Starting phenix.real_space_refine on Thu Sep 18 21:49:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bwd_30232/09_2025/7bwd_30232.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bwd_30232/09_2025/7bwd_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7bwd_30232/09_2025/7bwd_30232.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bwd_30232/09_2025/7bwd_30232.map" model { file = "/net/cci-nas-00/data/ceres_data/7bwd_30232/09_2025/7bwd_30232.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bwd_30232/09_2025/7bwd_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-2.0-5805/lib/python3.9/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: 3.79, per 1000 atoms: 0.24 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: 1.43 Conformation dependent library (CDL) restraints added in 572.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 2.21 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: 2.97 Time building geometry restraints manager: 1.91 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=" 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 bond pdb=" CA TYR K 136 " pdb=" CB TYR K 136 " ideal model delta sigma weight residual 1.526 1.582 -0.056 1.53e-02 4.27e+03 1.33e+01 bond pdb=" C2 SAH K 501 " pdb=" N3 SAH K 501 " ideal model delta sigma weight residual 1.322 1.374 -0.052 2.00e-02 2.50e+03 6.76e+00 bond pdb=" C6 SAH K 501 " pdb=" N1 SAH K 501 " ideal model delta sigma weight residual 1.338 1.383 -0.045 2.00e-02 2.50e+03 5.15e+00 bond pdb=" C3' DC J 75 " pdb=" O3' DC J 75 " ideal model delta sigma weight residual 1.422 1.486 -0.064 3.00e-02 1.11e+03 4.56e+00 ... (remaining 16930 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 23715 2.72 - 5.44: 360 5.44 - 8.17: 43 8.17 - 10.89: 8 10.89 - 13.61: 3 Bond angle restraints: 24129 Sorted by residual: 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=" C THR B 30 " pdb=" N LYS B 31 " pdb=" CA LYS B 31 " ideal model delta sigma weight residual 120.09 125.62 -5.53 1.25e+00 6.40e-01 1.96e+01 angle pdb=" C PRO K 274 " pdb=" N LEU K 275 " pdb=" CA LEU K 275 " ideal model delta sigma weight residual 121.54 129.45 -7.91 1.91e+00 2.74e-01 1.72e+01 angle pdb=" CG SAH K 501 " pdb=" SD SAH K 501 " pdb=" C5' SAH K 501 " ideal model delta sigma weight residual 101.77 90.01 11.76 3.00e+00 1.11e-01 1.54e+01 angle pdb=" C LEU F 22 " pdb=" N ARG F 23 " pdb=" CA ARG F 23 " ideal model delta sigma weight residual 120.38 126.10 -5.72 1.46e+00 4.69e-01 1.53e+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: 2633 0.117 - 0.233: 92 0.233 - 0.350: 2 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: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 16.880 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 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= 0.387 Angle : 0.927 13.611 24129 Z= 0.521 Chirality : 0.054 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 aren 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 covalent geometry : bond 0.00854 (16935) covalent geometry : angle 0.92729 (24129) hydrogen bonds : bond 0.31091 ( 463) hydrogen bonds : angle 11.84672 ( 1175) Misc. bond : bond 0.00489 ( 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 : 0.337 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: -0.1388 (mtt) REVERT: F 29 ILE cc_start: 0.9049 (mm) cc_final: 0.8763 (mm) REVERT: F 50 ILE cc_start: 0.9271 (mm) cc_final: 0.8987 (mm) REVERT: G 15 LYS cc_start: 0.8178 (ttpt) cc_final: 0.7441 (mmtt) REVERT: G 84 GLN cc_start: 0.8994 (tp-100) cc_final: 0.8583 (tp40) REVERT: H 111 VAL cc_start: 0.9189 (OUTLIER) cc_final: 0.8890 (t) REVERT: E 68 GLN cc_start: 0.9028 (tt0) cc_final: 0.8128 (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: 0.8141 (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: 0.7793 (mttp) REVERT: C 90 ASP cc_start: 0.8087 (m-30) cc_final: 0.7855 (m-30) REVERT: C 95 LYS cc_start: 0.8998 (mtpp) cc_final: 0.8706 (mttt) REVERT: B 35 ARG cc_start: 0.7818 (ttm-80) cc_final: 0.7494 (ttm-80) REVERT: B 44 LYS cc_start: 0.9460 (tttt) cc_final: 0.9203 (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: 0.8165 (m-30) REVERT: B 92 ARG cc_start: 0.8400 (ptm160) cc_final: 0.7845 (ttp80) REVERT: B 98 TYR cc_start: 0.9064 (m-10) cc_final: 0.8806 (m-80) outliers start: 32 outliers final: 6 residues processed: 291 average time/residue: 0.1801 time to fit residues: 71.1358 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 : 0.495 ------------------------------------------------------------------------------- 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: 3.