Starting phenix.real_space_refine on Sun Sep 13 11:38:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xct_33127/09_2026/7xct_33127.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xct_33127/09_2026/7xct_33127.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xct_33127/09_2026/7xct_33127.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xct_33127/09_2026/7xct_33127.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7xct_33127/09_2026/7xct_33127.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xct_33127/09_2026/7xct_33127.cif" model { file = "/net/cci-nas-00/data/ceres_data/7xct_33127/09_2026/7xct_33127.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xct_33127/09_2026/7xct_33127.cif" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.107 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5945 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 290 5.49 5 S 40 5.16 5 C 10853 2.51 5 N 3399 2.21 5 O 4051 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.18s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18633 Number of models: 1 Model: "" Number of chains: 16 Chain: "L" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "F" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 707 Classifications: {'peptide': 88} Link IDs: {'CIS': 2, 'PTRANS': 1, 'TRANS': 84} Chain: "G" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 718 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "K" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2656 Classifications: {'peptide': 326} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 307} Chain: "E" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'NLE:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'NLE:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "C" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "I" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "M" Number of atoms: 2671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2671 Classifications: {'peptide': 328} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 308} Chain: "N" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Chain: "M" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N LEU L 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU L 73 " occ=0.45 residue: pdb=" N ARG L 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG L 74 " occ=0.45 residue: pdb=" N GLY L 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY L 75 " occ=0.25 residue: pdb=" N GLY L 76 " occ=0.25 ... (3 atoms not shown) pdb=" OXT GLY L 76 " occ=0.25 residue: pdb=" N LEU N 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU N 73 " occ=0.45 residue: pdb=" N ARG N 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG N 74 " occ=0.45 residue: pdb=" N GLY N 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY N 75 " occ=0.25 residue: pdb=" N GLY N 76 " occ=0.25 ... (3 atoms not shown) pdb=" OXT GLY N 76 " occ=0.25 Time building chain proxies: 3.80, per 1000 atoms: 0.20 Number of scatterers: 18633 At special positions: 0 Unit cell: (151.2, 123.12, 150.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 P 290 15.00 O 4051 8.00 N 3399 7.00 C 10853 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 557.3 milliseconds 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2966 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 14 sheets defined 51.5% alpha, 6.9% beta 125 base pairs and 260 stacking pairs defined. Time for finding SS restraints: 3.20 Creating SS restraints... Processing helix chain 'L' and resid 22 through 34 removed outlier: 4.357A pdb=" N GLN L 31 " --> pdb=" O LYS L 27 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP L 32 " --> pdb=" O ALA L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 60 removed outlier: 3.803A pdb=" N ASN L 60 " --> pdb=" O SER L 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 35 Processing helix chain 'F' and resid 36 through 41 removed outlier: 3.726A pdb=" N ARG F 40 " --> pdb=" O ARG F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 54 removed outlier: 3.588A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.517A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.553A pdb=" N GLU H 71 " --> pdb=" O ASN H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 Processing helix chain 'K' and resid 36 through 45 removed outlier: 3.689A pdb=" N ARG K 42 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TRP K 43 " --> pdb=" O GLU K 39 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL K 44 " --> pdb=" O THR K 40 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 55 Processing helix chain 'K' and resid 68 through 73 Processing helix chain 'K' and resid 75 through 80 Processing helix chain 'K' and resid 82 through 87 Processing helix chain 'K' and resid 88 through 90 No H-bonds generated for 'chain 'K' and resid 88 through 90' Processing helix chain 'K' and resid 105 through 119 removed outlier: 3.599A pdb=" N HIS K 109 " --> pdb=" O GLY K 105 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN K 116 " --> pdb=" O GLN K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 127 Processing helix chain 'K' and resid 140 through 152 Processing helix chain 'K' and resid 167 through 175 removed outlier: 3.577A pdb=" N LEU K 171 " --> pdb=" O GLY K 167 " (cutoff:3.500A) Processing helix chain 'K' and resid 188 through 209 removed outlier: 3.540A pdb=" N GLU K 196 " --> pdb=" O ALA K 192 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR K 197 " --> pdb=" O LYS K 193 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG K 203 " --> pdb=" O ASP K 199 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR K 209 " --> pdb=" O TRP K 205 " (cutoff:3.500A) Processing helix chain 'K' and resid 225 through 234 removed outlier: 4.366A pdb=" N GLU K 230 " --> pdb=" O GLU K 226 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG K 231 " --> pdb=" O GLU K 227 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA K 233 " --> pdb=" O ARG K 229 " (cutoff:3.500A) Processing helix chain 'K' and resid 246 through 255 removed outlier: 3.738A pdb=" N GLU K 255 " --> pdb=" O HIS K 251 " (cutoff:3.500A) Processing helix chain 'K' and resid 256 through 260 removed outlier: 3.817A pdb=" N ASN K 259 " --> pdb=" O ARG K 256 " (cutoff:3.500A) Processing helix chain 'K' and resid 286 through 289 Processing helix chain 'K' and resid 320 through 325 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 75 Processing helix chain 'E' and resid 76 through 79 removed outlier: 3.614A pdb=" N NLE E 79 " --> pdb=" O GLN E 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 