Starting phenix.real_space_refine on Thu Mar 5 04:26:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zzq_15039/03_2026/7zzq_15039.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zzq_15039/03_2026/7zzq_15039.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zzq_15039/03_2026/7zzq_15039.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zzq_15039/03_2026/7zzq_15039.map" model { file = "/net/cci-nas-00/data/ceres_data/7zzq_15039/03_2026/7zzq_15039.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zzq_15039/03_2026/7zzq_15039.cif" } resolution = 2.6 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= 0.001 sd= 0.026 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 106 5.16 5 C 12331 2.51 5 N 3366 2.21 5 O 3724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19527 Number of models: 1 Model: "" Number of chains: 46 Chain: "A" Number of atoms: 1088 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1080 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 138, 1080 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 1 bond proxies already assigned to first conformer: 1092 Chain: "B" Number of atoms: 1112 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 141, 1104 Classifications: {'peptide': 141} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 132} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 141, 1104 Classifications: {'peptide': 141} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 132} Chain breaks: 1 bond proxies already assigned to first conformer: 1116 Chain: "C" Number of atoms: 1099 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1080 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 138, 1080 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 1 bond proxies already assigned to first conformer: 1080 Chain: "D" Number of atoms: 1083 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 136, 1075 Classifications: {'peptide': 136} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 127} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 136, 1075 Classifications: {'peptide': 136} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 127} Chain breaks: 2 bond proxies already assigned to first conformer: 1085 Chain: "E" Number of atoms: 1088 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1080 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 138, 1080 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 1 bond proxies already assigned to first conformer: 1092 Chain: "F" Number of atoms: 1133 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 144, 1122 Classifications: {'peptide': 144} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 135} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 144, 1122 Classifications: {'peptide': 144} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 135} Chain breaks: 1 bond proxies already assigned to first conformer: 1131 Chain: "G" Number of atoms: 1088 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1080 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 138, 1080 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 1 bond proxies already assigned to first conformer: 1092 Chain: "H" Number of atoms: 1115 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 141, 1104 Classifications: {'peptide': 141} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 132} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 141, 1104 Classifications: {'peptide': 141} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 132} Chain breaks: 1 bond proxies already assigned to first conformer: 1113 Chain: "I" Number of atoms: 1099 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1080 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 138, 1080 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 1 bond proxies already assigned to first conformer: 1080 Chain: "J" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1098 Classifications: {'peptide': 140} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 131} Chain breaks: 1 Chain: "K" Number of atoms: 1083 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 137, 1075 Classifications: {'peptide': 137} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 128} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 137, 1075 Classifications: {'peptide': 137} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 128} Chain breaks: 1 bond proxies already assigned to first conformer: 1087 Chain: "L" Number of atoms: 1133 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 144, 1122 Classifications: {'peptide': 144} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 135} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 144, 1122 Classifications: {'peptide': 144} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 135} Chain breaks: 1 bond proxies already assigned to first conformer: 1131 Chain: "M" Number of atoms: 1099 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1080 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 138, 1080 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 1 bond proxies already assigned to first conformer: 1080 Chain: "N" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1104 Classifications: {'peptide': 141} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 132} Chain breaks: 1 Chain: "O" Number of atoms: 1099 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1080 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 138, 1080 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 1 bond proxies already assigned to first conformer: 1080 Chain: "P" Number of atoms: 1096 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1085 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 138, 1085 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 2 bond proxies already assigned to first conformer: 1092 Chain: "Q" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 259 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 3, 'TRANS': 30} Chain: "R" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 266 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 3, 'TRANS': 31} Chain: "S" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 187 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 2, 'TRANS': 22} Chain breaks: 1 Chain: "T" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 2, 'TRANS': 25} Chain breaks: 1 Chain: "U" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 103 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "V" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 84 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "W" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 42 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "X" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 99 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "Y" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 91 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 1, 'TRANS': 9} Chain: "Z" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 103 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "a" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 84 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "b" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 151 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 1, 'TRANS': 19} Chain: "c" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 42 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "d" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 84 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "G" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "H" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "I" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "J" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "K" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "L" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "M" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "N" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "O" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "P" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Residues with excluded nonbonded symmetry interactions: 18 residue: pdb=" N AMET A 46 " occ=0.63 ... (14 atoms not shown) pdb=" CE BMET A 46 " occ=0.37 residue: pdb=" N AMET B 46 " occ=0.73 ... (14 atoms not shown) pdb=" CE BMET B 46 " occ=0.27 residue: pdb=" N AMET C 46 " occ=0.54 ... (14 atoms not shown) pdb=" CE BMET C 46 " occ=0.46 residue: pdb=" N AARG C 114 " occ=0.53 ... (20 atoms not shown) pdb=" NH2BARG C 114 " occ=0.47 residue: pdb=" N AMET D 46 " occ=0.47 ... (14 atoms not shown) pdb=" CE BMET D 46 " occ=0.53 residue: pdb=" N AMET E 46 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET E 46 " occ=0.50 residue: pdb=" N AARG F 39 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG F 39 " occ=0.50 residue: pdb=" N AMET G 46 " occ=0.43 ... (14 atoms not shown) pdb=" CE BMET G 46 " occ=0.57 residue: pdb=" N AARG H 84 " occ=0.34 ... (20 atoms not shown) pdb=" NH2BARG H 84 " occ=0.66 residue: pdb=" N AMET I 46 " occ=0.55 ... (14 atoms not shown) pdb=" CE BMET I 46 " occ=0.45 residue: pdb=" N AARG I 114 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG I 114 " occ=0.50 residue: pdb=" N AMET K 46 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET K 46 " occ=0.50 ... (remaining 6 not shown) Time building chain proxies: 7.93, per 1000 atoms: 0.41 Number of scatterers: 19527 At special positions: 0 Unit cell: (105.714, 107.392, 193.809, 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 106 16.00 O 3724 8.00 N 3366 7.00 C 12331 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.70 Conformation dependent library (CDL) restraints added in 1.5 seconds 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4516 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 16 sheets defined 50.0% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 10 through 25 Processing helix chain 'A' and resid 27 through 43 