C 196 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS C 209 " --> pdb=" O CYS C 196 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL C 207 " --> pdb=" O VAL C 198 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 4 through 8 removed outlier: 6.649A pdb=" N ILE D 53 " --> pdb=" O CYS D 5 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR D 7 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL D 51 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU D 66 " --> pdb=" O LYS D 54 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LYS E 24 " --> pdb=" O GLU E 11 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N THR E 13 " --> pdb=" O THR E 22 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N THR E 22 " --> pdb=" O THR E 13 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY E 62 " --> pdb=" O GLU E 29 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB7, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.710A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AB9, first strand: chain 'H' and resid 127 through 131 removed outlier: 6.431A pdb=" N TYR H 183 " --> pdb=" O ASP H 151 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 127 through 131 removed outlier: 6.431A pdb=" N TYR H 183 " --> pdb=" O ASP H 151 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER H 184 " --> pdb=" O VAL H 176 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 158 through 161 removed outlier: 4.526A pdb=" N TYR H 201 " --> pdb=" O VAL H 218 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.666A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.645A pdb=" N MET L 97 " --> pdb=" O SER L 92 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 116 through 120 removed outlier: 5.787A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 156 through 157 removed outlier: 4.846A pdb=" N TRP L 150 " --> pdb=" O GLN L 157 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR L 194 " --> pdb=" O PHE L 211 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS L 196 " --> pdb=" O LYS L 209 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS L 209 " --> pdb=" O CYS L 196 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL L 207 " --> pdb=" O VAL L 198 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 4 through 8 removed outlier: 6.726A pdb=" N ILE E 53 " --> pdb=" O CYS E 5 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N THR E 7 " --> pdb=" O VAL E 51 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL E 51 " --> pdb=" O THR E 7 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU E 66 " --> pdb=" O LYS E 54 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LYS F 24 " --> pdb=" O GLU F 11 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N THR F 13 " --> pdb=" O THR F 22 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N THR F 22 " --> pdb=" O THR F 13 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY F 62 " --> pdb=" O GLU F 29 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 4 through 8 removed outlier: 6.726A pdb=" N ILE E 53 " --> pdb=" O CYS E 5 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N THR E 7 " --> pdb=" O VAL E 51 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL E 51 " --> pdb=" O THR E 7 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU E 66 " --> pdb=" O LYS E 54 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE F 53 " --> pdb=" O CYS F 5 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N THR F 7 " --> pdb=" O VAL F 51 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL F 51 " --> pdb=" O THR F 7 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU F 66 " --> pdb=" O LYS F 54 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TYR G 12 " --> pdb=" O LYS G 24 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY G 62 " --> pdb=" O GLU G 29 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AD2, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.715A pdb=" N ILE I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N TRP I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 10 through 12 Processing sheet with id=AD4, first strand: chain 'I' and resid 127 through 131 removed outlier: 6.367A pdb=" N TYR I 183 " --> pdb=" O ASP I 151 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 127 through 131 removed outlier: 6.367A pdb=" N TYR I 183 " --> pdb=" O ASP I 151 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER I 184 " --> pdb=" O VAL I 176 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL I 176 " --> pdb=" O SER I 184 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 158 through 161 removed outlier: 4.509A pdb=" N TYR I 201 " --> pdb=" O VAL I 218 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AD8, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.632A pdb=" N LEU M 33 " --> pdb=" O TYR M 49 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N TYR M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 10 through 13 removed outlier: 3.660A pdb=" N MET M 97 " --> pdb=" O SER M 92 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'M' and resid 116 through 120 removed outlier: 3.578A pdb=" N VAL M 135 " --> pdb=" O PHE M 120 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N TYR M 175 " --> pdb=" O ASN M 140 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 147 through 152 removed outlier: 3.630A pdb=" N TYR M 194 " --> pdb=" O PHE M 211 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYS M 196 " --> pdb=" O LYS M 209 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS M 209 " --> pdb=" O CYS M 196 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL M 207 " --> pdb=" O VAL M 198 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AE4, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.701A pdb=" N ILE J 34 " --> pdb=" O TRP J 50 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N TRP J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 10 through 12 Processing sheet with id=AE6, first strand: chain 'J' and resid 127 through 131 removed outlier: 6.416A pdb=" N TYR J 183 " --> pdb=" O ASP J 151 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 127 through 131 removed outlier: 6.416A pdb=" N TYR J 183 " --> pdb=" O ASP J 151 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER J 184 " --> pdb=" O VAL J 176 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL J 176 " --> pdb=" O SER J 184 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 158 through 161 removed outlier: 4.509A pdb=" N TYR J 201 " --> pdb=" O VAL J 218 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AF1, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.645A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'N' and resid 10 through 13 removed outlier: 3.653A pdb=" N MET N 97 " --> pdb=" O SER N 92 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 116 through 120 removed outlier: 5.725A pdb=" N TYR N 175 " --> pdb=" O ASN N 140 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'N' and resid 156 through 157 removed outlier: 4.811A pdb=" N TRP N 150 " --> pdb=" O GLN N 157 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR N 194 " --> pdb=" O PHE N 211 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N CYS N 196 " --> pdb=" O LYS N 209 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS N 209 " --> pdb=" O CYS N 196 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL N 207 " --> pdb=" O VAL N 198 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AF6, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.733A pdb=" N ILE K 34 