Starting phenix.real_space_refine on Sun Sep 13 03:33:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7bwd_30232/09_2026/7bwd_30232.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bwd_30232/09_2026/7bwd_30232.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7bwd_30232/09_2026/7bwd_30232.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bwd_30232/09_2026/7bwd_30232.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bwd_30232/09_2026/7bwd_30232.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bwd_30232/09_2026/7bwd_30232.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7bwd_30232/09_2026/7bwd_30232.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7bwd_30232/09_2026/7bwd_30232.cif" } resolution = 4.32 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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 5986 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 292 5.49 5 S 29 5.16 5 C 9189 2.51 5 N 2962 2.21 5 O 3570 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16042 Number of models: 1 Model: "" Number of chains: 14 Chain: "K" Number of atoms: 2671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2671 Classifications: {'peptide': 328} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 309} Chain: "F" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "G" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 844 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} 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: {'PTRANS': 4, 'TRANS': 94} Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "C" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 866 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "B" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 673 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "L" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 594 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 594 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Residues with excluded nonbonded symmetry interactions: 6 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 LEU M 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU M 73 " occ=0.45 residue: pdb=" N ARG M 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG M 74 " occ=0.45 residue: pdb=" N GLY M 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY M 75 " occ=0.25 Time building chain proxies: 3.12, per 1000 atoms: 0.19 Number of scatterers: 16042 At special positions: 0 Unit cell: (114.48, 143.64, 136.08, 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 29 16.00 P 292 15.00 O 3570 8.00 N 2962 7.00 C 9189 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=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 483.9 milliseconds 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2358 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 11 sheets defined 48.3% alpha, 4.4% beta 76 base pairs and 184 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'K' and resid 37 through 48 removed outlier: 3.700A pdb=" N ILE K 41 " --> pdb=" O ILE K 37 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ARG K 42 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TRP K 43 " --> pdb=" O GLU K 39 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL K 44 " --> pdb=" O THR K 40 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU K 46 " --> pdb=" O ARG K 42 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU K 47 " --> pdb=" O TRP K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 56 removed outlier: 3.889A pdb=" N ALA K 54 " --> pdb=" O ASP K 50 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU K 56 " --> pdb=" O LYS K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 68 through 73 removed outlier: 4.367A pdb=" N ARG K 73 " --> pdb=" O GLU K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 90 removed outlier: 3.542A pdb=" N LYS K 77 " --> pdb=" O ARG K 73 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE K 82 " --> pdb=" O TYR K 78 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ASP K 83 " --> pdb=" O ASN K 79 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER K 84 " --> pdb=" O ARG K 80 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN K 87 " --> pdb=" O ASP K 83 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU K 88 " --> pdb=" O SER K 84 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS K 90 " --> pdb=" O HIS K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 105 through 114 removed outlier: 3.840A pdb=" N HIS K 109 " --> pdb=" O GLY K 105 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU K 111 " --> pdb=" O LEU K 107 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLN K 113 " --> pdb=" O HIS K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 169 through 177 removed outlier: 4.179A pdb=" N ALA K 175 " --> pdb=" O LEU K 171 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR K 177 " --> pdb=" O VAL K 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 189 through 197 removed outlier: 3.621A pdb=" N TYR K 194 " --> pdb=" O ILE K 190 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ALA K 195 " --> pdb=" O PRO K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 198 through 200 No H-bonds generated for 'chain 'K' and resid 198 through 200' Processing helix chain 'K' and resid 201 through 210 removed outlier: 3.576A pdb=" N MET K 206 " --> pdb=" O PHE K 202 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LYS K 207 " --> pdb=" O ARG K 203 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TRP K 208 " --> pdb=" O LYS K 204 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR K 209 " --> pdb=" O TRP K 205 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY K 210 " --> pdb=" O MET K 206 " (cutoff:3.500A) Processing helix chain 'K' and resid 228 through 234 Processing helix chain 'K' and resid 246 through 254 removed outlier: 4.161A pdb=" N HIS K 251 " --> pdb=" O PRO K 247 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N GLN K 252 " --> pdb=" O GLU K 248 " (cutoff:3.500A) Processing helix chain 'K' and resid 319 through 324 Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.830A pdb=" N GLY F 28 " --> pdb=" O ASN F 25 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 25 through 29' Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.538A pdb=" N ARG F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG F 39 " --> pdb=" O ARG F 35 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ARG F 40 " --> pdb=" O ARG F 36 