Processing helix chain 'A' and resid 52 through 68 Processing helix chain 'A' and resid 78 through 81 Processing helix chain 'A' and resid 104 through 116 removed outlier: 3.503A pdb=" N LEU A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 25 Processing helix chain 'B' and resid 27 through 43 Processing helix chain 'B' and resid 52 through 68 Processing helix chain 'B' and resid 104 through 118 Processing helix chain 'C' and resid 10 through 25 Processing helix chain 'C' and resid 27 through 45 Processing helix chain 'C' and resid 52 through 68 removed outlier: 3.509A pdb=" N ILE C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 removed outlier: 3.809A pdb=" N VAL C 116 " --> pdb=" O TYR C 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 25 Processing helix chain 'D' and resid 26 through 45 Processing helix chain 'D' and resid 52 through 68 removed outlier: 3.559A pdb=" N ILE D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 118 removed outlier: 3.804A pdb=" N LEU D 108 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU D 109 " --> pdb=" O ALA D 105 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR D 117 " --> pdb=" O GLY D 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 26 Processing helix chain 'E' and resid 27 through 45 Processing helix chain 'E' and resid 52 through 68 Processing helix chain 'E' and resid 104 through 117 removed outlier: 3.596A pdb=" N THR E 117 " --> pdb=" O GLY E 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 25 Processing helix chain 'F' and resid 26 through 45 Processing helix chain 'F' and resid 52 through 68 removed outlier: 3.589A pdb=" N ILE F 67 " --> pdb=" O LEU F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 118 Processing helix chain 'G' and resid 10 through 25 Processing helix chain 'G' and resid 27 through 42 Processing helix chain 'G' and resid 52 through 68 Processing helix chain 'G' and resid 104 through 117 removed outlier: 3.564A pdb=" N THR G 117 " --> pdb=" O GLY G 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 25 Processing helix chain 'H' and resid 26 through 45 Processing helix chain 'H' and resid 52 through 68 removed outlier: 3.540A pdb=" N ILE H 67 " --> pdb=" O LEU H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 118 Processing helix chain 'I' and resid 10 through 26 Processing helix chain 'I' and resid 27 through 43 Processing helix chain 'I' and resid 52 through 68 Processing helix chain 'I' and resid 104 through 117 removed outlier: 3.580A pdb=" N THR I 117 " --> pdb=" O GLY I 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 25 Processing helix chain 'J' and resid 26 through 43 Processing helix chain 'J' and resid 52 through 68 removed outlier: 3.548A pdb=" N ILE J 67 " --> pdb=" O LEU J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 104 through 118 removed outlier: 3.637A pdb=" N LEU J 108 " --> pdb=" O LEU J 104 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR J 117 " --> pdb=" O GLY J 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 26 Processing helix chain 'K' and resid 27 through 43 Processing helix chain 'K' and resid 52 through 68 Processing helix chain 'K' and resid 104 through 116 removed outlier: 3.668A pdb=" N LEU K 108 " --> pdb=" O LEU K 104 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU K 109 " --> pdb=" O ALA K 105 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG K 114 " --> pdb=" O GLY K 110 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 25 Processing helix chain 'L' and resid 26 through 45 Processing helix chain 'L' and resid 52 through 68 removed outlier: 3.585A pdb=" N ILE L 67 " --> pdb=" O LEU L 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 104 through 118 Processing helix chain 'M' and resid 10 through 26 Processing helix chain 'M' and resid 27 through 43 Processing helix chain 'M' and resid 52 through 68 removed outlier: 3.564A pdb=" N ILE M 67 " --> pdb=" O LEU M 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 117 Processing helix chain 'N' and resid 10 through 25 Processing helix chain 'N' and resid 26 through 45 Processing helix chain 'N' and resid 52 through 68 removed outlier: 3.549A pdb=" N ILE N 67 " --> pdb=" O LEU N 63 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 118 removed outlier: 3.772A pdb=" N LEU N 108 " --> pdb=" O LEU N 104 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU N 109 " --> pdb=" O ALA N 105 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR N 117 " --> pdb=" O GLY N 113 " (cutoff:3.500A) Processing helix chain 'O' and resid 10 through 25 Processing helix chain 'O' and resid 27 through 45 Processing helix chain 'O' and resid 52 through 68 Processing helix chain 'O' and resid 104 through 117 removed outlier: 3.547A pdb=" N THR O 117 " --> pdb=" O GLY O 113 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 25 Processing helix chain 'P' and resid 26 through 45 Processing helix chain 'P' and resid 52 through 68 removed outlier: 3.535A pdb=" N ILE P 67 " --> pdb=" O LEU P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 104 through 118 Processing helix chain 'Q' and resid 317 through 326 removed outlier: 3.624A pdb=" N GLY Q 326 " --> pdb=" O PHE Q 322 " (cutoff:3.500A) Processing helix chain 'Q' and resid 328 through 333 Processing helix chain 'Q' and resid 338 through 346 Processing helix chain 'R' and resid 317 through 326 removed outlier: 3.544A pdb=" N GLY R 326 " --> pdb=" O PHE R 322 " (cutoff:3.500A) Processing helix chain 'R' and resid 328 through 333 Processing helix chain 'R' and resid 338 through 346 Processing helix chain 'S' and resid 317 through 327 Processing helix chain 'S' and resid 338 through 346 Processing helix chain 'T' and resid 317 through 327 Processing helix chain 'T' and resid 338 through 346 Processing helix chain 'U' and resid 317 through 327 Processing helix chain 'V' and resid 338 through 346 Processing helix chain 'X' and resid 317 through 326 Processing helix chain 'Y' and resid 338 through 345 removed outlier: 4.089A pdb=" N ARG Y 345 " --> pdb=" O GLU Y 341 " (cutoff:3.500A) Processing helix chain 'Z' and resid 317 through 327 Processing helix chain 'a' and resid 338 through 345 removed outlier: 3.551A pdb=" N ARG a 345 " --> pdb=" O GLU a 341 " (cutoff:3.500A) Processing helix chain 'b' and resid 317 through 326 removed outlier: 3.599A pdb=" N GLY b 326 " --> pdb=" O PHE b 322 " (cutoff:3.500A) Processing helix chain 'b' and resid 328 through 333 Processing helix chain 'd' and resid 338 through 346 Processing sheet with id=AA1, first strand: chain 'A' and resid 71 through 77 removed outlier: 3.874A pdb=" N TYR A 148 " --> pdb=" O THR A 129 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 71 through 77 removed outlier: 3.504A pdb=" N SER W 154 " --> pdb=" O GLY B 124 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N VAL B 128 " --> pdb=" O THR W 156 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 71 through 77 Processing sheet with id=AA4, first strand: chain 'D' and resid 71 through 77 Processing sheet with id=AA5, first strand: chain 'E' and resid 71 through 76 Processing sheet with id=AA6, first strand: chain 'F' and resid 71 through 77 Processing sheet with id=AA7, first strand: chain 'F' and resid 153 through 156 removed outlier: 6.468A pdb=" N SER F 154 " --> pdb=" O TYR J 126 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N VAL J 128 " --> pdb=" O SER F 154 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N THR F 156 " --> pdb=" O VAL J 128 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ARG J 130 " --> pdb=" O THR F 156 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 71 through 77 Processing sheet with id=AA9, first strand: chain 'H' and resid 71 through 77 removed outlier: 6.758A pdb=" N TYR H 126 " --> pdb=" O THR L 156 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 71 through 76 Processing sheet with id=AB2, first strand: chain 'K' and resid 71 through 77 Processing sheet with id=AB3, first strand: chain 'L' and resid 71 through 77 Processing sheet with id=AB4, first strand: chain 'M' and resid 71 through 77 Processing sheet with id=AB5, first strand: chain 'N' and resid 71 through 77 Processing sheet with id=AB6, first strand: chain 'O' and resid 71 through 77 Processing sheet with id=AB7, first strand: chain 'P' and resid 71 through 77 1162 hydrogen bonds defined for protein. 3329 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.57 Time building geometry restraints manager: 2.