Starting phenix.real_space_refine on Sun Sep 13 08:23:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6k0a_30036/09_2026/6k0a_30036.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k0a_30036/09_2026/6k0a_30036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6k0a_30036/09_2026/6k0a_30036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k0a_30036/09_2026/6k0a_30036.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6k0a_30036/09_2026/6k0a_30036.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6k0a_30036/09_2026/6k0a_30036.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6k0a_30036/09_2026/6k0a_30036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k0a_30036/09_2026/6k0a_30036.map" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 516 5.49 5 S 38 5.16 5 C 12184 2.51 5 N 4012 2.21 5 O 5524 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 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: 22276 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1059 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "C" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1875 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 4, 'TRANS': 221} Chain: "E" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 764 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain: "G" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1021 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "I" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 883 Classifications: {'peptide': 116} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 111} Chain: "X" Number of atoms: 5535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 5535 Classifications: {'RNAv2': 258} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 14, 'rna3p_pur': 131, 'rna3p_pyr': 99} Link IDs: {'rna2p': 28, 'rna3p': 229} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4232 SG CYS G 63 182.893 49.953 84.315 1.00123.20 S ATOM 4256 SG CYS G 66 180.141 52.933 85.267 1.00109.97 S ATOM 4470 SG CYS G 92 183.213 53.629 87.634 1.00128.27 S ATOM 4493 SG CYS G 95 181.038 50.386 87.761 1.00145.27 S Restraints were copied for chains: B, D, F, H, J, Y Time building chain proxies: 7.11, per 1000 atoms: 0.32 Number of scatterers: 22276 At special positions: 0 Unit cell: (245.25, 161.32, 109, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 38 16.00 P 516 15.00 O 5524 8.00 N 4012 7.00 C 12184 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: 1.60 Conformation dependent library (CDL) restraints added in 643.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 66 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 63 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 95 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 92 " pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 66 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 63 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 95 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 92 " Number of angles added : 12 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2600 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 10 sheets defined 46.3% alpha, 15.0% beta 120 base pairs and 324 stacking pairs defined. Time for finding SS restraints: 2.63 Creating SS restraints... Processing helix chain 'A' and resid 30 through 46 removed outlier: 3.597A pdb=" N ASN A 36 " --> pdb=" O GLY A 32 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU A 44 " --> pdb=" O LYS A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 55 removed outlier: 3.554A pdb=" N GLY A 50 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER A 52 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS A 53 " --> pdb=" O TRP A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 80 removed outlier: 3.675A pdb=" N VAL A 78 " --> pdb=" O ASN A 74 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA A 80 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 111 removed outlier: 3.960A pdb=" N ILE A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE A 111 " --> pdb=" O ALA A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 125 removed outlier: 4.061A pdb=" N VAL A 122 " --> pdb=" O LYS A 118 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG A 124 " --> pdb=" O TRP A 120 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG A 125 " --> pdb=" O PHE A 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 21 removed outlier: 3.542A pdb=" N LYS C 18 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU C 20 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS C 21 " --> pdb=" O LEU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 47 removed outlier: 3.583A pdb=" N GLU C 41 " --> pdb=" O ASP C 37 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS C 43 " --> pdb=" O TYR C 39 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA C 44 " --> pdb=" O GLU C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 75 removed outlier: 3.642A pdb=" N ASP C 69 " --> pdb=" O LYS C 65 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS C 70 " --> pdb=" O GLN C 66 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS C 72 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS C 73 " --> pdb=" O ASP C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 97 removed outlier: 3.993A pdb=" N VAL C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU C 96 " --> pdb=" O ARG C 92 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU C 97 " --> pdb=" O ALA C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 127 removed outlier: 3.515A pdb=" N ALA C 120 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG C 121 " --> pdb=" O HIS C 117 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER C 124 " --> pdb=" O ALA C 120 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASN C 125 " --> pdb=" O ARG C 121 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N HIS C 126 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 140 removed outlier: 3.515A pdb=" N ASN C 139 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS C 140 " --> pdb=" O LEU C 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 136 through 140' Processing helix chain 'C' and resid 141 through 162 removed outlier: 3.548A pdb=" N THR C 148 " --> pdb=" O GLU C 144 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS C 157 " --> pdb=" O ARG C 153 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU C 158 " --> pdb=" O ASN C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 192 removed outlier: 3.667A pdb=" N LEU C 184 " --> pdb=" O