Starting phenix.real_space_refine on Sat Sep 12 08:14:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pwf_20507/09_2026/6pwf_20507.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pwf_20507/09_2026/6pwf_20507.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6pwf_20507/09_2026/6pwf_20507.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pwf_20507/09_2026/6pwf_20507.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pwf_20507/09_2026/6pwf_20507.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pwf_20507/09_2026/6pwf_20507.map" } resolution = 4.07 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 292 5.49 5 S 27 5.16 5 C 8674 2.51 5 N 2812 2.21 5 O 3392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15197 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 671 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 86} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 798 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 723 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 626 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "G" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 807 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 743 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 3263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3263 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'PTRANS': 15, 'TRANS': 438} Chain breaks: 1 Unresolved non-hydrogen bonds: 463 Unresolved non-hydrogen angles: 580 Unresolved non-hydrogen dihedrals: 379 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'PHE:plan': 4, 'ARG:plan': 10, 'GLU:plan': 17, 'ASP:plan': 14, 'TYR:plan': 1, 'GLN:plan1': 14, 'ASN:plan1': 7, 'TRP:plan': 2, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 306 Time building chain proxies: 2.97, per 1000 atoms: 0.20 Number of scatterers: 15197 At special positions: 0 Unit cell: (111.72, 149.52, 115.92, 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 27 16.00 P 292 15.00 O 3392 8.00 N 2812 7.00 C 8674 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 493.3 milliseconds 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2268 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 8 sheets defined 53.5% alpha, 3.6% beta 79 base pairs and 216 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'A' and resid 50 through 55 Processing helix chain 'A' and resid 63 through 75 removed outlier: 3.900A pdb=" N GLU A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 88 through 112 removed outlier: 3.589A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU A 97 " --> pdb=" O GLN A 93 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN A 108 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N CYS A 110 " --> pdb=" O ASP A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 120 through 133 removed outlier: 3.701A pdb=" N LEU A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 4.105A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 41 removed outlier: 3.853A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG B 40 " --> pdb=" O ARG B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 62 removed outlier: 4.014A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE B 61 " --> pdb=" O VAL B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 76 removed outlier: 3.647A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N TYR B 72 " --> pdb=" O ASP B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 4.080A pdb=" N ARG B 92 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 35 removed outlier: 3.813A pdb=" N ARG C 34 " --> pdb=" O HIS C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 67 removed outlier: 3.565A pdb=" N ALA C 51 " --> pdb=" O PRO C 47 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 70 No H-bonds generated for 'chain 'C' and resid 68 through 70' Processing helix chain 'C' and resid 78 through 87 removed outlier: 3.947A pdb=" N LEU C 82 " --> pdb=" O ILE C 78 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN C 83 " --> pdb=" O PRO C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 96 removed outlier: 3.757A pdb=" N LEU C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 46 removed outlier: 3.650A pdb=" N VAL D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 61 removed outlier: 3.620A pdb=" N MET D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 81 removed outlier: 4.794A pdb=" N ALA D 72 " --> pdb=" O GLU D 68 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 97 removed outlier: 3.780A pdb=" N THR D 93 " --> pdb=" O ARG D 89 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA D 94 " --> pdb=" O GLU D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 119 removed outlier: 4.127A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR D 116 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS D 117 " --> pdb=" O LYS D 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 55 Processing helix chain 'E' and resid 63 through 75 removed outlier: 3.900A pdb=" N GLU E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 88 through 112 removed outlier: 3.590A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA E 95 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU E 97 " --> pdb=" O GLN E 93 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN E 108 " --> pdb=" O PHE E 104 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N CYS E 110 " --> pdb=" O ASP E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 