Starting phenix.real_space_refine on Fri Feb 6 04:49:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xct_33127/02_2026/7xct_33127.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xct_33127/02_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_33127/02_2026/7xct_33127.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xct_33127/02_2026/7xct_33127.map" model { file = "/net/cci-nas-00/data/ceres_data/7xct_33127/02_2026/7xct_33127.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xct_33127/02_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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: 3.54, per 1000 atoms: 0.19 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: 1.29 Conformation dependent library (CDL) restraints added in 439.5 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: 2.57 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: 3.33 Time building geometry restraints manager: 1.70 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 1.490 1.595 -0.105 3.00e-02 1.11e+03 1.22e+01 bond pdb=" CB THR H 96 " pdb=" CG2 THR H 96 " ideal model delta sigma weight residual 1.521 1.422 0.099 3.30e-02 9.18e+02 9.09e+00 bond pdb=" CA LYS F 79 " pdb=" C LYS F 79 " ideal model delta sigma weight residual 1.523 1.563 -0.040 1.34e-02 5.57e+03 8.89e+00 bond pdb=" CB THR B 71 " pdb=" CG2 THR B 71 " ideal model delta sigma weight residual 1.521 1.425 0.096 3.30e-02 9.18e+02 8.45e+00 bond pdb=" CB THR D 96 " pdb=" CG2 THR D 96 " ideal model delta sigma weight residual 1.521 1.430 0.091 3.30e-02 9.18e+02 7.62e+00 ... (remaining 19587 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.96: 27451 3.96 - 7.91: 226 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=" CA GLU K 47 " pdb=" C GLU K 47 " pdb=" N ILE K 48 " ideal model delta sigma weight residual 119.01 126.49 -7.48 1.38e+00 5.25e-01 2.94e+01 ... (remaining 27724 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 9745 35.58 - 71.16: 1342 71.16 - 106.74: 13 106.74 - 142.32: 1 142.32 - 177.90: 2 Dihedral angle restraints: 11103 sinusoidal: 6512 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 11100 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2424 0.071 - 0.142: 588 0.142 - 0.213: 88 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 17.240 Find NCS groups from input model: 0.200 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:6.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 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 0.111 19592 Z= 0.529 Angle : 1.114 19.779 27729 Z= 0.615 Chirality : 0.064 0.354 3117 Planarity : 0.008 0.081 2519 Dihedral : 22.813 177.902 8137 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 covalent geometry : bond 0.01218 (19592) covalent geometry : angle 1.11369 (27729) hydrogen bonds : bond 0.30837 ( 831) hydrogen bonds : angle 9.45175 ( 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 : 0.480 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: 0.7937 (m-30) REVERT: A 122 LYS cc_start: 0.8973 (pttt) cc_final: 0.8742 (pttp) REVERT: D 59 MET cc_start: 0.8960 (tpp) cc_final: 0.8684 (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: 0.3497 (tpp) outliers start: 8 outliers final: 4 residues processed: 274 average time/residue: 0.9418 time to fit residues: 277.0455 Evaluate side-chains 181 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 177 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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: 0.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 7.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 60 ASN F 18 HIS ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 K 315 HIS E 68 GLN E 76 GLN A 68 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 M 331 ASN N 60 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.175671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.130024 restraints weight = 22479.190| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.32 r_work: 0.3287 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3097 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3096 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19592 Z= 0.173 Angle : 0.698 15.303 27729 Z= 0.397 Chirality : 0.042 0.236 3117 Planarity : 0.006 0.073 2519 Dihedral : 27.845 172.968 4980 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.60 % Favored : 95.15 % Rotamer: Outliers : 3.76 % Allowed : 10.24 % Favored : 86.01 % 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: -2.42 (0.19), residues: 1545 helix: -1.49 (0.16), residues: 799 sheet: -0.68 (0.48), residues: 140 loop : -1.79 (0.23), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 101 TYR 0.014 0.001 TYR K 312 PHE 0.019 0.002 PHE K 223 TRP 0.017 0.002 TRP M 22 HIS 0.005 0.001 HIS G 82 Details of bonding type rmsd covalent geometry : bond 0.00380 (19592) covalent geometry : angle 0.69788 (27729) hydrogen bonds : bond 0.06372 ( 831) hydrogen bonds : angle 3.94609 ( 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 257 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 206 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: H 47 GLN cc_start: 0.8628 (mt0) cc_final: 0.8426 (mt0) REVERT: K 71 MET cc_start: 0.5120 (OUTLIER) cc_final: 0.4628 (mpp) REVERT: K 104 THR cc_start: 0.8560 (OUTLIER) cc_final: 0.8180 (t) REVERT: E 73 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8369 (tt0) REVERT: C 95 LYS cc_start: 0.9059 (mtpp) cc_final: 0.8856 (mmmt) REVERT: M 71 MET cc_start: 0.4963 (mmt) cc_final: 0.4305 (tpp) REVERT: M 248 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7445 (mm-30) outliers start: 51 outliers final: 14 residues processed: 234 average time/residue: 0.8439 time to fit residues: 214.0969 Evaluate side-chains 199 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 181 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 101 THR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain K residue 71 MET Chi-restraints excluded: chain K residue 104 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 96 THR Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 200 ARG Chi-restraints excluded: chain M residue 248 GLU 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: 5.9990 chunk 112 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 170 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 159 optimal weight: 20.0000 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 GLN A 68 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.169750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.121405 restraints weight = 22848.398| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.32 r_work: 0.3194 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 19592 Z= 0.270 Angle : 0.722 15.101 27729 Z= 0.405 Chirality : 0.046 0.251 3117 Planarity : 0.006 0.077 2519 Dihedral : 27.902 172.450 4978 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.37 % Favored : 94.43 % Rotamer: Outliers : 4.27 % Allowed : 12.37 % Favored : 83.36 % 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: -1.30 (0.21), residues: 1545 helix: -0.33 (0.19), residues: 798 sheet: -0.44 (0.49), residues: 140 loop : -1.59 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 101 TYR 0.021 0.002 TYR K 312 PHE 0.024 0.002 PHE K 223 TRP 0.013 0.002 TRP K 228 HIS 0.009 0.001 HIS F 18 Details of bonding type rmsd covalent geometry : bond 0.00624 (19592) covalent geometry : angle 0.72166 (27729) hydrogen bonds : bond 0.06464 ( 831) hydrogen bonds : angle 3.68828 ( 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 242 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 184 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 23 ARG cc_start: 0.7647 (ttm-80) cc_final: 0.7420 (tpp-160) REVERT: G 91 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8552 (tt0) REVERT: K 36 GLU cc_start: 0.5683 (OUTLIER) cc_final: 0.5476 (tt0) REVERT: K 104 THR cc_start: 0.8689 (OUTLIER) cc_final: 0.8318 (t) REVERT: K 276 ASN cc_start: 0.7561 (p0) cc_final: 0.7349 (p0) REVERT: E 49 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8555 (ttm170) REVERT: E 73 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8423 (tt0) REVERT: C 36 LYS cc_start: 0.8477 (mmmt) cc_final: 0.8191 (ptpt) REVERT: M 22 TRP cc_start: 0.3596 (OUTLIER) cc_final: 0.3258 (t-100) REVERT: M 71 MET cc_start: 0.5010 (mmt) cc_final: 0.4368 (tpp) outliers start: 58 outliers final: 27 residues processed: 216 average time/residue: 0.7905 time to fit residues: 186.4594 Evaluate side-chains 207 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 174 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 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 101 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain K residue 22 TRP Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 104 THR 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 49 ARG 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 D residue 88 THR Chi-restraints excluded: chain D residue 108 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 120 THR Chi-restraints excluded: chain M residue 200 ARG Chi-restraints excluded: chain M residue 297 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 104 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 165 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 143 optimal weight: 0.0870 chunk 45 optimal weight: 6.