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TRP K 50 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 10 through 12 Processing sheet with id=AF8, first strand: chain 'K' and resid 127 through 131 removed outlier: 6.352A pdb=" N TYR K 183 " --> pdb=" O ASP K 151 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 127 through 131 removed outlier: 6.352A pdb=" N TYR K 183 " --> pdb=" O ASP K 151 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER K 184 " --> pdb=" O VAL K 176 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL K 176 " --> pdb=" O SER K 184 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 158 through 161 removed outlier: 4.538A pdb=" N TYR K 201 " --> pdb=" O VAL K 218 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'O' and resid 4 through 7 Processing sheet with id=AG3, first strand: chain 'O' and resid 10 through 13 removed outlier: 6.290A pdb=" N LEU O 11 " --> pdb=" O GLU O 107 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU O 33 " --> pdb=" O TYR O 49 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N TYR O 49 " --> pdb=" O LEU O 33 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'O' and resid 10 through 13 removed outlier: 6.290A pdb=" N LEU O 11 " --> pdb=" O GLU O 107 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET O 97 " --> pdb=" O SER O 92 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'O' and resid 116 through 120 removed outlier: 3.511A pdb=" N VAL O 135 " --> pdb=" O PHE O 120 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N TYR O 175 " --> pdb=" O ASN O 140 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'O' and resid 156 through 157 removed outlier: 4.826A pdb=" N TRP O 150 " --> pdb=" O GLN O 157 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N CYS O 196 " --> pdb=" O LYS O 209 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS O 209 " --> pdb=" O CYS O 196 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL O 207 " --> pdb=" O VAL O 198 " (cutoff:3.500A) 947 hydrogen bonds defined for protein. 2373 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.09 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6271 1.34 - 1.46: 4845 1.46 - 1.58: 8569 1.58 - 1.70: 0 1.70 - 1.83: 120 Bond restraints: 19805 Sorted by residual: bond pdb=" C MET E 1 " pdb=" N THR E 2 " ideal model delta sigma weight residual 1.332 1.302 0.030 1.44e-02 4.82e+03 4.45e+00 bond pdb=" C GLN C 38 " pdb=" N LYS C 39 " ideal model delta sigma weight residual 1.331 1.312 0.019 1.48e-02 4.57e+03 1.59e+00 bond pdb=" N GLY A 71 " pdb=" CA GLY A 71 " ideal model delta sigma weight residual 1.449 1.465 -0.015 1.45e-02 4.76e+03 1.14e+00 bond pdb=" C GLN L 38 " pdb=" N LYS L 39 " ideal model delta sigma weight residual 1.329 1.310 0.019 1.86e-02 2.89e+03 1.06e+00 bond pdb=" N GLU O 79 " pdb=" CA GLU O 79 " ideal model delta sigma weight residual 1.453 1.445 0.008 8.30e-03 1.45e+04 1.03e+00 ... (remaining 19800 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 25919 1.32 - 2.63: 851 2.63 - 3.95: 142 3.95 - 5.27: 38 5.27 - 6.59: 5 Bond angle restraints: 26955 Sorted by residual: angle pdb=" N THR N 69 " pdb=" CA THR N 69 " pdb=" C THR N 69 " ideal model delta sigma weight residual 114.75 110.33 4.42 1.26e+00 6.30e-01 1.23e+01 angle pdb=" N THR L 69 " pdb=" CA THR L 69 " pdb=" C THR L 69 " ideal model delta sigma weight residual 114.75 110.41 4.34 1.26e+00 6.30e-01 1.19e+01 angle pdb=" N THR O 69 " pdb=" CA THR O 69 " pdb=" C THR O 69 " ideal model delta sigma weight residual 114.75 110.56 4.19 1.26e+00 6.30e-01 1.11e+01 angle pdb=" N THR M 69 " pdb=" CA THR M 69 " pdb=" C THR M 69 " ideal model delta sigma weight residual 114.75 110.74 4.01 1.26e+00 6.30e-01 1.01e+01 angle pdb=" C ILE K 102 " pdb=" N THR K 103 " pdb=" CA THR K 103 " ideal model delta sigma weight residual 123.05 127.94 -4.89 1.57e+00 4.06e-01 9.71e+00 ... (remaining 26950 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 11061 17.66 - 35.31: 613 35.31 - 52.97: 101 52.97 - 70.63: 20 70.63 - 88.28: 15 Dihedral angle restraints: 11810 sinusoidal: 4505 harmonic: 7305 Sorted by residual: dihedral pdb=" CA SER B 28 " pdb=" C SER B 28 " pdb=" N PHE B 29 " pdb=" CA PHE B 29 " ideal model delta harmonic sigma weight residual 180.00 -162.66 -17.34 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA SER I 28 " pdb=" C SER I 28 " pdb=" N PHE I 29 " pdb=" CA PHE I 29 " ideal model delta harmonic sigma weight residual 180.00 -162.76 -17.24 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA SER K 28 " pdb=" C SER K 28 " pdb=" N PHE K 29 " pdb=" CA PHE K 29 " ideal model delta harmonic sigma weight residual -180.00 -162.90 -17.10 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 11807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1966 0.036 - 0.071: 691 0.071 - 0.107: 318 0.107 - 0.142: 80 0.142 - 0.178: 10 Chirality restraints: 3065 Sorted by residual: chirality pdb=" CA THR I 103 " pdb=" N THR I 103 " pdb=" C THR I 103 " pdb=" CB THR I 103 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 7.88e-01 chirality pdb=" CA THR K 103 " pdb=" N THR K 103 " pdb=" C THR K 103 " pdb=" CB THR K 103 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.17 2.00e-01 2.50e+01 7.55e-01 chirality pdb=" CA THR B 103 " pdb=" N THR B 103 " pdb=" C THR B 103 " pdb=" CB THR B 103 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 7.16e-01 ... (remaining 3062 not shown) Planarity restraints: 3460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 155 " -0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO B 156 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 156 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 156 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL H 99 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.53e+00 pdb=" N PRO H 100 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO H 100 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO H 100 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU J 155 " -0.026 5.00e-02 4.00e+02 3.98e-02 2.53e+00 pdb=" N PRO J 156 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO J 156 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO J 156 " -0.020 5.00e-02 4.00e+02 ... (remaining 3457 not shown) Histogram of nonbonded interaction distances: 2.59 - 3.05: 11519 3.05 - 3.52: 18263 3.52 - 3.98: 30926 3.98 - 4.44: 36165 4.44 - 4.90: 59576 Nonbonded interactions: 156449 Sorted by model distance: nonbonded pdb=" O ILE K 102 " pdb=" OG1 THR K 103 " model vdw 2.594 3.040 nonbonded pdb=" N ASP I 106 " pdb=" O ASP I 106 " model vdw 2.604 2.496 nonbonded pdb=" N VAL I 99 " pdb=" CG1 VAL I 99 " model vdw 2.604 2.832 nonbonded pdb=" N VAL H 99 " pdb=" CG1 VAL H 99 " model vdw 2.607 2.832 nonbonded pdb=" N VAL J 99 " pdb=" CG1 VAL J 99 " model vdw 2.607 2.832 ... (remaining 156444 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.040 Process input model: 19.320 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 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 : 0.004 0.036 19830 Z= 0.175 Angle : 0.595 6.586 27005 Z= 0.327 Chirality : 0.045 0.178 3065 Planarity : 0.005 0.046 3460 Dihedral : 11.699 88.283 7055 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.79 % Allowed : 7.26 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.17), residues: 2515 helix: 1.16 (0.49), residues: 120 sheet: 1.29 (0.14), residues: 1325 loop : 0.16 (0.20), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 98 TYR 0.020 0.002 TYR H 33 PHE 0.016 0.002 PHE D 64 TRP 0.014 0.002 TRP F 35 HIS 0.003 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (19805) covalent