115 No H-bonds generated for 'chain 'E' and resid 113 through 115' Processing helix chain 'E' and resid 120 through 133 removed outlier: 3.701A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG E 129 " --> pdb=" O GLN E 125 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE E 130 " --> pdb=" O LEU E 126 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU E 133 " --> pdb=" O ARG E 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 41 removed outlier: 3.881A pdb=" N LEU F 37 " --> pdb=" O ALA F 33 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG F 40 " --> pdb=" O ARG F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 54 removed outlier: 3.744A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 62 removed outlier: 4.353A pdb=" N VAL F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE F 61 " --> pdb=" O VAL F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 76 removed outlier: 3.737A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N TYR F 72 " --> pdb=" O ASP F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.894A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 36 removed outlier: 4.300A pdb=" N ARG G 34 " --> pdb=" O HIS G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 57 removed outlier: 3.857A pdb=" N ALA G 52 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL G 53 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLU G 55 " --> pdb=" O ALA G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 65 Processing helix chain 'G' and resid 66 through 68 No H-bonds generated for 'chain 'G' and resid 66 through 68' Processing helix chain 'G' and resid 78 through 89 removed outlier: 3.885A pdb=" N LEU G 82 " --> pdb=" O ILE G 78 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN G 83 " --> pdb=" O PRO G 79 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN G 88 " --> pdb=" O LEU G 84 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP G 89 " --> pdb=" O ALA G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 96 removed outlier: 3.782A pdb=" N LYS G 94 " --> pdb=" O GLU G 90 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 46 removed outlier: 3.698A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 82 removed outlier: 3.898A pdb=" N SER H 57 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE H 58 " --> pdb=" O LYS H 54 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER H 61 " --> pdb=" O SER H 57 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL H 63 " --> pdb=" O MET H 59 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN H 64 " --> pdb=" O ASN H 60 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ASP H 65 " --> pdb=" O SER H 61 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG H 69 " --> pdb=" O ASP H 65 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ALA H 72 " --> pdb=" O GLU H 68 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU H 73 " --> pdb=" O ARG H 69 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG H 76 " --> pdb=" O ALA H 72 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N HIS H 79 " --> pdb=" O SER H 75 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TYR H 80 " --> pdb=" O ARG H 76 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 112 removed outlier: 3.561A pdb=" N VAL H 108 " --> pdb=" O ALA H 104 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N SER H 109 " --> pdb=" O LYS H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 120 removed outlier: 4.705A pdb=" N TYR H 118 " --> pdb=" O ALA H 114 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 186 through 191 Processing helix chain 'K' and resid 193 through 203 removed outlier: 3.787A pdb=" N SER K 198 " --> pdb=" O ASN K 194 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU K 199 " --> pdb=" O TRP K 195 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASN K 202 " --> pdb=" O SER K 198 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY K 203 " --> pdb=" O LEU K 199 " (cutoff:3.500A) Processing helix chain 'K' and resid 217 through 225 removed outlier: 3.894A pdb=" N SER K 222 " --> pdb=" O LEU K 218 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N PHE K 223 " --> pdb=" O GLN K 219 " (cutoff:3.500A) Processing helix chain 'K' and resid 225 through 230 removed outlier: 4.228A pdb=" N HIS K 229 " --> pdb=" O GLY K 225 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE K 230 " --> pdb=" O TYR K 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 225 through 230' Processing helix chain 'K' and resid 242 through 244 No H-bonds generated for 'chain 'K' and resid 242 through 244' Processing helix chain 'K' and resid 245 through 257 removed outlier: 3.816A pdb=" N TRP K 249 " --> pdb=" O THR K 245 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LYS K 250 " --> pdb=" O LEU K 246 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ARG K 251 " --> pdb=" O ASP K 247 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU K 254 " --> pdb=" O LYS K 250 " (cutoff:3.500A) Processing helix chain 'K' and resid 268 through 273 removed outlier: 4.197A pdb=" N HIS K 273 " --> pdb=" O LYS K 269 " (cutoff:3.500A) Processing helix chain 'K' and resid 273 through 278 removed outlier: 3.676A pdb=" N ASP K 278 " --> pdb=" O GLN K 274 " (cutoff:3.500A) Processing helix chain 'K' and resid 291 through 297 removed outlier: 4.032A pdb=" N LEU K 296 " --> pdb=" O TYR K 292 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG K 297 " --> pdb=" O