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3260 1.32 - 1.44: 4897 1.44 - 1.56: 11432 1.56 - 1.69: 0 1.69 - 1.81: 196 Bond restraints: 19785 Sorted by residual: bond pdb=" C PRO Q 335 " pdb=" O PRO Q 335 " ideal model delta sigma weight residual 1.233 1.197 0.036 1.34e-02 5.57e+03 7.36e+00 bond pdb=" CA SER Q 334 " pdb=" CB SER Q 334 " ideal model delta sigma weight residual 1.527 1.485 0.041 1.79e-02 3.12e+03 5.28e+00 bond pdb=" CA PRO Q 335 " pdb=" C PRO Q 335 " ideal model delta sigma weight residual 1.520 1.543 -0.022 1.09e-02 8.42e+03 4.10e+00 bond pdb=" N LEU Q 333 " pdb=" CA LEU Q 333 " ideal model delta sigma weight residual 1.456 1.479 -0.023 1.26e-02 6.30e+03 3.42e+00 bond pdb=" N SER Q 334 " pdb=" CA SER Q 334 " ideal model delta sigma weight residual 1.456 1.476 -0.021 1.57e-02 4.06e+03 1.72e+00 ... (remaining 19780 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 26234 1.18 - 2.35: 479 2.35 - 3.53: 150 3.53 - 4.70: 31 4.70 - 5.88: 6 Bond angle restraints: 26900 Sorted by residual: angle pdb=" C PRO Q 335 " pdb=" CA PRO Q 335 " pdb=" CB PRO Q 335 " ideal model delta sigma weight residual 111.71 117.59 -5.88 1.30e+00 5.92e-01 2.05e+01 angle pdb=" N LEU Q 333 " pdb=" CA LEU Q 333 " pdb=" C LEU Q 333 " ideal model delta sigma weight residual 112.92 108.80 4.12 1.23e+00 6.61e-01 1.12e+01 angle pdb=" N PRO Q 335 " pdb=" CA PRO Q 335 " pdb=" CB PRO Q 335 " ideal model delta sigma weight residual 103.17 100.29 2.88 8.90e-01 1.26e+00 1.05e+01 angle pdb=" C ASP K 125 " pdb=" CA ASP K 125 " pdb=" CB ASP K 125 " ideal model delta sigma weight residual 116.34 111.91 4.43 1.40e+00 5.10e-01 1.00e+01 angle pdb=" CB GLU P 59 " pdb=" CG GLU P 59 " pdb=" CD GLU P 59 " ideal model delta sigma weight residual 112.60 116.84 -4.24 1.70e+00 3.46e-01 6.22e+00 ... (remaining 26895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 10279 17.99 - 35.99: 1092 35.99 - 53.98: 368 53.98 - 71.98: 116 71.98 - 89.97: 50 Dihedral angle restraints: 11905 sinusoidal: 4887 harmonic: 7018 Sorted by residual: dihedral pdb=" CA ASP J 80 " pdb=" CB ASP J 80 " pdb=" CG ASP J 80 " pdb=" OD1 ASP J 80 " ideal model delta sinusoidal sigma weight residual -30.00 -89.45 59.45 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA ASP O 9 " pdb=" CB ASP O 9 " pdb=" CG ASP O 9 " pdb=" OD1 ASP O 9 " ideal model delta sinusoidal sigma weight residual -30.00 -88.14 58.14 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CB GLU E 20 " pdb=" CG GLU E 20 " pdb=" CD GLU E 20 " pdb=" OE1 GLU E 20 " ideal model delta sinusoidal sigma weight residual 0.00 89.97 -89.97 1 3.00e+01 1.11e-03 1.07e+01 ... (remaining 11902 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2077 0.030 - 0.059: 712 0.059 - 0.089: 210 0.089 - 0.118: 101 0.118 - 0.148: 21 Chirality restraints: 3121 Sorted by residual: chirality pdb=" CA ILE D 85 " pdb=" N ILE D 85 " pdb=" C ILE D 85 " pdb=" CB ILE D 85 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.48e-01 chirality pdb=" CA ILE P 85 " pdb=" N ILE P 85 " pdb=" C ILE P 85 " pdb=" CB ILE P 85 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA ILE C 85 " pdb=" N ILE C 85 " pdb=" C ILE C 85 " pdb=" CB ILE C 85 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.15e-01 ... (remaining 3118 not shown) Planarity restraints: 3455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU Q 332 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.24e+00 pdb=" C LEU Q 332 " -0.036 2.00e-02 2.50e+03 pdb=" O LEU Q 332 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU Q 333 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA M 105 " 0.027 5.00e-02 4.00e+02 4.06e-02 2.63e+00 pdb=" N PRO M 106 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO M 106 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO M 106 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 109 " -0.007 2.00e-02 2.50e+03 1.49e-02 2.21e+00 pdb=" C GLU A 109 " 0.026 2.00e-02 2.50e+03 pdb=" O GLU A 109 " -0.010 2.00e-02 2.50e+03 pdb=" N GLY A 110 " -0.009 2.00e-02 2.50e+03 ... (remaining 3452 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 255 2.66 - 3.22: 17133 3.22 - 3.78: 32677 3.78 - 4.34: 44986 4.34 - 4.90: 71962 Nonbonded interactions: 167013 Sorted by model distance: nonbonded pdb=" O GLY O 113 " pdb=" OG1 THR O 117 " model vdw 2.094 3.040 nonbonded pdb=" O GLY E 113 " pdb=" OG1 THR E 117 " model vdw 2.119 3.040 nonbonded pdb=" O GLY M 113 " pdb=" OG1 THR M 117 " model vdw 2.197 3.040 nonbonded pdb=" OD2 ASP A 54 " pdb=" NH2 ARG F 142 " model vdw 2.200 3.120 nonbonded pdb=" OE2 GLU I 36 " pdb=" NH1 ARG I 39 " model vdw 2.207 3.120 ... (remaining 167008 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' and (resid 7 through 34 or resid 36 through 38 or resid 40 through 45 \ or resid 47 through 83 or resid 85 through 113 or resid 115 through 119 or resi \ d 125 through 131 or resid 140 through 151)) selection = (chain 'B' and (resid 7 through 34 or resid 36 through 38 or resid 40 through 45 \ or resid 47 through 83 or resid 85 through 113 or resid 115 through 119 or resi \ d 125 through 131 or resid 140 through 151)) selection = (chain 'C' and (resid 7 through 34 or resid 36 through 38 or resid 40 through 45 \ or resid 47 through 83 or resid 85 through 113 or resid 115 through 119 or resi \ d 125 through 131 or resid 140 through 151)) selection = (chain 'D' and (resid 7 through 34 or resid 36 through 38 or resid 40 through 45 \ or resid 47 through 83 or resid 85 through 113 or resid 115 through 131 or resi \ d 140 through 151)) selection = (chain 'E' and (resid 7 through 34 or resid 36 through 38 or resid 40 through 45 \ or resid 47 through 83 or resid 85 through 113 or resid 115 through 119 or resi \ d 125 through 131 or resid 140 through 151)) selection = (chain 'F' and (resid 7 through 34 or resid 36 through 38 or resid 40 through 45 \ or resid 47 through 83 or resid 85 through 113 or resid 115 through 119 or resi \ d 125 through 131 or resid 140 through 151)) selection = (chain 'G' and (resid 7 through 34 or resid 36 through 38 or resid 40 through 45 \ or resid 47 through 83 or resid 85 through 113 or resid 115 through 119 or resi \ d 125 through 131 or resid 140 through 151)) selection = (chain 'H' and (resid 7 through 34 or resid 36 through 38 or resid 40 through 45 \ or resid 47 through 83 or resid 85 through 113 or resid 115 through 119 or resi \ d 125 through 131 or resid 140 through 151)) selection = (chain 'I' and (resid 7 through 34 or resid 36 through 38 or resid 40 through 45 \ or resid 47 through 83 or resid 85 through 113 or resid 115 through 119 or resi \ d 125 through 131 or resid 140 through 151)) selection = (chain 'J' and (resid 7 through 34 or resid 36 through 38 or resid 40 through 45 \ or resid 47 through 83 or resid 85 through 113 or resid 115 through 119 or resi \ d 125 through 131 or resid 140 through 151)) selection = (chain 'K' and (resid 7 through 34 or resid 36 through 38 or resid 40 through 45 \ or resid 47 through 83 or resid 85 through 113 or resid 115 through 119 or resi \ d 125 through 151)) selection = (chain 'L' and (resid 7 through 34 or resid 36 through 38 or resid 40 through 45 \ or resid 47 through 83 or resid 85 through 113 or resid 115 through 119 or resi \ d 125 through 131 or resid 140 through 151)) selection = (chain 'M' and (resid 7 through 34 or resid 36 through 38 or resid 40 through 45 \ or resid 47 through 83 or resid 85 through 113 or resid 115 through 119 or resi \ d 125 through 131 or resid 140 through 151)) selection = (chain 'N' and (resid 7 through 34 or resid 36 through 38 or resid 40 through 45 \ or resid 47 through 83 or resid 85 through 113 or resid 115 through 119 or resi \ d 125 through 131 or resid 140 through 151)) selection = (chain 'O' and (resid 7 through 34 or resid 36 through 38 or resid 40 through 45 \ or resid 47 through 83 or resid 85 through 113 or resid 115 through 119 or resi \ d 125 through 131 or resid 140 through 151)) selection = (chain 'P' and (resid 7 through 34 or resid 36 through 38 or resid 40 through 45 \ or resid 47 through 83 or resid 85 through 113 or resid 115 through 119 or resi \ d 125 through 131 or resid 140 through 151)) } ncs_group { reference = chain 'Q' selection = (chain 'R' and resid 313 through 346) } ncs_group { reference = chain 'S' selection = (chain 'T' and (resid 313 through 327 or resid 337 through 346)) } ncs_group { reference = (chain 'U' and resid 313 through 326) selection = chain 'X' selection = (chain 'Z' and resid 313 through 326) } ncs_group { reference = (chain 'V' and resid 337 through 345) selection = (chain 'Y' and resid 337 through 345) selection = (chain 'a' and resid 337 through 345) selection = (chain 'd' and resid 337 through 345) } ncs_group { reference = chain 'W' selection = chain 'c' } 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=0.27 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.370 Find NCS groups from input model: 0.400 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:9.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 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 : 0.002 0.041 19785 Z= 0.110 Angle : 0.456 5.879 26900 Z= 0.242 Chirality : 0.037 0.148 3121 Planarity : 0.004 0.041 3455 Dihedral : 18.367 89.973 7389 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.90 % Favored : 98.06 % Rotamer: Outliers : 1.18 % Allowed : 20.83 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 1.31 (0.17), residues: 2422 helix: 1.95 (0.15), residues: 1207 sheet: 0.99 (0.24), residues: 422 loop : -0.92 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG T 345 TYR 0.010 0.001 TYR C 112 PHE 0.009 0.001 PHE T 322 TRP 0.009 0.001 TRP N 19 HIS 0.002 0.001 HIS F 87 Details of bonding type rmsd covalent geometry : bond 0.00229 (19785) covalent geometry : angle 0.45590 (26900) hydrogen bonds : bond 0.14283 ( 1162) hydrogen bonds : angle 5.59822 ( 3329) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 568 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 153 SER cc_start: 0.8069 (m) cc_final: 0.7732 (m) outliers start: 18 outliers final: 16 residues processed: 582 average time/residue: 0.8840 time to fit residues: 560.5380 Evaluate side-chains 505 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 489 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain K residue 19 TRP Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain P residue 100 SER Chi-restraints excluded: chain S residue 345 ARG Chi-restraints excluded: chain T residue 345 ARG Chi-restraints excluded: chain U residue 321 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 24 GLN G 51 GLN H 24 GLN I 51 GLN J 24 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.051775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2526 r_free = 0.2526 target = 0.038701 restraints weight = 264643.044| |-----------------------------------------------------------------------------| r_work (start): 0.2499 rms_B_bonded: 5.55 r_work: 0.2297 rms_B_bonded: 5.16 restraints_weight: 2.0000 r_work (final): 0.2297 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2288 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2288 r_free = 0.2288 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2287 r_free = 0.2287 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2287 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9208 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19785 Z= 0.182 Angle : 0.610 9.629 26900 Z= 