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN A 76 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.171411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.123704 restraints weight = 22745.599| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.26 r_work: 0.3247 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2669 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= 0.158 Angle : 0.665 14.853 27729 Z= 0.377 Chirality : 0.041 0.243 3117 Planarity : 0.005 0.079 2519 Dihedral : 27.875 172.132 4978 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.18 % Favored : 94.63 % Rotamer: Outliers : 3.24 % Allowed : 14.06 % Favored : 82.70 % 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: -0.76 (0.22), residues: 1545 helix: 0.19 (0.19), residues: 801 sheet: -0.25 (0.49), residues: 140 loop : -1.42 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 71 TYR 0.010 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 covalent geometry : bond 0.00348 (19592) covalent geometry : angle 0.66543 (27729) hydrogen bonds : bond 0.05521 ( 831) hydrogen bonds : angle 3.50440 ( 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 223 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 179 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 23 ARG cc_start: 0.7596 (ttm-80) cc_final: 0.7368 (tpp-160) REVERT: H 47 GLN cc_start: 0.8738 (mt0) cc_final: 0.8431 (mt0) REVERT: K 104 THR cc_start: 0.8661 (OUTLIER) cc_final: 0.8299 (t) REVERT: E 73 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8350 (tt0) REVERT: A 59 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8314 (pm20) REVERT: A 120 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.7759 (mtt) REVERT: C 36 LYS cc_start: 0.8459 (mmmt) cc_final: 0.8165 (ptpt) REVERT: C 59 THR cc_start: 0.8991 (t) cc_final: 0.8768 (p) REVERT: M 22 TRP cc_start: 0.3788 (OUTLIER) cc_final: 0.3504 (t-100) REVERT: M 71 MET cc_start: 0.4971 (mmt) cc_final: 0.4364 (tpp) outliers start: 44 outliers final: 24 residues processed: 208 average time/residue: 0.8076 time to fit residues: 183.2771 Evaluate side-chains 207 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 178 time to evaluate : 0.409 ------------------------------------------------------------------------------- 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 101 THR Chi-restraints excluded: chain H residue 39 VAL 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 106 LEU 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 59 GLU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain D residue 39 VAL 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 297 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 49 optimal weight: 8.9990 chunk 145 optimal weight: 20.0000 chunk 135 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 123 optimal weight: 8.9990 chunk 168 optimal weight: 8.9990 chunk 73 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN D 84 ASN 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 = 0.4037 r_free = 0.4037 target = 0.167474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.119707 restraints weight = 22657.958| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.26 r_work: 0.3185 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 19592 Z= 0.322 Angle : 0.749 14.345 27729 Z= 0.418 Chirality : 0.048 0.241 3117 Planarity : 0.006 0.080 2519 Dihedral : 28.024 169.382 4978 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.89 % Favored : 93.92 % Rotamer: Outliers : 4.57 % Allowed : 13.33 % Favored : 82.11 % 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: -0.80 (0.22), residues: 1545 helix: 0.16 (0.19), residues: 801 sheet: -0.24 (0.48), residues: 140 loop : -1.47 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 131 TYR 0.017 0.002 TYR K 312 PHE 0.025 0.002 PHE K 223 TRP 0.014 0.002 TRP M 22 HIS 0.011 0.001 HIS F 18 Details of bonding type rmsd covalent geometry : bond 0.00746 (19592) covalent geometry : angle 0.74868 (27729) hydrogen bonds : bond 0.06684 ( 831) hydrogen bonds : angle 3.59300 ( 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 241 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 179 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 23 ARG cc_start: 0.7656 (ttm-80) cc_final: 0.7405 (tpp-160) REVERT: G 91 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8642 (tt0) REVERT: G 92 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8240 (mt-10) REVERT: H 37 TYR cc_start: 0.9268 (m-80) cc_final: 0.8968 (m-80) REVERT: K 104 THR cc_start: 0.8699 (OUTLIER) cc_final: 0.8327 (t) REVERT: K 276 ASN cc_start: 0.7615 (p0) cc_final: 0.7414 (p0) REVERT: E 73 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8417 (tt0) REVERT: A 59 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8256 (pm20) REVERT: A 120 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.7928 (mtt) REVERT: C 36 LYS cc_start: 0.8551 (mmmt) cc_final: 0.8278 (ptpt) REVERT: C 74 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8486 (mtpt) REVERT: M 22 TRP cc_start: 0.3789 (OUTLIER) cc_final: 0.3513 (t-100) REVERT: M 71 MET cc_start: 0.5015 (mmt) cc_final: 0.4340 (tpp) REVERT: M 278 ARG cc_start: 0.8005 (mtm-85) cc_final: 0.7570 (ptp90) outliers start: 62 outliers final: 32 residues processed: 217 average