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 63 removed outlier: 3.755A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU F 63 " --> pdb=" O LYS F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 76 removed outlier: 4.424A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS F 75 " --> pdb=" O THR F 71 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 91 Processing helix chain 'G' and resid 16 through 22 removed outlier: 3.714A pdb=" N ARG G 20 " --> pdb=" O THR G 16 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 35 removed outlier: 4.009A pdb=" N ARG G 35 " --> pdb=" O HIS G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 72 removed outlier: 3.785A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU G 63 " --> pdb=" O THR G 59 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN G 68 " --> pdb=" O GLU G 64 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 88 removed outlier: 3.974A pdb=" N ALA G 86 " --> pdb=" O HIS G 82 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG G 88 " --> pdb=" O GLN G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 95 removed outlier: 3.706A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 47 removed outlier: 3.812A pdb=" N TYR H 42 " --> pdb=" O SER H 38 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS H 43 " --> pdb=" O VAL H 39 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS H 46 " --> pdb=" O TYR H 42 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 79 removed outlier: 3.698A pdb=" N MET H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL H 66 " --> pdb=" O MET H 62 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASN H 67 " --> pdb=" O ASN H 63 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASP H 68 " --> pdb=" O SER H 64 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLU H 71 " --> pdb=" O ASN H 67 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA H 74 " --> pdb=" O PHE H 70 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 102 removed outlier: 3.698A pdb=" N ARG H 99 " --> pdb=" O GLN H 95 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU H 100 " --> pdb=" O THR H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.856A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N HIS H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N SER H 112 " --> pdb=" O LYS H 108 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS H 120 " --> pdb=" O LYS H 116 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 removed outlier: 3.676A pdb=" N GLU E 50 " --> pdb=" O VAL E 46 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN E 55 " --> pdb=" O ILE E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.649A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG E 72 " --> pdb=" O GLN E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 93 removed outlier: 4.084A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 97 Processing helix chain 'E' and resid 100 through 114 removed outlier: 3.685A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N CYS E 110 " --> pdb=" O ASP E 106 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA E 111 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 128 removed outlier: 3.712A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN E 125 " --> pdb=" O PRO E 121 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 55 removed outlier: 4.012A pdb=" N ARG A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN A 55 " --> pdb=" O ILE A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 75 removed outlier: 3.644A pdb=" N GLU A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.808A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN A 93 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU A 94 " --> pdb=" O MET A 90 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N CYS A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU A 97 " --> pdb=" O GLN A 93 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL A 101 " --> pdb=" O GLU A 97 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLY A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN A 108 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 130 removed outlier: 3.513A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LEU A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 127 " --> pdb=" O ASP A 123 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 47 removed outlier: 3.812A pdb=" N TYR D 42 " --> pdb=" O SER D 38 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS D 43 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS D 46 " --> pdb=" O TYR D 42 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 79 removed outlier: 3.697A pdb=" N MET D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL D 66 " --> pdb=" O MET D 62 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN D 67 " --> pdb=" O ASN D 63 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ASP D 68 " --> pdb=" O SER D 64 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLU D 71 " --> pdb=" O ASN D 67 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA D 74 " --> pdb=" O PHE D 70 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 102 removed outlier: 3.699A pdb=" N ARG D 99 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU D 100 " --> pdb=" O THR D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.856A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N HIS D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS D 120 " --> pdb=" O LYS D 116 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 36 removed outlier: 4.237A pdb=" N ARG C 35 " --> pdb=" O HIS C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 71 removed outlier: 3.667A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA C 53 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG C 71 " --> pdb=" O GLY C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 85 Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.753A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.585A pdb=" N ARG B 35 " --> pdb=" O LYS B 31 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG B 40 " --> pdb=" O ARG B 36 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.816A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 91 removed outlier: 3.858A pdb=" N VAL B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ALA B 89 " --> pdb=" O ASP B 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 35 removed outlier: 3.507A pdb=" N VAL L 26 " --> pdb=" O THR L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 