ASN C 180 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL C 192 " --> pdb=" O LEU C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 217 removed outlier: 3.540A pdb=" N LYS C 198 " --> pdb=" O PRO C 194 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS C 199 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE C 200 " --> pdb=" O TYR C 196 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N MET C 201 " --> pdb=" O ALA C 197 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU C 202 " --> pdb=" O LYS C 198 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N CYS C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET C 215 " --> pdb=" O ARG C 211 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASP C 217 " --> pdb=" O TYR C 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 87 removed outlier: 4.250A pdb=" N LYS E 86 " --> pdb=" O GLU E 82 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS E 87 " --> pdb=" O GLU E 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 82 through 87' Processing helix chain 'G' and resid 4 through 29 removed outlier: 3.777A pdb=" N GLU G 15 " --> pdb=" O LYS G 11 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP G 18 " --> pdb=" O TYR G 14 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU G 20 " --> pdb=" O ARG G 16 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET G 21 " --> pdb=" O ILE G 17 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU G 26 " --> pdb=" O SER G 22 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU G 27 " --> pdb=" O LEU G 23 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS G 29 " --> pdb=" O GLU G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 51 removed outlier: 3.543A pdb=" N VAL G 40 " --> pdb=" O ALA G 36 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N MET G 48 " --> pdb=" O ARG G 44 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS G 49 " --> pdb=" O ARG G 45 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N MET G 50 " --> pdb=" O ILE G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 121 removed outlier: 3.754A pdb=" N GLU G 109 " --> pdb=" O ARG G 105 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS G 110 " --> pdb=" O GLU G 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 25 removed outlier: 3.684A pdb=" N LYS I 15 " --> pdb=" O GLU I 11 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLU I 16 " --> pdb=" O GLU I 12 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA I 22 " --> pdb=" O LEU I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 30 through 41 removed outlier: 3.522A pdb=" N VAL I 34 " --> pdb=" O GLY I 30 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR I 35 " --> pdb=" O ALA I 31 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU I 39 " --> pdb=" O THR I 35 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG I 40 " --> pdb=" O LYS I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 54 through 58 removed outlier: 3.909A pdb=" N VAL I 57 " --> pdb=" O PRO I 54 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 69 removed outlier: 4.409A pdb=" N TYR I 63 " --> pdb=" O ALA I 59 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU I 67 " --> pdb=" O TYR I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 86 Processing helix chain 'I' and resid 99 through 101 No H-bonds generated for 'chain 'I' and resid 99 through 101' Processing helix chain 'I' and resid 102 through 110 removed outlier: 3.918A pdb=" N VAL I 107 " --> pdb=" O GLU I 103 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU I 108 " --> pdb=" O GLU I 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 117 removed outlier: 3.612A pdb=" N LEU I 115 " --> pdb=" O LYS I 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 46 removed outlier: 3.598A pdb=" N ASN B 36 " --> pdb=" O GLY B 32 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU B 44 " --> pdb=" O LYS B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.553A pdb=" N GLY B 50 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N SER B 52 " --> pdb=" O SER B 48 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS B 53 " --> pdb=" O TRP B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 80 removed outlier: 3.676A pdb=" N VAL B 78 " --> pdb=" O ASN B 74 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA B 80 " --> pdb=" O ASP B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 111 removed outlier: 3.958A pdb=" N ILE B 109 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE B 111 " --> pdb=" O ALA B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 125 removed outlier: 4.062A pdb=" N VAL B 122 " --> pdb=" O LYS B 118 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG B 124 " --> pdb=" O TRP B 120 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG B 125 " --> pdb=" O PHE B 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 21 removed outlier: 3.541A pdb=" N LYS D 18 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU D 20 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS D 21 " --> pdb=" O LEU D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 47 removed outlier: 3.584A pdb=" N GLU D 41 " --> pdb=" O ASP D 37 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS D 43 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA D 44 " --> pdb=" O GLU D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 75 removed outlier: 3.642A pdb=" N ASP D 69 " --> pdb=" O LYS D 65 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS D 70 " --> pdb=" O GLN D 66 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS D 72 " --> pdb=" O ARG D 68 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS D 73 " --> pdb=" O ASP D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 97 removed outlier: 3.993A pdb=" N VAL D 95 " --> pdb=" O ASN D 91 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU D 96 " --> pdb=" O ARG D 92 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU D 97 " --> pdb=" O ALA D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 127 removed outlier: 3.515A pdb=" N ALA D 120 " --> pdb=" O ASP D 116 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG D 121 " --> pdb=" O HIS D 117 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER D 124 " --> pdb=" O ALA D 120 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASN D 125 " --> pdb=" O ARG D 121 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS D 126 " --> pdb=" O LEU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 140 removed outlier: 3.514A pdb=" N ASN D 139 " --> pdb=" O THR D 136 