time/residue: 0.8076 time to fit residues: 191.2875 Evaluate side-chains 213 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 173 time to evaluate : 0.603 ------------------------------------------------------------------------------- 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 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 96 THR Chi-restraints excluded: chain K residue 22 TRP Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 100 THR Chi-restraints excluded: chain K residue 104 THR 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 294 VAL Chi-restraints excluded: chain E residue 73 GLU 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 D residue 39 VAL Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain C residue 74 LYS 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 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain M residue 22 TRP Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 120 THR 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: 3.9990 chunk 33 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 97 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 111 optimal weight: 10.0000 chunk 129 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 GLN E 85 GLN B 25 ASN M 113 GLN ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 252 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.170372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.121371 restraints weight = 22537.500| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.33 r_work: 0.3214 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3021 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3021 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19592 Z= 0.181 Angle : 0.681 14.588 27729 Z= 0.384 Chirality : 0.042 0.247 3117 Planarity : 0.005 0.081 2519 Dihedral : 28.000 169.397 4978 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.44 % Favored : 94.37 % Rotamer: Outliers : 3.68 % Allowed : 15.46 % Favored : 80.85 % 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: -0.57 (0.22), residues: 1545 helix: 0.38 (0.19), residues: 805 sheet: -0.15 (0.49), residues: 140 loop : -1.42 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 71 TYR 0.013 0.001 TYR M 209 PHE 0.018 0.001 PHE K 223 TRP 0.014 0.002 TRP M 22 HIS 0.007 0.001 HIS F 18 Details of bonding type rmsd covalent geometry : bond 0.00407 (19592) covalent geometry : angle 0.68121 (27729) hydrogen bonds : bond 0.05708 ( 831) hydrogen bonds : angle 3.44311 ( 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 235 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 185 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 23 ARG cc_start: 0.7654 (ttm-80) cc_final: 0.7333 (tpp-160) REVERT: K 51 LEU cc_start: 0.1453 (OUTLIER) cc_final: 0.0964 (mm) REVERT: K 55 MET cc_start: 0.3047 (mtm) cc_final: 0.1559 (mmt) REVERT: K 104 THR cc_start: 0.8658 (OUTLIER) cc_final: 0.8310 (t) REVERT: K 276 ASN cc_start: 0.7587 (p0) cc_final: 0.7360 (p0) REVERT: E 73 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8385 (tt0) REVERT: A 59 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8255 (pm20) REVERT: A 120 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.7956 (mtt) REVERT: C 36 LYS cc_start: 0.8499 (mmmt) cc_final: 0.8269 (ptpt) REVERT: C 59 THR cc_start: 0.9029 (t) cc_final: 0.8790 (p) REVERT: M 22 TRP cc_start: 0.3793 (OUTLIER) cc_final: 0.3458 (t-100) REVERT: M 71 MET cc_start: 0.4875 (mmt) cc_final: 0.4224 (tpp) REVERT: M 121 ASP cc_start: 0.7929 (t0) cc_final: 0.7555 (t70) REVERT: M 278 ARG cc_start: 0.7963 (mtm-85) cc_final: 0.7641 (ptp90) outliers start: 50 outliers final: 31 residues processed: 217 average time/residue: 0.7399 time to fit residues: 175.7913 Evaluate side-chains 215 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 178 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 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 51 LEU Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 100 THR 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 E residue 73 GLU 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 D residue 39 VAL Chi-restraints excluded: chain D residue 108 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 61 ILE Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 226 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 137 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 136 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 123 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN M 113 GLN ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.169147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.120890 restraints weight = 22814.553| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.28 r_work: 0.3210 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3008 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3008 