GLU K 293 " (cutoff:3.500A) Processing helix chain 'K' and resid 316 through 320 removed outlier: 3.795A pdb=" N LYS K 319 " --> pdb=" O HIS K 316 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN K 320 " --> pdb=" O ARG K 317 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 316 through 320' Processing helix chain 'K' and resid 325 through 330 Processing helix chain 'K' and resid 349 through 360 removed outlier: 3.743A pdb=" N TRP K 353 " --> pdb=" O LEU K 349 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU K 355 " --> pdb=" O GLU K 351 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE K 358 " --> pdb=" O ALA K 354 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU K 360 " --> pdb=" O LEU K 356 " (cutoff:3.500A) Processing helix chain 'K' and resid 363 through 368 removed outlier: 4.109A pdb=" N ASP K 368 " --> pdb=" O PHE K 364 " (cutoff:3.500A) Processing helix chain 'K' and resid 370 through 374 removed outlier: 3.738A pdb=" N PHE K 374 " --> pdb=" O ASP K 371 " (cutoff:3.500A) Processing helix chain 'K' and resid 388 through 393 Processing helix chain 'K' and resid 400 through 404 Processing helix chain 'K' and resid 430 through 436 Processing helix chain 'K' and resid 453 through 460 removed outlier: 3.852A pdb=" N ARG K 460 " --> pdb=" O VAL K 456 " (cutoff:3.500A) Processing helix chain 'K' and resid 490 through 501 removed outlier: 3.584A pdb=" N LEU K 494 " --> pdb=" O LYS K 490 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS K 496 " --> pdb=" O ILE K 492 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N LYS K 499 " --> pdb=" O ASP K 495 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG K 500 " --> pdb=" O LYS K 496 " (cutoff:3.500A) Processing helix chain 'K' and resid 514 through 526 removed outlier: 3.729A pdb=" N LEU K 518 " --> pdb=" O MET K 514 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE K 520 " --> pdb=" O ARG K 516 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP K 523 " --> pdb=" O ASP K 519 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS K 525 " --> pdb=" O LEU K 521 " (cutoff:3.500A) Processing helix chain 'K' and resid 540 through 552 removed outlier: 3.547A pdb=" N ILE K 545 " --> pdb=" O HIS K 541 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA K 547 " --> pdb=" O ASP K 543 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU K 550 " --> pdb=" O ALA K 546 " (cutoff:3.500A) Processing helix chain 'K' and resid 590 through 595 Processing helix chain 'K' and resid 596 through 599 Processing helix chain 'K' and resid 619 through 630 Processing helix chain 'K' and resid 634 through 640 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.330A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.788A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 41 through 42 removed outlier: 6.875A pdb=" N ARG C 41 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 76 through 77 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.965A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.654A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'K' and resid 207 through 209 removed outlier: 5.972A pdb=" N GLU K 308 " --> pdb=" O ASN K 336 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU K 338 " --> pdb=" O GLU K 308 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ILE K 310 " --> pdb=" O LEU K 338 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ILE K 340 " --> pdb=" O ILE K 310 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE K 312 " --> pdb=" O ILE K 340 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU K 238 " --> pdb=" O ILE K 311 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ASP K 313 " --> pdb=" O LEU K 238 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA K 240 " --> pdb=" O ASP K 313 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N HIS K 237 " --> pdb=" O CYS K 288 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N THR K 290 " --> pdb=" O HIS K 237 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL K 239 " --> pdb=" O THR K 290 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 532 through 534 removed outlier: 6.902A pdb=" N VAL K 508 " --> pdb=" O PHE K 561 " (cutoff:3.500A) 264 hydrogen bonds defined for protein. 777 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 184 hydrogen bonds 356 hydrogen bond angles 0 basepair planarities 79 basepair parallelities 216 stacking parallelities Total time for adding SS restraints: 2.99 Time building geometry restraints manager: 1.63 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: 2513 1.33 - 1.45: 5206 1.45 - 1.57: 7718 1.57 - 1.69: 582 1.69 - 1.81: 47 Bond restraints: 16066 Sorted by residual: bond pdb=" C1' DC I -71 " pdb=" N1 DC I -71 " ideal model delta sigma weight residual 1.468 1.550 -0.082 1.40e-02 5.10e+03 3.46e+01 bond pdb=" C3' DG J 25 " pdb=" O3' DG J 25 " ideal model delta sigma weight residual 1.435 1.499 -0.064 1.30e-02 5.92e+03 2.40e+01 bond pdb=" C3' DC J -4 " pdb=" O3' DC J -4 " ideal model delta sigma weight residual 1.435 1.377 0.058 1.30e-02 5.92e+03 2.01e+01 bond pdb=" C1' DA I -73 " pdb=" N9 DA I -73 " ideal model delta sigma weight residual 1.468 1.405 0.063 1.40e-02 5.10e+03 2.00e+01 bond pdb=" C3' DG J -34 " pdb=" O3' DG J -34 " ideal model delta sigma weight residual 1.435 1.489 -0.054 1.30e-02 5.92e+03 1.70e+01 ... (remaining 16061 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 22229 2.55 - 5.09: 670 5.09 - 7.64: 