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 A 68 GLN A 76 GLN A 85 GLN D 84 ASN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN C 104 GLN C 112 GLN L 60 ASN M 60 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.150644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.113920 restraints weight = 39401.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.111876 restraints weight = 48123.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.112538 restraints weight = 54961.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.112583 restraints weight = 33620.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.113003 restraints weight = 30104.160| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3397 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3394 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 16942 Z= 0.225 Angle : 0.703 9.320 24129 Z= 0.405 Chirality : 0.043 0.278 2729 Planarity : 0.006 0.062 2052 Dihedral : 29.864 178.628 4582 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.09 % Allowed : 4.85 % Favored : 95.06 % 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 aren not related in a simple way. whole: -3.80 (0.19), residues: 1234 helix: -2.92 (0.16), residues: 582 sheet: 0.42 (0.73), residues: 46 loop : -2.28 (0.22), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 72 TYR 0.017 0.001 TYR H 40 PHE 0.026 0.002 PHE K 245 TRP 0.009 0.001 TRP K 305 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00492 (16935) covalent geometry : angle 0.70285 (24129) hydrogen bonds : bond 0.09272 ( 463) hydrogen bonds : angle 5.44920 ( 1175) Misc. bond : bond 0.00507 ( 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 258 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 257 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 153 MET cc_start: 0.0953 (mpp) cc_final: -0.0505 (mtt) REVERT: F 29 ILE cc_start: 0.8956 (mm) cc_final: 0.8712 (mm) REVERT: F 30 THR cc_start: 0.9300 (t) cc_final: 0.8906 (m) REVERT: F 50 ILE cc_start: 0.9336 (mm) cc_final: 0.8870 (mm) REVERT: F 74 GLU cc_start: 0.8368 (tm-30) cc_final: 0.8165 (tm-30) REVERT: G 11 ARG cc_start: 0.7192 (ttt-90) cc_final: 0.6992 (ttt-90) REVERT: G 84 GLN cc_start: 0.8846 (tp-100) cc_final: 0.8305 (tp-100) REVERT: H 71 GLU cc_start: 0.8344 (tp30) cc_final: 0.8109 (tp30) REVERT: H 96 THR cc_start: 0.9715 (m) cc_final: 0.9455 (t) REVERT: E 79 LYS cc_start: 0.8723 (tptt) cc_final: 0.8103 (tppt) REVERT: E 124 ILE cc_start: 0.9571 (mt) cc_final: 0.9355 (mm) REVERT: D 88 THR cc_start: 0.8994 (p) cc_final: 0.8770 (p) REVERT: D 95 GLN cc_start: 0.8743 (tm-30) cc_final: 0.8431 (tm-30) REVERT: D 118 VAL cc_start: 0.9311 (t) cc_final: 0.9031 (p) REVERT: B 66 ILE cc_start: 0.9385 (mt) cc_final: 0.9132 (mm) REVERT: B 92 ARG cc_start: 0.8588 (ptm160) cc_final: 0.8352 (ttp80) outliers start: 1 outliers final: 1 residues processed: 258 average time/residue: 0.1586 time to fit residues: 57.9357 Evaluate side-chains 213 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 212 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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: 0.6980 chunk 63 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 16 optimal weight: 20.0000 chunk 114 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 95 optimal weight: 0.0570 chunk 108 optimal weight: 8.9990 overall best weight: 1.9504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 109 HIS ** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN A 68 GLN A 76 GLN A 108 ASN D 49 HIS 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 = 0.3997 r_free = 0.3997 target = 0.151071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.111766 restraints weight = 39451.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.110396 restraints weight = 34869.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.110952 restraints weight = 34744.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.110642 restraints weight = 24660.