Starting phenix.real_space_refine on Mon Jun 16 22:37:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zzq_15039/06_2025/7zzq_15039.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zzq_15039/06_2025/7zzq_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_15039/06_2025/7zzq_15039.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zzq_15039/06_2025/7zzq_15039.map" model { file = "/net/cci-nas-00/data/ceres_data/7zzq_15039/06_2025/7zzq_15039.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zzq_15039/06_2025/7zzq_15039.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 19.86, per 1000 atoms: 1.02 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: 4.81 Conformation dependent library (CDL) restraints added in 4.6 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: 1.95 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: 6.06 Time building geometry restraints manager: 5.74 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: 6.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.790 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 54.860 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.090 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (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 TRP 0.009 0.001 TRP N 19 HIS 0.002 0.001 HIS F 87 PHE 0.009 0.001 PHE T 322 TYR 0.010 0.001 TYR C 112 ARG 0.008 0.000 ARG T 345 Details of bonding type rmsd hydrogen bonds : bond 0.14283 ( 1162) hydrogen bonds : angle 5.59822 ( 3329) covalent geometry : bond 0.00229 (19785) covalent geometry : angle 0.45590 (26900) *********************** 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 : 2.218 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: 1.7148 time to fit residues: 1091.6856 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 : 2.103 ------------------------------------------------------------------------------- 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 196 optimal weight: 3.9990 chunk 176 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 182 optimal weight: 0.4980 chunk 70 optimal weight: 0.4980 chunk 111 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 211 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 G 51 GLN H 24 GLN I 51 GLN I 119 GLN J 24 GLN K 119 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.052687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.039634 restraints weight = 251446.298| |-----------------------------------------------------------------------------| r_work (start): 0.2524 rms_B_bonded: 5.45 r_work: 0.2325 rms_B_bonded: 5.14 restraints_weight: 2.0000 r_work (final): 0.2325 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2315 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2315 r_free = 0.2315 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2314 r_free = 0.2314 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2314 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9184 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19785 Z= 0.149 Angle : 0.602 9.651 26900 Z= 0.312 Chirality : 0.040 0.153 3121 Planarity : 0.005 0.046 3455 Dihedral : 4.760 89.531 2720 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.94 % Favored : 98.02 % Rotamer: Outliers : 2.44 % Allowed : 21.06 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.17), residues: 2422 helix: 2.09 (0.15), residues: 1235 sheet: 1.04 (0.23), residues: 416 loop : -0.86 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 103 HIS 0.002 0.000 HIS J 87 PHE 0.009 0.001 PHE N 123 TYR 0.010 0.001 TYR L 112 ARG 0.012 0.001 ARG D 114 Details of bonding type rmsd hydrogen bonds : bond 0.03900 ( 1162) hydrogen bonds : angle 4.40019 ( 3329) covalent geometry : bond 0.00345 (19785) covalent geometry : angle 0.60237 (26900) *********************** 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 551 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 507 time to evaluate : 2.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 80 ASP cc_start: 0.8690 (t0) cc_final: 0.8423 (t0) REVERT: B 125 ASP cc_start: 0.8604 (p0) cc_final: 0.8249 (p0) REVERT: B 152 ARG cc_start: 0.8961 (ttp-110) cc_final: 0.8681 (ttp80) REVERT: D 20 GLU cc_start: 0.9290 (tp30) cc_final: 0.8942 (tp30) REVERT: D 129 THR cc_start: 0.9364 (m) cc_final: 0.9139 (p) REVERT: E 9 ASP cc_start: 0.9389 (t0) cc_final: 0.9030 (t0) REVERT: I 78 SER cc_start: 0.9607 (m) cc_final: 0.9355 (p) REVERT: J 24 GLN cc_start: 0.9361 (OUTLIER) cc_final: 0.9019 (tp40) REVERT: L 130 ARG cc_start: 0.9338 (OUTLIER) cc_final: 0.7981 (ttm170) REVERT: M 20 GLU cc_start: 0.9381 (tp30) cc_final: 0.9092 (tp30) REVERT: M 75 GLU cc_start: 0.8636 (tm-30) cc_final: 0.8129 (tm-30) REVERT: M 80 ASP cc_start: 0.8477 (p0) cc_final: 0.8036 (p0) REVERT: M 88 GLU cc_start: 0.9113 (OUTLIER) cc_final: 0.8555 (mp0) REVERT: N 80 ASP cc_start: 0.9006 (t0) cc_final: 0.8739 (t0) REVERT: N 152 ARG cc_start: 0.9158 (ttp80) cc_final: 0.8242 (ttp80) REVERT: O 36 GLU cc_start: 0.9380 (mm-30) cc_final: 0.9149 (mm-30) REVERT: P 80 ASP cc_start: 0.9056 (t0) cc_final: 0.8792 (t0) REVERT: P 88 GLU cc_start: 0.9151 (OUTLIER) cc_final: 0.8927 (mt-10) REVERT: R 341 GLU cc_start: 0.9092 (OUTLIER) cc_final: 0.8888 (pm20) REVERT: R 345 ARG cc_start: 0.8371 (tpm170) cc_final: 0.8020 (tpm170) REVERT: S 320 GLU cc_start: 0.8951 (tm-30) cc_final: 0.8696 (tm-30) REVERT: S 340 ARG cc_start: 0.9174 (ttp80) cc_final: 0.8942 (ptp-110) REVERT: Y 336 ARG cc_start: 0.8697 (ttp80) cc_final: 0.8412 (ttp80) REVERT: Y 341 GLU cc_start: 0.9011 (mp0) cc_final: 0.8778 (mp0) REVERT: a 341 GLU cc_start: 0.9080 (mt-10) cc_final: 0.8761 (pt0) REVERT: b 320 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8448 (tm-30) REVERT: b 332 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8367 (mp) outliers start: 44 outliers final: 19 residues processed: 528 average time/residue: 1.8041 time to fit residues: 1046.2998 Evaluate side-chains 508 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 483 time to evaluate : 2.199 ------------------------------------------------------------------------------- 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 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 M residue 88 GLU Chi-restraints excluded: chain N residue 78 SER Chi-restraints