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS D 140 " --> pdb=" O LEU D 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 136 through 140' Processing helix chain 'D' and resid 141 through 162 removed outlier: 3.547A pdb=" N THR D 148 " --> pdb=" O GLU D 144 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS D 157 " --> pdb=" O ARG D 153 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU D 158 " --> pdb=" O ASN D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 192 removed outlier: 3.666A pdb=" N LEU D 184 " --> pdb=" O ASN D 180 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL D 192 " --> pdb=" O LEU D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 217 removed outlier: 3.540A pdb=" N LYS D 198 " --> pdb=" O PRO D 194 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS D 199 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE D 200 " --> pdb=" O TYR D 196 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N MET D 201 " --> pdb=" O ALA D 197 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU D 202 " --> pdb=" O LYS D 198 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N CYS D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE D 210 " --> pdb=" O LYS D 206 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET D 215 " --> pdb=" O ARG D 211 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASP D 217 " --> pdb=" O TYR D 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 87 removed outlier: 4.248A pdb=" N LYS F 86 " --> pdb=" O GLU F 82 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS F 87 " --> pdb=" O GLU F 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 82 through 87' Processing helix chain 'H' and resid 4 through 29 removed outlier: 3.777A pdb=" N GLU H 15 " --> pdb=" O LYS H 11 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP H 18 " --> pdb=" O TYR H 14 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU H 20 " --> pdb=" O ARG H 16 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET H 21 " --> pdb=" O ILE H 17 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU H 26 " --> pdb=" O SER H 22 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU H 27 " --> pdb=" O LEU H 23 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS H 29 " --> pdb=" O GLU H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 51 removed outlier: 3.545A pdb=" N VAL H 40 " --> pdb=" O ALA H 36 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N MET H 48 " --> pdb=" O ARG H 44 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS H 49 " --> pdb=" O ARG H 45 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N MET H 50 " --> pdb=" O ILE H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 121 removed outlier: 3.753A pdb=" N GLU H 109 " --> pdb=" O ARG H 105 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS H 110 " --> pdb=" O GLU H 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 25 removed outlier: 3.683A pdb=" N LYS J 15 " --> pdb=" O GLU J 11 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLU J 16 " --> pdb=" O GLU J 12 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA J 22 " --> pdb=" O LEU J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 41 removed outlier: 3.522A pdb=" N VAL J 34 " --> pdb=" O GLY J 30 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR J 35 " --> pdb=" O ALA J 31 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU J 39 " --> pdb=" O THR J 35 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG J 40 " --> pdb=" O LYS J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 58 removed outlier: 3.907A pdb=" N VAL J 57 " --> pdb=" O PRO J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 69 removed outlier: 4.409A pdb=" N TYR J 63 " --> pdb=" O ALA J 59 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU J 67 " --> pdb=" O TYR J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 78 through 86 Processing helix chain 'J' and resid 99 through 101 No H-bonds generated for 'chain 'J' and resid 99 through 101' Processing helix chain 'J' and resid 102 through 110 removed outlier: 3.919A pdb=" N VAL J 107 " --> pdb=" O GLU J 103 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU J 108 " --> pdb=" O GLU J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 117 removed outlier: 3.613A pdb=" N LEU J 115 " --> pdb=" O LYS J 111 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 60 removed outlier: 3.542A pdb=" N VAL A 59 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE A 67 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N TYR A 18 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL A 100 " --> pdb=" O TYR A 18 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA A 20 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 3 through 6 removed outlier: 6.442A pdb=" N ASP C 4 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N TYR C 28 " --> pdb=" O ASP C 4 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASN C 6 " --> pdb=" O TYR C 28 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N PHE C 25 " --> pdb=" O TYR C 54 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N GLY C 56 " --> pdb=" O PHE C 25 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N PHE C 27 " --> pdb=" O GLY C 56 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N LYS C 58 " --> pdb=" O PHE C 27 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE C 80 " --> pdb=" O SER C 55 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU C 82 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE C 59 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLU C 84 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ILE C 81 " --> pdb=" O ILE C 102 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N SER C 104 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE C 83 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N LEU C 103 " --> pdb=" O GLU C 131 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ASN C 133 " --> pdb=" O LEU C 103 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 223 through 225 removed outlier: 3.767A pdb=" N VAL C 224 " --> pdb=" O LYS E 71 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS E 71 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL E 60 " --> pdb=" O VAL E 20 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL E 20 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LYS E 16 " --> pdb=" O GLN E 64 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL E 43 " --> pdb=" O VAL E 35 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N GLU E 37 " --> pdb=" O