60 removed outlier: 3.640A pdb=" N TYR L 59 " --> pdb=" O LEU L 56 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 35 removed outlier: 3.506A pdb=" N VAL M 26 " --> pdb=" O THR M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 56 through 60 removed outlier: 3.642A pdb=" N TYR M 59 " --> pdb=" O LEU M 56 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 8 through 9 Processing sheet with id=AA2, first strand: chain 'K' and resid 159 through 160 removed outlier: 5.998A pdb=" N VAL K 160 " --> pdb=" O PHE K 239 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE K 238 " --> pdb=" O VAL K 267 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'K' and resid 183 through 184 Processing sheet with id=AA4, first strand: chain 'K' and resid 294 through 295 Processing sheet with id=AA5, first strand: chain 'F' and resid 96 through 97 removed outlier: 6.835A pdb=" N THR F 96 " --> pdb=" O THR C 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.123A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 101 through 102 removed outlier: 7.067A pdb=" N THR G 101 " --> pdb=" O TYR B 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'D' and resid 88 through 89 removed outlier: 3.515A pdb=" N ILE D 89 " --> pdb=" O ARG C 42 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'L' and resid 12 through 16 removed outlier: 4.669A pdb=" N SER L 65 " --> pdb=" O GLN L 2 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 12 through 16 removed outlier: 4.670A pdb=" N SER M 65 " --> pdb=" O GLN M 2 " (cutoff:3.500A) 279 hydrogen bonds defined for protein. 819 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 184 hydrogen bonds 356 hydrogen bond angles 0 basepair planarities 76 basepair parallelities 184 stacking parallelities Total time for adding SS restraints: 2.26 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3060 1.33 - 1.45: 5184 1.45 - 1.57: 8057 1.57 - 1.69: 583 1.69 - 1.81: 51 Bond restraints: 16935 Sorted by residual: bond pdb=" C3' DA I 52 " pdb=" O3' DA I 52 " ideal model delta sigma weight residual 1.435 1.381 0.054 1.30e-02 5.92e+03 1.72e+01 bond pdb=" C3' DG J 101 " pdb=" O3' DG J 101 " ideal model delta sigma weight residual 1.435 1.383 0.052 1.30e-02 5.92e+03 1.61e+01 bond pdb=" C3' DC J 75 " pdb=" O3' DC J 75 " ideal model delta sigma weight residual 1.435 1.486 -0.051 1.30e-02 5.92e+03 1.54e+01 bond pdb=" C3' DC I 140 " pdb=" O3' DC I 140 " ideal model delta sigma weight residual 1.435 1.486 -0.051 1.30e-02 5.92e+03 1.51e+01 bond pdb=" C8 SAH K 501 " pdb=" N7 SAH K 501 " ideal model delta sigma weight residual 1.299 1.374 -0.075 2.00e-02 2.50e+03 1.42e+01 ... (remaining 16930 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 23661 2.72 - 5.44: 411 5.44 - 8.17: 46 8.17 - 10.89: 8 10.89 - 13.61: 3 Bond angle restraints: 24129 Sorted by residual: angle pdb=" O4' DC J 126 " pdb=" C4' DC J 126 " pdb=" C3' DC J 126 " ideal model delta sigma weight residual 106.00 102.48 3.52 6.00e-01 2.78e+00 3.44e+01 angle pdb=" C THR F 30 " pdb=" N LYS F 31 " pdb=" CA LYS F 31 " ideal model delta sigma weight residual 120.09 126.73 -6.64 1.25e+00 6.40e-01 2.82e+01 angle pdb=" C3' DC I 140 " pdb=" O3' DC I 140 " pdb=" P DA I 141 " ideal model delta sigma weight residual 119.70 126.00 -6.30 1.20e+00 6.94e-01 2.75e+01 angle pdb=" C3' DG J 125 " pdb=" C2' DG J 125 " pdb=" C1' DG J 125 " ideal model delta sigma weight residual 102.50 96.60 5.90 1.20e+00 6.94e-01 2.42e+01 angle pdb=" O4' DT I 129 " pdb=" C1' DT I 129 " pdb=" N1 DT I 129 " ideal model delta sigma weight residual 108.00 111.37 -3.37 7.00e-01 2.04e+00 2.32e+01 ... (remaining 24124 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.64: 8016 35.64 - 71.28: 1400 71.28 - 106.92: 41 106.92 - 142.57: 0 142.57 - 178.21: 6 Dihedral angle restraints: 9463 sinusoidal: 5813 harmonic: 3650 Sorted by residual: dihedral pdb=" CA LYS C 13 " pdb=" C LYS C 13 " pdb=" N ALA C 14 " pdb=" CA ALA C 14 " ideal model delta harmonic sigma weight residual 180.00 146.55 33.45 0 5.00e+00 4.00e-02 4.48e+01 dihedral pdb=" CA GLN E 85 " pdb=" C GLN E 85 " pdb=" N SER E 86 " pdb=" CA SER E 86 " ideal model delta harmonic sigma weight residual -180.00 -153.85 -26.15 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA VAL L 17 " pdb=" C VAL L 17 " pdb=" N GLU L 18 " pdb=" CA GLU L 18 " ideal model delta harmonic sigma weight residual 180.00 156.08 23.92 0 5.00e+00 4.00e-02 2.29e+01 ... (remaining 9460 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 2569 0.117 - 0.233: 155 0.233 - 0.350: 3 0.350 - 0.466: 1 0.466 - 0.583: 1 Chirality restraints: 2729 Sorted by residual: chirality pdb=" C3' SAH K 501 " pdb=" C2' SAH K 501 " pdb=" C4' SAH K 501 " pdb=" O3' SAH K 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.12 -0.58 2.00e-01 2.50e+01 8.49e+00 chirality pdb=" CB VAL K 169 " pdb=" CA VAL K 169 " pdb=" CG1 VAL K 169 " pdb=" CG2 VAL K 169 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 3.99e+00 chirality pdb=" CB ILE K 190 " pdb=" CA ILE K 190 " pdb=" CG1 ILE K 190 " pdb=" CG2 ILE K 190 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 2726 not shown) Planarity restraints: 2052 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE K 223 " -0.022 2.00e-02 2.50e+03 2.11e-02 7.79e+00 pdb=" CG PHE K 223 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE K 223 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE K 223 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE K 223 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE K 223 " -0.021 2.00e-02 2.50e+03 pdb=" CZ PHE K 223 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA K 273 " 0.044 5.00e-02 4.00e+02 6.61e-02 6.98e+00 pdb=" N PRO K 274 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO K 274 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO K 274 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 65 " -0.038 5.00e-02 4.00e+02 5.73e-02 5.26e+00 pdb=" N PRO A 66 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " -0.033 5.00e-02 4.00e+02 ... (remaining 2049 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.06: 6 2.06 - 2.77: 3218 2.77 - 3.48: 20933 3.48 - 4.19: 41466 4.19 - 4.90: 60988 Nonbonded interactions: 126611 Sorted by model distance: nonbonded pdb=" OP2 DC J 126 " pdb=" CB ARG L 72 " model vdw 1.348 3.440 nonbonded pdb=" C4' DG J 125 " pdb=" NH2 ARG L 72 " model vdw 1.674 3.550 nonbonded pdb=" N ARG D 31 " pdb=" N CYS M 76 " model vdw 1.735 3.200 nonbonded pdb=" O4' DG J 125 " pdb=" NH2 ARG L 72 " model