0.316 Chirality : 0.040 0.152 3121 Planarity : 0.005 0.045 3455 Dihedral : 4.764 84.486 2720 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.07 % Favored : 97.89 % Rotamer: Outliers : 2.59 % Allowed : 21.02 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 1.56 (0.17), residues: 2422 helix: 2.15 (0.15), residues: 1228 sheet: 1.03 (0.23), residues: 416 loop : -0.80 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 114 TYR 0.011 0.001 TYR L 112 PHE 0.011 0.001 PHE E 123 TRP 0.012 0.001 TRP H 103 HIS 0.002 0.000 HIS J 87 Details of bonding type rmsd covalent geometry : bond 0.00423 (19785) covalent geometry : angle 0.60952 (26900) hydrogen bonds : bond 0.04031 ( 1162) hydrogen bonds : angle 4.40300 ( 3329) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 508 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8882 (mp0) cc_final: 0.8677 (pm20) REVERT: B 54 ASP cc_start: 0.9396 (t70) cc_final: 0.9019 (t0) REVERT: B 80 ASP cc_start: 0.8767 (t0) cc_final: 0.8481 (t0) REVERT: B 125 ASP cc_start: 0.8770 (p0) cc_final: 0.8301 (p0) REVERT: B 152 ARG cc_start: 0.9186 (tmm-80) cc_final: 0.8749 (ttp80) REVERT: D 20 GLU cc_start: 0.9299 (tp30) cc_final: 0.9078 (tp30) REVERT: D 80 ASP cc_start: 0.8793 (t0) cc_final: 0.8577 (t0) REVERT: D 129 THR cc_start: 0.9371 (m) cc_final: 0.9144 (p) REVERT: E 9 ASP cc_start: 0.9398 (t0) cc_final: 0.9038 (t0) REVERT: I 78 SER cc_start: 0.9634 (m) cc_final: 0.9393 (p) REVERT: J 24 GLN cc_start: 0.9378 (OUTLIER) cc_final: 0.9080 (tp40) REVERT: L 80 ASP cc_start: 0.9323 (t0) cc_final: 0.9114 (t0) REVERT: L 130 ARG cc_start: 0.9365 (OUTLIER) cc_final: 0.8012 (ttm170) REVERT: M 75 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8253 (tm-30) REVERT: M 80 ASP cc_start: 0.8505 (p0) cc_final: 0.8091 (p0) REVERT: M 88 GLU cc_start: 0.9151 (OUTLIER) cc_final: 0.8615 (mp0) REVERT: N 75 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8450 (tm-30) REVERT: N 80 ASP cc_start: 0.9046 (t0) cc_final: 0.8771 (t0) REVERT: N 152 ARG cc_start: 0.9141 (ttp80) cc_final: 0.8255 (ttp80) REVERT: O 36 GLU cc_start: 0.9389 (mm-30) cc_final: 0.9164 (mm-30) REVERT: P 75 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8272 (tm-30) REVERT: P 80 ASP cc_start: 0.9095 (t0) cc_final: 0.8827 (t0) REVERT: P 88 GLU cc_start: 0.9173 (OUTLIER) cc_final: 0.8950 (mt-10) REVERT: Q 341 GLU cc_start: 0.9308 (mt-10) cc_final: 0.8966 (mp0) REVERT: R 341 GLU cc_start: 0.9226 (mt-10) cc_final: 0.9023 (pm20) REVERT: R 345 ARG cc_start: 0.8409 (tpm170) cc_final: 0.8108 (tpm170) REVERT: S 313 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7329 (m-30) REVERT: S 320 GLU cc_start: 0.9006 (tm-30) cc_final: 0.8745 (tm-30) REVERT: S 340 ARG cc_start: 0.9193 (ttp80) cc_final: 0.8967 (ptp-110) REVERT: T 320 GLU cc_start: 0.9228 (tt0) cc_final: 0.8864 (tm-30) REVERT: Y 336 ARG cc_start: 0.8715 (ttp80) cc_final: 0.8429 (ttp80) REVERT: Y 341 GLU cc_start: 0.9006 (mp0) cc_final: 0.8787 (mp0) REVERT: a 341 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8739 (pt0) REVERT: b 320 GLU cc_start: 0.8743 (tm-30) cc_final: 0.8437 (tm-30) REVERT: b 332 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8327 (mp) outliers start: 47 outliers final: 21 residues processed: 531 average time/residue: 0.8410 time to fit residues: 488.8007 Evaluate side-chains 507 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 480 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain K residue 19 TRP Chi-restraints excluded: chain K residue 24 GLN Chi-restraints excluded: chain L residue 130 ARG Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain M residue 88 GLU Chi-restraints excluded: chain N residue 78 SER Chi-restraints excluded: chain O residue 78 SER Chi-restraints excluded: chain P residue 78 SER Chi-restraints excluded: chain P residue 88 GLU Chi-restraints excluded: chain S residue 313 ASP Chi-restraints excluded: chain S residue 345 ARG Chi-restraints excluded: chain T residue 323 MET Chi-restraints excluded: chain V residue 345 ARG Chi-restraints excluded: chain W residue 154 SER Chi-restraints excluded: chain b residue 332 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 50 optimal weight: 0.7980 chunk 187 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 221 optimal weight: 0.4980 chunk 135 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 156 optimal weight: 0.5980 chunk 141 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 129 optimal weight: 0.6980 chunk 165 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 24 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 GLN I 51 GLN K 119 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.051625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2529 r_free = 0.2529 target = 0.038586 restraints weight = 290219.525| |-----------------------------------------------------------------------------| r_work (start): 0.2498 rms_B_bonded: 5.70 r_work: 0.2291 rms_B_bonded: 5.27 restraints_weight: 2.0000 r_work (final): 0.2291 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2288 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2288 r_free = 0.2288 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2288 r_free = 0.2288 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2288 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9196 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19785 Z= 0.146 Angle : 0.613 12.480 26900 Z= 0.314 Chirality : 0.039 0.257 3121 Planarity : 0.004 0.055 3455 Dihedral : 4.020 57.292 2703 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.03 % Favored : 97.93 % Rotamer: Outliers : 2.44 % Allowed : 22.00 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 1.58 (0.17), residues: 2422 helix: 2.18 (0.15), residues: 1239 sheet: 1.01 (0.23), residues: 416 loop : -0.84 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 114 TYR 0.009 0.001 TYR I 112 PHE 0.012 0.001 PHE F 10 TRP 0.011 0.001 TRP K 69 HIS 0.001 0.000 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00344 (19785) covalent geometry : angle 0.61268 (26900) hydrogen bonds : bond 0.03630 ( 1162) hydrogen bonds : angle 4.22346 ( 3329) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 501 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 54 ASP cc_start: 0.9422 (t70) cc_final: 0.9073 (t0) REVERT: B 80 ASP cc_start: 0.8813 (t0) cc_final: 0.8485 (t0) REVERT: B 125 ASP cc_start: 0.8852 (p0) cc_final: 0.8384 (p0) REVERT: B 152 ARG cc_start: 0.9192 (tmm-80) cc_final: 0.8810 (ttp80) REVERT: D 80 ASP cc_start: 0.8897 (t0) cc_final: 0.8482 (t0) REVERT: E 9 ASP cc_start: 0.9382 (t0) cc_final: 0.9033 (t0) REVERT: E 80 ASP cc_start: 0.8893 (p0) cc_final: 0.8609 (p0) REVERT: G 51 GLN cc_start: 0.9229 (mm-40) cc_final: 0.8942 (mm-40) REVERT: I 75 GLU cc_start: 0.9138 (tt0) cc_final: 0.8749 (tm-30) REVERT: J 20 GLU cc_start: 0.9322 (tp30) cc_final: 0.9036 (tp30) REVERT: J 24 GLN cc_start: 0.9441 (OUTLIER) cc_final: 0.9161 (tp40) REVERT: J 114 ARG cc_start: 0.9221 (OUTLIER) cc_final: 0.8375 (tpm170) REVERT: L 59 GLU cc_start: 0.9589 (mm-30) cc_final: 0.9385 (mm-30) REVERT: L 80 ASP cc_start: 0.9410 (t0) cc_final: 0.9105 (t0) REVERT: M 75 GLU cc_start: 0.8746 (tm-30) cc_final: 0.8175 (tm-30) REVERT: M 79 GLU cc_start: 0.8790 (pm20) cc_final: 0.8553 (pm20) REVERT: M 80 ASP cc_start: 0.8455 (p0) cc_final: 0.8166 (p0) REVERT: N 59 GLU cc_start: 0.9492 (mm-30) cc_final: 0.9244 (mm-30) REVERT: N 75 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8533 (tm-30) REVERT: N 80 ASP cc_start: 0.9128 (t0) cc_final: 0.8810 (t0) REVERT: N 125 ASP cc_start: 0.8421 (p0) cc_final: 0.7691 (p0) REVERT: N 152 ARG cc_start: 0.9077 (ttp80) cc_final: 0.8531 (ttp80) REVERT: P 32 GLU cc_start: 0.9137 (tp30) cc_final: 0.8743 (tp30) REVERT: P 75 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8228 (tm-30) REVERT: P 80 ASP cc_start: 0.9200 (t0) cc_final: 0.8874 (t0) REVERT: P 88 GLU cc_start: 0.9182 (OUTLIER) cc_final: 0.8957 (mt-10) REVERT: R 341 GLU cc_start: 0.9227 (mt-10) cc_final: 0.8948 (pt0) REVERT: S 313 ASP cc_start: 0.7739 (OUTLIER) cc_final: 0.7347 (m-30) REVERT: S 320 GLU cc_start: 0.9058 (tm-30) cc_final: 0.8790 (tm-30) REVERT: S 340 ARG cc_start: 0.9169 (ttp80) cc_final: 0.8944 (ptp-110) REVERT: T 346 ARG cc_start: 0.7353 (mmm160) cc_final: 0.7016 (mmm160) REVERT: U 320 GLU cc_start: 0.9058 (tt0) cc_final: 0.8520 (tm-30) REVERT: Y 341 GLU cc_start: 0.9006 (mp0) cc_final: 0.8755 (mp0) REVERT: a 341 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8703 (pm20) REVERT: b 320 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8503 (tm-30) REVERT: b 332 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8281 (mp) outliers start: 44 outliers final: 21 residues processed: 524 average time/residue: 0.8431 time to fit residues: 483.4358 Evaluate side-chains 507 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 481 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain I residue 125 ASP Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain J residue 114 ARG Chi-restraints excluded: chain K residue 19 TRP Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain N residue 46 MET Chi-restraints excluded: chain N residue 78 SER Chi-restraints excluded: chain O residue 78 SER Chi-restraints excluded: chain P residue 46 MET Chi-restraints excluded: chain P residue 78 SER Chi-restraints excluded: chain P residue 88 GLU Chi-restraints excluded: chain S residue 313 ASP Chi-restraints excluded: chain S residue 345 ARG Chi-restraints excluded: chain V residue 344 LEU Chi-restraints excluded: chain b residue 332 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 79 optimal weight: 0.7980 chunk 123 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 190 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 192 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 37 optimal weight: 0.0770 chunk 231 optimal weight: 0.3980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 GLN F 24 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 