THR E 41 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N THR E 41 " --> pdb=" O GLU E 37 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE E 44 " --> pdb=" O VAL E 52 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 79 through 81 removed outlier: 3.697A pdb=" N ARG G 79 " --> pdb=" O VAL G 89 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 27 through 29 removed outlier: 4.483A pdb=" N LEU I 45 " --> pdb=" O ILE I 96 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL I 46 " --> pdb=" O ALA I 73 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL I 75 " --> pdb=" O VAL I 46 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE I 48 " --> pdb=" O VAL I 75 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 57 through 60 removed outlier: 3.543A pdb=" N VAL B 59 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ILE B 67 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N TYR B 18 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL B 100 " --> pdb=" O TYR B 18 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA B 20 " --> pdb=" O LEU B 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 3 through 6 removed outlier: 6.443A pdb=" N ASP D 4 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N TYR D 28 " --> pdb=" O ASP D 4 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASN D 6 " --> pdb=" O TYR D 28 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N PHE D 25 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N GLY D 56 " --> pdb=" O PHE D 25 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N PHE D 27 " --> pdb=" O GLY D 56 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N LYS D 58 " --> pdb=" O PHE D 27 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE D 80 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU D 82 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE D 59 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLU D 84 " --> pdb=" O ILE D 59 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ILE D 81 " --> pdb=" O ILE D 102 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N SER D 104 " --> pdb=" O ILE D 81 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE D 83 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LEU D 103 " --> pdb=" O GLU D 131 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ASN D 133 " --> pdb=" O LEU D 103 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 223 through 225 removed outlier: 3.775A pdb=" N VAL D 224 " --> pdb=" O LYS F 71 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS F 71 " --> pdb=" O VAL D 224 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL F 60 " --> pdb=" O VAL F 20 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL F 20 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LYS F 16 " --> pdb=" O GLN F 64 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL F 43 " --> pdb=" O VAL F 35 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N GLU F 37 " --> pdb=" O THR F 41 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N THR F 41 " --> pdb=" O GLU F 37 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE F 44 " --> pdb=" O VAL F 52 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 79 through 81 removed outlier: 3.697A pdb=" N ARG H 79 " --> pdb=" O VAL H 89 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 27 through 29 removed outlier: 4.484A pdb=" N LEU J 45 " --> pdb=" O ILE J 96 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL J 46 " --> pdb=" O ALA J 73 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL J 75 " --> pdb=" O VAL J 46 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE J 48 " --> pdb=" O VAL J 75 " (cutoff:3.500A) 362 hydrogen bonds defined for protein. 1068 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 302 hydrogen bonds 564 hydrogen bond angles 0 basepair planarities 120 basepair parallelities 324 stacking parallelities Total time for adding SS restraints: 3.62 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4782 1.34 - 1.45: 7556 1.45 - 1.57: 10348 1.57 - 1.69: 1030 1.69 - 1.81: 56 Bond restraints: 23772 Sorted by residual: bond pdb=" CA THR C 61 " pdb=" CB THR C 61 " ideal model delta sigma weight residual 1.527 1.557 -0.029 1.61e-02 3.86e+03 3.36e+00 bond pdb=" C3' U Y 198 " pdb=" O3' U Y 198 " ideal model delta sigma weight residual 1.415 1.452 -0.037 2.00e-02 2.50e+03 3.35e+00 bond pdb=" C3' U X 198 " pdb=" O3' U X 198 " ideal model delta sigma weight residual 1.415 1.451 -0.036 2.00e-02 2.50e+03 3.27e+00 bond pdb=" CA THR D 61 " pdb=" CB THR D 61 " ideal model delta sigma weight residual 1.527 1.556 -0.029 1.61e-02 3.86e+03 3.26e+00 bond pdb=" C THR C 105 " pdb=" N PRO C 106 " ideal model delta sigma weight residual 1.333 1.344 -0.011 7.80e-03 1.64e+04 2.01e+00 ... (remaining 23767 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 32869 2.31 - 4.62: 1514 4.62 - 6.93: 155 6.93 - 9.25: 28 9.25 - 11.56: 4 Bond angle restraints: 34570 Sorted by residual: angle pdb=" C3' U X 198 " pdb=" O3' U X 198 " pdb=" P U X 199 " ideal model delta sigma weight residual 119.70 126.54 -6.84 1.20e+00 6.94e-01 3.24e+01 angle pdb=" C3' U Y 198 " pdb=" O3' U Y 198 " pdb=" P U Y 199 " ideal model delta sigma weight residual 119.70 126.50 -6.80 1.20e+00 6.94e-01 3.21e+01 angle pdb=" C LYS C 60 " pdb=" N THR C 61 " pdb=" CA THR C 61 " ideal model delta sigma weight residual 122.82 130.31 -7.49 1.42e+00 4.96e-01 2.78e+01 angle pdb=" C LYS D 60 " pdb=" N THR D 61 " pdb=" CA THR D 61 " ideal model delta sigma weight residual 122.82 130.31 -7.49 1.42e+00 4.96e-01 2.78e+01 angle pdb=" C3' A X 224 " pdb=" O3' A X 224 " pdb=" P A X 225 " ideal model delta sigma weight residual 119.70 125.02 -5.32 1.20e+00 6.94e-01 1.96e+01 ... (remaining 34565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.23: 12232 34.23 - 68.46: 1010 68.46 - 102.69: 62 102.69 - 136.93: 0 136.93 - 171.16: 4 Dihedral angle restraints: 13308 sinusoidal: 9290 harmonic: 4018 Sorted by residual: dihedral pdb=" C4' G Y 37 " pdb=" C3' G Y 37 " pdb=" C2' G Y 37 " pdb=" C1' G Y 37 " ideal model delta sinusoidal sigma weight residual 36.35 -38.40 74.74 1 3.10e+00 1.04e-01 7.36e+02 dihedral pdb=" C4' G X 37 " pdb=" C3' G X 37 " pdb=" C2' G X 37 " pdb=" C1' G X 37 " ideal model delta sinusoidal sigma weight residual 36.34 -38.31 74.65 1 3.10e+00 1.04e-01 7.35e+02 dihedral pdb=" C4' C Y 101 " pdb=" C3' C Y 101 " pdb=" C2' C Y 101 " pdb=" C1' C Y 101 " ideal model delta sinusoidal sigma weight residual 36.34 -36.84 73.18 1 3.10e+00 1.04e-01 7.10e+02 ... (remaining 