vdw 1.914 3.120 nonbonded pdb=" N ARG D 31 " pdb=" C CYS M 76 " model vdw 1.963 3.350 ... (remaining 126606 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 37 through 133) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 19 through 102) } ncs_group { reference = (chain 'C' and resid 11 through 119) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'L' selection = chain 'M' } 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 group one per residue 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: 0.850 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: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.090 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 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 : 0.009 0.079 16942 Z= 0.709 Angle : 1.016 13.611 24129 Z= 0.747 Chirality : 0.062 0.583 2729 Planarity : 0.007 0.066 2052 Dihedral : 26.469 178.206 7105 Min Nonbonded Distance : 1.348 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.98 % Allowed : 9.04 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -5.07 (0.17), residues: 1234 helix: -4.36 (0.10), residues: 555 sheet: -1.47 (0.83), residues: 45 loop : -2.50 (0.21), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 11 TYR 0.022 0.002 TYR K 128 PHE 0.042 0.003 PHE K 223 TRP 0.013 0.001 TRP K 305 HIS 0.006 0.002 HIS K 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00917 / 0.71 (16935) covalent geometry : angle 1.01572 / 0.75 (24129) hydrogen bonds : bond 0.31091 / 20.02 ( 463) hydrogen bonds : angle 11.84672 / 8.09 ( 1175) Misc. bond : bond 0.00489 / 0.22 ( 7) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 272 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 153 MET cc_start: 0.0123 (mpp) cc_final: -0.1386 (mtt) REVERT: F 29 ILE cc_start: 0.9049 (mm) cc_final: 0.8759 (mm) REVERT: F 50 ILE cc_start: 0.9271 (mm) cc_final: 0.8984 (mm) REVERT: G 11 ARG cc_start: 0.7235 (ttt-90) cc_final: 0.6867 (ttt-90) REVERT: G 15 LYS cc_start: 0.8178 (ttpt) cc_final: 0.7445 (mmtt) REVERT: G 84 GLN cc_start: 0.8994 (tp-100) cc_final: 0.8590 (tp40) REVERT: H 111 VAL cc_start: 0.9188 (OUTLIER) cc_final: 0.8892 (t) REVERT: E 68 GLN cc_start: 0.9028 (tt0) cc_final: 0.8127 (tm-30) REVERT: E 79 LYS cc_start: 0.8793 (tptt) cc_final: 0.8366 (tptp) REVERT: A 50 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8142 (mt-10) REVERT: A 73 GLU cc_start: 0.8388 (pp20) cc_final: 0.7928 (pp20) REVERT: D 120 LYS cc_start: 0.8157 (mtpp) cc_final: 0.7795 (mttp) REVERT: C 90 ASP cc_start: 0.8087 (m-30) cc_final: 0.7857 (m-30) REVERT: C 95 LYS cc_start: 0.8998 (mtpp) cc_final: 0.8705 (mttt) REVERT: B 44 LYS cc_start: 0.9460 (tttt) cc_final: 0.9241 (ttmm) REVERT: B 66 ILE cc_start: 0.9442 (mt) cc_final: 0.9180 (mm) REVERT: B 85 ASP cc_start: 0.8719 (m-30) cc_final: 0.8163 (m-30) REVERT: B 92 ARG cc_start: 0.8400 (ptm160) cc_final: 0.7843 (ttp80) REVERT: B 98 TYR cc_start: 0.9065 (m-10) cc_final: 0.8808 (m-80) outliers start: 32 outliers final: 6 residues processed: 291 average time/residue: 0.1581 time to fit residues: 63.5055 Evaluate side-chains 213 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 206 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 21.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 57 ASN K 113 GLN K 117 HIS ** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 252 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN H 84 ASN H 95 GLN E 39 HIS A 68 GLN A 76 GLN A 85 GLN D 84 ASN D 95 GLN C 104 GLN C 112 GLN L 60 ASN M 60 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.150387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.111296 restraints weight = 38730.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.110833 restraints weight = 33044.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.111032 restraints weight = 31290.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.110702 restraints weight = 22801.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.111092 restraints weight = 20797.354| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3370 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 10 (16 function evaluations) r_final: 0.3367 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 16942 Z= 0.201 Angle : 0.801 8.523 24129 Z= 0.454 Chirality : 0.054 0.360 2729 Planarity : 0.006 0.073 2052 Dihedral : 29.999 178.120 4582 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.09 % Allowed : 4.38 % Favored : 95.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.94 (0.19), residues: 1234 helix: -3.04 (0.15), residues: 578 sheet: -0.95 (0.93), residues: 45 loop : -2.23 (0.22), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 53 TYR 0.021 0.002 TYR H 40 PHE 0.020 0.002 PHE K 223 TRP 0.008 0.001 TRP K 305 HIS 0.004 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.20 (16935) covalent geometry : angle 0.80089 / 0.45 (24129) hydrogen bonds : bond 0.10772 / 7.48 ( 463) hydrogen bonds : angle 5.70443 / 3.66 ( 1175) Misc. bond : bond 0.00866 / 0.35 ( 7) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 255 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 153 MET cc_start: 0.0802 (mpp) cc_final: -0.0763 (mtt) REVERT: F 29 ILE cc_start: 0.9033 (mm) cc_final: 0.8739 (mm) REVERT: F 30 THR cc_start: 0.9208 (t) cc_final: 0.8893 (m) REVERT: F 50 ILE cc_start: 0.9320 (mm) cc_final: 0.8909 (mm) REVERT: F 74 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8189 (tm-30) REVERT: G 84 GLN cc_start: 0.8887 (tp-100) cc_final: 0.8317 (tp-100) REVERT: H 71 GLU cc_start: 0.8471 (tp30) cc_final: 0.8163 (tp30) REVERT: E 79 LYS cc_start: 0.8732 (tptt) cc_final: 0.8429 (tptp) REVERT: E 113 HIS cc_start: 0.8713 (t-90) cc_final: 0.8512 (t-90) REVERT: E 124 ILE cc_start: 0.9611 (mt) cc_final: 0.9392 (mm) REVERT: A 73 GLU cc_start: 0.8609 (pp20) cc_final: 0.8366 (pp20) REVERT: D 118 VAL cc_start: 0.9409 (t) cc_final: 0.9096 (p) REVERT: B 66 ILE cc_start: 0.9468 (mt) cc_final: 0.9218 (mm) REVERT: B 73 THR cc_start: 0.9532 (p) cc_final: 0.9311 (t) REVERT: B 92 ARG cc_start: 0.8635 (ptm160) cc_final: 0.8318 (ttp80) REVERT: B 98 TYR cc_start: 0.9172 (m-10) cc_final: 0.8940 (m-80) outliers start: 1 outliers final: 1 residues processed: 256 average time/residue: 0.1422 time to fit residues: 52.0302 Evaluate side-chains 210 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 209 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 91 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 114 optimal weight: 30.0000 chunk 94 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 108 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 109 HIS ** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN H 95 GLN A 68 GLN A 76 GLN A 108 ASN C 38 ASN C 112 GLN M 41 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.149191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.112326 restraints weight = 39607.