119 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.051854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.038722 restraints weight = 330778.257| |-----------------------------------------------------------------------------| r_work (start): 0.2506 rms_B_bonded: 5.98 r_work: 0.2298 rms_B_bonded: 5.40 restraints_weight: 2.0000 r_work (final): 0.2298 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2291 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2291 r_free = 0.2291 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2291 r_free = 0.2291 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2291 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9219 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19785 Z= 0.142 Angle : 0.612 11.172 26900 Z= 0.311 Chirality : 0.039 0.142 3121 Planarity : 0.004 0.039 3455 Dihedral : 3.948 52.436 2702 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.11 % Favored : 97.85 % Rotamer: Outliers : 1.88 % Allowed : 22.76 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 1.65 (0.17), residues: 2422 helix: 2.25 (0.15), residues: 1238 sheet: 1.02 (0.23), residues: 416 loop : -0.84 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 346 TYR 0.009 0.001 TYR L 112 PHE 0.008 0.001 PHE E 123 TRP 0.009 0.001 TRP K 69 HIS 0.001 0.000 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00338 (19785) covalent geometry : angle 0.61233 (26900) hydrogen bonds : bond 0.03464 ( 1162) hydrogen bonds : angle 4.12984 ( 3329) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 500 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 51 GLN cc_start: 0.9194 (mt0) cc_final: 0.8788 (mp10) REVERT: B 54 ASP cc_start: 0.9460 (t70) cc_final: 0.9128 (t0) REVERT: B 80 ASP cc_start: 0.8884 (t0) cc_final: 0.8537 (t0) REVERT: B 125 ASP cc_start: 0.8898 (p0) cc_final: 0.8476 (p0) REVERT: B 129 THR cc_start: 0.9544 (m) cc_final: 0.9187 (p) REVERT: B 152 ARG cc_start: 0.9212 (tmm-80) cc_final: 0.8849 (ttp80) REVERT: D 80 ASP cc_start: 0.8934 (t0) cc_final: 0.8469 (t0) REVERT: E 9 ASP cc_start: 0.9407 (t0) cc_final: 0.9078 (t0) REVERT: E 20 GLU cc_start: 0.9090 (mm-30) cc_final: 0.8670 (mm-30) REVERT: E 24 GLN cc_start: 0.9150 (mt0) cc_final: 0.8844 (mt0) REVERT: G 24 GLN cc_start: 0.9306 (OUTLIER) cc_final: 0.9091 (mt0) REVERT: G 51 GLN cc_start: 0.9255 (mm-40) cc_final: 0.9003 (mm-40) REVERT: I 75 GLU cc_start: 0.9200 (tt0) cc_final: 0.8794 (tm-30) REVERT: I 78 SER cc_start: 0.9656 (m) cc_final: 0.9422 (p) REVERT: J 20 GLU cc_start: 0.9323 (tp30) cc_final: 0.9061 (tp30) REVERT: J 59 GLU cc_start: 0.9589 (mm-30) cc_final: 0.9376 (mm-30) REVERT: L 46 MET cc_start: 0.9190 (mmm) cc_final: 0.8968 (mmp) REVERT: L 59 GLU cc_start: 0.9592 (mm-30) cc_final: 0.9344 (mm-30) REVERT: L 80 ASP cc_start: 0.9469 (t0) cc_final: 0.9125 (t0) REVERT: M 75 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8293 (tm-30) REVERT: N 59 GLU cc_start: 0.9506 (mm-30) cc_final: 0.9252 (mm-30) REVERT: N 75 GLU cc_start: 0.8812 (tm-30) cc_final: 0.8556 (tm-30) REVERT: N 80 ASP cc_start: 0.9216 (t0) cc_final: 0.8907 (t0) REVERT: N 125 ASP cc_start: 0.8639 (p0) cc_final: 0.7776 (p0) REVERT: N 152 ARG cc_start: 0.9177 (ttp80) cc_final: 0.8541 (ttp80) REVERT: P 32 GLU cc_start: 0.9131 (tp30) cc_final: 0.8727 (tp30) REVERT: P 75 GLU cc_start: 0.8599 (tm-30) cc_final: 0.8255 (tm-30) REVERT: P 80 ASP cc_start: 0.9249 (t0) cc_final: 0.8906 (t0) REVERT: S 313 ASP cc_start: 0.7548 (OUTLIER) cc_final: 0.7165 (m-30) REVERT: S 320 GLU cc_start: 0.9126 (tm-30) cc_final: 0.8831 (tm-30) REVERT: S 341 GLU cc_start: 0.9116 (OUTLIER) cc_final: 0.8858 (pm20) REVERT: U 320 GLU cc_start: 0.9062 (tt0) cc_final: 0.8547 (tm-30) REVERT: Y 336 ARG cc_start: 0.8746 (ttp80) cc_final: 0.8466 (ttp80) REVERT: Y 341 GLU cc_start: 0.9003 (mp0) cc_final: 0.8792 (pm20) REVERT: a 341 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8757 (pm20) REVERT: b 320 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8498 (tm-30) REVERT: b 332 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8240 (mp) outliers start: 32 outliers final: 13 residues processed: 514 average time/residue: 0.8418 time to fit residues: 473.4063 Evaluate side-chains 496 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 479 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain I residue 125 ASP Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain K residue 19 TRP Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain N residue 46 MET Chi-restraints excluded: chain N residue 78 SER Chi-restraints excluded: chain P residue 46 MET Chi-restraints excluded: chain S residue 313 ASP Chi-restraints excluded: chain S residue 341 GLU Chi-restraints excluded: chain T residue 323 MET Chi-restraints excluded: chain W residue 154 SER Chi-restraints excluded: chain b residue 325 LEU Chi-restraints excluded: chain b residue 332 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 118 optimal weight: 5.9990 chunk 168 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 184 optimal weight: 0.5980 chunk 108 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 187 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 154 optimal weight: 0.4980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 24 GLN F 81 GLN I 51 GLN I 119 GLN K 51 GLN K 119 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.050766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2516 r_free = 0.2516 target = 0.037857 restraints weight = 299616.160| |-----------------------------------------------------------------------------| r_work (start): 0.2479 rms_B_bonded: 5.71 r_work: 0.2270 rms_B_bonded: 5.37 restraints_weight: 2.0000 r_work (final): 0.2270 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2272 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2272 r_free = 0.2272 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2272 r_free = 0.2272 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2272 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9241 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19785 Z= 0.175 Angle : 0.644 11.163 26900 Z= 0.328 Chirality : 0.040 0.142 3121 Planarity : 0.004 0.038 3455 Dihedral : 3.742 40.802 2697 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.32 % Favored : 97.64 % Rotamer: Outliers : 2.30 % Allowed : 23.27 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 1.70 (0.17), residues: 2422 helix: 2.26 (0.15), residues: 1243 sheet: 1.08 (0.23), residues: 416 loop : -0.77 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 39 TYR 0.008 0.001 TYR I 112 PHE 0.010 0.001 PHE E 123 TRP 0.007 0.001 TRP I 19 HIS 0.001 0.000 HIS F 87 Details of bonding type rmsd covalent geometry : bond 0.00419 (19785) covalent geometry : angle 0.64361 (26900) hydrogen bonds : bond 0.03700 ( 1162) hydrogen bonds : angle 4.12597 ( 3329) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 484 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8928 (mp0) cc_final: 0.8677 (mp0) REVERT: A 80 ASP cc_start: 0.9313 (m-30) cc_final: 0.8772 (t0) REVERT: B 51 GLN cc_start: 0.9163 (mt0) cc_final: 0.8764 (mp10) REVERT: B 54 ASP cc_start: 0.9473 (t70) cc_final: 0.9140 (t0) REVERT: B 75 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8318 (tm-30) REVERT: B 80 ASP cc_start: 0.8992 (t0) cc_final: 0.8627 (t0) REVERT: B 125 ASP cc_start: 0.8905 (p0) cc_final: 0.8443 (p0) REVERT: B 129 THR cc_start: 0.9538 (m) cc_final: 0.9182 (p) REVERT: B 152 ARG cc_start: 0.9176 (tmm-80) cc_final: 0.8783 (ttp80) REVERT: D 80 ASP cc_start: 0.9075 (t0) cc_final: 0.8596 (t0) REVERT: E 9 ASP cc_start: 0.9408 (t0) cc_final: 0.8987 (t0) REVERT: E 20 GLU cc_start: 0.9130 (mm-30) cc_final: 0.8665 (mm-30) REVERT: E 24 GLN cc_start: 0.9170 (mt0) cc_final: 0.8853 (mt0) REVERT: F 131 ASP cc_start: 0.9108 (t0) cc_final: 0.8884 (t0) REVERT: G 24 GLN cc_start: 0.9294 (OUTLIER) cc_final: 0.8969 (mt0) REVERT: G 51 GLN cc_start: 0.9330 (mm-40) cc_final: 0.9065 (mm-40) REVERT: I 75 GLU cc_start: 0.9191 (tt0) cc_final: 0.8768 (tm-30) REVERT: I 78 SER cc_start: 0.9665 (m) cc_final: 0.9442 (p) REVERT: I 119 GLN cc_start: 0.9260 (mm-40) cc_final: 0.9049 (mp10) REVERT: J 20 GLU cc_start: 0.9364 (tp30) cc_final: 0.9084 (tp30) REVERT: L 46 MET cc_start: 0.9145 (mmm) cc_final: 0.8911 (mmp) REVERT: L 59 GLU cc_start: 0.9580 (mm-30) cc_final: 0.9367 (mm-30) REVERT: L 80 ASP cc_start: 0.9484 (t0) cc_final: 0.9134 (t0) REVERT: M 75 GLU cc_start: 0.8828 (tm-30) cc_final: 0.8326 (tm-30) REVERT: N 59 GLU cc_start: 0.9500 (mm-30) cc_final: 0.9228 (mm-30) REVERT: N 75 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8613 (tm-30) REVERT: N 80 ASP cc_start: 0.9260 (t0) cc_final: 0.8916 (t0) REVERT: N 125 ASP cc_start: 0.8719 (p0) cc_final: 0.7886 (p0) REVERT: N 152 ARG cc_start: 0.9156 (ttp80) cc_final: 0.8508 (ttp80) REVERT: P 32 GLU cc_start: 0.9109 (tp30) cc_final: 0.8742 (tp30) REVERT: P 75 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8197 (tm-30) REVERT: P 80 ASP cc_start: 0.9293 (t0) cc_final: 0.8946 (t0) REVERT: P 88 GLU cc_start: 0.9205 (OUTLIER) cc_final: 0.8970 (mt-10) REVERT: R 341 GLU cc_start: 0.9212 (mt-10) cc_final: 0.8951 (pm20) REVERT: S 313 ASP cc_start: 0.7752 (OUTLIER) cc_final: 0.7324 (m-30) REVERT: S 320 GLU cc_start: 0.9150 (tm-30) cc_final: 0.8836 (tm-30) REVERT: S 341 GLU cc_start: 0.9133 (OUTLIER) cc_final: 0.8854 (pm20) REVERT: U 320 GLU cc_start: 0.9044 (tt0) cc_final: 0.8601 (tm-30) REVERT: Y 336 ARG cc_start: 0.8773 (ttp80) cc_final: 0.8499 (ttp80) REVERT: Y 341 GLU cc_start: 0.9018 (mp0) cc_final: 0.8756 (pm20) REVERT: a 341 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8684 (pm20) REVERT: b 320 GLU cc_start: 0.8851 (tm-30) cc_final: 0.8523 (tm-30) REVERT: b 332 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8292 (mp) outliers start: 41 outliers final: 19 residues processed: 507 average time/residue: 0.8045 time to fit residues: 446.9689 Evaluate side-chains 497 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 