85 7.64 - 10.18: 11 10.18 - 12.73: 1 Bond angle restraints: 22996 Sorted by residual: angle pdb=" O4' DA J -31 " pdb=" C4' DA J -31 " pdb=" C3' DA J -31 " ideal model delta sigma weight residual 106.00 101.58 4.42 6.00e-01 2.78e+00 5.43e+01 angle pdb=" C ARG B 19 " pdb=" N LYS B 20 " pdb=" CA LYS B 20 " ideal model delta sigma weight residual 120.79 129.01 -8.22 1.39e+00 5.18e-01 3.50e+01 angle pdb=" O4' DT I 54 " pdb=" C4' DT I 54 " pdb=" C3' DT I 54 " ideal model delta sigma weight residual 106.00 102.60 3.40 6.00e-01 2.78e+00 3.21e+01 angle pdb=" O4' DT J -28 " pdb=" C4' DT J -28 " pdb=" C3' DT J -28 " ideal model delta sigma weight residual 106.00 102.66 3.34 6.00e-01 2.78e+00 3.09e+01 angle pdb=" O4' DA I -43 " pdb=" C4' DA I -43 " pdb=" C3' DA I -43 " ideal model delta sigma weight residual 106.00 102.69 3.31 6.00e-01 2.78e+00 3.05e+01 ... (remaining 22991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.28: 7439 35.28 - 70.56: 1390 70.56 - 105.83: 49 105.83 - 141.11: 2 141.11 - 176.39: 8 Dihedral angle restraints: 8888 sinusoidal: 5378 harmonic: 3510 Sorted by residual: dihedral pdb=" CA LYS H 31 " pdb=" C LYS H 31 " pdb=" N GLU H 32 " pdb=" CA GLU H 32 " ideal model delta harmonic sigma weight residual 180.00 146.87 33.13 0 5.00e+00 4.00e-02 4.39e+01 dihedral pdb=" CA HIS K 465 " pdb=" C HIS K 465 " pdb=" N PRO K 466 " pdb=" CA PRO K 466 " ideal model delta harmonic sigma weight residual -180.00 -150.58 -29.42 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA ALA K 369 " pdb=" C ALA K 369 " pdb=" N PHE K 370 " pdb=" CA PHE K 370 " ideal model delta harmonic sigma weight residual 180.00 150.82 29.18 0 5.00e+00 4.00e-02 3.41e+01 ... (remaining 8885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1895 0.063 - 0.126: 627 0.126 - 0.190: 102 0.190 - 0.253: 14 0.253 - 0.316: 2 Chirality restraints: 2640 Sorted by residual: chirality pdb=" CB ILE K 310 " pdb=" CA ILE K 310 " pdb=" CG1 ILE K 310 " pdb=" CG2 ILE K 310 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" C3' DA I -3 " pdb=" C4' DA I -3 " pdb=" O3' DA I -3 " pdb=" C2' DA I -3 " both_signs ideal model delta sigma weight residual False -2.73 -2.43 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" C3' DG J -34 " pdb=" C4' DG J -34 " pdb=" O3' DG J -34 " pdb=" C2' DG J -34 " both_signs ideal model delta sigma weight residual False -2.73 -2.48 -0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 2637 not shown) Planarity restraints: 1909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO K 476 " -0.057 5.00e-02 4.00e+02 8.49e-02 1.15e+01 pdb=" N PRO K 477 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO K 477 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO K 477 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU K 360 " 0.050 5.00e-02 4.00e+02 7.53e-02 9.08e+00 pdb=" N PRO K 361 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO K 361 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO K 361 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG K 393 " -0.044 5.00e-02 4.00e+02 6.68e-02 7.14e+00 pdb=" N PRO K 394 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO K 394 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO K 394 " -0.038 5.00e-02 4.00e+02 ... (remaining 1906 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 268 2.63 - 3.20: 12437 3.20 - 3.77: 25605 3.77 - 4.33: 33907 4.33 - 4.90: 49504 Nonbonded interactions: 121721 Sorted by model distance: nonbonded pdb=" OP1 DA J 23 " pdb=" ND2 ASN K 588 " model vdw 2.066 3.120 nonbonded pdb=" OD2 ASP D 65 " pdb=" OH TYR F 98 " model vdw 2.265 3.040 nonbonded pdb=" O TYR C 38 " pdb=" OG SER D 75 " model vdw 2.288 3.040 nonbonded pdb=" OD1 ASP K 536 " pdb=" OG1 THR K 539 " model vdw 2.289 3.040 nonbonded pdb=" N2 DG I -21 " pdb=" O2 DC J 22 " model vdw 2.295 3.120 ... (remaining 121716 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' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 24 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 14 through 117) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 30 through 121) } 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=0.00 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: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.120 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 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 : 0.010 0.085 16066 Z= 0.707 Angle : 1.102 12.731 22996 Z= 0.808 Chirality : 0.062 0.316 2640 Planarity : 0.008 0.085 1909 Dihedral : 26.976 176.386 6620 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 0.11 % Allowed : 3.52 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.10 (0.16), residues: 1188 helix: -4.62 (0.09), residues: 644 sheet: -2.34 (0.67), residues: 48 loop : -3.19 (0.23), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG B 40 TYR 0.040 0.004 TYR K 583 PHE 0.035 0.005 PHE K 613 TRP 0.018 0.004 TRP K 427 HIS 0.011 0.003 HIS K 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00958 / 0.71 (16066) covalent geometry : angle 1.10218 / 0.81 (22996) hydrogen bonds : bond 0.30242 / 19.41 ( 448) hydrogen bonds : angle 11.01938 / 7.64 ( 1133) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 277 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 47 SER cc_start: 0.8385 (t) cc_final: 0.8070 (t) REVERT: E 87 SER cc_start: 0.9233 (p) cc_final: 0.8867 (t) REVERT: H 54 LYS cc_start: 0.9011 (tttp) cc_final: 0.8449 (tptt) REVERT: K 221 ILE cc_start: 0.6891 (mt) cc_final: 0.6680 (mt) REVERT: K 294 MET cc_start: 0.8923 (mmp) cc_final: 0.8238 (mmt) REVERT: K 631 LEU cc_start: 0.7781 (mt) cc_final: 0.7400 (tp) outliers start: 1 outliers final: 0 residues processed: 277 average time/residue: 0.1688 time to fit residues: 63.3851 Evaluate side-chains 158 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 30.0000 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 20.0000 chunk 55 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 389 HIS K 487 ASN K 513 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.155494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.136824 restraints weight = 28209.