76 through 79' Processing helix chain 'E' and resid 85 through 113 removed outlier: 3.576A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.626A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 75 removed outlier: 3.525A pdb=" N LEU A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.605A pdb=" N ASP A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.655A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.551A pdb=" N ILE D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS D 82 " --> pdb=" O SER D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 124 removed outlier: 3.612A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.746A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N HIS B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.601A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 36 through 45 removed outlier: 3.690A pdb=" N ARG M 42 " --> pdb=" O ILE M 38 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TRP M 43 " --> pdb=" O GLU M 39 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL M 44 " --> pdb=" O THR M 40 " (cutoff:3.500A) Processing helix chain 'M' and resid 50 through 55 Processing helix chain 'M' and resid 68 through 73 Processing helix chain 'M' and resid 75 through 80 Processing helix chain 'M' and resid 82 through 87 Processing helix chain 'M' and resid 88 through 90 No H-bonds generated for 'chain 'M' and resid 88 through 90' Processing helix chain 'M' and resid 105 through 119 removed outlier: 3.599A pdb=" N HIS M 109 " --> pdb=" O GLY M 105 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN M 116 " --> pdb=" O GLN M 112 " (cutoff:3.500A) Processing helix chain 'M' and resid 121 through 127 Processing helix chain 'M' and resid 140 through 152 Processing helix chain 'M' and resid 167 through 175 removed outlier: 3.577A pdb=" N LEU M 171 " --> pdb=" O GLY M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 188 through 209 removed outlier: 3.540A pdb=" N GLU M 196 " --> pdb=" O ALA M 192 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR M 197 " --> pdb=" O LYS M 193 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG M 203 " --> pdb=" O ASP M 199 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR M 209 " --> pdb=" O TRP M 205 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 234 removed outlier: 4.366A pdb=" N GLU M 230 " --> pdb=" O GLU M 226 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG M 231 " --> pdb=" O GLU M 227 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA M 233 " --> pdb=" O ARG M 229 " (cutoff:3.500A) Processing helix chain 'M' and resid 246 through 255 removed outlier: 3.737A pdb=" N GLU M 255 " --> pdb=" O HIS M 251 " (cutoff:3.500A) Processing helix chain 'M' and resid 256 through 260 removed outlier: 3.817A pdb=" N ASN M 259 " --> pdb=" O ARG M 256 " (cutoff:3.500A) Processing helix chain 'M' and resid 286 through 289 Processing helix chain 'M' and resid 320 through 325 Processing helix chain 'N' and resid 22 through 34 removed outlier: 4.357A pdb=" N GLN N 31 " --> pdb=" O LYS N 27 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP N 32 " --> pdb=" O ALA N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 60 removed outlier: 3.802A pdb=" N ASN N 60 " --> pdb=" O SER N 57 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 12 through 15 removed outlier: 3.566A pdb=" N VAL L 5 " --> pdb=" O ILE L 13 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE L 4 " --> pdb=" O LEU L 67 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LEU L 69 " --> pdb=" O PHE L 4 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LYS L 6 " --> pdb=" O LEU L 69 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LEU L 71 " --> pdb=" O LYS L 6 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS L 68 " --> pdb=" O ILE L 44 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 45 through 46 removed outlier: 7.167A pdb=" N ARG F 45 " --> pdb=" O ILE E 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'F' and resid 96 through 98 removed outlier: 6.417A pdb=" N THR F 96 " --> pdb=" O THR C 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.147A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'G' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'K' and resid 7 through 8 removed outlier: 3.558A pdb=" N LEU K 7 " --> pdb=" O TYR K 20 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 215 through 220 removed outlier: 6.418A pdb=" N HIS K 182 " --> pdb=" O THR K 217 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N GLU K 219 " --> pdb=" O HIS K 182 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLY K 184 " --> pdb=" O GLU K 219 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N PHE K 159 " --> pdb=" O TYR K 183 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL K 185 " --> pdb=" O PHE K 159 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ASP K 161 " --> pdb=" O VAL K 185 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE K 238 " --> pdb=" O VAL K 267 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AB1, first strand: chain 'D' and resid 53 through 54 removed outlier: 7.199A pdb=" N GLY D 53 " --> pdb=" O ILE C 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 88 through 89 Processing sheet with id=AB3, first strand: chain 'M' and resid 7 through 8 removed outlier: 3.559A pdb=" N LEU M 7 " --> pdb=" O TYR M 20 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 215 through 220 removed outlier: 6.417A pdb=" N HIS M 182 " --> pdb=" O THR M 217 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N GLU M 219 " --> pdb=" O HIS M 182 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLY M 184 " --> pdb=" O GLU M 219 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N PHE M 159 " --> pdb=" O TYR M 183 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N VAL M 185 " --> pdb=" O PHE M 159 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASP M 161 " --> pdb=" O VAL M 185 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE M 238 " --> pdb=" O VAL M 267 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 12 through 15 removed outlier: 3.566A pdb=" N VAL N 5 " --> pdb=" O ILE N 13 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE N 4 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU N 69 " --> pdb=" O PHE N 4 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N LYS N 6 " --> pdb=" O LEU N 69 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LEU N 71 " --> pdb=" O LYS N 6 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS N 68 " --> pdb=" O ILE N 44 " (cutoff:3.500A) 526 hydrogen bonds defined for protein. 