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 19592 Z= 0.234 Angle : 0.681 14.257 27729 Z= 0.382 Chirality : 0.044 0.246 3117 Planarity : 0.006 0.082 2519 Dihedral : 27.877 166.940 4978 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.83 % Favored : 93.98 % Rotamer: Outliers : 3.98 % Allowed : 15.02 % 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: -0.49 (0.22), residues: 1545 helix: 0.44 (0.19), residues: 802 sheet: -0.00 (0.49), residues: 140 loop : -1.38 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 71 TYR 0.013 0.002 TYR D 37 PHE 0.020 0.002 PHE K 223 TRP 0.014 0.002 TRP M 22 HIS 0.008 0.001 HIS F 18 Details of bonding type rmsd covalent geometry : bond 0.00537 (19592) covalent geometry : angle 0.68104 (27729) hydrogen bonds : bond 0.05752 ( 831) hydrogen bonds : angle 3.38870 ( 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 233 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 179 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 91 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7641 (ttmt) REVERT: G 91 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8626 (tt0) REVERT: G 92 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8281 (mt-10) REVERT: K 55 MET cc_start: 0.3014 (mtm) cc_final: 0.1615 (mmt) REVERT: K 104 THR cc_start: 0.8741 (OUTLIER) cc_final: 0.8436 (t) REVERT: A 120 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.7949 (mtt) REVERT: A 129 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7512 (tpt-90) REVERT: C 36 LYS cc_start: 0.8502 (mmmt) cc_final: 0.8239 (ptpt) REVERT: C 74 LYS cc_start: 0.8800 (mttm) cc_final: 0.8429 (mtpt) REVERT: M 22 TRP cc_start: 0.3836 (OUTLIER) cc_final: 0.3539 (t-100) REVERT: M 71 MET cc_start: 0.4964 (mmt) cc_final: 0.4296 (tpp) REVERT: M 121 ASP cc_start: 0.7919 (t0) cc_final: 0.7546 (t70) REVERT: M 278 ARG cc_start: 0.7972 (mtm-85) cc_final: 0.7564 (ptp90) outliers start: 54 outliers final: 30 residues processed: 212 average time/residue: 0.7529 time to fit residues: 174.8606 Evaluate side-chains 212 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 175 time to evaluate : 0.552 ------------------------------------------------------------------------------- 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 91 GLU Chi-restraints excluded: chain G residue 92 GLU 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 56 SER Chi-restraints excluded: chain K residue 22 TRP Chi-restraints excluded: chain K residue 100 THR 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 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 D residue 108 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 61 ILE Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 226 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 62 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 90 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 4 optimal weight: 30.0000 chunk 127 optimal weight: 8.9990 chunk 28 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 170 optimal weight: 9.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN M 113 GLN ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.170355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.121463 restraints weight = 22572.911| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.32 r_work: 0.3214 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3017 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3017 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 19592 Z= 0.191 Angle : 0.664 14.513 27729 Z= 0.374 Chirality : 0.042 0.246 3117 Planarity : 0.005 0.082 2519 Dihedral : 27.871 166.540 4978 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.83 % Favored : 93.98 % Rotamer: Outliers : 3.61 % Allowed : 15.76 % Favored : 80.63 % 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: -0.39 (0.22), residues: 1545 helix: 0.53 (0.19), residues: 802 sheet: 0.07 (0.49), residues: 140 loop : -1.36 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 86 TYR 0.011 0.001 TYR D 37 PHE 0.018 0.001 PHE K 223 TRP 0.014 0.002 TRP M 22 HIS 0.007 0.001 HIS F 18 Details of bonding type rmsd covalent geometry : bond 0.00436 (19592) covalent geometry : angle 0.66442 (27729) hydrogen bonds : bond 0.05513 ( 831) hydrogen bonds : angle 3.34616 ( 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 222 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 173 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 91 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7562 (ttmt) REVERT: G 91 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8619 (tt0) REVERT: K 51 LEU cc_start: 0.1412 (OUTLIER) cc_final: 0.0989 (mm) REVERT: K 55 MET cc_start: 0.3092 (mtm) cc_final: 0.1647 (mmt) REVERT: K 104 THR cc_start: 0.8724 (OUTLIER) cc_final: 0.8426 (t) REVERT: A 120 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.7963 (mtt) REVERT: A 129 