excluded: chain P residue 73 THR Chi-restraints excluded: chain P residue 78 SER Chi-restraints excluded: chain P residue 88 GLU Chi-restraints excluded: chain R residue 341 GLU Chi-restraints excluded: chain S residue 345 ARG Chi-restraints excluded: chain T residue 323 MET Chi-restraints excluded: chain T residue 345 ARG 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 21 optimal weight: 4.9990 chunk 97 optimal weight: 0.0670 chunk 198 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 188 optimal weight: 0.7980 chunk 126 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 176 optimal weight: 0.6980 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.052363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.039225 restraints weight = 292354.389| |-----------------------------------------------------------------------------| r_work (start): 0.2519 rms_B_bonded: 5.78 r_work: 0.2315 rms_B_bonded: 5.30 restraints_weight: 2.0000 r_work (final): 0.2315 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2311 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2311 r_free = 0.2311 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2311 r_free = 0.2311 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2311 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9225 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19785 Z= 0.141 Angle : 0.606 12.533 26900 Z= 0.312 Chirality : 0.039 0.276 3121 Planarity : 0.004 0.079 3455 Dihedral : 4.180 58.817 2706 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.90 % Favored : 98.06 % Rotamer: Outliers : 2.54 % Allowed : 21.96 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.17), residues: 2422 helix: 2.18 (0.15), residues: 1239 sheet: 1.01 (0.23), residues: 416 loop : -0.83 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 69 HIS 0.001 0.000 HIS B 87 PHE 0.008 0.001 PHE E 123 TYR 0.009 0.001 TYR I 112 ARG 0.009 0.001 ARG D 114 Details of bonding type rmsd hydrogen bonds : bond 0.03542 ( 1162) hydrogen bonds : angle 4.20623 ( 3329) covalent geometry : bond 0.00331 (19785) covalent geometry : angle 0.60581 (26900) *********************** 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 547 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 501 time to evaluate : 2.272 Fit side-chains revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8349 (pm20) cc_final: 0.8001 (pp20) REVERT: B 54 ASP cc_start: 0.9428 (t70) cc_final: 0.9083 (t0) REVERT: B 80 ASP cc_start: 0.8808 (t0) cc_final: 0.8481 (t0) REVERT: B 125 ASP cc_start: 0.8747 (p0) cc_final: 0.8433 (p0) REVERT: B 152 ARG cc_start: 0.8998 (ttp-110) cc_final: 0.8765 (ttp80) REVERT: D 20 GLU cc_start: 0.9300 (tp30) cc_final: 0.8977 (tp30) REVERT: D 24 GLN cc_start: 0.9431 (mt0) cc_final: 0.8952 (mt0) REVERT: E 9 ASP cc_start: 0.9404 (t0) cc_final: 0.9082 (t0) REVERT: G 24 GLN cc_start: 0.9304 (OUTLIER) cc_final: 0.9060 (mt0) REVERT: G 51 GLN cc_start: 0.9242 (mm-40) cc_final: 0.8955 (mm-40) REVERT: H 46 MET cc_start: 0.9277 (OUTLIER) cc_final: 0.9062 (mpp) REVERT: I 78 SER cc_start: 0.9620 (m) cc_final: 0.9371 (p) REVERT: J 24 GLN cc_start: 0.9417 (OUTLIER) cc_final: 0.9199 (tp40) REVERT: M 75 GLU cc_start: 0.8800 (tm-30) cc_final: 0.8263 (tm-30) REVERT: M 79 GLU cc_start: 0.8826 (pm20) cc_final: 0.8562 (pm20) REVERT: M 80 ASP cc_start: 0.8465 (p0) cc_final: 0.8168 (p0) REVERT: N 32 GLU cc_start: 0.9084 (tp30) cc_final: 0.8875 (mm-30) REVERT: N 80 ASP cc_start: 0.9143 (t0) cc_final: 0.8839 (t0) REVERT: N 125 ASP cc_start: 0.8532 (p0) cc_final: 0.7783 (p0) REVERT: N 152 ARG cc_start: 0.9136 (ttp80) cc_final: 0.8533 (ttp80) REVERT: P 32 GLU cc_start: 0.9140 (tp30) cc_final: 0.8739 (tp30) REVERT: P 75 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8359 (tm-30) REVERT: P 80 ASP cc_start: 0.9219 (t0) cc_final: 0.8894 (t0) REVERT: Q 341 GLU cc_start: 0.9367 (mt-10) cc_final: 0.8962 (mp0) REVERT: R 341 GLU cc_start: 0.9151 (OUTLIER) cc_final: 0.8875 (pm20) REVERT: S 320 GLU cc_start: 0.9056 (tm-30) cc_final: 0.8800 (tm-30) REVERT: S 340 ARG cc_start: 0.9182 (ttp80) cc_final: 0.8969 (ptp-110) REVERT: U 320 GLU cc_start: 0.9076 (tt0) cc_final: 0.8520 (tm-30) REVERT: Y 336 ARG cc_start: 0.8698 (ttp80) cc_final: 0.8377 (ttp80) REVERT: Y 341 GLU cc_start: 0.8984 (mp0) cc_final: 0.8768 (mp0) REVERT: a 341 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8730 (pm20) REVERT: b 320 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8519 (tm-30) REVERT: b 332 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8236 (mp) outliers start: 46 outliers final: 20 residues processed: 523 average time/residue: 1.9108 time to fit residues: 1099.2006 Evaluate side-chains 502 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 477 time to evaluate : 2.780 ------------------------------------------------------------------------------- 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 32 GLU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain D residue 78 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 H residue 46 MET 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 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 M residue 27 ILE 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 R residue 341 GLU 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 200 optimal weight: 0.9990 chunk 204 optimal weight: 3.9990 chunk 80 optimal weight: 0.3980 chunk 209 optimal weight: 2.9990 chunk 36 optimal weight: 0.3980 chunk 25 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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** I 51 GLN K 51 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 = 0.2889 r_free = 0.2889 target = 0.051647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2538 r_free = 0.2538 target = 0.038599 restraints weight = 286283.308| |-----------------------------------------------------------------------------| r_work (start): 0.2503 rms_B_bonded: 5.71 r_work: 0.2299 rms_B_bonded: 5.24 restraints_weight: 2.0000 r_work (final): 0.2299 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2292 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2292 r_free = 0.2292 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2292 r_free = 0.2292 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2292 