geometry : angle 0.59340 / 0.33 (26955) SS BOND : bond 0.00582 / 0.38 ( 25) SS BOND : angle 1.19651 / 0.84 ( 50) hydrogen bonds : bond 0.18721 / 12.20 ( 815) hydrogen bonds : angle 8.40923 / 5.82 ( 2373) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 261 time to evaluate : 0.760 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 150 LYS cc_start: 0.7358 (mtpm) cc_final: 0.7111 (tttt) REVERT: C 167 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8344 (mm-30) REVERT: L 167 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8250 (mm-30) REVERT: I 82 GLU cc_start: 0.9246 (tt0) cc_final: 0.9023 (tt0) REVERT: M 192 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8555 (tmtp) REVERT: F 27 ASP cc_start: 0.9130 (p0) cc_final: 0.8850 (p0) REVERT: J 171 HIS cc_start: 0.8261 (m-70) cc_final: 0.7984 (m-70) REVERT: N 192 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8671 (tmtp) REVERT: O 167 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8207 (mm-30) outliers start: 83 outliers final: 38 residues processed: 331 average time/residue: 0.6991 time to fit residues: 256.5915 Evaluate side-chains 254 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 214 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 136 LYS Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 192 LYS Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 112 GLN Chi-restraints excluded: chain I residue 136 LYS Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 151 LYS Chi-restraints excluded: chain M residue 192 LYS Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 112 GLN Chi-restraints excluded: chain J residue 136 LYS Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 151 LYS Chi-restraints excluded: chain N residue 192 LYS Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 105 VAL Chi-restraints excluded: chain K residue 112 GLN Chi-restraints excluded: chain K residue 136 LYS Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 151 LYS Chi-restraints excluded: chain O residue 165 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: [216, 98, 194, 227, 107, 10, 66, 247, 130, 124, 103] chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 40.0000 chunk 194 optimal weight: 30.0000 chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 247 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN B 1 GLN B 35 HIS B 178 GLN B 199 GLN C 42 GLN ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 ASN D 36 ASN H 1 GLN H 35 HIS H 178 GLN H 199 GLN L 102 GLN ** L 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN I 1 GLN I 35 HIS I 199 GLN M 42 GLN M 53 ASN ** M 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN J 1 GLN ** J 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 112 GLN J 199 GLN N 53 ASN G 36 ASN K 1 GLN K 35 HIS K 199 GLN O 53 ASN O 102 GLN O 212 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.131236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.067451 restraints weight = 30519.611| |-----------------------------------------------------------------------------| r_work (start): 0.2433 rms_B_bonded: 2.55 r_work: 0.2334 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2237 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 19830 Z= 0.291 Angle : 0.728 7.595 27005 Z= 0.392 Chirality : 0.052 0.198 3065 Planarity : 0.006 0.051 3460 Dihedral : 7.360 58.799 2799 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.84 % Allowed : 9.45 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.17), residues: 2515 helix: 1.13 (0.47), residues: 130 sheet: 1.46 (0.14), residues: 1265 loop : -0.06 (0.19), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG N 24 TYR 0.030 0.003 TYR I 33 PHE 0.021 0.003 PHE D 64 TRP 0.020 0.003 TRP F 35 HIS 0.006 0.002 HIS A 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00672 / 0.29 (19805) covalent geometry : angle 0.72209 / 0.39 (26955) SS BOND : bond 0.00852 / 0.54 ( 25) SS BOND : angle 2.21829 / 1.50 ( 50) hydrogen bonds : bond 0.05116 / 3.39 ( 815) hydrogen bonds : angle 6.56074 / 4.53 ( 2373) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 213 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 GLN cc_start: 0.8979 (mt0) cc_final: 0.8714 (mt0) REVERT: B 150 LYS cc_start: 0.6921 (mtpm) cc_final: 0.6647 (tmtt) REVERT: C 79 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8048 (mt-10) REVERT: L 79 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8174 (mt-10) REVERT: L 167 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8260 (mm-30) REVERT: L 192 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8720 (tmtp) REVERT: M 79 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8013 (mt-10) REVERT: M 192 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8559 (tmtp) REVERT: J 112 GLN cc_start: 0.9315 (OUTLIER) cc_final: 0.7780 (pp30) REVERT: J 150 LYS cc_start: 0.6860 (OUTLIER) cc_final: 0.6649 (tmtt) REVERT: J 171 HIS cc_start: 0.8326 (m-70) cc_final: 0.8085 (m-70) REVERT: N 79 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8021 (mt-10) REVERT: N 192 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8629 (tmtp) REVERT: O 79 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8202 (mt-10) REVERT: O 111 THR cc_start: 0.8620 (OUTLIER) cc_final: 0.8396 (p) outliers start: 106 outliers final: 65 residues processed: 300 average time/residue: 0.6166 time to fit residues: 207.6090 Evaluate side-chains 279 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 203 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 136 LYS Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 156 LEU Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 192 LYS Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 112 GLN Chi-restraints excluded: chain I residue 117 THR Chi-restraints excluded: chain I residue 136 LYS Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 79 GLU Chi-restraints excluded: chain M residue 109 LYS Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 151 LYS Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain M residue 192 LYS Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 112 GLN Chi-restraints excluded: chain J residue 117 THR Chi-restraints excluded: chain J residue 136 LYS Chi-restraints excluded: chain J residue 150 LYS Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 79 GLU Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 151 LYS Chi-restraints excluded: chain N residue 156 LEU Chi-restraints excluded: chain N residue 192 LYS Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 105 VAL Chi-restraints excluded: chain K residue 112 GLN Chi-restraints excluded: chain K residue 136 LYS Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 27 GLN Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 79 GLU Chi-restraints excluded: chain O residue 109 LYS Chi-restraints excluded: chain O residue 111 THR Chi-restraints excluded: chain O residue 151 LYS Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain O residue 165 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: [71, 6, 38, 119, 75, 190, 114, 2, 24, 35, 17] chunk 71 optimal weight: 20.0000 chunk 6 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 119 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 190 optimal weight: 8.9990 chunk 114 optimal weight: 2.9990 chunk 2 optimal weight: 0.1980 chunk 24 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 42 GLN C 102 GLN ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 168 GLN ** J 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 178 GLN O 102 