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.109687 restraints weight = 55784.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.111050 restraints weight = 55295.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.110428 restraints weight = 36248.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.111074 restraints weight = 32875.305| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3366 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3366 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16942 Z= 0.241 Angle : 0.761 8.868 24129 Z= 0.430 Chirality : 0.051 0.355 2729 Planarity : 0.006 0.070 2052 Dihedral : 30.107 177.924 4582 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.07 (0.21), residues: 1234 helix: -2.12 (0.19), residues: 582 sheet: 0.59 (0.74), residues: 46 loop : -2.12 (0.23), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 72 TYR 0.018 0.002 TYR D 40 PHE 0.030 0.002 PHE K 223 TRP 0.010 0.001 TRP K 305 HIS 0.005 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.24 (16935) covalent geometry : angle 0.76096 / 0.43 (24129) hydrogen bonds : bond 0.09266 / 6.35 ( 463) hydrogen bonds : angle 5.42179 / 3.53 ( 1175) Misc. bond : bond 0.00932 / 0.52 ( 7) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 71 MET cc_start: 0.1335 (tpt) cc_final: 0.1087 (tpt) REVERT: K 153 MET cc_start: 0.1011 (mpp) cc_final: -0.0460 (mtt) REVERT: K 220 ARG cc_start: 0.5017 (mtt90) cc_final: 0.4446 (ttm110) REVERT: F 29 ILE cc_start: 0.9016 (mm) cc_final: 0.8745 (mm) REVERT: F 74 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8220 (tm-30) REVERT: G 84 GLN cc_start: 0.8833 (tp-100) cc_final: 0.8338 (tp-100) REVERT: H 40 TYR cc_start: 0.8764 (m-80) cc_final: 0.8555 (m-10) REVERT: H 71 GLU cc_start: 0.8532 (tp30) cc_final: 0.8208 (tp30) REVERT: H 96 THR cc_start: 0.9704 (m) cc_final: 0.9487 (t) REVERT: E 79 LYS cc_start: 0.8768 (tptt) cc_final: 0.7983 (tppt) REVERT: E 93 GLN cc_start: 0.8993 (tm-30) cc_final: 0.8435 (tm-30) REVERT: E 120 MET cc_start: 0.8223 (mtt) cc_final: 0.7951 (mtt) REVERT: D 88 THR cc_start: 0.9206 (p) cc_final: 0.9005 (p) REVERT: D 95 GLN cc_start: 0.9033 (tm-30) cc_final: 0.8488 (tm-30) REVERT: D 96 THR cc_start: 0.9534 (m) cc_final: 0.9333 (m) REVERT: D 118 VAL cc_start: 0.9355 (t) cc_final: 0.9039 (p) REVERT: B 66 ILE cc_start: 0.9470 (mt) cc_final: 0.9188 (mm) REVERT: B 92 ARG cc_start: 0.8712 (ptm160) cc_final: 0.8255 (ttp80) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.1319 time to fit residues: 46.0261 Evaluate side-chains 209 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 141 optimal weight: 50.0000 chunk 69 optimal weight: 0.0020 chunk 68 optimal weight: 9.9990 chunk 24 optimal weight: 50.0000 chunk 12 optimal weight: 10.0000 chunk 138 optimal weight: 40.0000 chunk 102 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 chunk 95 optimal weight: 0.7980 chunk 22 optimal weight: 9.9990 overall best weight: 4.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN H 63 ASN H 95 GLN A 68 GLN A 76 GLN C 112 GLN L 41 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.148013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.109349 restraints weight = 39604.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.107284 restraints weight = 37604.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.107913 restraints weight = 39514.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.107703 restraints weight = 27503.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.108395 restraints weight = 24389.741| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3321 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3321 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16942 Z= 0.233 Angle : 0.743 10.651 24129 Z= 0.420 Chirality : 0.050 0.324 2729 Planarity : 0.005 0.056 2052 Dihedral : 30.173 170.814 4582 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.71 (0.22), residues: 1234 helix: -1.66 (0.20), residues: 580 sheet: -0.61 (0.62), residues: 58 loop : -2.00 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 53 TYR 0.032 0.002 TYR B 98 PHE 0.021 0.002 PHE E 84 TRP 0.006 0.001 TRP K 43 HIS 0.005 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.23 (16935) covalent geometry : angle 0.74265 / 0.42 (24129) hydrogen bonds : bond 0.08294 / 5.81 ( 463) hydrogen bonds : angle 5.09170 / 3.34 ( 1175) Misc. bond : bond 0.00410 / 0.24 ( 7) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 71 MET cc_start: 0.1303 (tpt) cc_final: 0.1064 (tpt) REVERT: K 153 MET cc_start: 0.0683 (mpp) cc_final: -0.0617 (mtt) REVERT: F 74 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8336 (tm-30) REVERT: G 25 PHE cc_start: 0.8742 (m-10) cc_final: 0.8521 (m-10) REVERT: G 84 GLN cc_start: 0.8928 (tp-100) cc_final: 0.8414 (tp-100) REVERT: H 71 GLU cc_start: 0.8417 (tp30) cc_final: 0.8014 (tp30) REVERT: E 93 GLN cc_start: 0.8909 (tm-30) cc_final: 0.8478 (tm-30) REVERT: A 93 GLN cc_start: 0.7782 (tm-30) cc_final: 0.7460 (tm-30) REVERT: D 62 MET cc_start: 0.9433 (mmm) cc_final: 0.9186 (mmp) REVERT: D 118 VAL cc_start: 0.9413 (t) cc_final: 0.9128 (p) REVERT: C 72 ASP cc_start: 0.8852 (m-30) cc_final: 0.8621 (m-30) REVERT: C 74 LYS cc_start: 0.9195 (mmtt) cc_final: 0.8108 (tppt) REVERT: B 66 ILE cc_start: 0.9532 (mt) cc_final: 0.9207 (mm) REVERT: B 92 ARG cc_start: 0.8805 (ptm160) cc_final: 0.8291 (ttp80) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.1328 time to fit residues: 46.3274 Evaluate side-chains 197 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 43 optimal weight: 0.2980 chunk 35 optimal weight: 1.9990 chunk 3 optimal weight: 40.0000 chunk 54 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 28 optimal weight: 20.0000 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN G 112 GLN H 95 GLN A 68 GLN C 112 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.151305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.113613 restraints weight = 39471.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.111842 restraints weight = 39423.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.112438 restraints weight = 42771.