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9218 moved from start: 0.2607 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= 0.161 Angle : 0.622 10.845 26900 Z= 0.316 Chirality : 0.039 0.141 3121 Planarity : 0.004 0.040 3455 Dihedral : 3.942 53.827 2701 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.32 % Favored : 97.64 % Rotamer: Outliers : 2.07 % Allowed : 22.52 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.17), residues: 2422 helix: 2.25 (0.15), residues: 1238 sheet: 1.04 (0.22), residues: 416 loop : -0.81 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 69 HIS 0.002 0.000 HIS F 87 PHE 0.009 0.001 PHE E 123 TYR 0.010 0.001 TYR L 112 ARG 0.011 0.001 ARG S 346 Details of bonding type rmsd hydrogen bonds : bond 0.03575 ( 1162) hydrogen bonds : angle 4.14542 ( 3329) covalent geometry : bond 0.00383 (19785) covalent geometry : angle 0.62211 (26900) *********************** 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 528 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 492 time to evaluate : 2.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 54 ASP cc_start: 0.9448 (t70) cc_final: 0.9086 (t0) REVERT: B 80 ASP cc_start: 0.8872 (t0) cc_final: 0.8525 (t0) REVERT: B 125 ASP cc_start: 0.8811 (p0) cc_final: 0.8490 (p0) REVERT: B 152 ARG cc_start: 0.9002 (ttp-110) cc_final: 0.8794 (ttp80) REVERT: C 7 LYS cc_start: 0.8475 (mmpt) cc_final: 0.8101 (mtmm) REVERT: D 20 GLU cc_start: 0.9287 (tp30) cc_final: 0.8920 (tp30) REVERT: D 24 GLN cc_start: 0.9435 (mt0) cc_final: 0.8935 (mt0) REVERT: D 114 ARG cc_start: 0.9127 (mmm160) cc_final: 0.8903 (mmm160) REVERT: E 9 ASP cc_start: 0.9404 (t0) cc_final: 0.9068 (t0) REVERT: E 20 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8601 (mm-30) REVERT: E 24 GLN cc_start: 0.9147 (mt0) cc_final: 0.8766 (mm-40) REVERT: F 81 GLN cc_start: 0.9479 (mt0) cc_final: 0.9251 (mt0) REVERT: G 24 GLN cc_start: 0.9310 (OUTLIER) cc_final: 0.9099 (mt0) REVERT: G 51 GLN cc_start: 0.9278 (mm-40) cc_final: 0.9004 (mm-40) REVERT: G 75 GLU cc_start: 0.8223 (pm20) cc_final: 0.7933 (pm20) REVERT: I 78 SER cc_start: 0.9658 (m) cc_final: 0.9426 (p) REVERT: L 46 MET cc_start: 0.9181 (mmm) cc_final: 0.8962 (mmp) REVERT: M 75 GLU cc_start: 0.8772 (tm-30) cc_final: 0.8283 (tm-30) REVERT: N 59 GLU cc_start: 0.9506 (mm-30) cc_final: 0.9234 (mm-30) REVERT: N 80 ASP cc_start: 0.9191 (t0) cc_final: 0.8866 (t0) REVERT: N 125 ASP cc_start: 0.8638 (p0) cc_final: 0.7729 (p0) REVERT: N 152 ARG cc_start: 0.9166 (ttp80) cc_final: 0.8508 (ttp80) REVERT: P 32 GLU cc_start: 0.9118 (tp30) cc_final: 0.8747 (tp30) REVERT: P 75 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8327 (tm-30) REVERT: P 80 ASP cc_start: 0.9253 (t0) cc_final: 0.8905 (t0) REVERT: P 88 GLU cc_start: 0.9169 (OUTLIER) cc_final: 0.8938 (mt-10) REVERT: R 341 GLU cc_start: 0.9174 (OUTLIER) cc_final: 0.8880 (pm20) REVERT: S 320 GLU cc_start: 0.9100 (tm-30) cc_final: 0.8813 (tm-30) REVERT: U 320 GLU cc_start: 0.9059 (tt0) cc_final: 0.8520 (tm-30) REVERT: Y 336 ARG cc_start: 0.8752 (ttp80) cc_final: 0.8458 (ttp80) REVERT: Y 341 GLU cc_start: 0.9110 (mp0) cc_final: 0.8811 (mp0) REVERT: a 341 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8735 (pm20) REVERT: b 320 GLU cc_start: 0.8797 (tm-30) cc_final: 0.8493 (tm-30) REVERT: b 332 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8277 (mp) outliers start: 36 outliers final: 13 residues processed: 508 average time/residue: 2.0280 time to fit residues: 1129.2182 Evaluate side-chains 492 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 475 time to evaluate : 4.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain D residue 78 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 L residue 140 VAL Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain P residue 78 SER Chi-restraints excluded: chain P residue 88 GLU Chi-restraints excluded: chain R residue 341 GLU Chi-restraints excluded: chain W residue 154 SER 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 188 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 213 optimal weight: 5.9990 chunk 111 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 145 optimal weight: 0.6980 chunk 31 optimal weight: 0.0980 chunk 230 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 119 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 = 0.2895 r_free = 0.2895 target = 0.051741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.038726 restraints weight = 317293.311| |-----------------------------------------------------------------------------| r_work (start): 0.2513 rms_B_bonded: 5.89 r_work: 0.2307 rms_B_bonded: 5.44 restraints_weight: 2.0000 r_work (final): 0.2307 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2301 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2301 r_free = 0.2301 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2301 r_free = 0.2301 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9215 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19785 Z= 0.143 Angle : 0.635 11.384 26900 Z= 0.323 Chirality : 0.039 0.141 3121 Planarity : 0.004 0.038 3455 Dihedral : 3.701 41.063 2697 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.11 % Favored : 97.85 % Rotamer: Outliers : 1.88 % Allowed : 23.60 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.17), residues: 2422 helix: 2.27 (0.15), residues: 1242 sheet: 1.10 (0.23), residues: 416 loop : -0.78 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 69 HIS 0.001 0.000 HIS B 87 PHE 0.007 0.001 PHE E 123 TYR 0.008 0.001 TYR I 112 ARG 0.007 0.000 ARG R 340 Details of bonding type rmsd hydrogen bonds : bond 0.03363 ( 1162) hydrogen bonds : angle 4.05186 ( 3329) covalent geometry : bond 0.00342 (19785) covalent geometry : angle 0.63471 (26900) *********************** 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 531 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 499 time to evaluate : 2.