13305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 3500 0.098 - 0.196: 154 0.196 - 0.295: 617 0.295 - 0.393: 15 0.393 - 0.491: 2 Chirality restraints: 4288 Sorted by residual: chirality pdb=" P U Y 199 " pdb=" OP1 U Y 199 " pdb=" OP2 U Y 199 " pdb=" O5' U Y 199 " both_signs ideal model delta sigma weight residual True 2.17 -2.66 -0.49 2.00e-01 2.50e+01 6.02e+00 chirality pdb=" P U X 199 " pdb=" OP1 U X 199 " pdb=" OP2 U X 199 " pdb=" O5' U X 199 " both_signs ideal model delta sigma weight residual True 2.17 -2.66 -0.49 2.00e-01 2.50e+01 5.90e+00 chirality pdb=" P A X 225 " pdb=" OP1 A X 225 " pdb=" OP2 A X 225 " pdb=" O5' A X 225 " both_signs ideal model delta sigma weight residual True 2.17 -2.54 -0.37 2.00e-01 2.50e+01 3.43e+00 ... (remaining 4285 not shown) Planarity restraints: 2404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 63 " -0.045 5.00e-02 4.00e+02 6.85e-02 7.51e+00 pdb=" N PRO A 64 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 64 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 64 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 63 " -0.045 5.00e-02 4.00e+02 6.84e-02 7.49e+00 pdb=" N PRO B 64 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 64 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 64 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 180 " 0.040 5.00e-02 4.00e+02 6.07e-02 5.90e+00 pdb=" N PRO D 181 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO D 181 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 181 " 0.034 5.00e-02 4.00e+02 ... (remaining 2401 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 6327 2.83 - 3.35: 16876 3.35 - 3.87: 40547 3.87 - 4.38: 47212 4.38 - 4.90: 66607 Nonbonded interactions: 177569 Sorted by model distance: nonbonded pdb=" OP1 U X 16 " pdb=" OH TYR D 182 " model vdw 2.316 3.040 nonbonded pdb=" OH TYR J 4 " pdb=" O ALA J 49 " model vdw 2.328 3.040 nonbonded pdb=" OH TYR I 4 " pdb=" O ALA I 49 " model vdw 2.329 3.040 nonbonded pdb=" OP2 G Y 76 " pdb=" O2' A Y 252 " model vdw 2.359 3.040 nonbonded pdb=" OP2 G X 76 " pdb=" O2' A X 252 " model vdw 2.360 3.040 ... (remaining 177564 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'X' selection = chain 'Y' } Set up NCS constraints Number of NCS constrained groups: 6 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' } pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'D' } pdb_interpretation.ncs_group { reference = chain 'E' selection = chain 'F' } pdb_interpretation.ncs_group { reference = chain 'G' selection = chain 'H' } pdb_interpretation.ncs_group { reference = chain 'I' selection = chain 'J' } pdb_interpretation.ncs_group { reference = chain 'X' selection = chain 'Y' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 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: 1.780 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 24.810 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6024 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 : 0.006 0.317 23780 Z= 0.240 Angle : 0.998 37.092 34582 Z= 0.457 Chirality : 0.101 0.491 4288 Planarity : 0.005 0.069 2404 Dihedral : 19.079 171.157 10708 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.83 % Allowed : 7.79 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -4.65 (0.17), residues: 1344 helix: -4.88 (0.07), residues: 512 sheet: -0.44 (0.36), residues: 190 loop : -2.25 (0.19), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 105 TYR 0.019 0.002 TYR B 46 PHE 0.012 0.001 PHE D 152 TRP 0.006 0.001 TRP D 22 HIS 0.003 0.001 HIS J 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.17 (23772) covalent geometry : angle 0.93405 / 0.45 (34570) hydrogen bonds : bond 0.30575 / 19.61 ( 664) hydrogen bonds : angle 9.61124 / 6.46 ( 1632) metal coordination : bond 0.26123 / 11.06 ( 8) metal coordination : angle 18.82681 / 11.24 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7499 (mp0) cc_final: 0.7028 (mp0) REVERT: A 49 TRP cc_start: 0.7122 (t60) cc_final: 0.5839 (m-90) REVERT: A 79 LYS cc_start: 0.8873 (ttmt) cc_final: 0.8356 (tttt) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.0713 time to fit residues: 3.4805 Evaluate side-chains 26 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.043 Evaluate side-chains 72 residues out of total 205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 30 TYR cc_start: 0.6726 (p90) cc_final: 0.6084 (p90) REVERT: C 62 GLU cc_start: 0.6451 (mp0) cc_final: 0.5298 (tm-30) outliers start: 4 outliers final: 2 residues processed: 70 average time/residue: 0.0968 time to fit residues: 7.4007 Evaluate side-chains 46 residues out of total 205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.078 Evaluate side-chains 29 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 15 LEU cc_start: 0.7892 (mt) cc_final: 0.7444 (mp) REVERT: E 42 LEU cc_start: 0.8314 (mt) cc_final: 0.7911 (mt) REVERT: E 62 LEU cc_start: 0.8204 (tt) cc_final: 0.7806 (mt) outliers start: 1 outliers final: 1 residues processed: 28 average time/residue: 0.1407 time to fit residues: 4.0784 Evaluate side-chains 17 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.034 Evaluate side-chains 46 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 49 LYS cc_start: 0.8682 (mmtt) cc_final: 0.8317 (tmtt) REVERT: G 106 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8345 (mt-10) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1250 time to fit residues: 6.0113 Evaluate side-chains 32 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.027 Evaluate side-chains 20 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.037 Fit side-chains revert: symmetry clash REVERT: I 45 LEU cc_start: 0.8017 (mt) cc_final: 0.7784 (mt) REVERT: I 80 ASP cc_start: 0.8690 (t70) cc_final: 0.8485 (p0) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0561 time to fit residues: 1.2322 Evaluate side-chains 10 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.033 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.056 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0724 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 6.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 91 ASN C 125 ASN E 64 GLN ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.114288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.090769 restraints weight = 3879.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.093548 restraints weight = 2698.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.095440 restraints weight = 2033.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.096948 restraints weight = 1632.