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.111290 restraints weight = 22288.654| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16942 Z= 0.184 Angle : 0.632 10.746 24129 Z= 0.364 Chirality : 0.040 0.257 2729 Planarity : 0.005 0.049 2052 Dihedral : 29.835 176.605 4582 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.09 % Allowed : 3.63 % Favored : 96.27 % 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 aren not related in a simple way. whole: -2.96 (0.22), residues: 1234 helix: -2.02 (0.19), residues: 582 sheet: -1.11 (0.56), residues: 88 loop : -1.91 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 49 TYR 0.021 0.001 TYR H 40 PHE 0.034 0.002 PHE K 245 TRP 0.006 0.001 TRP K 89 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00402 (16935) covalent geometry : angle 0.63235 (24129) hydrogen bonds : bond 0.06874 ( 463) hydrogen bonds : angle 4.69753 ( 1175) Misc. bond : bond 0.00441 ( 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 261 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 260 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 153 MET cc_start: 0.0545 (mpp) cc_final: -0.0735 (mtt) REVERT: F 29 ILE cc_start: 0.9117 (mm) cc_final: 0.8765 (mm) REVERT: F 30 THR cc_start: 0.9290 (t) cc_final: 0.8822 (m) REVERT: F 50 ILE cc_start: 0.9336 (mm) cc_final: 0.8881 (mm) REVERT: F 52 GLU cc_start: 0.8019 (tp30) cc_final: 0.7761 (tp30) REVERT: G 84 GLN cc_start: 0.8905 (tp-100) cc_final: 0.8382 (tp-100) REVERT: H 67 ASN cc_start: 0.8941 (m-40) cc_final: 0.8350 (t0) REVERT: H 71 GLU cc_start: 0.8385 (tp30) cc_final: 0.7975 (tp30) REVERT: H 96 THR cc_start: 0.9753 (m) cc_final: 0.9543 (t) REVERT: E 79 LYS cc_start: 0.8568 (tptt) cc_final: 0.7961 (tppt) REVERT: A 93 GLN cc_start: 0.7659 (tm-30) cc_final: 0.7437 (tm-30) REVERT: A 106 ASP cc_start: 0.8030 (m-30) cc_final: 0.7795 (m-30) REVERT: D 118 VAL cc_start: 0.9316 (t) cc_final: 0.9024 (p) REVERT: C 74 LYS cc_start: 0.9172 (mmtt) cc_final: 0.8192 (tppt) REVERT: B 52 GLU cc_start: 0.7737 (pp20) cc_final: 0.7484 (pp20) REVERT: B 92 ARG cc_start: 0.8797 (ptm160) cc_final: 0.8419 (ttp80) outliers start: 1 outliers final: 0 residues processed: 260 average time/residue: 0.1576 time to fit residues: 57.9424 Evaluate side-chains 218 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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: 0.0570 chunk 68 optimal weight: 8.9990 chunk 24 optimal weight: 0.0570 chunk 12 optimal weight: 10.0000 chunk 138 optimal weight: 40.0000 chunk 102 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 95 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 overall best weight: 4.4222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS G 112 GLN H 63 ASN H 95 GLN A 68 GLN D 49 HIS D 84 ASN C 38 ASN C 112 GLN L 31 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.147822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.108329 restraints weight = 39797.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.106947 restraints weight = 36165.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.107509 restraints weight = 34658.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.107083 restraints weight = 25206.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.107643 restraints weight = 22927.973| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3314 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3314 r_free = 0.3314 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3314 r_free = 0.3314 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3314 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 16942 Z= 0.274 Angle : 0.693 9.878 24129 Z= 0.391 Chirality : 0.043 0.213 2729 Planarity : 0.005 0.049 2052 Dihedral : 29.790 177.929 4582 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.09 % Allowed : 4.75 % Favored : 95.15 % 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 aren not related in a simple way. whole: -2.57 (0.23), residues: 1234 helix: -1.59 (0.20), residues: 581 sheet: -0.44 (0.61), residues: 62 loop : -1.90 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 49 TYR 0.024 0.002 TYR B 98 PHE 0.024 0.002 PHE K 245 TRP 0.008 0.001 TRP K 89 HIS 0.005 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00611 (16935) covalent geometry : angle 