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.131087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.067769 restraints weight = 30770.735| |-----------------------------------------------------------------------------| r_work (start): 0.2440 rms_B_bonded: 2.46 r_work: 0.2325 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2211 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 19830 Z= 0.251 Angle : 0.682 10.679 27005 Z= 0.363 Chirality : 0.049 0.193 3065 Planarity : 0.006 0.054 3460 Dihedral : 7.275 58.253 2795 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.75 % Allowed : 11.32 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.17), residues: 2515 helix: 1.24 (0.48), residues: 130 sheet: 1.31 (0.14), residues: 1245 loop : -0.12 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG N 24 TYR 0.026 0.003 TYR I 33 PHE 0.020 0.003 PHE D 64 TRP 0.017 0.003 TRP F 35 HIS 0.006 0.001 HIS A 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.25 (19805) covalent geometry : angle 0.67716 / 0.36 (26955) SS BOND : bond 0.00814 / 0.52 ( 25) SS BOND : angle 2.06291 / 1.39 ( 50) hydrogen bonds : bond 0.04791 / 3.18 ( 815) hydrogen bonds : angle 6.14884 / 4.24 ( 2373) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 201 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 GLN cc_start: 0.9080 (mt0) cc_final: 0.8869 (mt0) REVERT: C 79 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8081 (mt-10) REVERT: L 79 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8193 (mt-10) REVERT: L 192 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8706 (tmtp) REVERT: I 3 GLN cc_start: 0.9115 (mt0) cc_final: 0.8887 (mt0) REVERT: M 1 GLU cc_start: 0.7777 (tp30) cc_final: 0.7565 (tp30) REVERT: M 79 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8094 (mt-10) REVERT: M 81 GLU cc_start: 0.8593 (pm20) cc_final: 0.8384 (pm20) REVERT: M 192 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8630 (tmtp) REVERT: J 112 GLN cc_start: 0.9350 (OUTLIER) cc_final: 0.7869 (pp30) REVERT: J 150 LYS cc_start: 0.6935 (OUTLIER) cc_final: 0.6714 (tmtt) REVERT: J 171 HIS cc_start: 0.8322 (m-70) cc_final: 0.8065 (m-70) REVERT: N 79 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8148 (mt-10) REVERT: N 192 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8623 (tmtp) REVERT: O 79 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8336 (mt-10) outliers start: 104 outliers final: 64 residues processed: 282 average time/residue: 0.6491 time to fit residues: 204.6195 Evaluate side-chains 273 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 199 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 136 LYS Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 192 LYS Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 112 GLN Chi-restraints excluded: chain I residue 136 LYS Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 79 GLU Chi-restraints excluded: chain M residue 108 ILE Chi-restraints excluded: chain M residue 109 LYS Chi-restraints excluded: chain M residue 151 LYS Chi-restraints excluded: chain M residue 192 LYS Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 112 GLN Chi-restraints excluded: chain J residue 117 THR Chi-restraints excluded: chain J residue 136 LYS Chi-restraints excluded: chain J residue 150 LYS Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 79 GLU Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 151 LYS Chi-restraints excluded: chain N residue 156 LEU Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain N residue 192 LYS Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 105 VAL Chi-restraints excluded: chain K residue 112 GLN Chi-restraints excluded: chain K residue 136 LYS Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 27 GLN Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 79 GLU Chi-restraints excluded: chain O residue 109 LYS Chi-restraints excluded: chain O residue 151 LYS Chi-restraints excluded: chain O residue 165 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: [83, 17, 113, 153, 227, 212, 40, 89, 148, 200, 214] chunk 83 optimal weight: 0.0670 chunk 17 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 227 optimal weight: 3.9990 chunk 212 optimal weight: 1.9990 chunk 40 optimal weight: 20.0000 chunk 89 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 chunk 200 optimal weight: 2.9990 chunk 214 optimal weight: 0.8980 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 42 GLN ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 35 HIS ** N 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 102 GLN O 168 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.132263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.069106 restraints weight = 30540.840| |-----------------------------------------------------------------------------| r_work (start): 0.2479 rms_B_bonded: 2.55 r_work: 0.2362 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2249 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19830 Z= 0.147 Angle : 0.583 8.839 27005 Z= 0.306 Chirality : 0.045 0.172 3065 Planarity : 0.005 0.048 3460 Dihedral : 7.030 57.739 2795 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.02 % Allowed : 12.19 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.17), residues: 2515 helix: 1.46 (0.48), residues: 130 sheet: 1.32 (0.14), residues: 1245 loop : -0.04 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG N 24 TYR 0.017 0.002 TYR I 33 PHE 0.017 0.002 PHE K 173 TRP 0.011 0.002 TRP F 35 HIS 0.004 0.001 HIS A 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (19805) covalent geometry : angle 0.57970 / 0.31 (26955) SS BOND : bond 0.00604 / 0.39 ( 25) SS BOND : angle 1.52774 / 1.02 ( 50) hydrogen bonds : bond 0.03862 / 2.58 ( 815) hydrogen bonds : angle 5.72729 / 3.94 ( 2373) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 206 time to evaluate : 0.583 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 3 GLN cc_start: 0.9085 (mt0) cc_final: 0.8881 (mt0) REVERT: C 79 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8142 (mt-10) REVERT: L 79 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8183 (mt-10) REVERT: L 105 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8501 (ttmm) REVERT: L 192 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8670 (tmtp) REVERT: I 3 GLN cc_start: 0.9095 (mt0) cc_final: 0.8886 (mt0) REVERT: M 79 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8073 (mt-10) REVERT: M 192 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8652 (tmtp) REVERT: J 112 GLN cc_start: 0.9314 (OUTLIER) cc_final: 0.7847 (pp30) REVERT: J 171 HIS cc_start: 0.8444 (m-70) cc_final: 0.8155 (m-70) REVERT: N 79 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8188 (mt-10) REVERT: N 192 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8628 (tmtp) outliers start: 88 outliers final: 57 residues processed: 276 average time/residue: 0.6746 time to fit residues: 207.0272 Evaluate side-chains 270 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 204 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 136 LYS Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 105 LYS Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 192 LYS Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 112 GLN Chi-restraints excluded: chain I residue 117 THR Chi-restraints excluded: chain I residue 136 LYS Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 79 GLU Chi-restraints excluded: chain M residue 109 LYS Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 151 LYS Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain M residue 167 GLU Chi-restraints