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.097975 restraints weight = 1362.514| |-----------------------------------------------------------------------------| r_work (final): 0.3853 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.116487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.100556 restraints weight = 7681.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.103004 restraints weight = 5299.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.104744 restraints weight = 3979.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.105956 restraints weight = 3162.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.106922 restraints weight = 2648.013| |-----------------------------------------------------------------------------| r_work (final): 0.4079 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.096491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.085041 restraints weight = 4895.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.086552 restraints weight = 3837.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.087873 restraints weight = 3136.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.088910 restraints weight = 2605.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.089587 restraints weight = 2200.063| |-----------------------------------------------------------------------------| r_work (final): 0.3955 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.077014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.064502 restraints weight = 5913.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.065701 restraints weight = 4444.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.066605 restraints weight = 3544.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.067300 restraints weight = 2970.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.067775 restraints weight = 2581.650| |-----------------------------------------------------------------------------| r_work (final): 0.3610 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.080299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.057786 restraints weight = 4345.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.059173 restraints weight = 3540.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.060317 restraints weight = 3045.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.061437 restraints weight = 2695.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.062398 restraints weight = 2406.252| |-----------------------------------------------------------------------------| r_work (final): 0.3524 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.090207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.088378 restraints weight = 1020030.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.088495 restraints weight = 729773.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.088480 restraints weight = 644234.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.088484 restraints weight = 629813.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.088471 restraints weight = 619166.998| |-----------------------------------------------------------------------------| r_work (final): 0.4222 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3955 r_free = 0.3955 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3918 r_free = 0.3918 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 13 (19 function evaluations) r_final: 0.3918 r_start: 0.3604 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3604 r_free = 0.3604 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3600 r_free = 0.3600 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 11 (15 function evaluations) r_final: 0.3600 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5611 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 23780 Z= 0.178 Angle : 1.099 18.872 34582 Z= 0.449 Chirality : 0.087 1.327 4288 Planarity : 0.006 0.073 2404 Dihedral : 17.974 160.211 7708 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.17 % Allowed : 4.64 % Favored : 95.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.92 (0.20), residues: 1344 helix: -2.84 (0.15), residues: 528 sheet: 0.04 (0.38), residues: 196 loop : -1.64 (0.22), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 9 TYR 0.023 0.002 TYR D 176 PHE 0.017 0.002 PHE C 210 TRP 0.020 0.002 TRP B 120 HIS 0.008 0.001 HIS F 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.18 (23772) covalent geometry : angle 1.09498 / 0.45 (34570) hydrogen bonds : bond 0.07701 / 4.98 ( 664) hydrogen bonds : angle 4.19513 / 2.86 ( 1632) metal coordination : bond 0.00699 / 0.30 ( 8) metal coordination : angle 5.32688 / 3.11 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 LEU cc_start: 0.8594 (tp) cc_final: 0.8307 (tp) REVERT: B 37 LEU cc_start: 0.9299 (pp) cc_final: 0.8705 (mp) REVERT: B 62 ASP cc_start: 0.4311 (p0) cc_final: 0.3708 (p0) REVERT: B 79 LYS cc_start: 0.9352 (ttmt) cc_final: 0.8830 (tttt) REVERT: B 100 VAL cc_start: 0.6586 (m) cc_final: 0.6135 (t) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0428 time to fit residues: 1.6745 Evaluate side-chains 24 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.046 Evaluate side-chains 42 residues out of total 205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.076 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 74 PHE cc_start: 0.9033 (m-10) cc_final: 0.8746 (m-10) REVERT: D 214 LEU cc_start: 0.8961 (tp) cc_final: 0.8585 (pp) outliers start: 1 outliers final: 0 residues processed: 41 average time/residue: 0.1006 time to fit residues: 4.5830 Evaluate side-chains 30 residues out of total 205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.092 Evaluate side-chains 19 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 15 LEU cc_start: 0.7889 (mt) cc_final: 0.7218 (mp) REVERT: F 42 LEU cc_start: 0.8141 (mt) cc_final: 0.7907 (mt) REVERT: F 90 LYS cc_start: 0.7037 (tptt) cc_final: 0.6571 (tptp) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.1306 time to fit residues: 2.5860 Evaluate side-chains 12 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.029 Evaluate side-chains 35 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 49 LYS cc_start: 0.9091 (mmtt) cc_final: 0.8879 (tmtt) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0796 time to fit residues: 3.0040 Evaluate side-chains 30 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.044 Evaluate side-chains 14 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.038 Fit side-chains revert: symmetry clash REVERT: J 45 LEU cc_start: 0.9498 (mt) cc_final: 0.9251 (mt) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0569 time to fit residues: 0.9020 Evaluate side-chains 8 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.034 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.056 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0722 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 142 optimal weight: 0.0030 chunk 169 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 146 optimal weight: 0.0970 chunk 65 optimal weight: 10.0000 chunk 178 optimal weight: 9.9990 chunk 131 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 overall best weight: 4.