0.69332 (24129) hydrogen bonds : bond 0.06963 ( 463) hydrogen bonds : angle 4.93570 ( 1175) Misc. bond : bond 0.00616 ( 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 226 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 225 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: K 153 MET cc_start: 0.0772 (mpp) cc_final: -0.0555 (mtt) REVERT: F 29 ILE cc_start: 0.9126 (mm) cc_final: 0.8834 (mm) REVERT: G 84 GLN cc_start: 0.8923 (tp-100) cc_final: 0.8485 (tp-100) REVERT: G 104 GLN cc_start: 0.9082 (mp10) cc_final: 0.8623 (mp10) REVERT: H 71 GLU cc_start: 0.8447 (tp30) cc_final: 0.8199 (tp30) REVERT: H 96 THR cc_start: 0.9764 (m) cc_final: 0.9550 (t) REVERT: A 74 ILE cc_start: 0.9350 (tp) cc_final: 0.9111 (tp) REVERT: D 62 MET cc_start: 0.9465 (mmm) cc_final: 0.9156 (mmp) REVERT: D 95 GLN cc_start: 0.9315 (tm-30) cc_final: 0.8863 (tm-30) REVERT: D 118 VAL cc_start: 0.9409 (t) cc_final: 0.9164 (p) REVERT: C 74 LYS cc_start: 0.9158 (mmtt) cc_final: 0.8227 (tppt) REVERT: B 35 ARG cc_start: 0.7949 (mtp85) cc_final: 0.7706 (mtt90) REVERT: B 68 ASP cc_start: 0.7894 (m-30) cc_final: 0.7579 (m-30) REVERT: B 92 ARG cc_start: 0.8939 (ptm160) cc_final: 0.8497 (ttp80) outliers start: 1 outliers final: 0 residues processed: 225 average time/residue: 0.1531 time to fit residues: 49.4475 Evaluate side-chains 194 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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: 0.9990 chunk 35 optimal weight: 0.9980 chunk 3 optimal weight: 40.0000 chunk 54 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN H 95 GLN A 68 GLN A 76 GLN D 95 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.153583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.118420 restraints weight = 39949.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.115827 restraints weight = 70117.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.116621 restraints weight = 63060.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.116910 restraints weight = 38730.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.117070 restraints weight = 36792.847| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3462 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3462 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16942 Z= 0.152 Angle : 0.592 9.457 24129 Z= 0.340 Chirality : 0.038 0.229 2729 Planarity : 0.004 0.047 2052 Dihedral : 29.601 178.092 4582 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % 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 aren not related in a simple way. whole: -2.12 (0.23), residues: 1234 helix: -1.20 (0.21), residues: 583 sheet: -1.16 (0.57), residues: 85 loop : -1.56 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 99 TYR 0.016 0.001 TYR D 40 PHE 0.041 0.002 PHE K 223 TRP 0.006 0.001 TRP K 89 HIS 0.003 0.001 HIS K 181 Details of bonding type rmsd covalent geometry : bond 0.00331 (16935) covalent geometry : angle 0.59154 (24129) hydrogen bonds : bond 0.05992 ( 463) hydrogen bonds : angle 4.15792 ( 1175) Misc. bond : bond 0.00313 ( 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 254 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 153 MET cc_start: 0.0875 (mpp) cc_final: -0.0555 (mtt) REVERT: F 29 ILE cc_start: 0.9091 (mm) cc_final: 0.8715 (mm) REVERT: F 30 THR cc_start: 0.9321 (t) cc_final: 0.8791 (m) REVERT: G 84 GLN cc_start: 0.9079 (tp-100) cc_final: 0.8829 (tp-100) REVERT: G 104 GLN cc_start: 0.9085 (mp10) cc_final: 0.8680 (mp10) REVERT: H 67 ASN cc_start: 0.8754 (m-40) cc_final: 0.8550 (t0) REVERT: H 71 GLU cc_start: 0.8317 (tp30) cc_final: 0.7965 (tp30) REVERT: E 93 GLN cc_start: 0.9013 (tm-30) cc_final: 0.8783 (tm-30) REVERT: E 126 LEU cc_start: 0.9046 (tt) cc_final: 0.7560 (mp) REVERT: A 93 GLN cc_start: 0.7608 (tm-30) cc_final: 0.7350 (tm-30) REVERT: D 62 MET cc_start: 0.9313 (mmm) cc_final: 0.9075 (mmp) REVERT: D 85 LYS cc_start: 0.7754 (mmtt) cc_final: 0.7548 (mmtm) REVERT: D 118 VAL cc_start: 0.9207 (t) cc_final: 0.8988 (p) REVERT: C 74 LYS cc_start: 0.8836 (mmtt) cc_final: 0.8065 (tppt) REVERT: C 78 ILE cc_start: 0.8696 (mt) cc_final: 0.8447 (mt) REVERT: B 35 ARG cc_start: 0.7805 (mtp85) cc_final: 0.7585 (mtp85) REVERT: B 52 GLU cc_start: 0.7633 (pp20) cc_final: 0.7433 (pp20) REVERT: B 92 ARG cc_start: 0.8518 (ptm160) cc_final: 0.8226 (ttp80) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.1557 time to fit residues: 55.9712 Evaluate side-chains 211 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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: 9.9990 chunk 31 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 80 optimal weight: 0.2980 chunk 142 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 143 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 30 optimal weight: 30.0000 chunk 111 optimal weight: 10.0000 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 63 ASN A 68 GLN ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN D 95 GLN C 84 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.150119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.113511 restraints weight = 40072.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.111767 restraints weight = 52205.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.112222 restraints weight = 54288.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.111943 restraints weight = 34223.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.112275 restraints weight = 31973.899| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3384 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3384 r_free = 0.3384 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3384 r_free = 0.3384 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3384 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 16942 Z= 0.247 Angle : 0.662 10.649 24129 Z= 0.374 Chirality : 0.042 0.244 2729 Planarity : 0.004 0.047 2052 Dihedral : 29.615 175.137 4582 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % 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 aren not related in a simple way. whole: -2.03 (0.23), residues: 1234 helix: -1.07 (0.21), residues: 582 sheet: -0.38 (0.63), residues: 64 loop : -1.67 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 99 TYR 0.023 0.002 TYR B 98 PHE 0.025 0.002 PHE K 223 TRP 0.006 0.001 TRP K 89 HIS 0.004 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00551 (16935) covalent geometry : angle 0.66234 (24129) hydrogen bonds : bond 0.06355 ( 463) hydrogen bonds : angle 4.57741 ( 1175) Misc. bond : bond 0.00244 ( 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 217 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 153 MET cc_start: 0.1017 (mpp) cc_final: -0.0259 (mtt) REVERT: F 29 ILE cc_start: 0.9143 (mm) cc_final: 0.8844 (mm) REVERT: G 84 GLN cc_start: 0.8898 (tp-100) cc_final: 0.8495 (tp-100) REVERT: G 104 GLN cc_start: 0.9094 (mp10) cc_final: 0.8631 (mp10) REVERT: H 71 GLU cc_start: 0.8400 (tp30) cc_final: 0.8110 (tp30) REVERT: A 74 ILE cc_start: 0.9395 (tp) cc_final: 0.9163 (tp) REVERT: D 118 VAL cc_start: 0.9304 (t) cc_final: 0.9076 (p) REVERT: C 74 LYS cc_start: 0.9008 (mmtt) cc_final: 0.8155 (tppt) REVERT: B 92 ARG cc_start: 0.8751 (ptm160) cc_final: 0.8426 (ttp80) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.1366 time to fit residues: 43.6826 Evaluate side-chains 186 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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: 8.9990 chunk 35 optimal weight: 0.9980 chunk 131 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 chunk 109 optimal weight: 7.9990 chunk 141 optimal weight: 30.0000 chunk 27 optimal weight: 9.9990 chunk 117 optimal weight: 8.9990 chunk 72 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 172 GLN G 112 GLN H 63 ASN A 68 GLN A 76 GLN D 95 GLN L 41 GLN M 31 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.147462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.101088 restraints weight = 40110.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.097090 restraints weight = 34511.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.097996 restraints weight = 29206.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.097961 restraints weight = 24916.