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 51 GLN cc_start: 0.9212 (mt0) cc_final: 0.8824 (mp10) REVERT: B 54 ASP cc_start: 0.9462 (t70) cc_final: 0.9096 (t0) REVERT: B 80 ASP cc_start: 0.8926 (t0) cc_final: 0.8538 (t0) REVERT: B 125 ASP cc_start: 0.8821 (p0) cc_final: 0.8520 (p0) REVERT: B 152 ARG cc_start: 0.8990 (ttp-110) cc_final: 0.8789 (ttp80) REVERT: D 20 GLU cc_start: 0.9295 (tp30) cc_final: 0.9074 (tp30) REVERT: D 24 GLN cc_start: 0.9445 (mt0) cc_final: 0.9123 (mt0) REVERT: D 80 ASP cc_start: 0.8699 (t0) cc_final: 0.8400 (t0) REVERT: E 9 ASP cc_start: 0.9410 (t0) cc_final: 0.9076 (t0) REVERT: E 20 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8577 (mm-30) REVERT: E 24 GLN cc_start: 0.9142 (mt0) cc_final: 0.8772 (mm-40) REVERT: G 24 GLN cc_start: 0.9293 (OUTLIER) cc_final: 0.9065 (mt0) REVERT: G 51 GLN cc_start: 0.9307 (mm-40) cc_final: 0.9046 (mm-40) REVERT: H 46 MET cc_start: 0.9295 (OUTLIER) cc_final: 0.9065 (mpp) REVERT: I 78 SER cc_start: 0.9650 (m) cc_final: 0.9403 (p) REVERT: I 119 GLN cc_start: 0.9264 (mm-40) cc_final: 0.9047 (mp10) REVERT: J 59 GLU cc_start: 0.9588 (mm-30) cc_final: 0.9372 (mm-30) REVERT: L 46 MET cc_start: 0.9142 (mmm) cc_final: 0.8906 (mmp) REVERT: M 75 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8343 (tm-30) REVERT: N 20 GLU cc_start: 0.9227 (tp30) cc_final: 0.8987 (tp30) REVERT: N 59 GLU cc_start: 0.9499 (mm-30) cc_final: 0.9239 (mm-30) REVERT: N 80 ASP cc_start: 0.9229 (t0) cc_final: 0.8872 (t0) REVERT: N 125 ASP cc_start: 0.8684 (p0) cc_final: 0.7843 (p0) REVERT: N 152 ARG cc_start: 0.9157 (ttp80) cc_final: 0.8497 (ttp80) REVERT: P 32 GLU cc_start: 0.9079 (tp30) cc_final: 0.8713 (tp30) REVERT: P 75 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8285 (tm-30) REVERT: P 80 ASP cc_start: 0.9255 (t0) cc_final: 0.8923 (t0) REVERT: R 341 GLU cc_start: 0.9196 (OUTLIER) cc_final: 0.8908 (pm20) REVERT: S 320 GLU cc_start: 0.9160 (tm-30) cc_final: 0.8848 (tm-30) REVERT: S 341 GLU cc_start: 0.9096 (pt0) cc_final: 0.8809 (pm20) REVERT: U 320 GLU cc_start: 0.9047 (tt0) cc_final: 0.8573 (tm-30) REVERT: Y 336 ARG cc_start: 0.8723 (ttp80) cc_final: 0.8451 (ttp80) REVERT: Y 341 GLU cc_start: 0.9154 (mp0) cc_final: 0.8822 (mp0) REVERT: a 341 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8692 (pt0) REVERT: b 320 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8484 (tm-30) REVERT: b 332 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8214 (mp) outliers start: 32 outliers final: 17 residues processed: 515 average time/residue: 1.6389 time to fit residues: 930.4084 Evaluate side-chains 500 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 479 time to evaluate : 2.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE 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 D residue 129 THR 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 J residue 78 SER Chi-restraints excluded: chain K residue 24 GLN Chi-restraints excluded: chain L residue 140 VAL 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 Q residue 332 LEU Chi-restraints excluded: chain R 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 76 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 211 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 157 optimal weight: 0.7980 chunk 184 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 158 optimal weight: 0.9990 chunk 148 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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** I 51 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 = 0.2888 r_free = 0.2888 target = 0.051439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.038434 restraints weight = 322308.467| |-----------------------------------------------------------------------------| r_work (start): 0.2495 rms_B_bonded: 5.90 r_work: 0.2286 rms_B_bonded: 5.40 restraints_weight: 2.0000 r_work (final): 0.2286 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2286 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2286 r_free = 0.2286 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 = 0.2286 r_free = 0.2286 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9216 moved from start: 0.2838 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= 0.160 Angle : 0.649 11.690 26900 Z= 0.329 Chirality : 0.039 0.142 3121 Planarity : 0.004 0.039 3455 Dihedral : 3.579 23.912 2695 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.45 % Favored : 97.51 % Rotamer: Outliers : 1.79 % Allowed : 24.40 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.17), residues: 2422 helix: 2.29 (0.15), residues: 1246 sheet: 1.15 (0.23), residues: 416 loop : -0.81 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 19 HIS 0.001 0.000 HIS B 87 PHE 0.008 0.001 PHE E 123 TYR 0.011 0.001 TYR L 112 ARG 0.011 0.001 ARG S 346 Details of bonding type rmsd hydrogen bonds : bond 0.03463 ( 1162) hydrogen bonds : angle 4.04057 ( 3329) covalent geometry : bond 0.00385 (19785) covalent geometry : angle 0.64905 (26900) *********************** 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 517 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 487 time to evaluate : 2.265 Fit side-chains revert: symmetry clash REVERT: B 51 GLN cc_start: 0.9214 (mt0) cc_final: 0.8774 (mp10) REVERT: B 54 ASP cc_start: 0.9454 (t70) cc_final: 0.9112 (t0) REVERT: B 80 ASP cc_start: 0.8935 (t0) cc_final: 0.8618 (t0) REVERT: B 125 ASP cc_start: 0.8865 (p0) cc_final: 0.8518 (p0) REVERT: B 129 THR cc_start: 0.9533 (m) cc_final: 0.9201 (p) REVERT: B 152 ARG cc_start: 0.8964 (ttp-110) cc_final: 0.8742 (ttp80) REVERT: D 20 GLU cc_start: 0.9301 (tp30) cc_final: 0.9078 (tp30) REVERT: D 24 GLN cc_start: 0.9446 (mt0) cc_final: 0.9116 (mt0) REVERT: D 80 ASP cc_start: 0.8813 (t0) cc_final: 0.8540 (t0) REVERT: E 9 ASP cc_start: 0.9407 (t0) cc_final: 0.8991 (t0) REVERT: E 20 GLU cc_start: 0.9116 (mm-30) cc_final: 0.8599 (mm-30) REVERT: E 24 GLN cc_start: 0.9157 (mt0) cc_final: 0.8769 (mm-40) REVERT: G 24 GLN cc_start: 0.9295 (OUTLIER) cc_final: 0.9087 (mt0) REVERT: G 51 GLN cc_start: 0.9333 (mm-40) cc_final: 0.9067 (mm-40) REVERT: G 75 GLU cc_start: 0.8364 (pm20) cc_final: 0.8104 (pm20) REVERT: H 46 MET cc_start: 0.9304 (OUTLIER) cc_final: 0.8728 (mpt) REVERT: I 75 GLU cc_start: 0.9158 (tt0) cc_final: 0.8747 (tm-30) REVERT: I 78 SER cc_start: 0.9670 (m) cc_final: 0.9421 (p) REVERT: J 59 GLU cc_start: 0.9594 (mm-30) cc_final: 0.9367 (mm-30) REVERT: L 7 LYS cc_start: 0.8689 (mppt) cc_final: 0.8489 (pmmt) REVERT: M 75 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8203 (tm-30) REVERT: N 59 GLU cc_start: 0.9516 (mm-30) cc_final: 0.9236 (mm-30) REVERT: N 80 ASP cc_start: 0.9242 (t0) cc_final: 0.8909 (t0) REVERT: N 125 ASP cc_start: 0.8721 (p0) cc_final: 0.7860 (p0) REVERT: N 152 ARG cc_start: 0.9175 (ttp80) cc_final: 0.8555 (ttp80) REVERT: P 32 GLU cc_start: 0.9093 (tp30) cc_final: 0.8731 (tp30) REVERT: P 75 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8245 (tm-30) REVERT: P 80 ASP cc_start: 0.9305 (t0) cc_final: 0.8943 (t0) REVERT: P 131 ASP cc_start: 0.9102 (t70) cc_final: 0.8822 (t0) REVERT: R 341 GLU cc_start: 0.9163 (OUTLIER) cc_final: 0.8885 (pm20) REVERT: S 320 GLU cc_start: 0.9155 (tm-30) cc_final: 0.8830 (tm-30) REVERT: S 341 GLU cc_start: 0.9105 (pt0) cc_final: 0.8788 (pm20) REVERT: U 320 GLU cc_start: 0.9022 (tt0) cc_final: 0.8584 (tm-30) REVERT: Y 336 ARG cc_start: 0.8740 (ttp80) cc_final: 0.8478 (ttp80) REVERT: Y 341 GLU cc_start: 0.9141 (mp0) cc_final: 0.8794 (mp0) REVERT: a 341 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8708 (pt0) REVERT: b 320 GLU cc_start: 0.8855 (tm-30) cc_final: 0.8513 (tm-30) REVERT: b 332 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8255 (mp) outliers start: 30 outliers final: 16 residues processed: 505 average time/residue: 1.6620 time to fit residues: 923.1848 Evaluate side-chains 497 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 477 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP 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 G residue 73 THR 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 N residue 78 SER Chi-restraints excluded: chain P residue 78 SER Chi-restraints excluded: chain R residue 325 LEU Chi-restraints excluded: chain R residue 341 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 147 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** I 51 GLN I 119 GLN J 24 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 = 0.2845 r_free = 0.2845 target = 0.049655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2489 r_free = 0.2489 target = 0.036926 restraints weight = 291242.404| |-----------------------------------------------------------------------------| r_work (start): 0.2452 rms_B_bonded: 5.59 r_work: 0.2242 rms_B_bonded: 5.25 restraints_weight: 2.0000 r_work (final): 0.2242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2240 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2240 r_free = 0.2240 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2240 r_free = 0.2240 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2240 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9235 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 19785 Z= 0.243 Angle : 0.704 12.439 26900 Z= 0.357 Chirality : 0.041 0.146 3121 Planarity : 0.004 0.038 3455 Dihedral : 3.696 26.973 2695 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.49 % Favored : 97.47 % Rotamer: Outliers : 1.88 % Allowed : 24.87 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.17), residues: 2422 helix: 2.31 (0.15), residues: 1230 sheet: 1.08 (0.22), residues: 416 loop : -0.77 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 19 HIS 0.002 0.001 HIS M 87 PHE 0.013 0.001 PHE E 123 TYR 0.009 0.001 TYR O 112 ARG 0.010 0.001 ARG A 39 Details of bonding type rmsd hydrogen bonds : bond 0.04126 ( 1162) hydrogen bonds : angle 4.21480 ( 3329) covalent geometry : bond 0.00577 (19785) covalent geometry : angle 0.70377 (26900) *********************** 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 500 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 468 time to evaluate : 2.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 GLN cc_start: 0.9157 (mt0) cc_final: 0.8729 (mp10) REVERT: B 54 ASP cc_start: 0.9489 (t70) cc_final: 0.9133 (t0) REVERT: B 80 ASP cc_start: 0.9039 (t0) cc_final: 0.8687 (t0) REVERT: B 125 ASP cc_start: 0.8841 (p0) cc_final: 0.8524 (p0) REVERT: D 20 GLU cc_start: 0.9300 (tp30) cc_final: 0.9058 (tp30) REVERT: D 24 GLN cc_start: 0.9439 (mt0) cc_final: 0.9162 (mt0) REVERT: D 32 GLU cc_start: 0.9243 (tp30) cc_final: 0.8859 (tp30) REVERT: D 80 ASP cc_start: 0.8967 (t0) cc_final: 0.8658 (t0) REVERT: E 9 ASP cc_start: 0.9412 (t0) cc_final: 0.8968 (t0) REVERT: E 20 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8655 (mm-30) REVERT: E 24 GLN cc_start: 0.9195 (mt0) cc_final: 0.8798 (mm-40) REVERT: G 24 GLN cc_start: 0.9299 (OUTLIER) cc_final: 0.9064 (mt0) REVERT: G 51 GLN cc_start: 0.9362 (mm-40) cc_final: 0.9072 (mm-40) REVERT: G 75 GLU cc_start: 0.8345 (pm20) cc_final: 0.7885 (pm20) REVERT: I 75 GLU cc_start: 0.9187 (tt0) cc_final: 0.8753 (tm-30) REVERT: M 75 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8197 (tm-30) REVERT: M 149 MET cc_start: 0.9505 (mmp) cc_final: 0.9279 (mmp) REVERT: N 59 GLU cc_start: 0.9504 (mm-30) cc_final: 0.9299 (mm-30) REVERT: N 80 ASP cc_start: 0.9270 (t0) cc_final: 0.8940 (t0) REVERT: N 125 ASP cc_start: 0.8733 (p0) cc_final: 0.7792 (p0) REVERT: N 152 ARG cc_start: 0.9125 (ttp80) cc_final: 0.8428 (ttp80) REVERT: O 36 GLU cc_start: 0.9393 (mm-30) cc_final: 0.9140 (mm-30) REVERT: P 32 GLU cc_start: 0.9095 (tp30) cc_final: 0.8734 (tp30) REVERT: P 75 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8323 (tm-30) REVERT: P 80 ASP cc_start: 0.9303 (t0) cc_final: 0.8975 (t0) REVERT: P 131 ASP cc_start: 0.9108 (t70) cc_final: 0.8812 (t0) REVERT: R 341 GLU cc_start: 0.9185 (OUTLIER) cc_final: 0.8898 (pm20) REVERT: S 320 GLU cc_start: 0.9170 (tm-30) cc_final: 0.8848 (tm-30) REVERT: S 341 GLU cc_start: 0.9080 (pt0) cc_final: 0.8774 (pm20) REVERT: S 346 ARG cc_start: 0.7455 (mmm160) cc_final: 0.7076 (mmm160) REVERT: T 340 ARG cc_start: 0.9004 (ttm-80) cc_final: 0.8794 (ttm-80) REVERT: U 320 GLU cc_start: 0.9038 (tt0) cc_final: 0.8621 (tm-30) REVERT: Y 336 ARG cc_start: 0.8763 (ttp80) cc_final: 0.8489 (ttp80) REVERT: Y 341 GLU cc_start: 0.9134 (mp0) cc_final: 0.8775 (mp0) REVERT: a 341 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8617 (pt0) REVERT: b 320 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8569 (tm-30) REVERT: b 332 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8351 (mp) outliers start: 32 outliers final: 19 residues processed: 493 average time/residue: 1.6330 time to fit residues: 885.0119 Evaluate side-chains 479 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 457 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain B residue 78 SER 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 132 VAL Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain L residue 25 VAL 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 R residue 325 LEU Chi-restraints excluded: chain R 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 183 optimal weight: 0.0270 chunk 113 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 126 optimal weight: 0.9980 chunk 174 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.9640 ------------------------------------------------------------------------------- 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 51 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.2867 r_free = 0.2867 target = 0.050491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2518 r_free = 0.2518 target = 0.037732 restraints weight = 271624.307| |-----------------------------------------------------------------------------| r_work (start): 0.2478 rms_B_bonded: 5.55 r_work: 0.2276 rms_B_bonded: 5.16 restraints_weight: 2.0000 r_work (final): 0.2276 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2268 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2268 r_free = 0.2268 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2268 r_free = 0.2268 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2268 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9242 moved from start: 0.2941 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= 0.172 Angle : 0.704 12.471 26900 Z= 0.356 Chirality : 0.040 0.232 3121 Planarity : 0.004 0.038 3455 Dihedral : 3.656 16.398 2694 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.53 % Favored : 97.42 % Rotamer: Outliers : 1.74 % Allowed : 25.58 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.17), residues: 2422 helix: 2.30 (0.15), residues: 1234 sheet: 1.06 (0.22), residues: 416 loop : -0.85 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 19 HIS 0.001 0.000 HIS M 87 PHE 0.009 0.001 PHE E 123 TYR 0.012 0.001 TYR L 112 ARG 0.011 0.001 ARG B 152 Details of bonding type rmsd hydrogen bonds : bond 0.03691 ( 1162) hydrogen bonds : angle 4.13893 ( 3329) covalent geometry : bond 0.00414 (19785) covalent geometry : angle 0.70387 (26900) *********************** 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 504 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 475 time to evaluate : 2.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 GLN cc_start: 0.9169 (mt0) cc_final: 0.8725 (mp10) REVERT: B 54 ASP cc_start: 0.9479 (t70) cc_final: 0.9138 (t0) REVERT: B 80 ASP cc_start: 0.9048 (t0) cc_final: 0.8736 (t0) REVERT: B 125 ASP cc_start: 0.8870 (p0) cc_final: 0.8450 (p0) REVERT: B 129 THR cc_start: 0.9523 (m) cc_final: 0.9159 (p) REVERT: B 152 ARG cc_start: 0.9084 (ttp80) cc_final: 0.8672 (ttp80) REVERT: D 20 GLU cc_start: 0.9314 (tp30) cc_final: 0.9056 (tp30) REVERT: D 24 GLN cc_start: 0.9456 (mt0) cc_final: 0.9070 (mt0) REVERT: D 80 ASP cc_start: 0.8955 (t0) cc_final: 0.8640 (t0) REVERT: E 9 ASP cc_start: 0.9391 (t0) cc_final: 0.8974 (t0) REVERT: E 20 GLU cc_start: 0.9158 (mm-30) cc_final: 0.8617 (mm-30) REVERT: E 24 GLN cc_start: 0.9165 (mt0) cc_final: 0.8762 (mm-40) REVERT: G 51 GLN cc_start: 0.9360 (mm-40) cc_final: 0.9081 (mm-40) REVERT: G 75 GLU cc_start: 0.8375 (pm20) cc_final: 0.8005 (pm20) REVERT: H 59 GLU cc_start: 0.9575 (mm-30) cc_final: 0.9370 (mm-30) REVERT: I 75 GLU cc_start: 0.9188 (tt0) cc_final: 0.8770 (tm-30) REVERT: J 20 GLU cc_start: 0.9366 (tp30) cc_final: 0.9126 (tp30) REVERT: J 59 GLU cc_start: 0.9578 (mm-30) cc_final: 0.9344 (mm-30) REVERT: L 7 LYS cc_start: 0.8623 (mppt) cc_final: 0.8362 (ptpp) REVERT: M 75 GLU cc_start: 0.8779 (tm-30) cc_final: 0.8158 (tm-30) REVERT: M 149 MET cc_start: 0.9451 (mmp) cc_final: 0.9235 (mmp) REVERT: N 59 GLU cc_start: 0.9495 (mm-30) cc_final: 0.9287 (mm-30) REVERT: N 80 ASP cc_start: 0.9272 (t0) cc_final: 0.8937 (t0) REVERT: N 125 ASP cc_start: 0.8745 (p0) cc_final: 0.7787 (p0) REVERT: N 152 ARG cc_start: 0.9142 (ttp80) cc_final: 0.8448 (ttp80) REVERT: O 36 GLU cc_start: 0.9392 (mm-30) cc_final: 0.9139 (mm-30) REVERT: P 32 GLU cc_start: 0.9068 (tp30) cc_final: 0.8688 (tp30) REVERT: P 75 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8389 (tm-30) REVERT: P 80 ASP cc_start: 0.9292 (t0) cc_final: 0.9008 (t0) REVERT: P 131 ASP cc_start: 0.9141 (t70) cc_final: 0.8839 (t0) REVERT: R 341 GLU cc_start: 0.9154 (OUTLIER) cc_final: 0.8917 (pm20) REVERT: R 344 LEU cc_start: 0.9300 (mt) cc_final: 0.9086 (mm) REVERT: S 320 GLU cc_start: 0.9184 (tm-30) cc_final: 0.8852 (tm-30) REVERT: S 341 GLU cc_start: 0.9082 (pt0) cc_final: 0.8779 (pm20) REVERT: U 320 GLU cc_start: 0.9010 (tt0) cc_final: 0.8601 (tm-30) REVERT: Y 336 ARG cc_start: 0.8732 (ttp80) cc_final: 0.8428 (ttp80) REVERT: Y 341 GLU cc_start: 0.9113 (mp0) cc_final: 0.8752 (mp0) REVERT: a 341 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8647 (pt0) REVERT: b 320 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8557 (tm-30) REVERT: b 323 MET cc_start: 0.8958 (mtp) cc_final: 0.8726 (mtp) REVERT: b 332 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8317 (mp) outliers start: 29 outliers final: 13 residues processed: 495 average time/residue: 2.2304 time to fit residues: 1211.6712 Evaluate side-chains 479 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 464 time to evaluate : 2.