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.136414 restraints weight = 38521.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.136657 restraints weight = 36882.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.136708 restraints weight = 31043.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.136779 restraints weight = 29327.732| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 16066 Z= 0.271 Angle : 0.911 10.475 22996 Z= 0.500 Chirality : 0.060 0.413 2640 Planarity : 0.007 0.065 1909 Dihedral : 31.760 177.633 4513 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.19 (0.19), residues: 1188 helix: -3.82 (0.13), residues: 652 sheet: -1.95 (0.79), residues: 48 loop : -2.82 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 69 TYR 0.030 0.003 TYR B 88 PHE 0.024 0.003 PHE H 67 TRP 0.009 0.002 TRP K 307 HIS 0.008 0.002 HIS K 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.27 (16066) covalent geometry : angle 0.91110 / 0.50 (22996) hydrogen bonds : bond 0.09132 / 5.78 ( 448) hydrogen bonds : angle 5.63005 / 3.85 ( 1133) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: C 37 ASN cc_start: 0.8588 (m110) cc_final: 0.8194 (m110) REVERT: C 49 TYR cc_start: 0.8422 (t80) cc_final: 0.8142 (t80) REVERT: D 119 THR cc_start: 0.7043 (p) cc_final: 0.6389 (m) REVERT: E 87 SER cc_start: 0.9302 (p) cc_final: 0.9100 (t) REVERT: H 85 THR cc_start: 0.8268 (p) cc_final: 0.7850 (p) REVERT: H 90 GLU cc_start: 0.7756 (mp0) cc_final: 0.7173 (mt-10) REVERT: K 294 MET cc_start: 0.8900 (mmp) cc_final: 0.8562 (mmt) REVERT: K 355 LEU cc_start: 0.8343 (mm) cc_final: 0.8115 (mm) REVERT: K 460 ARG cc_start: 0.7957 (ttm110) cc_final: 0.7176 (ttm-80) REVERT: K 506 SER cc_start: 0.8648 (m) cc_final: 0.8236 (p) REVERT: K 631 LEU cc_start: 0.8161 (mt) cc_final: 0.7908 (tp) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.1363 time to fit residues: 42.7650 Evaluate side-chains 150 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 4 optimal weight: 8.9990 chunk 74 optimal weight: 30.0000 chunk 46 optimal weight: 0.9990 chunk 79 optimal weight: 20.0000 chunk 111 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 1 optimal weight: 0.4980 chunk 73 optimal weight: 20.0000 chunk 59 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 64 ASN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 ASN K 237 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.161055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.143527 restraints weight = 28646.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.143175 restraints weight = 42093.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.143479 restraints weight = 38320.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.143507 restraints weight = 33841.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.143628 restraints weight = 31644.092| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 16066 Z= 0.155 Angle : 0.714 9.599 22996 Z= 0.406 Chirality : 0.052 0.357 2640 Planarity : 0.005 0.046 1909 Dihedral : 31.450 179.798 4513 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.51 (0.21), residues: 1188 helix: -3.29 (0.15), residues: 655 sheet: -1.79 (0.83), residues: 46 loop : -2.45 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 89 TYR 0.017 0.002 TYR K 467 PHE 0.015 0.001 PHE G 24 TRP 0.008 0.001 TRP K 307 HIS 0.004 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.16 (16066) covalent geometry : angle 0.71433 / 0.41 (22996) hydrogen bonds : bond 0.06918 / 4.26 ( 448) hydrogen bonds : angle 4.65492 / 3.16 ( 1133) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: C 37 ASN cc_start: 0.8524 (m110) cc_final: 0.8081 (m110) REVERT: C 88 ASN cc_start: 0.7306 (t0) cc_final: 0.7046 (t0) REVERT: D 105 LYS cc_start: 0.8405 (mmtt) cc_final: 0.8164 (mttt) REVERT: E 87 SER cc_start: 0.9300 (p) cc_final: 0.9082 (t) REVERT: K 506 SER cc_start: 0.8493 (m) cc_final: 0.8096 (p) REVERT: K 631 LEU cc_start: 0.8115 (mt) cc_final: 0.7764 (tp) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.1376 time to fit residues: 41.4025 Evaluate side-chains 148 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 126 optimal weight: 0.7980 chunk 117 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 71 optimal weight: 30.0000 chunk 83 optimal weight: 30.0000 chunk 78 optimal weight: 40.0000 chunk 56 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 81 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.161940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.143653 restraints weight = 28844.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.143448 restraints weight = 40542.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.143671 restraints weight = 36519.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.143722 restraints weight = 33874.