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 55 ASN B 94 ASN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN D 125 ASN D 180 ASN F 64 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.093558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.074668 restraints weight = 4564.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.076710 restraints weight = 3088.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.078210 restraints weight = 2287.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.079319 restraints weight = 1796.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.079835 restraints weight = 1481.514| |-----------------------------------------------------------------------------| r_work (final): 0.3551 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.095304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.080136 restraints weight = 7741.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.082064 restraints weight = 5613.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.083408 restraints weight = 4352.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.084594 restraints weight = 3567.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.085398 restraints weight = 3002.511| |-----------------------------------------------------------------------------| r_work (final): 0.3744 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.080367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.070407 restraints weight = 5514.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.071724 restraints weight = 4134.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.072673 restraints weight = 3273.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.073480 restraints weight = 2707.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.074105 restraints weight = 2297.274| |-----------------------------------------------------------------------------| r_work (final): 0.3727 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.066932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.056040 restraints weight = 6918.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.057170 restraints weight = 5173.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.058031 restraints weight = 4140.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.058644 restraints weight = 3467.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.059098 restraints weight = 3037.563| |-----------------------------------------------------------------------------| r_work (final): 0.3421 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.070652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.051008 restraints weight = 4771.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.052296 restraints weight = 3837.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.053314 restraints weight = 3242.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.054182 restraints weight = 2832.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.054868 restraints weight = 2530.685| |-----------------------------------------------------------------------------| r_work (final): 0.3359 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.082898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.075733 restraints weight = 75863.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.075647 restraints weight = 53319.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.076060 restraints weight = 44738.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.076052 restraints weight = 39640.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.076188 restraints weight = 36855.032| |-----------------------------------------------------------------------------| r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3727 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3727 r_free = 0.3727 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3721 r_free = 0.3721 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (10 function evaluations) r_final: 0.3721 r_start: 0.3431 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3430 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6518 moved from start: 0.6522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 23780 Z= 0.251 Angle : 1.119 19.766 34582 Z= 0.478 Chirality : 0.072 0.589 4288 Planarity : 0.007 0.096 2404 Dihedral : 18.381 160.394 7708 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 25.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.83 % Allowed : 8.96 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.21), residues: 1344 helix: -1.08 (0.20), residues: 532 sheet: -0.36 (0.33), residues: 242 loop : -1.59 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 16 TYR 0.039 0.004 TYR D 182 PHE 0.023 0.003 PHE C 152 TRP 0.033 0.004 TRP A 120 HIS 0.007 0.002 HIS H 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.25 (23772) covalent geometry : angle 1.09956 / 0.48 (34570) hydrogen bonds : bond 0.07497 / 4.76 ( 664) hydrogen bonds : angle 4.49195 / 2.99 ( 1632) metal coordination : bond 0.02560 / 1.11 ( 8) metal coordination : angle 11.22517 / 6.52 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.046 Fit side-chains REVERT: B 62 ASP cc_start: 0.5208 (p0) cc_final: 0.4783 (p0) REVERT: B 79 LYS cc_start: 0.9362 (ttmt) cc_final: 0.8843 (tttt) REVERT: B 100 VAL cc_start: 0.6722 (OUTLIER) cc_final: 0.6399 (t) REVERT: B 104 ILE cc_start: 0.8042 (mm) cc_final: 0.7780 (pt) outliers start: 2 outliers final: 0 residues processed: 22 average time/residue: 0.0372 time to fit residues: 0.9873 Evaluate side-chains 15 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 14 time to evaluate : 0.045 Evaluate side-chains 39 residues out of total 205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 175 LYS cc_start: 0.8045 (mmtm) cc_final: 0.7391 (pptt) outliers start: 1 outliers final: 0 residues processed: 39 average time/residue: 