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.112357 restraints weight = 29412.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.112995 restraints weight = 26106.310| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3403 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3403 r_free = 0.3403 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3403 r_free = 0.3403 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3403 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16942 Z= 0.152 Angle : 0.648 9.636 24129 Z= 0.376 Chirality : 0.046 0.321 2729 Planarity : 0.005 0.050 2052 Dihedral : 30.000 173.302 4582 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.38 (0.23), residues: 1234 helix: -1.42 (0.20), residues: 583 sheet: -0.58 (0.61), residues: 58 loop : -1.78 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 92 TYR 0.032 0.002 TYR B 98 PHE 0.017 0.002 PHE G 25 TRP 0.008 0.001 TRP K 89 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.15 (16935) covalent geometry : angle 0.64759 / 0.38 (24129) hydrogen bonds : bond 0.07359 / 5.13 ( 463) hydrogen bonds : angle 4.42573 / 2.87 ( 1175) Misc. bond : bond 0.00531 / 0.29 ( 7) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 153 MET cc_start: 0.0818 (mpp) cc_final: -0.0574 (mtt) REVERT: F 29 ILE cc_start: 0.9016 (mm) cc_final: 0.8732 (mm) REVERT: F 30 THR cc_start: 0.9301 (t) cc_final: 0.8865 (m) REVERT: F 50 ILE cc_start: 0.9285 (mm) cc_final: 0.8888 (mm) REVERT: G 11 ARG cc_start: 0.6976 (ttt-90) cc_final: 0.6650 (ttt-90) REVERT: G 84 GLN cc_start: 0.8820 (tp40) cc_final: 0.8404 (tp-100) REVERT: H 67 ASN cc_start: 0.8971 (m-40) cc_final: 0.8738 (t0) REVERT: H 71 GLU cc_start: 0.8417 (tp30) cc_final: 0.8053 (tp30) REVERT: E 82 LEU cc_start: 0.9243 (mt) cc_final: 0.8923 (mp) REVERT: E 93 GLN cc_start: 0.8942 (tm-30) cc_final: 0.8449 (tm-30) REVERT: E 126 LEU cc_start: 0.9167 (tt) cc_final: 0.7535 (mp) REVERT: A 50 GLU cc_start: 0.8750 (tp30) cc_final: 0.8202 (mm-30) REVERT: A 77 ASP cc_start: 0.8607 (p0) cc_final: 0.8186 (p0) REVERT: A 120 MET cc_start: 0.8850 (mmm) cc_final: 0.8565 (mmm) REVERT: D 118 VAL cc_start: 0.9247 (t) cc_final: 0.8982 (p) REVERT: C 33 LEU cc_start: 0.9155 (mp) cc_final: 0.8853 (tt) REVERT: C 74 LYS cc_start: 0.9039 (mmtt) cc_final: 0.8127 (tppt) REVERT: C 90 ASP cc_start: 0.7884 (m-30) cc_final: 0.7683 (m-30) REVERT: B 44 LYS cc_start: 0.9492 (tttt) cc_final: 0.9252 (tttp) REVERT: B 92 ARG cc_start: 0.8576 (ptm160) cc_final: 0.8135 (ttp80) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.1452 time to fit residues: 51.2653 Evaluate side-chains 209 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 19 optimal weight: 20.0000 chunk 31 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 142 optimal weight: 50.0000 chunk 15 optimal weight: 9.9990 chunk 143 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 111 optimal weight: 30.0000 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN A 76 GLN C 84 GLN C 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.151104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.115534 restraints weight = 40141.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.112959 restraints weight = 67434.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.114134 restraints weight = 65554.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.113406 restraints weight = 43813.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.113824 restraints weight = 42012.344| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3408 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3408 r_free = 0.3408 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3408 r_free = 0.3408 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3408 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16942 Z= 0.193 Angle : 0.665 9.975 24129 Z= 0.382 Chirality : 0.047 0.276 2729 Planarity : 0.004 0.050 2052 Dihedral : 30.002 175.516 4582 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.23), residues: 1234 helix: -1.17 (0.21), residues: 580 sheet: -0.55 (0.61), residues: 58 loop : -1.77 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 92 TYR 0.029 0.002 TYR B 98 PHE 0.015 0.002 PHE F 100 TRP 0.005 0.001 TRP K 208 HIS 0.004 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.19 (16935) covalent geometry : angle 0.66470 / 0.38 (24129) hydrogen bonds : bond 0.07197 / 5.01 ( 463) hydrogen bonds : angle 4.56550 / 2.98 ( 1175) Misc. bond : bond 0.00392 / 0.20 ( 7) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 153 MET cc_start: 0.0967 (mpp) cc_final: -0.0464 (mtt) REVERT: F 30 THR cc_start: 0.9307 (t) cc_final: 0.8887 (m) REVERT: G 84 GLN cc_start: 0.8813 (tp40) cc_final: 0.8432 (tp-100) REVERT: H 71 GLU cc_start: 0.8331 (tp30) cc_final: 0.8042 (tp30) REVERT: E 93 GLN cc_start: 0.8919 (tm-30) cc_final: 0.8638 (tm-30) REVERT: E 120 MET cc_start: 0.8335 (mtt) cc_final: 0.8069 (mtt) REVERT: E 126 LEU cc_start: 0.9096 (tt) cc_final: 0.7464 (mp) REVERT: A 50 GLU cc_start: 0.8662 (tp30) cc_final: 0.8433 (mm-30) REVERT: A 77 ASP cc_start: 0.8650 (p0) cc_final: 0.8207 (p0) REVERT: A 106 ASP cc_start: 0.7931 (m-30) cc_final: 0.7713 (m-30) REVERT: D 118 VAL cc_start: 0.9293 (t) cc_final: 0.9034 (p) REVERT: C 74 LYS cc_start: 0.9034 (mmtt) cc_final: 0.8112 (tppt) REVERT: B 66 ILE cc_start: 0.9518 (mt) cc_final: 0.9294 (mm) REVERT: B 68 ASP cc_start: 0.7763 (m-30) cc_final: 0.7452 (m-30) REVERT: B 92 ARG cc_start: 0.8652 (ptm160) cc_final: 0.8130 (ttp80) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.1374 time to fit residues: 46.2951 Evaluate side-chains 198 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 106 optimal weight: 30.0000 chunk 35 optimal weight: 0.2980 chunk 131 optimal weight: 30.0000 chunk 120 optimal weight: 40.0000 chunk 108 optimal weight: 20.0000 chunk 109 optimal weight: 30.0000 chunk 141 optimal weight: 50.0000 chunk 27 optimal weight: 8.9990 chunk 117 optimal weight: 20.0000 chunk 72 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 overall best weight: 7.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 172 GLN ** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS H 63 ASN A 68 GLN L 31 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.145454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.105411 restraints weight = 39807.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.103902 restraints weight = 33526.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.104551 restraints weight = 29726.