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.143833 restraints weight = 32130.817| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 16066 Z= 0.140 Angle : 0.656 9.690 22996 Z= 0.378 Chirality : 0.048 0.369 2640 Planarity : 0.004 0.047 1909 Dihedral : 31.204 178.260 4513 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.02 (0.22), residues: 1188 helix: -2.82 (0.17), residues: 660 sheet: -1.46 (0.87), residues: 46 loop : -2.34 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 129 TYR 0.029 0.002 TYR D 80 PHE 0.009 0.001 PHE K 332 TRP 0.015 0.002 TRP K 307 HIS 0.004 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.14 (16066) covalent geometry : angle 0.65596 / 0.38 (22996) hydrogen bonds : bond 0.05847 / 3.58 ( 448) hydrogen bonds : angle 4.23890 / 2.90 ( 1133) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.427 Fit side-chains REVERT: C 37 ASN cc_start: 0.8368 (m110) cc_final: 0.8115 (m110) REVERT: C 38 TYR cc_start: 0.8012 (m-80) cc_final: 0.7667 (m-80) REVERT: C 88 ASN cc_start: 0.7143 (t0) cc_final: 0.6872 (t0) REVERT: D 105 LYS cc_start: 0.8324 (mmtt) cc_final: 0.8114 (mttt) REVERT: E 106 ASP cc_start: 0.7712 (m-30) cc_final: 0.7250 (t0) REVERT: G 106 VAL cc_start: 0.9224 (p) cc_final: 0.9018 (t) REVERT: K 506 SER cc_start: 0.8362 (m) cc_final: 0.7953 (p) REVERT: K 631 LEU cc_start: 0.8212 (mt) cc_final: 0.7703 (tp) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.1267 time to fit residues: 38.7858 Evaluate side-chains 148 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 13 optimal weight: 7.9990 chunk 70 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 132 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 73 optimal weight: 20.0000 chunk 67 optimal weight: 7.9990 chunk 111 optimal weight: 0.0050 chunk 88 optimal weight: 30.0000 chunk 44 optimal weight: 2.9990 overall best weight: 3.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.156951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.138234 restraints weight = 28656.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.137882 restraints weight = 41685.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.138069 restraints weight = 39142.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.138207 restraints weight = 32492.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.138291 restraints weight = 31437.399| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 16066 Z= 0.205 Angle : 0.727 9.035 22996 Z= 0.405 Chirality : 0.052 0.392 2640 Planarity : 0.005 0.048 1909 Dihedral : 31.258 179.861 4513 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.78 (0.22), residues: 1188 helix: -2.63 (0.17), residues: 650 sheet: -1.61 (0.71), residues: 61 loop : -2.22 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 34 TYR 0.039 0.003 TYR D 80 PHE 0.041 0.003 PHE G 24 TRP 0.010 0.001 TRP K 307 HIS 0.006 0.001 HIS K 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.21 (16066) covalent geometry : angle 0.72696 / 0.40 (22996) hydrogen bonds : bond 0.06544 / 4.00 ( 448) hydrogen bonds : angle 4.42781 / 3.01 ( 1133) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: C 37 ASN cc_start: 0.8608 (m110) cc_final: 0.8167 (m110) REVERT: C 88 ASN cc_start: 0.7110 (t0) cc_final: 0.6765 (t0) REVERT: D 41 VAL cc_start: 0.8915 (p) cc_final: 0.8672 (t) REVERT: D 119 THR cc_start: 0.7091 (p) cc_final: 0.6737 (t) REVERT: G 63 GLU cc_start: 0.7421 (tp30) cc_final: 0.7050 (tt0) REVERT: K 506 SER cc_start: 0.8450 (m) cc_final: 0.8129 (p) REVERT: K 631 LEU cc_start: 0.8379 (mt) cc_final: 0.8041 (tp) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.1153 time to fit residues: 32.9017 Evaluate side-chains 146 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 61 optimal weight: 5.9990 chunk 85 optimal weight: 40.0000 chunk 7 optimal weight: 6.9990 chunk 9 optimal weight: 20.0000 chunk 133 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 109 optimal weight: 0.1980 chunk 87 optimal weight: 20.0000 chunk 129 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.160748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.143451 restraints weight = 28749.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.143144 restraints weight = 42307.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.143310 restraints weight = 38598.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.143333 restraints weight = 35996.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.143720 restraints weight = 32374.101| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 16066 Z= 0.140 Angle : 0.644 8.939 22996 Z= 0.369 Chirality : 0.048 0.348 2640 Planarity : 0.004 0.055 1909 Dihedral : 31.080 179.005 4513 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.53 (0.23), residues: 1188 helix: -2.46 (0.18), residues: 648 sheet: -1.47 (0.71), residues: 61 loop : -2.06 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 34 TYR 0.027 0.002 TYR D 80 PHE 0.015 0.001 PHE G 24 TRP 0.007 0.001 TRP K 307 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.14 (16066) covalent geometry : angle 0.64362 / 0.37 (22996) hydrogen bonds : bond 0.05692 / 3.49 ( 448) hydrogen bonds : angle 4.11436 / 2.80 ( 1133) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.458 Fit side-chains REVERT: C 37 ASN cc_start: 0.8537 (m110) cc_final: 0.8142 (m110) REVERT: C 88 ASN cc_start: 0.7022 (t0) cc_final: 0.6726 (t0) REVERT: D 41 VAL cc_start: 0.8979 (p) cc_final: 0.8688 (t) REVERT: E 106 ASP cc_start: 