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.098214 restraints weight = 21700.793| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 16942 Z= 0.347 Angle : 0.766 10.746 24129 Z= 0.424 Chirality : 0.046 0.340 2729 Planarity : 0.005 0.046 2052 Dihedral : 29.741 173.529 4582 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % 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 aren not related in a simple way. whole: -2.16 (0.23), residues: 1234 helix: -1.18 (0.21), residues: 582 sheet: -0.59 (0.61), residues: 73 loop : -1.74 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 71 TYR 0.026 0.002 TYR H 40 PHE 0.035 0.003 PHE K 245 TRP 0.007 0.001 TRP K 205 HIS 0.006 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00779 (16935) covalent geometry : angle 0.76640 (24129) hydrogen bonds : bond 0.06974 ( 463) hydrogen bonds : angle 5.09407 ( 1175) Misc. bond : bond 0.00347 ( 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 206 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 153 MET cc_start: -0.0300 (mpp) cc_final: -0.1515 (mtt) REVERT: K 260 MET cc_start: 0.0543 (mmm) cc_final: 0.0213 (mmm) REVERT: F 29 ILE cc_start: 0.9162 (mm) cc_final: 0.8928 (mm) REVERT: G 84 GLN cc_start: 0.8936 (tp-100) cc_final: 0.8570 (tp-100) REVERT: G 104 GLN cc_start: 0.9161 (mp10) cc_final: 0.8506 (mp10) REVERT: G 112 GLN cc_start: 0.8609 (mm-40) cc_final: 0.8379 (mm-40) REVERT: H 71 GLU cc_start: 0.8582 (tp30) cc_final: 0.8277 (tp30) REVERT: A 74 ILE cc_start: 0.9298 (tp) cc_final: 0.8997 (tp) REVERT: C 74 LYS cc_start: 0.9164 (mmtt) cc_final: 0.8313 (tppt) REVERT: B 92 ARG cc_start: 0.8763 (ptm160) cc_final: 0.8357 (ttp80) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.1462 time to fit residues: 43.7548 Evaluate side-chains 174 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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: 3.9990 chunk 71 optimal weight: 0.6980 chunk 15 optimal weight: 30.0000 chunk 141 optimal weight: 50.0000 chunk 65 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 136 optimal weight: 0.1980 chunk 90 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 chunk 30 optimal weight: 20.0000 chunk 142 optimal weight: 30.0000 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN A 68 GLN ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.152891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.115461 restraints weight = 39867.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.113684 restraints weight = 43398.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.114472 restraints weight = 43550.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.113839 restraints weight = 29514.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.114125 restraints weight = 28419.261| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3416 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3416 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16942 Z= 0.156 Angle : 0.609 10.215 24129 Z= 0.346 Chirality : 0.039 0.283 2729 Planarity : 0.004 0.047 2052 Dihedral : 29.529 176.214 4582 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % 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 aren not related in a simple way. whole: -1.75 (0.24), residues: 1234 helix: -0.77 (0.22), residues: 584 sheet: -0.62 (0.59), residues: 79 loop : -1.60 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 99 TYR 0.020 0.001 TYR H 40 PHE 0.018 0.002 PHE K 223 TRP 0.007 0.001 TRP K 305 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00343 (16935) covalent geometry : angle 0.60920 (24129) hydrogen bonds : bond 0.05908 ( 463) hydrogen bonds : angle 4.13603 ( 1175) Misc. bond : bond 0.00307 ( 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 232 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 153 MET cc_start: 0.0799 (mpp) cc_final: -0.0700 (mtt) REVERT: F 29 ILE cc_start: 0.9119 (mm) cc_final: 0.8784 (mm) REVERT: F 30 THR cc_start: 0.9317 (t) cc_final: 0.8789 (m) REVERT: G 25 PHE cc_start: 0.8781 (m-10) cc_final: 0.8547 (m-10) REVERT: G 84 GLN cc_start: 0.8810 (tp40) cc_final: 0.8486 (tp-100) REVERT: G 104 GLN cc_start: 0.9109 (mp10) cc_final: 0.8545 (mp10) REVERT: H 71 GLU cc_start: 0.8241 (tp30) cc_final: 0.7955 (tp30) REVERT: E 82 LEU cc_start: 0.9172 (mt) cc_final: 0.8880 (mp) REVERT: E 129 ARG cc_start: 0.7503 (tpt170) cc_final: 0.7210 (tpt170) REVERT: A 77 ASP cc_start: 0.8659 (p0) cc_final: 0.7861 (m-30) REVERT: D 111 VAL cc_start: 0.9560 (m) cc_final: 0.9213 (p) REVERT: C 74 LYS cc_start: 0.8792 (mmtt) cc_final: 0.8054 (tppt) REVERT: B 88 TYR cc_start: 0.7754 (m-80) cc_final: 0.7511 (m-80) REVERT: B 92 ARG cc_start: 0.8533 (ptm160) cc_final: 0.8096 (ttp80) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.1362 time to fit residues: 45.9096 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 : 0.462 ------------------------------------------------------------------------------- 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: 0.9990 chunk 30 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 144 optimal weight: 50.0000 chunk 80 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN E 68 GLN A 68 GLN A 76 GLN D 84 ASN D 95 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.150705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.113793 restraints weight = 40428.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.111267 restraints weight = 56069.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.112320 restraints weight = 54136.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.111493 restraints weight = 37039.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.111933 restraints weight = 35067.797| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3373 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3373 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 16942 Z= 0.220 Angle : 0.649 10.588 24129 Z= 0.365 Chirality : 0.041 0.306 2729 Planarity : 0.004 0.048 2052 Dihedral : 29.534 174.766 4582 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % 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 aren not related in a simple way. whole: -1.73 (0.24), residues: 1234 helix: -0.74 (0.22), residues: 588 sheet: -0.46 (0.62), residues: 73 loop : -1.62 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 71 TYR 0.035 0.002 TYR E 54 PHE 0.017 0.002 PHE A 78 TRP 0.004 0.001 TRP K 208 HIS 0.006 0.001 HIS K 181 Details of bonding type rmsd covalent geometry : bond 0.00495 (16935) covalent geometry : angle 0.64942 (24129) hydrogen bonds : bond 0.06081 ( 463) hydrogen bonds : angle 4.37429 ( 1175) Misc. bond : bond 0.00242 ( 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 223 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 153 MET cc_start: 0.0684 (mpp) cc_final: -0.0853 (mtt) REVERT: F 29 ILE cc_start: 0.9121 (mm) cc_final: 0.8818 (mm) REVERT: G 25 PHE cc_start: 0.8742 (m-10) cc_final: 0.8444 (m-10) REVERT: G 93 LEU cc_start: 0.8832 (mt) cc_final: 0.8621 (mt) REVERT: G 104 GLN cc_start: 0.9134 (mp10) cc_final: 0.8563 (mp10) REVERT: H 71 GLU cc_start: 0.8362 (tp30) cc_final: 0.8045 (tp30) REVERT: H 79 ARG cc_start: 0.7510 (ttm-80) cc_final: 0.7229 (ttm110) REVERT: E 129 ARG cc_start: 0.7750 (tpt170) cc_final: 0.7460 (tpt170) REVERT: A 74 ILE cc_start: 0.9439 (tp) cc_final: 0.9101 (tp) REVERT: D 111 VAL cc_start: 0.9574 (m) cc_final: 0.9211 (p) REVERT: C 74 LYS cc_start: 0.8882 (mmtt) cc_final: 0.8117 (tppt) REVERT: B 92 ARG cc_start: 0.8759 (ptm160) cc_final: 0.8439 (ttp80) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.1226 time to fit residues: 41.2634 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 : 0.358 ------------------------------------------------------------------------------- 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: 10.0000 chunk 82 optimal weight: 0.4980 chunk 145 optimal weight: 40.0000 chunk 78 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 28 optimal weight: 10.0000 chunk 123 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 144 optimal weight: 50.0000 chunk 46 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN A 68 GLN A 76 GLN D 95 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.153642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.115241 restraints weight = 39051.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.113676 restraints weight = 36652.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.114160 restraints weight = 34662.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.113959 restraints weight = 28602.