1518 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 305 hydrogen bonds 590 hydrogen bond angles 0 basepair planarities 125 basepair parallelities 260 stacking parallelities Total time for adding SS restraints: 3.64 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2539 1.31 - 1.44: 6617 1.44 - 1.56: 9780 1.56 - 1.69: 582 1.69 - 1.81: 74 Bond restraints: 19592 Sorted by residual: bond pdb=" C1' DC J 65 " pdb=" N1 DC J 65 " ideal model delta sigma weight residual 1.468 1.595 -0.127 1.40e-02 5.10e+03 8.22e+01 bond pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " ideal model delta sigma weight residual 1.435 1.498 -0.063 1.30e-02 5.92e+03 2.38e+01 bond pdb=" N1 DC I 70 " pdb=" C6 DC I 70 " ideal model delta sigma weight residual 1.367 1.338 0.029 6.00e-03 2.78e+04 2.31e+01 bond pdb=" C3' DG J 69 " pdb=" O3' DG J 69 " ideal model delta sigma weight residual 1.435 1.374 0.061 1.30e-02 5.92e+03 2.21e+01 bond pdb=" C3' DA I 69 " pdb=" O3' DA I 69 " ideal model delta sigma weight residual 1.435 1.376 0.059 1.30e-02 5.92e+03 2.05e+01 ... (remaining 19587 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.96: 27438 3.96 - 7.91: 239 7.91 - 11.87: 45 11.87 - 15.82: 3 15.82 - 19.78: 4 Bond angle restraints: 27729 Sorted by residual: angle pdb=" C GLU M 47 " pdb=" N ILE M 48 " pdb=" CA ILE M 48 " ideal model delta sigma weight residual 121.70 141.48 -19.78 1.80e+00 3.09e-01 1.21e+02 angle pdb=" C GLU K 47 " pdb=" N ILE K 48 " pdb=" CA ILE K 48 " ideal model delta sigma weight residual 121.70 141.47 -19.77 1.80e+00 3.09e-01 1.21e+02 angle pdb=" C ARG F 67 " pdb=" N ASP F 68 " pdb=" CA ASP F 68 " ideal model delta sigma weight residual 121.54 135.56 -14.02 1.91e+00 2.74e-01 5.39e+01 angle pdb=" C TYR F 88 " pdb=" CA TYR F 88 " pdb=" CB TYR F 88 " ideal model delta sigma weight residual 109.83 103.87 5.96 9.90e-01 1.02e+00 3.62e+01 angle pdb=" O4' DC J 65 " pdb=" C1' DC J 65 " pdb=" N1 DC J 65 " ideal model delta sigma weight residual 108.00 111.85 -3.85 7.00e-01 2.04e+00 3.03e+01 ... (remaining 27724 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 9703 35.58 - 71.16: 1320 71.16 - 106.74: 13 106.74 - 142.32: 1 142.32 - 177.90: 2 Dihedral angle restraints: 11039 sinusoidal: 6448 harmonic: 4591 Sorted by residual: dihedral pdb=" CA TRP K 22 " pdb=" C TRP K 22 " pdb=" N PRO K 23 " pdb=" CA PRO K 23 " ideal model delta harmonic sigma weight residual -180.00 -106.89 -73.11 0 5.00e+00 4.00e-02 2.14e+02 dihedral pdb=" CA TRP M 22 " pdb=" C TRP M 22 " pdb=" N PRO M 23 " pdb=" CA PRO M 23 " ideal model delta harmonic sigma weight residual -180.00 -106.90 -73.10 0 5.00e+00 4.00e-02 2.14e+02 dihedral pdb=" CA GLN F 27 " pdb=" C GLN F 27 " pdb=" N GLY F 28 " pdb=" CA GLY F 28 " ideal model delta harmonic sigma weight residual 180.00 115.38 64.62 0 5.00e+00 4.00e-02 1.67e+02 ... (remaining 11036 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2243 0.071 - 0.142: 757 0.142 - 0.213: 100 0.213 - 0.284: 13 0.284 - 0.354: 4 Chirality restraints: 3117 Sorted by residual: chirality pdb=" CB VAL F 43 " pdb=" CA VAL F 43 " pdb=" CG1 VAL F 43 " pdb=" CG2 VAL F 43 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" CB ILE M 48 " pdb=" CA ILE M 48 " pdb=" CG1 ILE M 48 " pdb=" CG2 ILE M 48 " both_signs ideal model delta sigma weight residual False 2.64 2.97 -0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CB ILE K 48 " pdb=" CA ILE K 48 " pdb=" CG1 ILE K 48 " pdb=" CG2 ILE K 48 " both_signs ideal model delta sigma weight residual False 2.64 2.97 -0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 3114 not shown) Planarity restraints: 2519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP K 22 " -0.054 5.00e-02 4.00e+02 8.13e-02 1.06e+01 pdb=" N PRO K 23 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO K 23 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO K 23 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 25 " -0.025 2.00e-02 2.50e+03 2.45e-02 1.05e+01 pdb=" CG PHE G 25 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE G 25 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE G 25 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE G 25 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE G 25 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE G 25 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP M 22 " 0.054 5.00e-02 4.00e+02 8.11e-02 1.05e+01 pdb=" N PRO M 23 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO M 23 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO M 23 " 0.044 5.00e-02 4.00e+02 ... (remaining 2516 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2964 2.76 - 3.29: 15464 3.29 - 3.83: 33115 3.83 - 4.36: 42587 4.36 - 4.90: 63026 Nonbonded interactions: 157156 Sorted by model distance: nonbonded pdb=" OG1 THR F 82 " pdb=" O MET F 84 " model vdw 2.220 3.040 nonbonded pdb=" OP1 DG J 125 " pdb=" O LEU N 73 " model vdw 2.253 3.040 nonbonded pdb=" OG1 THR H 90 " pdb=" OE1 GLU H 93 " model vdw 2.285 3.040 nonbonded pdb=" OE2 GLU K 186 " pdb=" O2' SAM K 500 " model vdw 2.302 3.040 nonbonded pdb=" OE2 GLU M 186 " pdb=" O2' SAM M 500 " model vdw 2.303 3.040 ... (remaining 157151 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 38 through 135) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 20 through 102) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 33 through 124) selection = chain 'H' } ncs_group { reference = chain 'K' selection = (chain 'M' and (resid 5 through 330 or resid 500)) } ncs_group { reference = chain 'L' selection = chain 'N' } 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=0.25 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 19.480 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 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 : 0.012 0.127 19592 Z= 0.877 Angle : 1.181 19.779 27729 Z= 0.798 Chirality : 0.068 0.354 3117 Planarity : 0.008 0.081 2519 Dihedral : 22.726 177.902 8073 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.31 % Favored : 94.30 % Rotamer: Outliers : 0.59 % Allowed : 3.83 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 3.12 % Twisted General : 0.33 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.11 (0.15), residues: 1545 helix: -4.25 (0.08), residues: 783 sheet: -1.05 (0.48), residues: 142 loop : -2.50 (0.20), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG B 78 TYR 0.046 0.003 TYR M 312 PHE 0.056 0.004 PHE G 25 TRP 0.036 0.005 TRP K 22 HIS 0.018 0.003 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.01249 / 0.88 (19592) covalent geometry : angle 1.18093 / 0.80 (27729) hydrogen bonds : bond 0.30837 / 20.57 ( 831) hydrogen bonds : angle 9.45175 / 6.53 ( 2108) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 266 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 77 ASP cc_start: 0.8156 (m-30) cc_final: 0.7938 (m-30) REVERT: A 122 LYS cc_start: 0.8973 (pttt) cc_final: 0.8743 (pttp) REVERT: D 59 MET cc_start: 0.8960 (tpp) cc_final: 0.8685 (tpp) REVERT: D 88 THR cc_start: 0.9058 (t) cc_final: 0.8647 (m) REVERT: M 71 MET cc_start: 0.4126 (mmt) cc_final: 0.3495 (tpp) outliers start: 8 outliers final: 4 residues processed: 274 average time/residue: 0.9275 time to fit residues: 274.1743 Evaluate side-chains 183 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 179 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 30.0000 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 7.