0.7806 (m-30) cc_final: 0.7588 (t70) REVERT: G 38 TYR cc_start: 0.8069 (m-80) cc_final: 0.7683 (m-80) REVERT: G 63 GLU cc_start: 0.6975 (tp30) cc_final: 0.6773 (tt0) REVERT: K 308 GLU cc_start: 0.5495 (mp0) cc_final: 0.5196 (mp0) REVERT: K 506 SER cc_start: 0.8370 (m) cc_final: 0.8059 (p) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.1180 time to fit residues: 35.1571 Evaluate side-chains 145 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 34 optimal weight: 1.9990 chunk 140 optimal weight: 7.9990 chunk 118 optimal weight: 0.0980 chunk 93 optimal weight: 30.0000 chunk 17 optimal weight: 7.9990 chunk 98 optimal weight: 40.0000 chunk 23 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 79 optimal weight: 20.0000 chunk 130 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.159869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.142249 restraints weight = 28755.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.141776 restraints weight = 43602.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.142038 restraints weight = 37631.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.142112 restraints weight = 32957.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.142171 restraints weight = 31386.793| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16066 Z= 0.157 Angle : 0.665 9.500 22996 Z= 0.375 Chirality : 0.049 0.371 2640 Planarity : 0.004 0.047 1909 Dihedral : 31.064 177.917 4513 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.34 (0.23), residues: 1188 helix: -2.25 (0.18), residues: 651 sheet: -1.43 (0.67), residues: 66 loop : -2.03 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 76 TYR 0.037 0.002 TYR D 80 PHE 0.026 0.002 PHE G 24 TRP 0.005 0.001 TRP K 427 HIS 0.010 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.16 (16066) covalent geometry : angle 0.66543 / 0.37 (22996) hydrogen bonds : bond 0.05776 / 3.54 ( 448) hydrogen bonds : angle 4.14788 / 2.82 ( 1133) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 37 ASN cc_start: 0.8270 (m110) cc_final: 0.7989 (m110) REVERT: C 88 ASN cc_start: 0.6932 (t0) cc_final: 0.6680 (t0) REVERT: D 41 VAL cc_start: 0.8962 (p) cc_final: 0.8706 (t) REVERT: E 106 ASP cc_start: 0.7836 (m-30) cc_final: 0.7593 (t70) REVERT: G 38 TYR cc_start: 0.8050 (m-80) cc_final: 0.7609 (m-80) REVERT: G 63 GLU cc_start: 0.7093 (tp30) cc_final: 0.6792 (tt0) REVERT: K 308 GLU cc_start: 0.5426 (mp0) cc_final: 0.5214 (mp0) REVERT: K 506 SER cc_start: 0.8452 (m) cc_final: 0.8122 (p) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.1200 time to fit residues: 34.1981 Evaluate side-chains 145 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 43 optimal weight: 7.9990 chunk 4 optimal weight: 0.5980 chunk 90 optimal weight: 30.0000 chunk 126 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 116 optimal weight: 0.0670 chunk 60 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 overall best weight: 1.5324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.161089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.143472 restraints weight = 28826.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.143188 restraints weight = 40817.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.143381 restraints weight = 37302.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.143448 restraints weight = 34279.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.143589 restraints weight = 31382.701| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16066 Z= 0.141 Angle : 0.628 7.343 22996 Z= 0.360 Chirality : 0.047 0.352 2640 Planarity : 0.004 0.047 1909 Dihedral : 30.934 177.358 4513 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.14 (0.23), residues: 1188 helix: -2.11 (0.18), residues: 656 sheet: -1.30 (0.68), residues: 66 loop : -1.92 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 34 TYR 0.027 0.001 TYR C 56 PHE 0.010 0.001 PHE K 511 TRP 0.005 0.001 TRP K 307 HIS 0.004 0.001 HIS K 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.14 (16066) covalent geometry : angle 0.62838 / 0.36 (22996) hydrogen bonds : bond 0.05478 / 3.39 ( 448) hydrogen bonds : angle 4.01498 / 2.75 ( 1133) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: D 30 ARG cc_start: 0.6351 (ptp-170) cc_final: 0.5903 (ptt90) REVERT: D 41 VAL cc_start: 0.8997 (p) cc_final: 0.8727 (t) REVERT: E 106 ASP cc_start: 0.7753 (m-30) cc_final: 0.7118 (t0) REVERT: G 38 TYR cc_start: 0.8045 (m-80) cc_final: 0.7699 (m-80) REVERT: G 63 GLU cc_start: 0.6970 (tp30) cc_final: 0.6737 (tt0) REVERT: H 42 LEU cc_start: 0.8677 (tp) cc_final: 0.8405 (tp) REVERT: K 490 LYS cc_start: 0.7443 (mmtt) cc_final: 0.6806 (mmtt) REVERT: K 506 SER cc_start: 0.8296 (m) cc_final: 0.8031 (p) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.1233 time to fit residues: 36.4963 Evaluate side-chains 148 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 19 optimal weight: 9.9990 chunk 139 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 76 optimal weight: 20.0000 chunk 119 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 143 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.158592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.140109 restraints weight = 28718.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.139795 restraints weight = 43543.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.139991 restraints weight = 38030.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.140103 restraints weight = 32858.