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.103871 restraints weight = 23315.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.104065 restraints weight = 21453.619| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3255 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3255 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.076 16942 Z= 0.377 Angle : 0.877 10.246 24129 Z= 0.478 Chirality : 0.055 0.296 2729 Planarity : 0.006 0.065 2052 Dihedral : 30.141 179.428 4582 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.23), residues: 1234 helix: -1.37 (0.21), residues: 579 sheet: -0.40 (0.61), residues: 58 loop : -1.85 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 88 TYR 0.037 0.003 TYR B 98 PHE 0.026 0.003 PHE F 100 TRP 0.008 0.001 TRP K 205 HIS 0.008 0.002 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00810 / 0.38 (16935) covalent geometry : angle 0.87678 / 0.48 (24129) hydrogen bonds : bond 0.08259 / 5.68 ( 463) hydrogen bonds : angle 5.43019 / 3.60 ( 1175) Misc. bond : bond 0.00694 / 0.33 ( 7) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.481 Fit side-chains revert: symmetry clash REVERT: K 71 MET cc_start: 0.1375 (tpt) cc_final: 0.1096 (tpt) REVERT: K 153 MET cc_start: 0.0792 (mpp) cc_final: -0.0509 (mtt) REVERT: G 84 GLN cc_start: 0.8893 (tp40) cc_final: 0.8449 (tp-100) REVERT: H 71 GLU cc_start: 0.8620 (tp30) cc_final: 0.8255 (tp30) REVERT: E 93 GLN cc_start: 0.9095 (tm-30) cc_final: 0.8877 (tm-30) REVERT: A 50 GLU cc_start: 0.8804 (tp30) cc_final: 0.8517 (mm-30) REVERT: A 77 ASP cc_start: 0.8666 (p0) cc_final: 0.8436 (p0) REVERT: D 118 VAL cc_start: 0.9474 (t) cc_final: 0.9271 (p) REVERT: C 72 ASP cc_start: 0.8913 (m-30) cc_final: 0.8644 (m-30) REVERT: C 74 LYS cc_start: 0.9170 (mmtt) cc_final: 0.8297 (tppt) REVERT: B 84 MET cc_start: 0.8810 (mmm) cc_final: 0.7938 (mmt) REVERT: B 92 ARG cc_start: 0.9009 (ptm160) cc_final: 0.8454 (ttp80) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.1453 time to fit residues: 45.5472 Evaluate side-chains 181 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 54 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 15 optimal weight: 0.0070 chunk 141 optimal weight: 40.0000 chunk 65 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 90 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 142 optimal weight: 20.0000 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 172 GLN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN A 68 GLN A 76 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.152994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.117465 restraints weight = 40074.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.114494 restraints weight = 67563.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.115483 restraints weight = 60564.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.115425 restraints weight = 37599.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.115730 restraints weight = 36685.847| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3433 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3433 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16942 Z= 0.152 Angle : 0.664 9.240 24129 Z= 0.384 Chirality : 0.046 0.286 2729 Planarity : 0.005 0.048 2052 Dihedral : 29.918 179.945 4582 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.94 (0.23), residues: 1234 helix: -0.98 (0.22), residues: 581 sheet: -0.68 (0.62), residues: 60 loop : -1.60 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 53 TYR 0.026 0.002 TYR B 98 PHE 0.018 0.002 PHE F 100 TRP 0.006 0.001 TRP K 89 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.15 (16935) covalent geometry : angle 0.66399 / 0.38 (24129) hydrogen bonds : bond 0.07116 / 4.98 ( 463) hydrogen bonds : angle 4.35191 / 2.81 ( 1175) Misc. bond : bond 0.00477 / 0.27 ( 7) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 71 MET cc_start: 0.1391 (tpt) cc_final: 0.1125 (tpt) REVERT: K 153 MET cc_start: 0.0953 (mpp) cc_final: -0.0498 (mtt) REVERT: K 206 MET cc_start: -0.2925 (ttt) cc_final: -0.3525 (tpt) REVERT: F 29 ILE cc_start: 0.9020 (mm) cc_final: 0.8784 (mm) REVERT: G 84 GLN cc_start: 0.8958 (tp40) cc_final: 0.8608 (tp-100) REVERT: G 100 VAL cc_start: 0.9179 (t) cc_final: 0.8902 (t) REVERT: G 104 GLN cc_start: 0.9060 (mp10) cc_final: 0.8787 (mp10) REVERT: H 71 GLU cc_start: 0.8237 (tp30) cc_final: 0.7962 (tp30) REVERT: H 79 ARG cc_start: 0.7622 (ttm-80) cc_final: 0.7336 (ttm110) REVERT: E 126 LEU cc_start: 0.9001 (tt) cc_final: 0.7483 (mp) REVERT: A 60 LEU cc_start: 0.8842 (mt) cc_final: 0.8632 (mt) REVERT: A 76 GLN cc_start: 0.8099 (tp40) cc_final: 0.7846 (tp-100) REVERT: A 77 ASP cc_start: 0.8461 (p0) cc_final: 0.8185 (p0) REVERT: A 93 GLN cc_start: 0.7607 (tm-30) cc_final: 0.7367 (tm-30) REVERT: A 120 MET cc_start: 0.8782 (mmm) cc_final: 0.8491 (mmm) REVERT: D 111 VAL cc_start: 0.9557 (m) cc_final: 0.9228 (p) REVERT: D 118 VAL cc_start: 0.9341 (t) cc_final: 0.9110 (p) REVERT: C 74 LYS cc_start: 0.8968 (mmtt) cc_final: 0.8056 (tppt) REVERT: C 84 GLN cc_start: 0.8891 (tp40) cc_final: 0.8688 (tp40) REVERT: B 52 GLU cc_start: 0.7782 (pp20) cc_final: 0.7565 (pp20) REVERT: B 92 ARG cc_start: 0.8671 (ptm160) cc_final: 0.8125 (ttp80) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.1318 time to fit residues: 47.2534 Evaluate side-chains 201 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 102 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 132 optimal weight: 40.0000 chunk 112 optimal weight: 20.0000 chunk 119 optimal weight: 40.0000 chunk 52 optimal weight: 0.3980 chunk 144 optimal weight: 40.0000 chunk 80 optimal weight: 0.8980 chunk 9 optimal weight: 40.0000 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.152412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.117476 restraints weight = 40336.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.115259 restraints weight = 68540.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.116305 restraints weight = 65241.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.115685 restraints weight = 43859.