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 60 ASN F 18 HIS F 64 ASN G 24 GLN G 73 ASN G 82 HIS H 63 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 HIS K 79 ASN K 112 GLN K 113 GLN E 68 GLN E 76 GLN A 113 HIS ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS C 24 GLN C 82 HIS B 25 ASN M 31 HIS M 79 ASN M 117 HIS ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 331 ASN N 60 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.173783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.127547 restraints weight = 23338.040| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.33 r_work: 0.3289 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19592 Z= 0.185 Angle : 0.815 15.280 27729 Z= 0.450 Chirality : 0.054 0.296 3117 Planarity : 0.006 0.075 2519 Dihedral : 27.975 169.840 4916 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.72 % Favored : 94.95 % Rotamer: Outliers : 2.95 % Allowed : 10.46 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 3.12 % Twisted General : 0.40 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.19), residues: 1545 helix: -1.64 (0.16), residues: 799 sheet: -0.73 (0.49), residues: 140 loop : -1.85 (0.23), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 36 TYR 0.017 0.001 TYR K 312 PHE 0.022 0.002 PHE K 223 TRP 0.020 0.002 TRP M 22 HIS 0.006 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.19 (19592) covalent geometry : angle 0.81465 / 0.45 (27729) hydrogen bonds : bond 0.08175 / 5.44 ( 831) hydrogen bonds : angle 4.23806 / 2.89 ( 2108) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 199 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: G 13 LYS cc_start: 0.8018 (mmtt) cc_final: 0.7739 (tptt) REVERT: G 91 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8505 (tt0) REVERT: G 95 LYS cc_start: 0.8789 (mtpp) cc_final: 0.8565 (ttmm) REVERT: H 47 GLN cc_start: 0.8741 (mt0) cc_final: 0.8489 (mt0) REVERT: K 71 MET cc_start: 0.5122 (OUTLIER) cc_final: 0.4663 (mpp) REVERT: K 177 THR cc_start: 0.7950 (OUTLIER) cc_final: 0.7582 (p) REVERT: K 212 LYS cc_start: 0.7495 (mmmt) cc_final: 0.7283 (mtpt) REVERT: E 73 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8442 (tt0) REVERT: A 120 MET cc_start: 0.8913 (mtm) cc_final: 0.8453 (mtm) REVERT: A 122 LYS cc_start: 0.9096 (pttt) cc_final: 0.8883 (pttp) REVERT: D 88 THR cc_start: 0.9044 (t) cc_final: 0.8551 (m) REVERT: C 95 LYS cc_start: 0.8984 (mtpp) cc_final: 0.8783 (mmmt) REVERT: B 26 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8366 (tp) REVERT: M 71 MET cc_start: 0.4917 (mmt) cc_final: 0.4219 (tpp) REVERT: M 101 ARG cc_start: 0.6818 (mtt90) cc_final: 0.6451 (mmt-90) outliers start: 40 outliers final: 12 residues processed: 221 average time/residue: 0.9130 time to fit residues: 218.9116 Evaluate side-chains 201 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 184 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain K residue 71 MET Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 255 GLU Chi-restraints excluded: chain K residue 286 ASP Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain M residue 297 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 40 optimal weight: 20.0000 chunk 75 optimal weight: 2.9990 chunk 112 optimal weight: 30.0000 chunk 131 optimal weight: 9.9990 chunk 6 optimal weight: 0.2980 chunk 87 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 170 optimal weight: 7.9990 chunk 151 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 159 optimal weight: 4.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN G 73 ASN H 84 ASN K 112 GLN ** K 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS A 68 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN M 99 ASN ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 315 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.172041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.123010 restraints weight = 22898.972| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.35 r_work: 0.3245 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3051 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3051 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19592 Z= 0.176 Angle : 0.731 14.928 27729 Z= 0.405 Chirality : 0.051 0.345 3117 Planarity : 0.005 0.076 2519 Dihedral : 28.218 162.663 4916 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.44 % Favored : 94.37 % Rotamer: Outliers : 3.68 % Allowed : 12.37 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 3.12 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.21), residues: 1545 helix: -0.28 (0.19), residues: 801 sheet: -0.43 (0.49), residues: 140 loop : -1.57 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 71 TYR 0.017 0.002 TYR M 209 PHE 0.022 0.002 PHE K 223 TRP 0.015 0.002 TRP M 22 HIS 0.006 0.001 HIS F 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.18 (19592) covalent geometry : angle 0.73144 / 0.40 (27729) hydrogen bonds : bond 0.06478 / 4.29 ( 831) hydrogen bonds : angle 3.67742 / 2.50 ( 2108) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 187 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 23 ARG cc_start: 0.7619 (ttm-80) cc_final: 0.7353 (tpp-160) REVERT: G 13 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7731 (mmmt) REVERT: H 47 GLN cc_start: 0.8772 (mt0) cc_final: 0.8542 (mt0) REVERT: K 71 MET cc_start: 0.5150 (OUTLIER) cc_final: 0.4624 (mpp) REVERT: K 104 THR cc_start: 0.8669 (OUTLIER) cc_final: 0.8286 (t) REVERT: E 73 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8349 (tt0) REVERT: D 96 THR cc_start: 0.8865 (t) cc_final: 0.8644 (p) REVERT: C 36 LYS cc_start: 0.8401 (mmmt) cc_final: 0.8137 (ptpt) REVERT: M 22 TRP cc_start: 0.3364 (OUTLIER) cc_final: 0.2508 (t-100) REVERT: M 71 MET cc_start: 0.5023 (mmt) cc_final: 0.4384 (tpp) outliers start: 50 outliers final: 20 residues processed: 216 average time/residue: 0.7864 time to fit residues: 186.6026 Evaluate side-chains 201 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 71 MET Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 248 GLU Chi-restraints excluded: chain K residue 255 GLU Chi-restraints excluded: chain K residue 286 ASP Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain M residue 22 TRP Chi-restraints excluded: chain M residue 200 ARG Chi-restraints excluded: chain M residue 297 SER Chi-restraints excluded: chain M residue 329 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 104 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 165 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 111 optimal weight: 30.0000 chunk 143 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN K 112 GLN A 68 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 113 GLN ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.170789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.121851 restraints weight = 22790.030| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.32 r_work: 0.3211 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 19592 Z= 0.204 Angle : 0.745 14.672 27729 Z= 0.407 Chirality : 0.052 0.332 3117 Planarity : 0.006 0.086 2519 Dihedral : 28.252 160.959 4914 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.50 % Favored : 94.30 % Rotamer: Outliers : 3.98 % Allowed : 13.11 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 3.12 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.21), residues: 1545 helix: 0.12 (0.19), residues: 802 sheet: -0.22 (0.49), residues: 140 loop : -1.53 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 101 TYR 0.016 0.002 TYR M 209 PHE 0.022 0.002 PHE K 223 TRP 0.013 0.002 TRP M 22 HIS 0.008 0.001 HIS F 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.20 (19592) covalent geometry : angle 0.74535 / 0.41 (27729) hydrogen bonds : bond 0.06424 / 4.27 ( 831) hydrogen bonds : angle 3.58244 / 2.44 ( 2108) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 180 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 23 ARG cc_start: 0.7611 (ttm-80) cc_final: 0.7358 (tpp-160) REVERT: G 91 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8546 (tt0) REVERT: G 92 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8259 (mt-10) REVERT: K 55 MET cc_start: 0.2756 (mtm) cc_final: 0.1259 (mmp) REVERT: K 71 MET cc_start: 0.5237 (OUTLIER) cc_final: 0.4698 (mpp) REVERT: K 104 THR cc_start: 0.8694 (OUTLIER) cc_final: 0.8330 (t) REVERT: K 129 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8059 (tt0) REVERT: K 276 ASN cc_start: 0.7515 (p0) cc_final: 0.7260 (p0) REVERT: E 73 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8373 (tt0) REVERT: D 96 THR cc_start: 0.8881 (t) cc_final: 0.8657 (p) REVERT: C 36 LYS cc_start: 0.8463 (mmmt) cc_final: 0.8197 (ptpt) REVERT: M 22 TRP cc_start: 0.3453 (OUTLIER) cc_final: 0.2355 (t-100) REVERT: M 55 MET cc_start: 0.0473 (mtt) cc_final: -0.0222 (mmt) REVERT: M 71 MET cc_start: 0.5080 (mmt) cc_final: 0.4442 (tpp) outliers start: 54 outliers final: 25 residues processed: 212 average time/residue: 0.7546 time to fit residues: 174.9439 Evaluate side-chains 210 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 178 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain K residue 71 MET Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 129 GLU Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 248 GLU Chi-restraints excluded: chain K residue 255 GLU Chi-restraints excluded: chain K residue 286 ASP Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain M residue 22 TRP Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 297 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 49 optimal weight: 7.9990 chunk 145 optimal weight: 7.9990 chunk 135 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 chunk 133 optimal weight: 9.9990 chunk 153 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 123 optimal weight: 30.0000 chunk 168 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN K 112 GLN E 68 GLN E 85 GLN A 68 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 113 GLN ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.167080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.118810 restraints weight = 22556.074| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.25 r_work: 0.3112 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2973 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 19592 Z= 0.332 Angle : 0.863 14.740 27729 Z= 0.460 Chirality : 0.059 0.339 3117 Planarity : 0.007 0.083 2519 Dihedral : 28.457 155.656 4914 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.83 % Favored : 93.92 % Rotamer: Outliers : 4.93 % Allowed : 13.03 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 3.12 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.21), residues: 1545 helix: -0.07 (0.19), residues: 810 sheet: -0.25 (0.48), residues: 140 loop : -1.56 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 40 TYR 0.020 0.002 TYR K 312 PHE 0.028 0.003 PHE K 223 TRP 0.015 0.003 TRP M 22 HIS 0.014 0.002 HIS F 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00748 / 0.33 (19592) covalent geometry : angle 0.86256 / 0.46 (27729) hydrogen bonds : bond 0.07731 / 5.17 ( 831) hydrogen bonds : angle 3.73408 / 2.54 ( 2108) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 180 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 36 LYS cc_start: 0.8828 (mmpt) cc_final: 0.8625 (pttt) REVERT: G 91 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8627 (tt0) REVERT: G 92 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8358 (mt-10) REVERT: K 55 MET cc_start: 0.2082 (mtm) cc_final: 0.0870 (mmt) REVERT: K 104 THR cc_start: 0.8747 (OUTLIER) cc_final: 0.8353 (t) REVERT: K 276 ASN cc_start: 0.7616 (p0) cc_final: 0.7362 (p0) REVERT: A 120 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8610 (mtm) REVERT: A 129 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.7510 (tpt-90) REVERT: D 99 ARG cc_start: 0.8804 (mtm110) cc_final: 0.8521 (mtm110) REVERT: C 36 LYS cc_start: 0.8592 (mmmt) cc_final: 0.8210 (ptpt) REVERT: M 22 TRP cc_start: 0.3833 (OUTLIER) cc_final: 0.3583 (t-100) REVERT: M 71 MET cc_start: 0.4975 (mmt) cc_final: 0.4288 (tpp) outliers start: 67 outliers final: 36 residues processed: 224 average time/residue: 0.7408 time to fit residues: 182.0771 Evaluate side-chains 216 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 174 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 248 GLU Chi-restraints excluded: chain K residue 255 GLU Chi-restraints excluded: chain K residue 286 ASP Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain M residue 22 TRP Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 200 ARG Chi-restraints excluded: chain M residue 226 GLU Chi-restraints excluded: chain M residue 297 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 135 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 111 optimal weight: 40.0000 chunk 129 optimal weight: 9.