473 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain K residue 24 GLN Chi-restraints excluded: chain K residue 129 THR Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain N residue 78 SER Chi-restraints excluded: chain P residue 78 SER Chi-restraints excluded: chain P residue 88 GLU Chi-restraints excluded: chain P residue 129 THR Chi-restraints excluded: chain R residue 325 LEU Chi-restraints excluded: chain S residue 313 ASP Chi-restraints excluded: chain S residue 341 GLU Chi-restraints excluded: chain T residue 323 MET Chi-restraints excluded: chain U residue 323 MET Chi-restraints excluded: chain W residue 154 SER Chi-restraints excluded: chain b residue 325 LEU Chi-restraints excluded: chain b residue 332 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 15 optimal weight: 0.9980 chunk 185 optimal weight: 1.9990 chunk 199 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 150 optimal weight: 0.4980 chunk 152 optimal weight: 1.9990 chunk 158 optimal weight: 0.7980 chunk 187 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 GLN ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 GLN I 51 GLN J 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.051072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2527 r_free = 0.2527 target = 0.038206 restraints weight = 285063.782| |-----------------------------------------------------------------------------| r_work (start): 0.2499 rms_B_bonded: 5.65 r_work: 0.2298 rms_B_bonded: 5.20 restraints_weight: 2.0000 r_work (final): 0.2298 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2291 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2291 r_free = 0.2291 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2291 r_free = 0.2291 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2291 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9218 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19785 Z= 0.151 Angle : 0.643 11.660 26900 Z= 0.326 Chirality : 0.039 0.142 3121 Planarity : 0.004 0.038 3455 Dihedral : 3.589 24.512 2695 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.07 % Favored : 97.89 % Rotamer: Outliers : 1.79 % Allowed : 24.59 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 1.74 (0.17), residues: 2422 helix: 2.31 (0.15), residues: 1242 sheet: 1.15 (0.23), residues: 416 loop : -0.85 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG S 346 TYR 0.012 0.001 TYR L 112 PHE 0.008 0.001 PHE E 123 TRP 0.008 0.001 TRP I 19 HIS 0.002 0.000 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00362 (19785) covalent geometry : angle 0.64290 (26900) hydrogen bonds : bond 0.03427 ( 1162) hydrogen bonds : angle 4.05667 ( 3329) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 492 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8914 (mp0) cc_final: 0.8678 (mp0) REVERT: A 80 ASP cc_start: 0.9299 (m-30) cc_final: 0.8816 (t0) REVERT: B 51 GLN cc_start: 0.9212 (mt0) cc_final: 0.8785 (mp10) REVERT: B 54 ASP cc_start: 0.9460 (t70) cc_final: 0.9111 (t0) REVERT: B 80 ASP cc_start: 0.8993 (t0) cc_final: 0.8682 (t0) REVERT: B 125 ASP cc_start: 0.8905 (p0) cc_final: 0.8431 (p0) REVERT: B 129 THR cc_start: 0.9524 (m) cc_final: 0.9155 (p) REVERT: B 152 ARG cc_start: 0.9169 (tmm-80) cc_final: 0.8785 (ttp80) REVERT: D 80 ASP cc_start: 0.9063 (t0) cc_final: 0.8580 (t0) REVERT: E 9 ASP cc_start: 0.9400 (t0) cc_final: 0.8981 (t0) REVERT: E 20 GLU cc_start: 0.9100 (mm-30) cc_final: 0.8639 (mm-30) REVERT: E 24 GLN cc_start: 0.9156 (mt0) cc_final: 0.8840 (mt0) REVERT: F 131 ASP cc_start: 0.9108 (t0) cc_final: 0.8899 (t0) REVERT: G 24 GLN cc_start: 0.9276 (OUTLIER) cc_final: 0.9059 (mt0) REVERT: H 46 MET cc_start: 0.9298 (OUTLIER) cc_final: 0.8748 (mpt) REVERT: I 75 GLU cc_start: 0.9195 (tt0) cc_final: 0.8774 (tm-30) REVERT: J 20 GLU cc_start: 0.9357 (tp30) cc_final: 0.9097 (tp30) REVERT: J 59 GLU cc_start: 0.9593 (mm-30) cc_final: 0.9362 (mm-30) REVERT: L 7 LYS cc_start: 0.8643 (mppt) cc_final: 0.8388 (ptpp) REVERT: L 59 GLU cc_start: 0.9572 (mm-30) cc_final: 0.9357 (mm-30) REVERT: L 80 ASP cc_start: 0.9499 (t0) cc_final: 0.9150 (t0) REVERT: M 75 GLU cc_start: 0.8788 (tm-30) cc_final: 0.8197 (tm-30) REVERT: M 149 MET cc_start: 0.9526 (mmp) cc_final: 0.9294 (mmp) REVERT: N 59 GLU cc_start: 0.9487 (mm-30) cc_final: 0.9218 (mm-30) REVERT: N 75 GLU cc_start: 0.8869 (tm-30) cc_final: 0.8628 (tm-30) REVERT: N 80 ASP cc_start: 0.9252 (t0) cc_final: 0.8907 (t0) REVERT: N 125 ASP cc_start: 0.8718 (p0) cc_final: 0.7867 (p0) REVERT: N 152 ARG cc_start: 0.9182 (ttp80) cc_final: 0.8531 (ttp80) REVERT: P 32 GLU cc_start: 0.9064 (tp30) cc_final: 0.8691 (tp30) REVERT: P 75 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8159 (tm-30) REVERT: P 80 ASP cc_start: 0.9301 (t0) cc_final: 0.8976 (t0) REVERT: R 341 GLU cc_start: 0.9196 (mt-10) cc_final: 0.8978 (pt0) REVERT: R 344 LEU cc_start: 0.9363 (mt) cc_final: 0.9114 (mm) REVERT: S 313 ASP cc_start: 0.7866 (OUTLIER) cc_final: 0.7498 (m-30) REVERT: S 320 GLU cc_start: 0.9155 (tm-30) cc_final: 0.8822 (tm-30) REVERT: S 341 GLU cc_start: 0.9158 (OUTLIER) cc_final: 0.8868 (pm20) REVERT: U 320 GLU cc_start: 0.9005 (tt0) cc_final: 0.8593 (tm-30) REVERT: Y 336 ARG cc_start: 0.8758 (ttp80) cc_final: 0.8421 (ttp80) REVERT: a 341 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8709 (pt0) REVERT: b 320 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8508 (tm-30) REVERT: b 332 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8276 (mp) outliers start: 30 outliers final: 13 residues processed: 509 average time/residue: 0.8189 time to fit residues: 456.9301 Evaluate side-chains 498 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 480 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain H residue 46 MET Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain M residue 80 ASP Chi-restraints excluded: chain N residue 78 SER Chi-restraints excluded: chain O residue 7 LYS Chi-restraints excluded: chain P residue 78 SER Chi-restraints excluded: chain S residue 313 ASP Chi-restraints excluded: chain S residue 341 GLU Chi-restraints excluded: chain T residue 323 MET Chi-restraints excluded: chain W residue 154 SER Chi-restraints excluded: chain b residue 332 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 113 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 116 optimal weight: 0.0670 chunk 155 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 chunk 143 optimal weight: 0.5980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 24 GLN F 81 GLN G 51 GLN I 119 GLN J 24 GLN K 51 GLN K 119 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.051225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.038342 restraints weight = 310533.971| |-----------------------------------------------------------------------------| r_work (start): 0.2503 rms_B_bonded: 5.81 r_work: 0.2295 rms_B_bonded: 5.40 restraints_weight: 2.0000 r_work (final): 0.2295 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2291 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2291 r_free = 0.2291 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2291 r_free = 0.2291 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2291 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9205 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19785 Z= 0.151 Angle : 0.666 12.007 26900 Z= 0.337 Chirality : 0.039 0.138 3121 Planarity : 0.004 0.037 3455 Dihedral : 3.593 23.770 2695 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.32 % Favored : 97.64 % Rotamer: Outliers : 1.93 % Allowed : 25.25 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 1.77 (0.17), residues: 2422 helix: 2.35 (0.15), residues: 1242 sheet: 1.15 (0.23), residues: 416 loop : -0.84 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG d 346 TYR 0.008 0.001 TYR K 112 PHE 0.007 0.001 PHE T 322 TRP 0.008 0.001 TRP I 19 HIS 0.002 0.000 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00366 (19785) covalent geometry : angle 0.66646 (26900) hydrogen bonds : bond 0.03382 ( 1162) hydrogen bonds : angle 4.03374 ( 3329) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 483 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 ASP cc_start: 0.9297 (m-30) cc_final: 0.8836 (OUTLIER) REVERT: B 51 GLN cc_start: 0.9203 (mt0) cc_final: 0.8755 (mp10) REVERT: B 54 ASP cc_start: 0.9466 (t70) cc_final: 0.9121 (t0) REVERT: B 80 ASP cc_start: 0.8992 (t0) cc_final: 0.8642 (t0) REVERT: B 125 ASP cc_start: 0.8908 (p0) cc_final: 0.8406 (p0) REVERT: B 129 THR cc_start: 0.9507 (m) cc_final: 0.9157 (p) REVERT: B 152 ARG cc_start: 0.9161 (tmm-80) cc_final: 0.8770 (ttp80) REVERT: D 80 ASP cc_start: 0.9063 (t0) cc_final: 0.8573 (t0) REVERT: E 9 ASP cc_start: 0.9400 (t0) cc_final: 0.8976 (t0) REVERT: E 20 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8627 (mm-30) REVERT: E 24 GLN cc_start: 0.9162 (mt0) cc_final: 0.8871 (mm-40) REVERT: G 24 GLN cc_start: 0.9273 (OUTLIER) cc_final: 0.9049 (mt0) REVERT: H 46 MET cc_start: 0.9305 (OUTLIER) cc_final: 0.8747 (mpt) REVERT: I 75 GLU cc_start: 0.9211 (tt0) cc_final: 0.8774 (tm-30) REVERT: J 20 GLU cc_start: 0.9353 (tp30) cc_final: 0.9144 (tp30) REVERT: J 59 GLU cc_start: 0.9591 (mm-30) cc_final: 0.9364 (mm-30) REVERT: L 7 LYS cc_start: 0.8680 (mppt) cc_final: 0.8460 (ptpp) REVERT: L 59 GLU cc_start: 0.9570 (mm-30) cc_final: 0.9345 (mm-30) REVERT: L 80 ASP cc_start: 0.9502 (t0) cc_final: 0.9141 (t0) REVERT: M 75 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8189 (tm-30) REVERT: M 149 MET cc_start: 0.9524 (mmp) cc_final: 0.9295 (mmp) REVERT: N 59 GLU cc_start: 0.9468 (mm-30) cc_final: 0.9189 (mm-30) REVERT: N 75 GLU cc_start: 0.8873 (tm-30) cc_final: 0.8631 (tm-30) REVERT: N 80 ASP cc_start: 0.9253 (t0) cc_final: 0.8900 (t0) REVERT: N 125 ASP cc_start: 0.8741 (p0) cc_final: 0.7841 (p0) REVERT: N 152 ARG cc_start: 0.9157 (ttp80) cc_final: 0.8491 (ttp80) REVERT: O 36 GLU cc_start: 0.9387 (mm-30) cc_final: 0.9148 (mm-30) REVERT: P 32 GLU cc_start: 0.9059 (tp30) cc_final: 0.8690 (tp30) REVERT: P 75 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8156 (tm-30) REVERT: P 80 ASP cc_start: 0.9288 (t0) cc_final: 0.8951 (t0) REVERT: R 341 GLU cc_start: 0.9209 (mt-10) cc_final: 0.9003 (pt0) REVERT: S 313 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7563 (m-30) REVERT: S 320 GLU cc_start: 0.9157 (tm-30) cc_final: 0.8825 (tm-30) REVERT: S 341 GLU cc_start: 0.9155 (OUTLIER) cc_final: 0.8916 (pm20) REVERT: U 320 GLU cc_start: 0.8990 (tt0) cc_final: 0.8577 (tm-30) REVERT: V 340 ARG cc_start: 0.8700 (ttm-80) cc_final: 0.8262 (ttm-80) REVERT: Y 336 ARG cc_start: 0.8740 (ttp80) cc_final: 0.8467 (ttp80) REVERT: Y 341 GLU cc_start: 0.9020 (mp0) cc_final: 0.8751 (pm20) REVERT: a 341 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8693 (pt0) REVERT: b 320 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8507 (tm-30) REVERT: b 332 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8144 (mp) outliers start: 33 outliers final: 17 residues processed: 506 average time/residue: 0.8454 time to fit residues: 468.7510 Evaluate side-chains 497 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 476 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain H residue 46 MET Chi-restraints excluded: chain K residue 129 THR Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain M residue 80 ASP Chi-restraints excluded: chain N residue 46 MET Chi-restraints excluded: chain P residue 78 SER Chi-restraints excluded: chain S residue 313 ASP Chi-restraints excluded: chain S residue 341 GLU Chi-restraints excluded: chain T residue 323 MET Chi-restraints excluded: chain W residue 154 SER Chi-restraints excluded: chain b residue 332 LEU Chi-restraints excluded: chain c residue 154 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 102 optimal weight: 0.8980 chunk 183 optimal weight: 0.1980 chunk 137 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 36 optimal weight: 0.4980 chunk 174 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 GLN ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 GLN I 51 GLN J 24 GLN K 119 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.051422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.038501 restraints weight = 305117.963| |-----------------------------------------------------------------------------| r_work (start): 0.2513 rms_B_bonded: 5.82 r_work: 0.2309 rms_B_bonded: 5.39 restraints_weight: 2.0000 r_work (final): 0.2309 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2304 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2304 r_free = 0.2304 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2304 r_free = 0.2304 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2304 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9220 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19785 Z= 0.145 Angle : 0.686 12.333 26900 Z= 0.344 Chirality : 0.039 0.228 3121 Planarity : 0.004 0.037 3455 Dihedral : 3.563 22.261 2695 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.15 % Favored : 97.80 % Rotamer: Outliers : 1.22 % Allowed : 26.14 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 1.79 (0.17), residues: 2422 helix: 2.36 (0.15), residues: 1243 sheet: 1.20 (0.23), residues: 416 loop : -0.85 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG d 346 TYR 0.011 0.001 TYR L 112 PHE 0.009 0.001 PHE C 10 TRP 0.008 0.001 TRP I 19 HIS 0.002 0.000 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00353 (19785) covalent geometry : angle 0.68586 (26900) hydrogen bonds : bond 0.03246 ( 1162) hydrogen bonds : angle 3.99435 ( 3329) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 488 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASP cc_start: 0.9269 (m-30) cc_final: 0.8849 (t0) REVERT: B 51 GLN cc_start: 0.9200 (mt0) cc_final: 0.8769 (mp10) REVERT: B 54 ASP cc_start: 0.9477 (t70) cc_final: 0.9140 (t0) REVERT: B 80 ASP cc_start: 0.9004 (t0) cc_final: 0.8684 (t0) REVERT: B 125 ASP cc_start: 0.8913 (p0) cc_final: 0.8412 (p0) REVERT: B 129 THR cc_start: 0.9517 (m) cc_final: 0.9236 (p) REVERT: B 152 ARG cc_start: 0.9138 (tmm-80) cc_final: 0.8744 (ttp80) REVERT: D 24 GLN cc_start: 0.9272 (mt0) cc_final: 0.8930 (mt0) REVERT: D 80 ASP cc_start: 0.9075 (t0) cc_final: 0.8590 (t0) REVERT: E 9 ASP cc_start: 0.9406 (t0) cc_final: 0.8995 (t0) REVERT: E 20 GLU cc_start: 0.9168 (mm-30) cc_final: 0.8676 (mm-30) REVERT: E 24 GLN cc_start: 0.9145 (mt0) cc_final: 0.8867 (mm-40) REVERT: G 24 GLN cc_start: 0.9290 (tt0) cc_final: 0.9071 (mt0) REVERT: G 51 GLN cc_start: 0.9318 (mm-40) cc_final: 0.9079 (mm-40) REVERT: G 142 ARG cc_start: 0.9442 (tpp80) cc_final: 0.9218 (tpp80) REVERT: H 46 MET cc_start: 0.9272 (OUTLIER) cc_final: 0.9000 (mpp) REVERT: I 75 GLU cc_start: 0.9227 (tt0) cc_final: 0.8786 (tm-30) REVERT: J 20 GLU cc_start: 0.9353 (tp30) cc_final: 0.9146 (tp30) REVERT: J 59 GLU cc_start: 0.9591 (mm-30) cc_final: 0.9373 (mm-30) REVERT: L 59 GLU cc_start: 0.9579 (mm-30) cc_final: 0.9301 (mm-30) REVERT: L 80 ASP cc_start: 0.9524 (t0) cc_final: 0.9182 (t0) REVERT: M 75 GLU cc_start: 0.8816 (tm-30) cc_final: 0.8240 (tm-30) REVERT: M 149 MET cc_start: 0.9528 (mmp) cc_final: 0.9311 (mmp) REVERT: N 59 GLU cc_start: 0.9467 (mm-30) cc_final: 0.9204 (mm-30) REVERT: N 75 GLU cc_start: 0.8879 (tm-30) cc_final: 0.8651 (tm-30) REVERT: N 80 ASP cc_start: 0.9256 (t0) cc_final: 0.8890 (t0) REVERT: N 125 ASP cc_start: 0.8771 (p0) cc_final: 0.7877 (p0) REVERT: N 152 ARG cc_start: 0.9151 (ttp80) cc_final: 0.8466 (ttp80) REVERT: O 36 GLU cc_start: 0.9421 (mm-30) cc_final: 0.9158 (mm-30) REVERT: P 32 GLU cc_start: 0.9056 (tp30) cc_final: 0.8668 (tp30) REVERT: P 75 GLU cc_start: 0.8688 (tm-30) cc_final: 0.8162 (tm-30) REVERT: P 80 ASP cc_start: 0.9271 (t0) cc_final: 0.8956 (t0) REVERT: P 131 ASP cc_start: 0.9089 (t70) cc_final: 0.8803 (t0) REVERT: R 341 GLU cc_start: 0.9256 (mt-10) cc_final: 0.8981 (pt0) REVERT: S 313 ASP cc_start: 0.7977 (OUTLIER) cc_final: 0.7609 (m-30) REVERT: S 320 GLU cc_start: 0.9164 (tm-30) cc_final: 0.8830 (tm-30) REVERT: S 341 GLU cc_start: 0.9162 (pt0) cc_final: 0.8946 (pm20) REVERT: U 320 GLU cc_start: 0.8991 (tt0) cc_final: 0.8594 (tm-30) REVERT: V 340 ARG cc_start: 0.8736 (ttm-80) cc_final: 0.8329 (ttm-80) REVERT: Y 336 ARG cc_start: 0.8746 (ttp80) cc_final: 0.8426 (ttp80) REVERT: Y 341 GLU cc_start: 0.9134 (mp0) cc_final: 0.8807 (mp0) REVERT: b 320 GLU cc_start: 0.8891 (tm-30) cc_final: 0.8545 (tm-30) REVERT: b 332 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8274 (mp) outliers start: 18 outliers final: 14 residues processed: 500 average time/residue: 0.8537 time to fit residues: 467.8100 Evaluate side-chains 493 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 476 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain D residue 9 ASP Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain H residue 46 MET Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 154 SER Chi-restraints excluded: chain M residue 80 ASP Chi-restraints excluded: chain N residue 46 MET Chi-restraints excluded: chain P residue 78 SER Chi-restraints excluded: chain S residue 313 ASP Chi-restraints excluded: chain T residue 323 MET Chi-restraints excluded: chain b residue 325 LEU Chi-restraints excluded: chain b residue 332 LEU Chi-restraints excluded: chain c residue 154 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 186 optimal weight: 0.0670 chunk 230 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 163 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 88 optimal weight: 0.3980 chunk 227 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 188 optimal weight: 0.7980 chunk 164 optimal weight: 1.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 24 GLN ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 GLN I 119 GLN J 24 GLN K 51 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.051681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.038775 restraints weight = 301587.271| |-----------------------------------------------------------------------------| r_work (start): 0.2519 rms_B_bonded: 5.80 r_work: 0.2315 rms_B_bonded: 5.34 restraints_weight: 2.0000 r_work (final): 0.2315 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2306 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2306 r_free = 0.2306 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2306 r_free = 0.2306 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2306 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9224 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19785 Z= 0.150 Angle : 0.709 12.559 26900 Z= 0.356 Chirality : 0.039 0.287 3121 Planarity : 0.004 0.037 3455 Dihedral : 3.573 21.630 2695 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.20 % Favored : 97.76 % Rotamer: Outliers : 1.50 % Allowed : 25.91 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 1.79 (0.17), residues: 2422 helix: 2.35 (0.15), residues: 1243 sheet: 1.21 (0.22), residues: 416 loop : -0.83 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG T 346 TYR 0.008 0.001 TYR K 112 PHE 0.019 0.001 PHE D 10 TRP 0.008 0.001 TRP I 19 HIS 0.002 0.000 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00368 (19785) covalent geometry : angle 0.70899 (26900) hydrogen bonds : bond 0.03239 ( 1162) hydrogen bonds : angle 3.98975 ( 3329) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 483 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 51 GLN cc_start: 0.9237 (mt0) cc_final: 0.8787 (mp10) REVERT: B 54 ASP cc_start: 0.9468 (t70) cc_final: 0.9102 (t0) REVERT: B 80 ASP cc_start: 0.9013 (t0) cc_final: 0.8686 (t0) REVERT: B 125 ASP cc_start: 0.8935 (p0) cc_final: 0.8444 (p0) REVERT: B 129 THR cc_start: 0.9524 (m) cc_final: 0.9247 (p) REVERT: B 152 ARG cc_start: 0.9144 (tmm-80) cc_final: 0.8768 (ttp80) REVERT: D 24 GLN cc_start: 0.9313 (mt0) cc_final: 0.8882 (mt0) REVERT: D 80 ASP cc_start: 0.9095 (t0) cc_final: 0.8579 (t0) REVERT: E 9 ASP cc_start: 0.9399 (t0) cc_final: 0.8997 (t0) REVERT: E 20 