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain N residue 78 SER Chi-restraints excluded: chain P residue 9 ASP Chi-restraints excluded: chain R residue 325 LEU Chi-restraints excluded: chain R 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 183 optimal weight: 0.1980 chunk 7 optimal weight: 0.9980 chunk 153 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 76 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 212 optimal weight: 1.9990 chunk 223 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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** I 51 GLN I 119 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 = 0.2878 r_free = 0.2878 target = 0.050919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2529 r_free = 0.2529 target = 0.038026 restraints weight = 302628.425| |-----------------------------------------------------------------------------| r_work (start): 0.2493 rms_B_bonded: 5.75 r_work: 0.2291 rms_B_bonded: 5.27 restraints_weight: 2.0000 r_work (final): 0.2291 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2282 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2282 r_free = 0.2282 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2282 r_free = 0.2282 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2282 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9237 moved from start: 0.2993 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= 0.159 Angle : 0.718 12.763 26900 Z= 0.364 Chirality : 0.040 0.260 3121 Planarity : 0.004 0.038 3455 Dihedral : 3.627 15.864 2694 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.36 % Favored : 97.59 % Rotamer: Outliers : 1.41 % Allowed : 25.91 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.17), residues: 2422 helix: 2.30 (0.15), residues: 1241 sheet: 1.09 (0.23), residues: 416 loop : -0.88 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 19 HIS 0.001 0.000 HIS M 87 PHE 0.036 0.001 PHE P 10 TYR 0.008 0.001 TYR I 112 ARG 0.010 0.001 ARG B 152 Details of bonding type rmsd hydrogen bonds : bond 0.03453 ( 1162) hydrogen bonds : angle 4.07564 ( 3329) covalent geometry : bond 0.00386 (19785) covalent geometry : angle 0.71849 (26900) *********************** 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 497 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 475 time to evaluate : 3.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 GLN cc_start: 0.9199 (mt0) cc_final: 0.8750 (mp10) REVERT: B 54 ASP cc_start: 0.9475 (t70) cc_final: 0.9126 (t0) REVERT: B 80 ASP cc_start: 0.9049 (t0) cc_final: 0.8713 (t0) REVERT: B 125 ASP cc_start: 0.8869 (p0) cc_final: 0.8506 (p0) REVERT: B 129 THR cc_start: 0.9518 (m) cc_final: 0.9237 (p) REVERT: D 20 GLU cc_start: 0.9307 (tp30) cc_final: 0.9068 (tp30) REVERT: D 24 GLN cc_start: 0.9456 (mt0) cc_final: 0.9126 (mt0) REVERT: D 80 ASP cc_start: 0.8985 (t0) cc_final: 0.8657 (t0) REVERT: E 9 ASP cc_start: 0.9402 (t0) cc_final: 0.9000 (t0) REVERT: E 20 GLU cc_start: 0.9150 (mm-30) cc_final: 0.8592 (mm-30) REVERT: E 24 GLN cc_start: 0.9118 (mt0) cc_final: 0.8756 (mm-40) REVERT: G 75 GLU cc_start: 0.8374 (pm20) cc_final: 0.8070 (pm20) REVERT: H 59 GLU cc_start: 0.9581 (mm-30) cc_final: 0.9378 (mm-30) REVERT: I 75 GLU cc_start: 0.9205 (tt0) cc_final: 0.8777 (tm-30) REVERT: J 20 GLU cc_start: 0.9359 (tp30) cc_final: 0.9139 (tp30) REVERT: J 59 GLU cc_start: 0.9593 (mm-30) cc_final: 0.9369 (mm-30) REVERT: L 7 LYS cc_start: 0.8665 (mppt) cc_final: 0.8404 (ptpp) REVERT: M 75 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8169 (tm-30) REVERT: N 59 GLU cc_start: 0.9476 (mm-30) cc_final: 0.9196 (mm-30) REVERT: N 80 ASP cc_start: 0.9283 (t0) cc_final: 0.8947 (t0) REVERT: N 125 ASP cc_start: 0.8775 (p0) cc_final: 0.7799 (p0) REVERT: N 152 ARG cc_start: 0.9159 (ttp80) cc_final: 0.8457 (ttp80) REVERT: O 36 GLU cc_start: 0.9417 (mm-30) cc_final: 0.9146 (mm-30) REVERT: P 32 GLU cc_start: 0.9067 (tp30) cc_final: 0.8660 (tp30) REVERT: P 75 GLU cc_start: 0.8616 (tm-30) cc_final: 0.8232 (tm-30) REVERT: P 80 ASP cc_start: 0.9330 (t0) cc_final: 0.8984 (t0) REVERT: P 131 ASP cc_start: 0.9140 (t70) cc_final: 0.8832 (t0) REVERT: Q 341 GLU cc_start: 0.9217 (mt-10) cc_final: 0.9005 (mt-10) REVERT: R 344 LEU cc_start: 0.9323 (mt) cc_final: 0.9113 (mm) REVERT: S 320 GLU cc_start: 0.9176 (tm-30) cc_final: 0.8847 (tm-30) REVERT: S 341 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8843 (pm20) REVERT: U 320 GLU cc_start: 0.9016 (tt0) cc_final: 0.8622 (tm-30) REVERT: Y 336 ARG cc_start: 0.8734 (ttp80) cc_final: 0.8431 (ttp80) REVERT: Y 341 GLU cc_start: 0.9133 (mp0) cc_final: 0.8766 (mp0) REVERT: a 341 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8658 (pt0) REVERT: b 320 GLU cc_start: 0.8900 (tm-30) cc_final: 0.8541 (tm-30) REVERT: b 332 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8244 (mp) outliers start: 22 outliers final: 14 residues processed: 488 average time/residue: 2.0280 time to fit residues: 1089.0910 Evaluate side-chains 480 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 464 time to evaluate : 2.992 ------------------------------------------------------------------------------- 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 129 THR Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 80 ASP 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 R residue 325 LEU Chi-restraints excluded: chain R residue 341 GLU Chi-restraints excluded: chain S residue 341 GLU Chi-restraints excluded: chain T residue 323 MET Chi-restraints excluded: chain V residue 338 SER Chi-restraints excluded: chain W residue 154 SER Chi-restraints excluded: chain b residue 332 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 179 optimal weight: 0.5980 chunk 215 optimal weight: 1.9990 chunk 9 optimal weight: 0.0980 chunk 116 optimal weight: 0.0470 chunk 28 optimal weight: 0.9980 chunk 127 optimal weight: 0.4980 chunk 107 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 192 optimal weight: 0.8980 chunk 209 optimal weight: 3.9990 overall best weight: 0.4278 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 GLN J 24 GLN K 51 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.051385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2535 r_free = 0.2535 target = 0.038245 restraints weight = 297928.776| |-----------------------------------------------------------------------------| r_work (start): 0.2510 rms_B_bonded: 5.86 r_work: 0.2303 rms_B_bonded: 5.50 restraints_weight: 2.0000 r_work (final): 0.2303 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2299 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2299 r_free = 0.2299 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 = 0.2299 r_free = 0.2299 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2299 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9239 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 19785 Z= 0.149 Angle : 0.731 14.372 26900 Z= 0.368 Chirality : 0.040 0.281 3121 Planarity : 0.004 0.039 3455 Dihedral : 3.618 17.248 2694 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.28 % Favored : 97.68 % Rotamer: Outliers : 1.18 % Allowed : 26.33 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.17), residues: 2422 helix: 2.31 (0.15), residues: 1241 sheet: 1.13 (0.23), residues: 416 loop : -0.87 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 19 HIS 0.001 0.000 HIS B 87 PHE 0.006 0.001 PHE T 322 TYR 0.009 0.001 TYR L 112 ARG 0.010 0.001 ARG T 346 Details of bonding type rmsd hydrogen bonds : bond 0.03322 ( 1162) hydrogen bonds : angle 4.04976 ( 3329) covalent geometry : bond 0.00363 (19785) covalent geometry : angle 0.73120 (26900) ********************** 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 490 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 473 time to evaluate : 2.