excluded: chain M residue 192 LYS Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 112 GLN Chi-restraints excluded: chain J residue 117 THR Chi-restraints excluded: chain J residue 136 LYS Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 200 THR Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 79 GLU Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 151 LYS Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain N residue 167 GLU Chi-restraints excluded: chain N residue 192 LYS Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 105 VAL Chi-restraints excluded: chain K residue 112 GLN Chi-restraints excluded: chain K residue 136 LYS Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 27 GLN Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 108 ILE Chi-restraints excluded: chain O residue 109 LYS Chi-restraints excluded: chain O residue 151 LYS Chi-restraints excluded: chain O residue 165 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: [24, 154, 128, 149, 4, 177, 148, 30, 226, 56, 176] chunk 24 optimal weight: 9.9990 chunk 154 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 chunk 149 optimal weight: 0.1980 chunk 4 optimal weight: 1.9990 chunk 177 optimal weight: 10.0000 chunk 148 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 226 optimal weight: 20.0000 chunk 56 optimal weight: 3.9990 chunk 176 optimal weight: 6.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 62 HIS B 178 GLN C 42 GLN C 168 GLN ** L 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 42 GLN ** M 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 168 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.131154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.067334 restraints weight = 30576.635| |-----------------------------------------------------------------------------| r_work (start): 0.2438 rms_B_bonded: 2.52 r_work: 0.2334 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2239 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 19830 Z= 0.215 Angle : 0.654 10.171 27005 Z= 0.344 Chirality : 0.048 0.188 3065 Planarity : 0.005 0.050 3460 Dihedral : 7.156 58.962 2791 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.47 % Allowed : 12.79 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.16), residues: 2515 helix: 1.40 (0.48), residues: 130 sheet: 1.29 (0.14), residues: 1240 loop : -0.09 (0.18), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 24 TYR 0.023 0.003 TYR I 33 PHE 0.024 0.002 PHE J 173 TRP 0.014 0.002 TRP F 35 HIS 0.005 0.001 HIS A 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.21 (19805) covalent geometry : angle 0.64850 / 0.34 (26955) SS BOND : bond 0.00806 / 0.53 ( 25) SS BOND : angle 2.04815 / 1.41 ( 50) hydrogen bonds : bond 0.04336 / 2.88 ( 815) hydrogen bonds : angle 5.81383 / 4.00 ( 2373) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 201 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 GLN cc_start: 0.9008 (mt0) cc_final: 0.8775 (mt0) REVERT: C 1 GLU cc_start: 0.7682 (tp30) cc_final: 0.7481 (tp30) REVERT: C 79 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8146 (mt-10) REVERT: L 79 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8179 (mt-10) REVERT: L 192 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8632 (tmtp) REVERT: I 3 GLN cc_start: 0.9053 (mt0) cc_final: 0.8839 (mt0) REVERT: I 150 LYS cc_start: 0.7259 (tmtt) cc_final: 0.6983 (tmtt) REVERT: M 79 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8041 (mt-10) REVERT: M 192 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8613 (tmtp) REVERT: J 112 GLN cc_start: 0.9346 (OUTLIER) cc_final: 0.7879 (pp30) REVERT: J 171 HIS cc_start: 0.8351 (m-70) cc_final: 0.8038 (m-70) REVERT: N 79 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8241 (mt-10) REVERT: N 192 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8626 (tmtp) REVERT: O 79 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8217 (mt-10) REVERT: O 105 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8463 (mtmm) outliers start: 98 outliers final: 67 residues processed: 275 average time/residue: 0.6430 time to fit residues: 197.7911 Evaluate side-chains 276 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 199 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 136 LYS Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 192 LYS Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 112 GLN Chi-restraints excluded: chain I residue 117 THR Chi-restraints excluded: chain I residue 136 LYS Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 79 GLU Chi-restraints excluded: chain M residue 109 LYS Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 151 LYS Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain M residue 167 GLU Chi-restraints excluded: chain M residue 192 LYS Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 112 GLN Chi-restraints excluded: chain J residue 117 THR Chi-restraints excluded: chain J residue 136 LYS Chi-restraints excluded: chain J residue 200 THR Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 79 GLU Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 151 LYS Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain N residue 167 GLU Chi-restraints excluded: chain N residue 192 LYS Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 105 VAL Chi-restraints excluded: chain K residue 112 GLN Chi-restraints excluded: chain K residue 136 LYS Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 27 GLN Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 79 GLU Chi-restraints excluded: chain O residue 105 LYS Chi-restraints excluded: chain O residue 109 LYS Chi-restraints excluded: chain O residue 151 LYS Chi-restraints excluded: chain O residue 165 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: [87, 185, 102, 55, 140, 25, 235, 96, 60, 15, 20] chunk 87 optimal weight: 0.7980 chunk 185 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 140 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 235 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 20 optimal weight: 30.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 42 GLN C 168 GLN L 168 GLN ** M 168 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 = 0.3827 r_free = 0.3827 target = 0.131994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.068512 restraints weight = 30518.677| |-----------------------------------------------------------------------------| r_work (start): 0.2469 rms_B_bonded: 2.42 r_work: 0.2364 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2279 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19830 Z= 0.152 Angle : 0.584 9.495 27005 Z= 0.306 Chirality : 0.046 0.196 3065 Planarity : 0.005 0.048 3460 Dihedral : 6.978 59.100 2791 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.02 % Allowed : 13.38 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.17), residues: 2515 helix: 1.61 (0.48), residues: 130 sheet: 1.30 (0.14), residues: 1240 loop : -0.03 (0.18), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 24 TYR 0.018 0.002 TYR I 33 PHE 0.016 0.002 PHE D 64 TRP 0.010 0.002 TRP J 36 HIS 0.004 0.001 HIS A 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (19805) covalent geometry : angle 0.58013 / 0.30 (26955) SS BOND : bond 0.00623 / 0.40 ( 25) SS BOND : angle 1.59092 / 1.07 ( 50) hydrogen bonds : bond 0.03807 / 2.54 ( 815) hydrogen bonds : angle 5.53289 / 3.81 ( 2373) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 205 time to evaluate : 0.753 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 3 GLN cc_start: 0.8959 (mt0) cc_final: 0.8722 (mt0) REVERT: C 79 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8131 (mt-10) REVERT: L 79 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8167 (mt-10) REVERT: L 192 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8621 (tmtp) REVERT: I 3 GLN cc_start: 0.8969 (mt0) cc_final: 0.8742 (mt0) REVERT: M 1 GLU cc_start: 0.7484 (tp30) cc_final: 0.7216 (tp30) REVERT: M 192 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8640 (tmtp) REVERT: J 112 GLN cc_start: 0.9320 (OUTLIER) cc_final: 0.7864 (pp30) REVERT: J 171 HIS cc_start: 0.8246 (m-70) cc_final: 0.7950 (m-70) REVERT: N 192 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8654 (tmtp) REVERT: O 105 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8423 (mtmm) outliers start: 88 outliers final: 70 residues processed: 274 average time/residue: 0.6573 time to fit residues: 200.4578 Evaluate side-chains 276 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 199 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 67 ARG Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 136 LYS Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 192 LYS Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 112 GLN Chi-restraints excluded: chain I residue 136 LYS Chi-restraints excluded: chain M residue 13 LEU Chi-restraints excluded: chain M residue 27 GLN Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 109 LYS Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 151 LYS Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain M residue 167 GLU Chi-restraints excluded: chain M residue 192 LYS Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 112 GLN Chi-restraints excluded: chain J residue 136 LYS Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 200 THR Chi-restraints excluded: chain N residue 18 ARG Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 151 LYS Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain N residue 167 GLU Chi-restraints excluded: chain N residue 192 LYS Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 105 VAL Chi-restraints excluded: chain K residue 112 GLN Chi-restraints excluded: chain K residue 136 LYS Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 27 GLN Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 105 LYS Chi-restraints excluded: chain O residue 108 ILE Chi-restraints excluded: chain O residue 109 LYS Chi-restraints excluded: chain O residue 151 LYS Chi-restraints excluded: chain O residue 165 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: [182, 195, 164, 55, 7, 152, 79, 112, 105, 224, 97] chunk 182 optimal weight: 2.9990 chunk 195 optimal weight: 10.0000 chunk 164 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 112 optimal weight: 0.3980 chunk 105 optimal weight: 4.9990 chunk 224 optimal weight: 4.9990 chunk 97 optimal weight: 20.0000 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 62 HIS C 42 GLN C 168 GLN ** M 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 178 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 = 0.3807 r_free = 0.3807 target = 0.130691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.067238 restraints weight = 30508.458| |-----------------------------------------------------------------------------| r_work (start): 0.2459 rms_B_bonded: 2.41 r_work: 0.2349 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2240 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 19830 Z= 0.252 Angle : 0.679 10.605 27005 Z= 0.360 Chirality : 0.050 0.196 3065 Planarity : 0.006 0.052 3460 Dihedral : 7.253 59.323 2791 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.52 % Allowed : 12.92 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.16), residues: 2515 helix: 1.45 (0.47), residues: 130 sheet: 1.23 (0.14), residues: 1240 loop : -0.11 (0.18), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 24 TYR 0.027 0.003 TYR K 33 PHE 0.020 0.003 PHE D 64 TRP 0.016 0.003 TRP F 35 HIS 0.007 0.001 HIS A 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.25 (19805) covalent geometry : angle 0.67314 / 0.36 (26955) SS BOND : bond 0.00824 / 0.52 ( 25) SS BOND : angle 2.15613 / 1.45 ( 50) hydrogen bonds : bond 0.04524 / 3.00 ( 815) hydrogen bonds : angle 5.76006 / 3.97 ( 2373) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 204 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 GLN cc_start: 0.9007 (mt0) cc_final: 0.8765 (mt0) REVERT: B 150 LYS cc_start: 0.7756 (mmmt) cc_final: 0.6898 (tmtt) REVERT: C 79 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8091 (mt-10) REVERT: L 79 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8187 (mt-10) REVERT: L 192 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8625 (tmtp) REVERT: I 3 GLN cc_start: 0.9034 (mt0) cc_final: 0.8788 (mt0) REVERT: I 150 LYS cc_start: 0.7593 (tmtt) cc_final: 0.7382 (tmtt) REVERT: M 79 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8038 (mt-10) REVERT: M 192 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8599 (tmtp) REVERT: J 112 GLN cc_start: 0.9379 (OUTLIER) cc_final: 0.7967 (pp30) REVERT: J 150 LYS cc_start: 0.7595 (tmtt) cc_final: 0.7325 (tmtt) REVERT: J 171 HIS cc_start: 0.8430 (m-70) cc_final: 0.8197 (m-70) REVERT: N 79 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8207 (mt-10) REVERT: N 192 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8636 (tmtp) REVERT: K 150 LYS cc_start: 0.7158 (mtpm) cc_final: 0.6783 (tmtt) REVERT: O 79 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8273 (mt-10) outliers start: 99 outliers final: 73 residues processed: 282 average time/residue: 0.6585 time to fit residues: 207.2316 Evaluate side-chains 283 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 201 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 67 ARG Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 136 LYS Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 192 LYS Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 112 GLN Chi-restraints excluded: chain I residue 117 THR Chi-restraints excluded: chain I residue 136 LYS Chi-restraints excluded: chain M residue 13 LEU Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 79 GLU Chi-restraints excluded: chain M residue 109 LYS Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 151 LYS Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain M residue 167 GLU Chi-restraints excluded: chain M residue 192 LYS Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 112 GLN Chi-restraints excluded: chain J residue 136 LYS Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 200 THR Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 79 GLU Chi-restraints excluded: chain N residue 151 LYS Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain N residue 167 GLU Chi-restraints excluded: chain N residue 192 LYS Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 105 VAL Chi-restraints excluded: chain K residue 112 GLN Chi-restraints excluded: chain K residue 136 LYS Chi-restraints excluded: chain O residue 18 ARG Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 27 GLN Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 79 GLU Chi-restraints excluded: chain O residue 108 ILE Chi-restraints excluded: chain O residue 151 LYS Chi-restraints excluded: chain O residue 165 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: [166, 146, 221, 191, 7, 130, 149, 150, 244, 14, 98] chunk 166 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 chunk 221 optimal weight: 8.9990 chunk 191 optimal weight: 30.0000 chunk 7 optimal weight: 2.9990 chunk 130 optimal weight: 0.0770 chunk 149 optimal weight: 20.0000 chunk 150 optimal