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.140180 restraints weight = 32114.820| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16066 Z= 0.182 Angle : 0.684 13.509 22996 Z= 0.380 Chirality : 0.049 0.385 2640 Planarity : 0.005 0.053 1909 Dihedral : 30.981 179.347 4513 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.15 (0.23), residues: 1188 helix: -2.12 (0.18), residues: 655 sheet: -1.33 (0.67), residues: 66 loop : -1.91 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 34 TYR 0.031 0.002 TYR H 37 PHE 0.017 0.002 PHE E 104 TRP 0.005 0.001 TRP K 427 HIS 0.004 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.18 (16066) covalent geometry : angle 0.68367 / 0.38 (22996) hydrogen bonds : bond 0.05905 / 3.62 ( 448) hydrogen bonds : angle 4.20760 / 2.87 ( 1133) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.562 Fit side-chains revert: symmetry clash REVERT: C 37 ASN cc_start: 0.8273 (m110) cc_final: 0.7979 (m110) REVERT: D 41 VAL cc_start: 0.8956 (p) cc_final: 0.8750 (t) REVERT: E 106 ASP cc_start: 0.7781 (m-30) cc_final: 0.6747 (t0) REVERT: G 38 TYR cc_start: 0.8122 (m-80) cc_final: 0.7652 (m-80) REVERT: G 63 GLU cc_start: 0.7191 (tp30) cc_final: 0.6844 (tt0) REVERT: K 506 SER cc_start: 0.8492 (m) cc_final: 0.8178 (p) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.1226 time to fit residues: 34.7239 Evaluate side-chains 140 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 104 optimal weight: 10.0000 chunk 94 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 95 optimal weight: 30.0000 chunk 8 optimal weight: 0.1980 chunk 131 optimal weight: 2.9990 chunk 100 optimal weight: 0.0040 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 overall best weight: 1.0396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.162286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.145404 restraints weight = 28805.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.145066 restraints weight = 42116.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.145241 restraints weight = 39053.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.145360 restraints weight = 33953.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.145433 restraints weight = 31121.670| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 16066 Z= 0.134 Angle : 0.636 10.696 22996 Z= 0.359 Chirality : 0.046 0.344 2640 Planarity : 0.004 0.050 1909 Dihedral : 30.825 177.824 4513 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.11 % Allowed : 0.33 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.83 (0.23), residues: 1188 helix: -1.85 (0.19), residues: 653 sheet: -1.32 (0.71), residues: 61 loop : -1.77 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 34 TYR 0.024 0.002 TYR C 56 PHE 0.023 0.001 PHE G 24 TRP 0.006 0.001 TRP K 307 HIS 0.004 0.001 HIS K 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.13 (16066) covalent geometry : angle 0.63556 / 0.36 (22996) hydrogen bonds : bond 0.05236 / 3.24 ( 448) hydrogen bonds : angle 3.95408 / 2.69 ( 1133) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: D 30 ARG cc_start: 0.6458 (ptp-170) cc_final: 0.5972 (ptt90) REVERT: D 41 VAL cc_start: 0.8998 (p) cc_final: 0.8753 (t) REVERT: E 92 LEU cc_start: 0.9264 (mm) cc_final: 0.8855 (mt) REVERT: E 106 ASP cc_start: 0.7650 (m-30) cc_final: 0.6594 (t0) REVERT: G 38 TYR cc_start: 0.8033 (m-80) cc_final: 0.7713 (m-80) REVERT: G 63 GLU cc_start: 0.7132 (tp30) cc_final: 0.6803 (tt0) REVERT: K 506 SER cc_start: 0.8423 (m) cc_final: 0.8121 (p) outliers start: 1 outliers final: 0 residues processed: 191 average time/residue: 0.1229 time to fit residues: 35.1079 Evaluate side-chains 145 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 126 optimal weight: 0.8980 chunk 117 optimal weight: 0.9980 chunk 74 optimal weight: 30.0000 chunk 65 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 112 optimal weight: 0.9980 chunk 129 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 2 optimal weight: 0.0980 chunk 107 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 504 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.163508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.145483 restraints weight = 28182.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.145196 restraints weight = 40172.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.145357 restraints weight = 37564.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.145470 restraints weight = 32649.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.145551 restraints weight = 30645.953| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.4649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 16066 Z= 0.126 Angle : 0.609 8.860 22996 Z= 0.346 Chirality : 0.045 0.357 2640 Planarity : 0.004 0.055 1909 Dihedral : 30.750 177.683 4513 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.24), residues: 1188 helix: -1.65 (0.19), residues: 655 sheet: -1.30 (0.65), residues: 73 loop : -1.62 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 89 TYR 0.031 0.001 TYR H 37 PHE 0.019 0.001 PHE K 561 TRP 0.044 0.002 TRP K 307 HIS 0.005 0.001 HIS K 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.13 (16066) covalent geometry : angle 0.60898 / 0.35 (22996) hydrogen bonds : bond 0.05005 / 3.10 ( 448) hydrogen bonds : angle 3.86805 / 2.60 ( 1133) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2084.69 seconds wall clock time: 36 minutes 52.76 seconds (2212.76 seconds total)