GLU cc_start: 0.9191 (mm-30) cc_final: 0.8870 (mm-30) REVERT: E 24 GLN cc_start: 0.9177 (mt0) cc_final: 0.8922 (mm-40) REVERT: G 24 GLN cc_start: 0.9296 (OUTLIER) cc_final: 0.9077 (mt0) REVERT: G 142 ARG cc_start: 0.9439 (tpp80) cc_final: 0.9224 (tpp80) REVERT: H 46 MET cc_start: 0.9276 (OUTLIER) cc_final: 0.8955 (mpp) REVERT: I 75 GLU cc_start: 0.9248 (tt0) cc_final: 0.8793 (tm-30) REVERT: J 20 GLU cc_start: 0.9345 (tp30) cc_final: 0.9130 (tp30) REVERT: J 59 GLU cc_start: 0.9585 (mm-30) cc_final: 0.9323 (mm-30) REVERT: L 59 GLU cc_start: 0.9585 (mm-30) cc_final: 0.9305 (mm-30) REVERT: L 80 ASP cc_start: 0.9524 (t0) cc_final: 0.9184 (t0) REVERT: M 75 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8218 (tm-30) REVERT: N 46 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.8462 (mpp) REVERT: N 59 GLU cc_start: 0.9463 (mm-30) cc_final: 0.9191 (mm-30) REVERT: N 75 GLU cc_start: 0.8862 (tm-30) cc_final: 0.8633 (tm-30) REVERT: N 80 ASP cc_start: 0.9264 (t0) cc_final: 0.8906 (t0) REVERT: N 125 ASP cc_start: 0.8799 (p0) cc_final: 0.7913 (p0) REVERT: N 152 ARG cc_start: 0.9164 (ttp80) cc_final: 0.8472 (ttp80) REVERT: O 36 GLU cc_start: 0.9402 (mm-30) cc_final: 0.9140 (mm-30) REVERT: P 32 GLU cc_start: 0.9044 (tp30) cc_final: 0.8643 (tp30) REVERT: P 75 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8173 (tm-30) REVERT: P 80 ASP cc_start: 0.9287 (t0) cc_final: 0.8985 (t0) REVERT: P 131 ASP cc_start: 0.9102 (t70) cc_final: 0.8817 (t0) REVERT: R 346 ARG cc_start: 0.7699 (tpm170) cc_final: 0.7478 (tpp-160) REVERT: S 313 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.7478 (m-30) REVERT: S 320 GLU cc_start: 0.9174 (tm-30) cc_final: 0.8845 (tm-30) REVERT: U 320 GLU cc_start: 0.9005 (tt0) cc_final: 0.8617 (tm-30) REVERT: V 340 ARG cc_start: 0.8739 (ttm-80) cc_final: 0.8446 (ttm-80) REVERT: Y 336 ARG cc_start: 0.8738 (ttp80) cc_final: 0.8430 (ttp80) REVERT: Y 341 GLU cc_start: 0.9140 (mp0) cc_final: 0.8762 (mp0) REVERT: a 341 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8645 (pt0) REVERT: b 320 GLU cc_start: 0.8903 (tm-30) cc_final: 0.8565 (tm-30) REVERT: b 332 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8192 (mp) outliers start: 24 outliers final: 12 residues processed: 497 average time/residue: 0.8374 time to fit residues: 455.8036 Evaluate side-chains 491 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 474 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain H residue 46 MET Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain K residue 129 THR Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 154 SER Chi-restraints excluded: chain N residue 46 MET Chi-restraints excluded: chain P residue 78 SER Chi-restraints excluded: chain S residue 313 ASP Chi-restraints excluded: chain b residue 325 LEU Chi-restraints excluded: chain b residue 332 LEU Chi-restraints excluded: chain c residue 154 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 127 optimal weight: 0.7980 chunk 123 optimal weight: 0.3980 chunk 105 optimal weight: 4.9990 chunk 97 optimal weight: 0.1980 chunk 126 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 135 optimal weight: 0.5980 chunk 168 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 158 optimal weight: 0.0970 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 GLN ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 GLN G 51 GLN I 51 GLN J 24 GLN K 119 GLN N 24 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.052163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.039241 restraints weight = 301988.549| |-----------------------------------------------------------------------------| r_work (start): 0.2536 rms_B_bonded: 5.83 r_work: 0.2332 rms_B_bonded: 5.43 restraints_weight: 2.0000 r_work (final): 0.2332 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2329 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2329 r_free = 0.2329 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2329 r_free = 0.2329 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9224 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 19785 Z= 0.146 Angle : 0.728 14.161 26900 Z= 0.365 Chirality : 0.040 0.361 3121 Planarity : 0.004 0.039 3455 Dihedral : 3.540 15.428 2694 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.20 % Favored : 97.76 % Rotamer: Outliers : 1.03 % Allowed : 26.38 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 1.79 (0.17), residues: 2422 helix: 2.35 (0.15), residues: 1246 sheet: 1.24 (0.22), residues: 416 loop : -0.87 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG T 346 TYR 0.009 0.001 TYR L 112 PHE 0.005 0.001 PHE E 123 TRP 0.008 0.001 TRP I 19 HIS 0.002 0.000 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00360 (19785) covalent geometry : angle 0.72802 (26900) hydrogen bonds : bond 0.03141 ( 1162) hydrogen bonds : angle 3.96846 ( 3329) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 491 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 GLN cc_start: 0.9246 (mt0) cc_final: 0.8806 (mp10) REVERT: B 54 ASP cc_start: 0.9471 (t70) cc_final: 0.9125 (t0) REVERT: B 80 ASP cc_start: 0.9007 (t0) cc_final: 0.8631 (t0) REVERT: B 125 ASP cc_start: 0.8941 (p0) cc_final: 0.8556 (p0) REVERT: B 129 THR cc_start: 0.9530 (m) cc_final: 0.9244 (p) REVERT: B 152 ARG cc_start: 0.9132 (tmm-80) cc_final: 0.8846 (ttp80) REVERT: C 39 ARG cc_start: 0.9050 (ttm-80) cc_final: 0.8681 (mtm-85) REVERT: C 54 ASP cc_start: 0.9065 (t70) cc_final: 0.8725 (t0) REVERT: D 24 GLN cc_start: 0.9387 (mt0) cc_final: 0.8916 (mt0) REVERT: D 80 ASP cc_start: 0.9139 (t0) cc_final: 0.8642 (t0) REVERT: E 9 ASP cc_start: 0.9402 (t0) cc_final: 0.9017 (t0) REVERT: E 20 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8891 (mm-30) REVERT: E 24 GLN cc_start: 0.9163 (mt0) cc_final: 0.8940 (mm-40) REVERT: G 24 GLN cc_start: 0.9305 (OUTLIER) cc_final: 0.9089 (mt0) REVERT: I 75 GLU cc_start: 0.9236 (tt0) cc_final: 0.8793 (tm-30) REVERT: J 24 GLN cc_start: 0.9360 (OUTLIER) cc_final: 0.9023 (tp40) REVERT: J 59 GLU cc_start: 0.9588 (mm-30) cc_final: 0.9323 (mm-30) REVERT: L 59 GLU cc_start: 0.9592 (mm-30) cc_final: 0.9319 (mm-30) REVERT: L 80 ASP cc_start: 0.9538 (t0) cc_final: 0.9205 (t0) REVERT: M 75 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8264 (tm-30) REVERT: N 46 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8462 (mpp) REVERT: N 59 GLU cc_start: 0.9466 (mm-30) cc_final: 0.9194 (mm-30) REVERT: N 75 GLU cc_start: 0.8876 (tm-30) cc_final: 0.8652 (tm-30) REVERT: N 80 ASP cc_start: 0.9255 (t0) cc_final: 0.8912 (t0) REVERT: N 125 ASP cc_start: 0.8827 (p0) cc_final: 0.7978 (p0) REVERT: N 152 ARG cc_start: 0.9175 (ttp80) cc_final: 0.8468 (ttp80) REVERT: O 36 GLU cc_start: 0.9408 (mm-30) cc_final: 0.9156 (mm-30) REVERT: P 32 GLU cc_start: 0.9044 (tp30) cc_final: 0.8570 (tp30) REVERT: P 75 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8195 (tm-30) REVERT: P 80 ASP cc_start: 0.9290 (t0) cc_final: 0.8957 (t0) REVERT: P 131 ASP cc_start: 0.9094 (t70) cc_final: 0.8805 (t0) REVERT: Q 341 GLU cc_start: 0.9229 (mt-10) cc_final: 0.8989 (mp0) REVERT: S 320 GLU cc_start: 0.9183 (tm-30) cc_final: 0.8775 (tm-30) REVERT: T 346 ARG cc_start: 0.7248 (mmm160) cc_final: 0.6904 (mmm160) REVERT: U 320 GLU cc_start: 0.9010 (tt0) cc_final: 0.8650 (tm-30) REVERT: V 340 ARG cc_start: 0.8777 (ttm-80) cc_final: 0.8555 (ttm-80) REVERT: Y 336 ARG cc_start: 0.8759 (ttp80) cc_final: 0.8461 (ttp80) REVERT: Y 341 GLU cc_start: 0.9101 (mp0) cc_final: 0.8715 (mp0) REVERT: b 320 GLU cc_start: 0.8900 (tm-30) cc_final: 0.8567 (tm-30) REVERT: b 332 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8184 (mp) outliers start: 14 outliers final: 6 residues processed: 500 average time/residue: 0.8544 time to fit residues: 467.7047 Evaluate side-chains 488 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 478 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain M residue 80 ASP Chi-restraints excluded: chain N residue 46 MET Chi-restraints excluded: chain b residue 332 LEU Chi-restraints excluded: chain c residue 154 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 94 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 146 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 209 optimal weight: 3.9990 chunk 61 optimal weight: 0.0970 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 GLN I 119 GLN J 24 GLN K 51 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.051788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.038847 restraints weight = 327315.423| |-----------------------------------------------------------------------------| r_work (start): 0.2524 rms_B_bonded: 5.92 r_work: 0.2319 rms_B_bonded: 5.47 restraints_weight: 2.0000 r_work (final): 0.2319 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2313 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2313 r_free = 0.2313 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2313 r_free = 0.2313 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2313 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9228 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19785 Z= 0.153 Angle : 0.718 12.299 26900 Z= 0.362 Chirality : 0.040 0.341 3121 Planarity : 0.004 0.057 3455 Dihedral : 3.550 16.522 2694 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.15 % Favored : 97.80 % Rotamer: Outliers : 1.08 % Allowed : 26.66 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 1.82 (0.17), residues: 2422 helix: 2.36 (0.15), residues: 1242 sheet: 1.26 (0.22), residues: 416 loop : -0.81 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 39 TYR 0.008 0.001 TYR I 126 PHE 0.006 0.001 PHE E 123 TRP 0.007 0.001 TRP I 19 HIS 0.001 0.000 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00374 (19785) covalent geometry : angle 0.71767 (26900) hydrogen bonds : bond 0.03235 ( 1162) hydrogen bonds : angle 3.97272 ( 3329) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9952.31 seconds wall clock time: 169 minutes 31.79 seconds (10171.79 seconds total)