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.116099 restraints weight = 41029.185| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3434 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3434 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16942 Z= 0.159 Angle : 0.643 9.643 24129 Z= 0.371 Chirality : 0.045 0.291 2729 Planarity : 0.004 0.049 2052 Dihedral : 29.907 179.273 4582 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.24), residues: 1234 helix: -0.74 (0.22), residues: 579 sheet: -0.44 (0.63), residues: 64 loop : -1.58 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 99 TYR 0.020 0.001 TYR B 98 PHE 0.021 0.002 PHE K 245 TRP 0.006 0.001 TRP K 208 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.16 (16935) covalent geometry : angle 0.64296 / 0.37 (24129) hydrogen bonds : bond 0.06674 / 4.65 ( 463) hydrogen bonds : angle 4.33035 / 2.81 ( 1175) Misc. bond : bond 0.00503 / 0.18 ( 7) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 153 MET cc_start: 0.0992 (mpp) cc_final: -0.0425 (mtt) REVERT: F 29 ILE cc_start: 0.9010 (mm) cc_final: 0.8738 (mm) REVERT: G 25 PHE cc_start: 0.8744 (m-10) cc_final: 0.8425 (m-10) REVERT: G 84 GLN cc_start: 0.8811 (tp40) cc_final: 0.8436 (tp-100) REVERT: H 71 GLU cc_start: 0.8234 (tp30) cc_final: 0.7936 (tp30) REVERT: E 126 LEU cc_start: 0.8954 (tt) cc_final: 0.7338 (mp) REVERT: E 129 ARG cc_start: 0.7736 (tpt170) cc_final: 0.7399 (tpt170) REVERT: A 45 THR cc_start: 0.9047 (m) cc_final: 0.8736 (t) REVERT: A 77 ASP cc_start: 0.8565 (p0) cc_final: 0.8207 (p0) REVERT: D 118 VAL cc_start: 0.9308 (t) cc_final: 0.9093 (p) REVERT: C 74 LYS cc_start: 0.8865 (mmtt) cc_final: 0.8127 (tppt) REVERT: B 52 GLU cc_start: 0.7696 (pp20) cc_final: 0.7423 (pp20) REVERT: B 92 ARG cc_start: 0.8743 (ptm160) cc_final: 0.8201 (ttp80) REVERT: B 98 TYR cc_start: 0.8865 (m-80) cc_final: 0.8657 (m-80) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.1340 time to fit residues: 45.3203 Evaluate side-chains 192 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 128 optimal weight: 30.0000 chunk 82 optimal weight: 0.1980 chunk 145 optimal weight: 50.0000 chunk 78 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 28 optimal weight: 0.0470 chunk 123 optimal weight: 30.0000 chunk 52 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 chunk 46 optimal weight: 0.0980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.155181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.119412 restraints weight = 39751.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.117009 restraints weight = 54803.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.118173 restraints weight = 50823.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.117291 restraints weight = 35169.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.117617 restraints weight = 34157.196| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3458 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3458 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16942 Z= 0.137 Angle : 0.629 9.167 24129 Z= 0.362 Chirality : 0.044 0.339 2729 Planarity : 0.004 0.048 2052 Dihedral : 29.750 179.244 4582 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.24), residues: 1234 helix: -0.60 (0.22), residues: 581 sheet: -0.73 (0.61), residues: 81 loop : -1.45 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 99 TYR 0.011 0.001 TYR D 40 PHE 0.021 0.002 PHE K 245 TRP 0.006 0.001 TRP K 89 HIS 0.005 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.14 (16935) covalent geometry : angle 0.62932 / 0.36 (24129) hydrogen bonds : bond 0.06433 / 4.51 ( 463) hydrogen bonds : angle 3.97061 / 2.54 ( 1175) Misc. bond : bond 0.00326 / 0.15 ( 7) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 153 MET cc_start: 0.0942 (mpp) cc_final: -0.0523 (mtt) REVERT: F 29 ILE cc_start: 0.9068 (mm) cc_final: 0.8764 (mm) REVERT: F 100 PHE cc_start: 0.8502 (m-80) cc_final: 0.8213 (m-10) REVERT: G 23 LEU cc_start: 0.8307 (mm) cc_final: 0.7803 (mt) REVERT: G 84 GLN cc_start: 0.8752 (tp40) cc_final: 0.8404 (tp-100) REVERT: H 46 LYS cc_start: 0.9039 (mmpt) cc_final: 0.8774 (tppt) REVERT: H 71 GLU cc_start: 0.8064 (tp30) cc_final: 0.7773 (tp30) REVERT: E 126 LEU cc_start: 0.8754 (tt) cc_final: 0.7318 (mp) REVERT: E 129 ARG cc_start: 0.7607 (tpt170) cc_final: 0.7273 (tpt170) REVERT: D 118 VAL cc_start: 0.9231 (t) cc_final: 0.8967 (p) REVERT: C 74 LYS cc_start: 0.8792 (mmtt) cc_final: 0.7986 (tppt) REVERT: C 78 ILE cc_start: 0.8576 (mt) cc_final: 0.8292 (mm) REVERT: B 52 GLU cc_start: 0.7565 (pp20) cc_final: 0.7247 (pp20) REVERT: B 92 ARG cc_start: 0.8479 (ptm160) cc_final: 0.7866 (ttp80) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.1251 time to fit residues: 45.6183 Evaluate side-chains 200 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 70 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 82 optimal weight: 7.9990 chunk 57 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 146 optimal weight: 30.0000 chunk 141 optimal weight: 50.0000 chunk 65 optimal weight: 0.9990 chunk 120 optimal weight: 40.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN H 67 ASN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 76 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.154927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.119414 restraints weight = 40038.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.117365 restraints weight = 60554.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.118358 restraints weight = 55183.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.117585 restraints weight = 38326.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.117906 restraints weight = 37021.557| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3459 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3459 r_free = 0.3459 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3459 r_free = 0.3459 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3459 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16942 Z= 0.133 Angle : 0.604 9.630 24129 Z= 0.349 Chirality : 0.044 0.407 2729 Planarity : 0.004 0.049 2052 Dihedral : 29.755 178.844 4582 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.09 % Allowed : 0.19 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.24), residues: 1234 helix: -0.48 (0.22), residues: 587 sheet: -0.69 (0.61), residues: 81 loop : -1.40 (0.27), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 99 TYR 0.018 0.001 TYR B 98 PHE 0.021 0.002 PHE K 245 TRP 0.012 0.001 TRP K 205 HIS 0.007 0.001 HIS K 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.13 (16935) covalent geometry : angle 0.60407 / 0.35 (24129) hydrogen bonds : bond 0.06072 / 4.23 ( 463) hydrogen bonds : angle 3.99296 / 2.57 ( 1175) Misc. bond : bond 0.00284 / 0.13 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2283.08 seconds wall clock time: 40 minutes 14.45 seconds (2414.45 seconds total)