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7518 (tpt-90) REVERT: C 36 LYS cc_start: 0.8590 (mmmt) cc_final: 0.8242 (ptpt) REVERT: C 74 LYS cc_start: 0.8773 (mttm) cc_final: 0.8398 (mtpt) REVERT: M 22 TRP cc_start: 0.3826 (OUTLIER) cc_final: 0.3466 (t-100) REVERT: M 71 MET cc_start: 0.4934 (mmt) cc_final: 0.4224 (tpp) REVERT: M 121 ASP cc_start: 0.7901 (t0) cc_final: 0.7585 (t70) REVERT: M 248 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7651 (mm-30) REVERT: M 278 ARG cc_start: 0.7900 (mtm-85) cc_final: 0.7579 (ptp90) outliers start: 49 outliers final: 32 residues processed: 206 average time/residue: 0.7500 time to fit residues: 168.8630 Evaluate side-chains 213 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 173 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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 91 GLU 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 56 SER Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 100 THR 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 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 D residue 108 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 61 ILE Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 226 GLU Chi-restraints excluded: chain M residue 248 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 29 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 174 optimal weight: 6.9990 chunk 133 optimal weight: 3.9990 chunk 125 optimal weight: 20.0000 chunk 90 optimal weight: 0.6980 chunk 155 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 GLN A 68 GLN M 113 GLN ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 252 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.170938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.122231 restraints weight = 22526.428| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.70 r_work: 0.3202 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 19592 Z= 0.169 Angle : 0.658 14.323 27729 Z= 0.370 Chirality : 0.041 0.253 3117 Planarity : 0.005 0.096 2519 Dihedral : 27.847 166.247 4978 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.89 % Favored : 93.92 % Rotamer: Outliers : 3.46 % Allowed : 16.20 % Favored : 80.34 % 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: -0.27 (0.22), residues: 1545 helix: 0.64 (0.19), residues: 802 sheet: 0.10 (0.49), residues: 140 loop : -1.33 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 86 TYR 0.009 0.001 TYR B 51 PHE 0.017 0.001 PHE K 223 TRP 0.025 0.002 TRP K 22 HIS 0.006 0.001 HIS F 18 Details of bonding type rmsd covalent geometry : bond 0.00380 (19592) covalent geometry : angle 0.65786 (27729) hydrogen bonds : bond 0.05322 ( 831) hydrogen bonds : angle 3.31388 ( 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 223 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 176 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 91 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8726 (tt0) REVERT: K 51 LEU cc_start: 0.1422 (OUTLIER) cc_final: 0.0982 (mm) REVERT: K 55 MET cc_start: 0.3054 (mtm) cc_final: 0.1645 (mmt) REVERT: K 104 THR cc_start: 0.8741 (OUTLIER) cc_final: 0.8435 (t) REVERT: K 170 VAL cc_start: 0.9204 (OUTLIER) cc_final: 0.8896 (t) REVERT: A 59 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8295 (pm20) REVERT: A 120 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.7998 (mtt) REVERT: A 129 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7557 (tpt-90) REVERT: C 36 LYS cc_start: 0.8636 (mmmt) cc_final: 0.8231 (ptpt) REVERT: C 74 LYS cc_start: 0.8771 (mttm) cc_final: 0.8390 (mtpt) REVERT: M 22 TRP cc_start: 0.3816 (OUTLIER) cc_final: 0.3454 (t-100) REVERT: M 71 MET cc_start: 0.4934 (mmt) cc_final: 0.4224 (tpp) REVERT: M 121 ASP cc_start: 0.7935 (t0) cc_final: 0.7600 (t70) REVERT: M 212 LYS cc_start: 0.6329 (pttt) cc_final: 0.5995 (pptt) REVERT: M 248 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7710 (mm-30) REVERT: M 278 ARG cc_start: 0.7951 (mtm-85) cc_final: 0.7611 (ptp90) outliers start: 47 outliers final: 29 residues processed: 206 average time/residue: 0.7678 time to fit residues: 173.5579 Evaluate side-chains 214 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 176 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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 91 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 51 LEU Chi-restraints excluded: chain K residue 100 THR Chi-restraints excluded: chain K residue 104 THR 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 A residue 133 GLU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 108 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 61 ILE Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 120 THR 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: 30.0000 chunk 173 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 chunk 175 optimal weight: 5.9990 