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 112 GLN K 113 GLN E 68 GLN E 85 GLN A 76 GLN D 84 ASN B 25 ASN M 99 ASN M 113 GLN ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 252 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.170470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.122574 restraints weight = 22480.291| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.27 r_work: 0.3233 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3035 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 19592 Z= 0.144 Angle : 0.735 14.674 27729 Z= 0.400 Chirality : 0.051 0.259 3117 Planarity : 0.005 0.087 2519 Dihedral : 28.424 161.665 4914 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.37 % Favored : 94.43 % Rotamer: Outliers : 3.68 % Allowed : 14.58 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 3.12 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.22), residues: 1545 helix: 0.32 (0.19), residues: 811 sheet: -0.11 (0.48), residues: 140 loop : -1.42 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 86 TYR 0.010 0.001 TYR M 209 PHE 0.017 0.001 PHE K 223 TRP 0.013 0.002 TRP M 22 HIS 0.005 0.001 HIS F 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 (19592) covalent geometry : angle 0.73542 / 0.40 (27729) hydrogen bonds : bond 0.05949 / 3.91 ( 831) hydrogen bonds : angle 3.49504 / 2.38 ( 2108) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 188 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 55 MET cc_start: 0.2031 (mtm) cc_final: 0.0723 (mmt) REVERT: K 104 THR cc_start: 0.8657 (OUTLIER) cc_final: 0.8304 (t) REVERT: K 129 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8114 (tt0) REVERT: K 276 ASN cc_start: 0.7529 (p0) cc_final: 0.7325 (p0) REVERT: A 59 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8287 (pm20) REVERT: D 96 THR cc_start: 0.8857 (t) cc_final: 0.8628 (p) REVERT: C 36 LYS cc_start: 0.8504 (mmmt) cc_final: 0.8246 (ptpt) REVERT: C 59 THR cc_start: 0.9009 (t) cc_final: 0.8805 (p) REVERT: C 75 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.8762 (mptp) REVERT: M 22 TRP cc_start: 0.3852 (OUTLIER) cc_final: 0.3579 (t-100) REVERT: M 71 MET cc_start: 0.5010 (mmt) cc_final: 0.4360 (tpp) REVERT: M 129 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7546 (tt0) outliers start: 50 outliers final: 29 residues processed: 222 average time/residue: 0.7263 time to fit residues: 177.1254 Evaluate side-chains 217 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 182 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain K residue 22 TRP Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 129 GLU Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 248 GLU Chi-restraints excluded: chain K residue 255 GLU Chi-restraints excluded: chain K residue 286 ASP Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain M residue 22 TRP Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 129 GLU Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 297 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 137 optimal weight: 20.0000 chunk 28 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 112 optimal weight: 30.0000 chunk 136 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 123 optimal weight: 30.0000 chunk 21 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 112 GLN K 113 GLN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 99 ASN M 113 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.170718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.123034 restraints weight = 22789.381| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.26 r_work: 0.3163 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3026 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3026 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19592 Z= 0.160 Angle : 0.704 14.583 27729 Z= 0.386 Chirality : 0.049 0.280 3117 Planarity : 0.005 0.090 2519 Dihedral : 28.250 158.903 4914 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.76 % Favored : 94.05 % Rotamer: Outliers : 3.83 % Allowed : 14.36 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 3.12 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.22), residues: 1545 helix: 0.54 (0.19), residues: 811 sheet: 0.01 (0.48), residues: 140 loop : -1.33 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 101 TYR 0.012 0.001 TYR F 72 PHE 0.017 0.001 PHE K 223 TRP 0.014 0.002 TRP M 22 HIS 0.006 0.001 HIS F 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.16 (19592) covalent geometry : angle 0.70354 / 0.39 (27729) hydrogen bonds : bond 0.05813 / 3.80 ( 831) hydrogen bonds : angle 3.35224 / 2.28 ( 2108) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 183 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 55 MET cc_start: 0.2474 (mtm) cc_final: 0.1128 (mmt) REVERT: K 104 THR cc_start: 0.8724 (OUTLIER) cc_final: 0.8397 (t) REVERT: K 129 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8181 (tt0) REVERT: K 170 VAL cc_start: 0.9188 (OUTLIER) cc_final: 0.8887 (t) REVERT: K 276 ASN cc_start: 0.7634 (p0) cc_final: 0.7430 (p0) REVERT: A 59 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8306 (pm20) REVERT: A 120 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8028 (mtt) REVERT: A 129 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.7531 (tpt-90) REVERT: D 96 THR cc_start: 0.8961 (t) cc_final: 0.8657 (p) REVERT: C 36 LYS cc_start: 0.8566 (mmmt) cc_final: 0.8209 (ptpt) REVERT: C 74 LYS cc_start: 0.8724 (mttm) cc_final: 0.8303 (mtpt) REVERT: C 75 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.8755 (mptp) REVERT: M 22 TRP cc_start: 0.3758 (OUTLIER) cc_final: 0.3481 (t-100) REVERT: M 71 MET cc_start: 0.4875 (mmt) cc_final: 0.4203 (tpp) REVERT: M 121 ASP cc_start: 0.7956 (t0) cc_final: 0.7613 (t70) REVERT: M 180 LYS cc_start: 0.7529 (OUTLIER) cc_final: 0.7327 (mmtm) REVERT: M 212 LYS cc_start: 0.6691 (OUTLIER) cc_final: 0.6310 (pptt) outliers start: 52 outliers final: 28 residues processed: 220 average time/residue: 0.7357 time to fit residues: 177.7384 Evaluate side-chains 217 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 179 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 129 GLU Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 248 GLU Chi-restraints excluded: chain K residue 255 GLU Chi-restraints excluded: chain K residue 286 ASP Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain M residue 22 TRP Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 180 LYS Chi-restraints excluded: chain M residue 212 LYS Chi-restraints excluded: chain M residue 297 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 62 optimal weight: 7.9990 chunk 115 optimal weight: 20.0000 chunk 59 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 4 optimal weight: 30.0000 chunk 127 optimal weight: 20.0000 chunk 28 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 5 optimal weight: 0.0020 chunk 170 optimal weight: 5.