weight: 2.9990 chunk 244 optimal weight: 20.0000 chunk 14 optimal weight: 0.8980 chunk 98 optimal weight: 8.9990 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 42 GLN C 168 GLN H 178 GLN M 42 GLN ** M 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 102 GLN O 168 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.130789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.067488 restraints weight = 30424.677| |-----------------------------------------------------------------------------| r_work (start): 0.2440 rms_B_bonded: 2.33 r_work: 0.2335 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2248 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 19830 Z= 0.208 Angle : 0.643 10.791 27005 Z= 0.338 Chirality : 0.048 0.184 3065 Planarity : 0.005 0.051 3460 Dihedral : 7.155 59.601 2791 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.16 % Allowed : 13.52 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.16), residues: 2515 helix: 1.53 (0.47), residues: 130 sheet: 1.22 (0.14), residues: 1240 loop : -0.12 (0.18), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 110 TYR 0.024 0.003 TYR I 33 PHE 0.019 0.002 PHE D 64 TRP 0.013 0.002 TRP F 35 HIS 0.004 0.001 HIS A 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.21 (19805) covalent geometry : angle 0.63839 / 0.34 (26955) SS BOND : bond 0.00770 / 0.50 ( 25) SS BOND : angle 1.94089 / 1.30 ( 50) hydrogen bonds : bond 0.04203 / 2.79 ( 815) hydrogen bonds : angle 5.59357 / 3.86 ( 2373) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 198 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 GLN cc_start: 0.8916 (mt0) cc_final: 0.8664 (mt0) REVERT: B 150 LYS cc_start: 0.7596 (mmmt) cc_final: 0.6823 (tmtt) REVERT: C 79 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8120 (mt-10) REVERT: L 79 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8131 (mt-10) REVERT: L 192 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8589 (tmtp) REVERT: I 3 GLN cc_start: 0.8957 (mt0) cc_final: 0.8723 (mt0) REVERT: I 150 LYS cc_start: 0.7385 (tmtt) cc_final: 0.7146 (tmtt) REVERT: M 79 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8008 (mt-10) REVERT: M 192 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8656 (tmtp) REVERT: J 112 GLN cc_start: 0.9374 (OUTLIER) cc_final: 0.7976 (pp30) REVERT: J 150 LYS cc_start: 0.7166 (tmtt) cc_final: 0.6865 (tmtt) REVERT: J 171 HIS cc_start: 0.8285 (m-70) cc_final: 0.8005 (m-70) REVERT: N 192 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8591 (tmtp) REVERT: K 150 LYS cc_start: 0.7001 (mtpm) cc_final: 0.6604 (tmtt) REVERT: O 18 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8531 (ptm160) REVERT: O 105 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8403 (mtmm) outliers start: 91 outliers final: 70 residues processed: 274 average time/residue: 0.6377 time to fit residues: 195.2548 Evaluate side-chains 272 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 193 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 67 ARG Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 136 LYS Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 192 LYS Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 112 GLN Chi-restraints excluded: chain I residue 117 THR Chi-restraints excluded: chain I residue 136 LYS Chi-restraints excluded: chain M residue 13 LEU Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 79 GLU Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 151 LYS Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain M residue 167 GLU Chi-restraints excluded: chain M residue 192 LYS Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 112 GLN Chi-restraints excluded: chain J residue 117 THR Chi-restraints excluded: chain J residue 136 LYS Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 200 THR Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 151 LYS Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain N residue 167 GLU Chi-restraints excluded: chain N residue 192 LYS Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 105 VAL Chi-restraints excluded: chain K residue 112 GLN Chi-restraints excluded: chain K residue 136 LYS Chi-restraints excluded: chain O residue 18 ARG Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 27 GLN Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 105 LYS Chi-restraints excluded: chain O residue 151 LYS Chi-restraints excluded: chain O residue 165 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: [25, 111, 87, 157, 32, 39, 12, 10, 20, 91, 79] chunk 25 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 91 optimal weight: 0.0970 chunk 79 optimal weight: 0.6980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 42 GLN C 102 GLN C 168 GLN ** I 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 168 GLN O 168 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.132094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.068974 restraints weight = 30530.535| |-----------------------------------------------------------------------------| r_work (start): 0.2483 rms_B_bonded: 2.43 r_work: 0.2377 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2259 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19830 Z= 0.123 Angle : 0.563 9.133 27005 Z= 0.292 Chirality : 0.045 0.165 3065 Planarity : 0.005 0.057 3460 Dihedral : 6.897 58.238 2791 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.56 % Allowed : 14.16 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.17), residues: 2515 helix: 1.73 (0.48), residues: 130 sheet: 1.28 (0.14), residues: 1240 loop : -0.02 (0.18), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 24 TYR 0.015 0.002 TYR H 33 PHE 0.014 0.002 PHE D 64 TRP 0.010 0.001 TRP J 36 HIS 0.004 0.001 HIS A 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (19805) covalent geometry : angle 0.55994 / 0.29 (26955) SS BOND : bond 0.00580 / 0.38 ( 25) SS BOND : angle 1.41445 / 0.93 ( 50) hydrogen bonds : bond 0.03523 / 2.35 ( 815) hydrogen bonds : angle 5.29822 / 3.65 ( 2373) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 216 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 GLN cc_start: 0.8951 (mt0) cc_final: 0.8709 (mt0) REVERT: B 150 LYS cc_start: 0.7740 (mmmt) cc_final: 0.6982 (tmtt) REVERT: C 79 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8142 (mt-10) REVERT: H 150 LYS cc_start: 0.7387 (mmmt) cc_final: 0.6693 (tmtt) REVERT: L 79 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8060 (mt-10) REVERT: L 192 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8570 (tmtp) REVERT: I 3 GLN cc_start: 0.8966 (mt0) cc_final: 0.8745 (mt0) REVERT: I 150 LYS cc_start: 0.7504 (tmtt) cc_final: 0.7248 (tmtt) REVERT: M 79 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.7988 (mt-10) REVERT: M 192 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8649 (tmtp) REVERT: J 112 GLN cc_start: 0.9316 (OUTLIER) cc_final: 0.7938 (pp30) REVERT: J 150 LYS cc_start: 0.7331 (tmtt) cc_final: 0.7004 (tmtt) REVERT: J 171 HIS cc_start: 0.8338 (m-70) cc_final: 0.8052 (m-70) REVERT: N 192 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8596 (tmtp) REVERT: K 150 LYS cc_start: 0.6888 (mtpm) cc_final: 0.6551 (tmtt) REVERT: O 18 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.8589 (ptm160) REVERT: O 105 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8446 (mtmm) outliers start: 78 outliers final: 61 residues processed: 281 average time/residue: 0.6521 time to fit residues: 204.3130 Evaluate side-chains 276 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 206 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain B residue 67 ARG Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 136 LYS Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 192 LYS Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 112 GLN Chi-restraints excluded: chain I residue 117 THR Chi-restraints excluded: chain I residue 136 LYS Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 79 GLU Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 151 LYS Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain M residue 167 GLU Chi-restraints excluded: chain M residue 192 LYS Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 112 GLN Chi-restraints excluded: chain J residue 117 THR Chi-restraints excluded: chain J residue 136 LYS Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 200 THR Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 151 LYS Chi-restraints excluded: chain N residue 167 GLU Chi-restraints excluded: chain N residue 192 LYS Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 105 VAL Chi-restraints excluded: chain K residue 112 GLN Chi-restraints excluded: chain K residue 136 LYS Chi-restraints excluded: chain O residue 18 ARG Chi-restraints excluded: chain O residue 27 GLN Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 105 LYS Chi-restraints excluded: chain O residue 151 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: [116, 174, 29, 200, 158, 226, 152, 107, 32, 69, 7] chunk 116 optimal weight: 1.9990 chunk 174 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 chunk 158 optimal weight: 0.6980 chunk 226 optimal weight: 30.0000 chunk 152 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 62 HIS C 42 GLN C 168 GLN H 57 HIS M 42 GLN ** M 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 168 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.130546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.066816 restraints weight = 30539.554| |-----------------------------------------------------------------------------| r_work (start): 0.2426 rms_B_bonded: 2.55 r_work: 0.2330 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2215 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 19830 Z= 0.243 Angle : 0.677 10.433 27005 Z= 0.357 Chirality : 0.049 0.194 3065 Planarity : 0.006 0.089 3460 Dihedral : 7.105 59.560 2787 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.61 % Allowed : 14.43 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.16), residues: 2515 helix: 1.61 (0.47), residues: 130 sheet: 1.18 (0.14), residues: 1235 loop : -0.07 (0.18), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 24 TYR 0.026 0.003 TYR K 33 PHE 0.019 0.002 PHE G 64 TRP 0.014 0.003 TRP F 35 HIS 0.006 0.001 HIS A 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.24 (19805) covalent geometry : angle 0.67148 / 0.35 (26955) SS BOND : bond 0.00837 / 0.54 ( 25) SS BOND : angle 2.11788 / 1.42 ( 50) hydrogen bonds : bond 0.04409 / 2.92 ( 815) hydrogen bonds : angle 5.61417 / 3.87 ( 2373) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 197 time to evaluate : 0.816 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 3 GLN cc_start: 0.8965 (mt0) cc_final: 0.8690 (mt0) REVERT: B 150 LYS cc_start: 0.7754 (mmmt) cc_final: 0.6949 (tmtt) REVERT: C 79 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8199 (mt-10) REVERT: H 150 LYS cc_start: 0.7434 (mmmt) cc_final: 0.6709 (tmtt) REVERT: L 79 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8257 (mt-10) REVERT: L 192 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8516 (tmtp) REVERT: I 3 GLN cc_start: 0.9008 (mt0) cc_final: 0.8760 (mt0) REVERT: I 150 LYS cc_start: 0.7551 (tmtt) cc_final: 0.7275 (tmtt) REVERT: M 79 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8040 (mt-10) REVERT: M 192 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8583 (tmtp) REVERT: J 112 GLN cc_start: 0.9374 (OUTLIER) cc_final: 0.8130 (pp30) REVERT: J 150 LYS cc_start: 0.7363 (tmtt) cc_final: 0.7016 (tmtt) REVERT: J 171 HIS cc_start: 0.8348 (m-70) cc_final: 0.8047 (m-70) REVERT: N 79 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8259 (mt-10) REVERT: N 192 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8577 (tmtp) REVERT: K 150 LYS cc_start: 0.7045 (mtpm) cc_final: 0.6654 (tmtt) outliers start: 79 outliers final: 65 residues processed: 262 average time/residue: 0.6687 time to fit residues: 195.1387 Evaluate side-chains 270 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 197 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain B residue 67 ARG Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 136 LYS Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 192 LYS Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 112 GLN Chi-restraints excluded: chain I residue 117 THR Chi-restraints excluded: chain I residue 136 LYS Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 79 GLU Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 151 LYS Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain M residue 167 GLU Chi-restraints excluded: chain M residue 192 LYS Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 112 GLN Chi-restraints excluded: chain J residue 117 THR Chi-restraints excluded: chain J residue 136 LYS Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 200 THR Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 79 GLU Chi-restraints excluded: chain N residue 151 LYS Chi-restraints excluded: chain N residue 167 GLU Chi-restraints excluded: chain N residue 192 LYS Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 105 VAL Chi-restraints excluded: chain K residue 112 GLN Chi-restraints excluded: chain K residue 136 LYS Chi-restraints excluded: chain O residue 18 ARG Chi-restraints excluded: chain O residue 27 GLN Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 151 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: [200, 52, 125, 211, 24, 171, 122, 80, 39, 147, 176] chunk 200 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 chunk 211 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 171 optimal weight: 10.0000 chunk 122 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 176 optimal weight: 30.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 42 GLN C 168 GLN ** M 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 168 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.130014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.066430 restraints weight = 30556.943| |-----------------------------------------------------------------------------| r_work (start): 0.2423 rms_B_bonded: 2.41 r_work: 0.2329 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2205 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 19830 Z= 0.244 Angle : 0.682 11.357 27005 Z= 0.359 Chirality : 0.049 0.192 3065 Planarity : 0.006 0.068 3460 Dihedral : 7.156 59.465 2787 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.70 % Allowed : 14.29 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.16), residues: 2515 helix: 1.57 (0.47), residues: 130 sheet: 1.13 (0.14), residues: 1235 loop : -0.13 (0.18), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG M 24 TYR 0.026 0.003 TYR K 33 PHE 0.020 0.002 PHE D 64 TRP 0.015 0.003 TRP F 35 HIS 0.006 0.001 HIS A 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.24 (19805) covalent geometry : angle 0.67597 / 0.36 (26955) SS BOND : bond 0.00867 / 0.56 ( 25) SS BOND : angle 2.13039 / 1.43 ( 50) hydrogen bonds : bond 0.04413 / 2.92 ( 815) hydrogen bonds : angle 5.59883 / 3.86 ( 2373) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9393.00 seconds wall clock time: 160 minutes 12.71 seconds (9612.71 seconds total)