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 GLN cc_start: 0.9194 (mt0) cc_final: 0.8744 (mp10) REVERT: B 54 ASP cc_start: 0.9480 (t70) cc_final: 0.9131 (t0) REVERT: B 80 ASP cc_start: 0.9034 (t0) cc_final: 0.8690 (t0) REVERT: B 125 ASP cc_start: 0.8806 (p0) cc_final: 0.8478 (p0) REVERT: B 129 THR cc_start: 0.9525 (m) cc_final: 0.9257 (p) REVERT: B 152 ARG cc_start: 0.9056 (ttp80) cc_final: 0.8621 (ttp80) REVERT: C 7 LYS cc_start: 0.8357 (mmpt) cc_final: 0.7955 (mmtm) REVERT: D 20 GLU cc_start: 0.9301 (tp30) cc_final: 0.9026 (tp30) REVERT: D 24 GLN cc_start: 0.9459 (mt0) cc_final: 0.9063 (mt0) REVERT: D 80 ASP cc_start: 0.9009 (t0) cc_final: 0.8689 (t0) REVERT: E 9 ASP cc_start: 0.9402 (t0) cc_final: 0.9013 (t0) REVERT: E 20 GLU cc_start: 0.9131 (mm-30) cc_final: 0.8591 (mm-30) REVERT: E 24 GLN cc_start: 0.9109 (mt0) cc_final: 0.8736 (mm-40) REVERT: G 75 GLU cc_start: 0.8370 (pm20) cc_final: 0.8075 (pm20) REVERT: H 46 MET cc_start: 0.9281 (OUTLIER) cc_final: 0.8746 (mpt) REVERT: H 59 GLU cc_start: 0.9581 (mm-30) cc_final: 0.9379 (mm-30) REVERT: I 75 GLU cc_start: 0.9218 (tt0) cc_final: 0.8781 (tm-30) REVERT: J 20 GLU cc_start: 0.9360 (tp30) cc_final: 0.9146 (tp30) REVERT: J 59 GLU cc_start: 0.9584 (mm-30) cc_final: 0.9368 (mm-30) REVERT: K 114 ARG cc_start: 0.9309 (tpp-160) cc_final: 0.9085 (tpp-160) REVERT: L 7 LYS cc_start: 0.8633 (mppt) cc_final: 0.8397 (ptpp) REVERT: M 75 GLU cc_start: 0.8832 (tm-30) cc_final: 0.8247 (tm-30) REVERT: N 59 GLU cc_start: 0.9477 (mm-30) cc_final: 0.9214 (mm-30) REVERT: N 75 GLU cc_start: 0.9218 (tt0) cc_final: 0.8797 (tm-30) REVERT: N 80 ASP cc_start: 0.9288 (t0) cc_final: 0.8944 (t0) REVERT: N 125 ASP cc_start: 0.8799 (p0) cc_final: 0.7860 (p0) REVERT: N 152 ARG cc_start: 0.9158 (ttp80) cc_final: 0.8449 (ttp80) REVERT: O 36 GLU cc_start: 0.9423 (mm-30) cc_final: 0.9167 (mm-30) REVERT: P 32 GLU cc_start: 0.9057 (tp30) cc_final: 0.8609 (tp30) REVERT: P 59 GLU cc_start: 0.9541 (mm-30) cc_final: 0.9329 (mm-30) REVERT: P 75 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8251 (tm-30) REVERT: P 80 ASP cc_start: 0.9298 (t0) cc_final: 0.8968 (t0) REVERT: P 131 ASP cc_start: 0.9135 (t70) cc_final: 0.8837 (t0) REVERT: S 320 GLU cc_start: 0.9198 (tm-30) cc_final: 0.8865 (tm-30) REVERT: S 341 GLU cc_start: 0.9012 (OUTLIER) cc_final: 0.8677 (pm20) REVERT: U 320 GLU cc_start: 0.9011 (tt0) cc_final: 0.8628 (tm-30) REVERT: Y 336 ARG cc_start: 0.8733 (ttp80) cc_final: 0.8480 (ttp80) REVERT: Y 341 GLU cc_start: 0.9149 (mp0) cc_final: 0.8775 (mp0) REVERT: b 320 GLU cc_start: 0.8930 (tm-30) cc_final: 0.8580 (tm-30) REVERT: b 332 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8254 (mp) outliers start: 17 outliers final: 13 residues processed: 485 average time/residue: 1.7105 time to fit residues: 922.8774 Evaluate side-chains 481 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 465 time to evaluate : 2.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain H residue 46 MET Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain M residue 80 ASP Chi-restraints excluded: chain N residue 9 ASP Chi-restraints excluded: chain N residue 78 SER Chi-restraints excluded: chain R residue 325 LEU Chi-restraints excluded: chain R residue 341 GLU Chi-restraints excluded: chain S residue 341 GLU Chi-restraints excluded: chain T residue 323 MET Chi-restraints excluded: chain V residue 338 SER Chi-restraints excluded: chain W residue 154 SER Chi-restraints excluded: chain b residue 332 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 73 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 153 optimal weight: 0.9980 chunk 213 optimal weight: 0.0070 chunk 232 optimal weight: 0.0070 chunk 47 optimal weight: 0.0170 chunk 163 optimal weight: 0.0570 chunk 131 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 200 optimal weight: 0.8980 overall best weight: 0.1972 ------------------------------------------------------------------------------- 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 51 GLN I 119 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 = 0.2906 r_free = 0.2906 target = 0.051886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.038975 restraints weight = 328882.487| |-----------------------------------------------------------------------------| r_work (start): 0.2527 rms_B_bonded: 5.94 r_work: 0.2318 rms_B_bonded: 5.56 restraints_weight: 2.0000 r_work (final): 0.2318 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2315 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2315 r_free = 0.2315 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 = 0.2315 r_free = 0.2315 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2315 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9226 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19785 Z= 0.145 Angle : 0.728 11.995 26900 Z= 0.366 Chirality : 0.040 0.265 3121 Planarity : 0.004 0.040 3455 Dihedral : 3.594 17.717 2694 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.28 % Favored : 97.68 % Rotamer: Outliers : 1.22 % Allowed : 26.23 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.17), residues: 2422 helix: 2.30 (0.15), residues: 1247 sheet: 1.18 (0.23), residues: 416 loop : -0.84 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 19 HIS 0.002 0.000 HIS B 87 PHE 0.009 0.001 PHE N 10 TYR 0.008 0.001 TYR I 126 ARG 0.010 0.001 ARG T 346 Details of bonding type rmsd hydrogen bonds : bond 0.03162 ( 1162) hydrogen bonds : angle 3.99298 ( 3329) covalent geometry : bond 0.00353 (19785) covalent geometry : angle 0.72816 (26900) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21242.51 seconds wall clock time: 371 minutes 14.08 seconds (22274.08 seconds total)