chunk 172 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 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 = 0.4056 r_free = 0.4056 target = 0.169118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.121012 restraints weight = 22612.173| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.27 r_work: 0.3208 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- 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 = 0.58 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 | |-----------------------------------------------------------------------------| r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19592 Z= 0.238 Angle : 0.690 14.366 27729 Z= 0.386 Chirality : 0.044 0.250 3117 Planarity : 0.006 0.085 2519 Dihedral : 27.845 162.331 4978 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.95 % Favored : 93.92 % Rotamer: Outliers : 3.53 % Allowed : 16.05 % Favored : 80.41 % 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: -0.28 (0.22), residues: 1545 helix: 0.61 (0.19), residues: 802 sheet: 0.12 (0.49), residues: 140 loop : -1.30 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 86 TYR 0.013 0.002 TYR D 37 PHE 0.020 0.002 PHE K 223 TRP 0.018 0.002 TRP K 22 HIS 0.009 0.001 HIS F 18 Details of bonding type rmsd covalent geometry : bond 0.00548 (19592) covalent geometry : angle 0.68972 (27729) hydrogen bonds : bond 0.05801 ( 831) hydrogen bonds : angle 3.35920 ( 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 225 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 177 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: G 91 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8653 (tt0) REVERT: H 37 TYR cc_start: 0.9195 (m-80) cc_final: 0.8885 (m-80) REVERT: K 55 MET cc_start: 0.3178 (mtm) cc_final: 0.1769 (mmt) REVERT: K 104 THR cc_start: 0.8705 (OUTLIER) cc_final: 0.8427 (t) REVERT: A 59 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8245 (pm20) REVERT: A 120 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.7799 (mtt) REVERT: A 129 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7488 (tpt-90) REVERT: C 11 ARG cc_start: 0.5740 (OUTLIER) cc_final: 0.5470 (ptt-90) REVERT: C 36 LYS cc_start: 0.8575 (mmmt) cc_final: 0.8290 (ptpt) REVERT: C 74 LYS cc_start: 0.8729 (mttm) cc_final: 0.8387 (mtpt) REVERT: M 22 TRP cc_start: 0.3730 (OUTLIER) cc_final: 0.3337 (t-100) REVERT: M 71 MET cc_start: 0.4806 (mmt) cc_final: 0.4108 (tpp) REVERT: M 121 ASP cc_start: 0.7928 (t0) cc_final: 0.7630 (t70) REVERT: M 212 LYS cc_start: 0.6295 (pttt) cc_final: 0.5998 (pptt) REVERT: M 248 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7657 (mm-30) REVERT: M 278 ARG cc_start: 0.7882 (mtm-85) cc_final: 0.7532 (ptp90) outliers start: 48 outliers final: 30 residues processed: 208 average time/residue: 0.7912 time to fit residues: 179.1508 Evaluate side-chains 213 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 175 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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 91 GLU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 100 THR Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 170 VAL 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 A residue 133 GLU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain C residue 11 ARG 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 61 ILE Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 120 THR 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: 8.9990 chunk 105 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 139 optimal weight: 30.0000 chunk 84 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 GLN A 39 HIS A 68 GLN M 113 GLN M 213 HIS M 252 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.168446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.120137 restraints weight = 22599.431| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.28 r_work: 0.3143 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 19592 Z= 0.272 Angle : 0.711 13.982 27729 Z= 0.396 Chirality : 0.045 0.273 3117 Planarity : 0.006 0.088 2519 Dihedral : 27.944 158.147 4978 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.02 % Favored : 93.79 % Rotamer: Outliers : 3.53 % Allowed : 16.27 % Favored : 80.19 % 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: -0.40 (0.22), residues: 1545 helix: 0.47 (0.19), residues: 808 sheet: 0.07 (0.49), residues: 140 loop : -1.31 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 131 TYR 0.015 0.002 TYR D 37 PHE 0.021 0.002 PHE K 223 TRP 0.015 0.002 TRP K 22 HIS 0.010 0.001 HIS F 18 Details of bonding type rmsd covalent geometry : bond 0.00629 (19592) covalent geometry : angle 0.71069 (27729) hydrogen bonds : bond 0.06013 ( 831) hydrogen bonds : angle 3.43468 ( 2108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8326.60 seconds wall clock time: 141 minutes 32.38 seconds (8492.38 seconds total)