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 112 GLN K 113 GLN M 113 GLN M 252 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.171341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.123900 restraints weight = 22554.567| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.25 r_work: 0.3176 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19592 Z= 0.135 Angle : 0.691 14.806 27729 Z= 0.379 Chirality : 0.048 0.289 3117 Planarity : 0.005 0.089 2519 Dihedral : 28.247 159.624 4914 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.50 % Favored : 94.30 % Rotamer: Outliers : 3.68 % Allowed : 15.24 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 3.12 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.22), residues: 1545 helix: 0.65 (0.19), residues: 811 sheet: 0.03 (0.48), residues: 140 loop : -1.28 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 101 TYR 0.023 0.001 TYR K 20 PHE 0.017 0.001 PHE K 223 TRP 0.013 0.002 TRP M 22 HIS 0.005 0.001 HIS F 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.14 (19592) covalent geometry : angle 0.69074 / 0.38 (27729) hydrogen bonds : bond 0.05573 / 3.63 ( 831) hydrogen bonds : angle 3.33109 / 2.27 ( 2108) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 182 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 36 LYS cc_start: 0.8791 (pttt) cc_final: 0.8579 (mmpt) REVERT: K 55 MET cc_start: 0.2409 (mtm) cc_final: 0.1096 (mmt) REVERT: K 104 THR cc_start: 0.8726 (OUTLIER) cc_final: 0.8393 (t) REVERT: K 129 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8160 (tt0) REVERT: K 170 VAL cc_start: 0.9186 (OUTLIER) cc_final: 0.8898 (t) REVERT: K 276 ASN cc_start: 0.7800 (p0) cc_final: 0.7591 (p0) REVERT: A 59 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8301 (pm20) REVERT: A 120 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8016 (mtt) REVERT: A 129 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7538 (tpt-90) REVERT: D 96 THR cc_start: 0.8964 (t) cc_final: 0.8655 (p) REVERT: C 36 LYS cc_start: 0.8543 (mmmt) cc_final: 0.8182 (ptpt) REVERT: C 75 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.8755 (mptp) REVERT: M 22 TRP cc_start: 0.3752 (OUTLIER) cc_final: 0.3471 (t-100) REVERT: M 71 MET cc_start: 0.4870 (mmt) cc_final: 0.4205 (tpp) REVERT: M 121 ASP cc_start: 0.7943 (t0) cc_final: 0.7613 (t70) REVERT: M 153 MET cc_start: 0.6659 (OUTLIER) cc_final: 0.5625 (ppp) REVERT: M 212 LYS cc_start: 0.6704 (OUTLIER) cc_final: 0.6331 (pptt) REVERT: M 248 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7694 (mm-30) REVERT: M 278 ARG cc_start: 0.8091 (mtm-85) cc_final: 0.7624 (ptp90) outliers start: 50 outliers final: 27 residues processed: 213 average time/residue: 0.7385 time to fit residues: 172.7635 Evaluate side-chains 219 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 181 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain K residue 22 TRP Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 129 GLU Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 248 GLU Chi-restraints excluded: chain K residue 255 GLU Chi-restraints excluded: chain K residue 286 ASP Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain M residue 22 TRP Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 153 MET Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 212 LYS Chi-restraints excluded: chain M residue 248 GLU Chi-restraints excluded: chain M residue 297 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 29 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 174 optimal weight: 0.1980 chunk 133 optimal weight: 10.0000 chunk 125 optimal weight: 50.0000 chunk 90 optimal weight: 0.7980 chunk 155 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 113 GLN ** K 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN M 113 GLN M 252 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.172217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.123246 restraints weight = 22568.288| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.34 r_work: 0.3237 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3041 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (14 function evaluations) r_final: 0.3041 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19592 Z= 0.145 Angle : 0.683 14.895 27729 Z= 0.374 Chirality : 0.048 0.316 3117 Planarity : 0.005 0.087 2519 Dihedral : 28.189 159.764 4914 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.50 % Favored : 94.30 % Rotamer: Outliers : 3.39 % Allowed : 15.61 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 3.12 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.22), residues: 1545 helix: 0.78 (0.19), residues: 807 sheet: 0.12 (0.48), residues: 140 loop : -1.21 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 101 TYR 0.013 0.001 TYR K 20 PHE 0.016 0.001 PHE K 223 TRP 0.013 0.002 TRP M 22 HIS 0.005 0.001 HIS F 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.15 (19592) covalent geometry : angle 0.68341 / 0.37 (27729) hydrogen bonds : bond 0.05486 / 3.57 ( 831) hydrogen bonds : angle 3.28065 / 2.23 ( 2108) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 179 time to evaluate : 0.564 Fit side-chains revert: symmetry clash REVERT: F 91 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7443 (ttmt) REVERT: K 55 MET cc_start: 0.2298 (mtm) cc_final: 0.1404 (mmt) REVERT: K 96 MET cc_start: 0.3936 (mtt) cc_final: 0.3211 (tpt) REVERT: K 104 THR cc_start: 0.8660 (OUTLIER) cc_final: 0.8371 (t) REVERT: K 129 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8096 (tt0) REVERT: K 170 VAL cc_start: 0.9194 (OUTLIER) cc_final: 0.8914 (t) REVERT: A 120 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.7983 (mtt) REVERT: A 129 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.7493 (tpt-90) REVERT: D 96 THR cc_start: 0.8888 (t) cc_final: 0.8599 (p) REVERT: C 36 LYS cc_start: 0.8474 (mmmt) cc_final: 0.8211 (ptpt) REVERT: C 75 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.8775 (mptp) REVERT: M 22 TRP cc_start: 0.3704 (OUTLIER) cc_final: 0.3376 (t-100) REVERT: M 71 MET cc_start: 0.4992 (mmt) cc_final: 0.4322 (tpp) REVERT: M 106 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7310 (tm) REVERT: M 121 ASP cc_start: 0.7940 (t0) cc_final: 0.7605 (t70) REVERT: M 129 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7480 (tt0) REVERT: M 212 LYS cc_start: 0.6749 (pptt) cc_final: 0.6372 (pptt) REVERT: M 248 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7647 (mm-30) REVERT: M 278 ARG cc_start: 0.8056 (mtm-85) cc_final: 0.7618 (ptp90) outliers start: 46 outliers final: 23 residues processed: 210 average time/residue: 0.7609 time to fit residues: 175.5575 Evaluate side-chains 209 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 175 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 22 TRP Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 129 GLU Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 248 GLU Chi-restraints excluded: chain K residue 255 GLU Chi-restraints excluded: chain K residue 286 ASP Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain M residue 22 TRP Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 129 GLU Chi-restraints excluded: chain M residue 248 GLU Chi-restraints excluded: chain M residue 297 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 177 optimal weight: 20.0000 chunk 173 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 121 optimal weight: 9.9990 chunk 14 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 143 optimal weight: 0.6980 chunk 175 optimal weight: 10.0000 chunk 172 optimal weight: 20.0000 chunk 23 optimal weight: 3.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 113 GLN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 113 GLN M 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.171129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.121961 restraints weight = 22593.874| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.33 r_work: 0.3232 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 19592 Z= 0.172 Angle : 0.700 15.031 27729 Z= 0.382 Chirality : 0.049 0.279 3117 Planarity : 0.005 0.088 2519 Dihedral : 28.198 158.623 4914 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.95 % Favored : 93.92 % Rotamer: Outliers : 2.95 % Allowed : 16.05 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 3.12 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.22), residues: 1545 helix: 0.74 (0.19), residues: 808 sheet: 0.16 (0.49), residues: 140 loop : -1.21 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 101 TYR 0.010 0.001 TYR B 51 PHE 0.018 0.001 PHE K 223 TRP 0.013 0.002 TRP M 22 HIS 0.007 0.001 HIS F 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (19592) covalent geometry : angle 0.69962 / 0.38 (27729) hydrogen bonds : bond 0.05744 / 3.77 ( 831) hydrogen bonds : angle 3.29865 / 2.25 ( 2108) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 176 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: L 1 MET cc_start: 0.1301 (ptt) cc_final: 0.1039 (ptt) REVERT: H 37 TYR cc_start: 0.9199 (m-80) cc_final: 0.8896 (m-80) REVERT: K 55 MET cc_start: 0.2788 (mtm) cc_final: 0.1361 (mmt) REVERT: K 96 MET cc_start: 0.3885 (mtt) cc_final: 0.3138 (tpt) REVERT: K 104 THR cc_start: 0.8632 (OUTLIER) cc_final: 0.8339 (t) REVERT: K 129 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8099 (tt0) REVERT: A 120 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.7958 (mtt) REVERT: A 129 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7477 (tpt-90) REVERT: D 96 THR cc_start: 0.8897 (t) cc_final: 0.8614 (p) REVERT: C 36 LYS cc_start: 0.8506 (mmmt) cc_final: 0.8216 (ptpt) REVERT: C 75 LYS cc_start: 0.9289 (OUTLIER) cc_final: 0.8786 (mptp) REVERT: M 22 TRP cc_start: 0.3705 (OUTLIER) cc_final: 0.3373 (t-100) REVERT: M 71 MET cc_start: 0.4731 (mmt) cc_final: 0.4036 (tpp) REVERT: M 121 ASP cc_start: 0.7964 (t0) cc_final: 0.7643 (t70) REVERT: M 212 LYS cc_start: 0.6892 (pptt) cc_final: 0.6469 (pptt) REVERT: M 248 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7673 (mm-30) REVERT: M 278 ARG cc_start: 0.7972 (mtm-85) cc_final: 0.7601 (ptp90) outliers start: 40 outliers final: 26 residues processed: 203 average time/residue: 0.8049 time to fit residues: 179.0852 Evaluate side-chains 209 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 22 TRP Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 129 GLU Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 248 GLU Chi-restraints excluded: chain K residue 255 GLU Chi-restraints excluded: chain K residue 286 ASP Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain M residue 22 TRP Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 248 GLU Chi-restraints excluded: chain M residue 297 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 163 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 139 optimal weight: 30.0000 chunk 84 optimal weight: 5.9990 chunk 133 optimal weight: 9.9990 chunk 161 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 85 GLN A 68 GLN M 113 GLN M 252 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.169639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.120311 restraints weight = 22596.091| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.32 r_work: 0.3204 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (14 function evaluations) r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 19592 Z= 0.220 Angle : 0.745 14.363 27729 Z= 0.402 Chirality : 0.052 0.291 3117 Planarity : 0.006 0.088 2519 Dihedral : 28.292 156.939 4914 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.02 % Favored : 93.85 % Rotamer: Outliers : 2.87 % Allowed : 15.98 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 3.12 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.22), residues: 1545 helix: 0.59 (0.19), residues: 809 sheet: 0.04 (0.48), residues: 142 loop : -1.28 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 101 TYR 0.013 0.002 TYR M 209 PHE 0.022 0.002 PHE K 223 TRP 0.013 0.002 TRP K 89 HIS 0.009 0.001 HIS F 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.22 (19592) covalent geometry : angle 0.74459 / 0.40 (27729) hydrogen bonds : bond 0.06249 / 4.14 ( 831) hydrogen bonds : angle 3.40074 / 2.31 ( 2108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8279.04 seconds wall clock time: 140 minutes 53.51 seconds (8453.51 seconds total)