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.114077 restraints weight = 24523.600| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3408 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3408 r_free = 0.3408 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3407 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.4763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16942 Z= 0.148 Angle : 0.600 10.426 24129 Z= 0.339 Chirality : 0.038 0.269 2729 Planarity : 0.004 0.048 2052 Dihedral : 29.433 176.422 4582 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % 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 aren not related in a simple way. whole: -1.50 (0.24), residues: 1234 helix: -0.50 (0.22), residues: 577 sheet: -0.57 (0.59), residues: 79 loop : -1.52 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 49 TYR 0.030 0.001 TYR E 54 PHE 0.043 0.002 PHE K 245 TRP 0.006 0.001 TRP K 208 HIS 0.006 0.001 HIS K 181 Details of bonding type rmsd covalent geometry : bond 0.00324 (16935) covalent geometry : angle 0.59999 (24129) hydrogen bonds : bond 0.05687 ( 463) hydrogen bonds : angle 3.96466 ( 1175) Misc. bond : bond 0.00397 ( 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 229 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 153 MET cc_start: 0.0668 (mpp) cc_final: -0.0815 (mtt) REVERT: F 29 ILE cc_start: 0.9198 (mm) cc_final: 0.8854 (mm) REVERT: F 30 THR cc_start: 0.9326 (t) cc_final: 0.8828 (m) REVERT: G 25 PHE cc_start: 0.8781 (m-10) cc_final: 0.8527 (m-10) REVERT: G 100 VAL cc_start: 0.9160 (t) cc_final: 0.8894 (t) REVERT: G 104 GLN cc_start: 0.9048 (mp10) cc_final: 0.8524 (mp10) REVERT: H 71 GLU cc_start: 0.8272 (tp30) cc_final: 0.7952 (tp30) REVERT: E 129 ARG cc_start: 0.7554 (tpt170) cc_final: 0.7353 (tpt170) REVERT: A 48 LEU cc_start: 0.8879 (mm) cc_final: 0.8575 (mm) REVERT: A 77 ASP cc_start: 0.8672 (p0) cc_final: 0.8350 (p0) REVERT: D 111 VAL cc_start: 0.9537 (m) cc_final: 0.9179 (p) REVERT: C 74 LYS cc_start: 0.8783 (mmtt) cc_final: 0.8007 (tppt) REVERT: C 102 ILE cc_start: 0.9393 (mm) cc_final: 0.9108 (mt) REVERT: B 92 ARG cc_start: 0.8427 (ptm160) cc_final: 0.8205 (ttp80) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.1322 time to fit residues: 45.1636 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 : 0.470 ------------------------------------------------------------------------------- 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: 3.9990 chunk 76 optimal weight: 0.9990 chunk 82 optimal weight: 0.0670 chunk 57 optimal weight: 7.9990 chunk 68 optimal weight: 0.1980 chunk 101 optimal weight: 0.3980 chunk 89 optimal weight: 0.0670 chunk 146 optimal weight: 50.0000 chunk 141 optimal weight: 40.0000 chunk 65 optimal weight: 0.4980 chunk 120 optimal weight: 10.0000 overall best weight: 0.2456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 315 HIS G 31 HIS H 67 ASN E 39 HIS A 68 GLN D 95 GLN C 31 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.156591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.120660 restraints weight = 39881.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.118308 restraints weight = 68424.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.119208 restraints weight = 56084.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.119202 restraints weight = 37901.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.119324 restraints weight = 35060.385| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3487 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3487 r_free = 0.3487 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3487 r_free = 0.3487 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3487 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16942 Z= 0.141 Angle : 0.586 10.370 24129 Z= 0.329 Chirality : 0.038 0.267 2729 Planarity : 0.004 0.048 2052 Dihedral : 29.248 177.147 4582 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % 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 aren not related in a simple way. whole: -1.10 (0.24), residues: 1234 helix: -0.22 (0.22), residues: 580 sheet: -0.43 (0.59), residues: 79 loop : -1.24 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 42 TYR 0.021 0.001 TYR B 98 PHE 0.019 0.002 PHE K 223 TRP 0.005 0.001 TRP K 208 HIS 0.006 0.001 HIS K 181 Details of bonding type rmsd covalent geometry : bond 0.00307 (16935) covalent geometry : angle 0.58632 (24129) hydrogen bonds : bond 0.05362 ( 463) hydrogen bonds : angle 3.68704 ( 1175) Misc. bond : bond 0.00412 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2379.21 seconds wall clock time: 41 minutes 54.19 seconds (2514.19 seconds total)