0.0876 time to fit residues: 3.8198 Evaluate side-chains 26 residues out of total 205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.082 Evaluate side-chains 16 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 42 LEU cc_start: 0.8498 (mt) cc_final: 0.8229 (mt) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0917 time to fit residues: 1.5630 Evaluate side-chains 9 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.033 Evaluate side-chains 32 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 21 MET cc_start: 0.9057 (tmm) cc_final: 0.8837 (tmm) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0714 time to fit residues: 2.4875 Evaluate side-chains 25 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.044 Evaluate side-chains 12 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 10 time to evaluate : 0.036 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 11 average time/residue: 0.0238 time to fit residues: 0.3597 Evaluate side-chains 8 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.055 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.060 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0773 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 75 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 129 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 159 optimal weight: 9.9990 chunk 10 optimal weight: 0.5980 chunk 86 optimal weight: 9.9990 chunk 154 optimal weight: 2.9990 chunk 22 optimal weight: 0.0980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN E 64 GLN ** G 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.099057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.078311 restraints weight = 4553.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.080361 restraints weight = 3225.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.081973 restraints weight = 2471.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.082956 restraints weight = 1998.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.083937 restraints weight = 1715.090| |-----------------------------------------------------------------------------| r_work (final): 0.3610 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.099368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.083967 restraints weight = 7838.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.086253 restraints weight = 5525.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.087952 restraints weight = 4159.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.089177 restraints weight = 3300.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.090164 restraints weight = 2743.232| |-----------------------------------------------------------------------------| r_work (final): 0.3829 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.082900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.070070 restraints weight = 5419.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.071343 restraints weight = 4024.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.072399 restraints weight = 3259.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.073167 restraints weight = 2760.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.073654 restraints weight = 2411.856| |-----------------------------------------------------------------------------| r_work (final): 0.3721 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.069426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.056351 restraints weight = 6927.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.057483 restraints weight = 5381.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.058397 restraints weight = 4447.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.059078 restraints weight = 3827.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.059607 restraints weight = 3399.238| |-----------------------------------------------------------------------------| r_work (final): 0.3424 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.069236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.048336 restraints weight = 4910.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.049633 restraints weight = 3986.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.050719 restraints weight = 3428.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.051341 restraints weight = 3033.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.052075 restraints weight = 2771.964| |-----------------------------------------------------------------------------| r_work (final): 0.3356 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.084349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.082833 restraints weight = 100858.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.082907 restraints weight = 79125.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.083000 restraints weight = 66068.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.083000 restraints weight = 56741.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.083000 restraints weight = 56719.663| |-----------------------------------------------------------------------------| r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3729 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3729 r_free = 0.3729 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3727 r_free = 0.3727 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (13 function evaluations) r_final: 0.3727 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6154 moved from start: 0.6946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23780 Z= 0.165 Angle : 0.921 11.902 34582 Z= 0.390 Chirality : 0.067 0.526 4288 Planarity : 0.006 0.076 2404 Dihedral : 18.123 159.388 7708 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 18.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.17 % Allowed : 4.81 % Favored : 95.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.22), residues: 1344 helix: 0.01 (0.21), residues: 536 sheet: -0.55 (0.32), residues: 256 loop : -1.70 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG H 38 TYR 0.018 0.002 TYR C 176 PHE 0.017 0.002 PHE D 152 TRP 0.037 0.004 TRP H 58 HIS 0.004 0.001 HIS F 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (23772) covalent geometry : angle 0.91768 / 0.39 (34570) hydrogen bonds : bond 0.05179 / 3.27 ( 664) hydrogen bonds : angle 4.17020 / 2.76 ( 1632) metal coordination : bond 0.01013 / 0.45 ( 8) metal coordination : angle 4.57017 / 2.56 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.049 Fit side-chains revert: symmetry clash REVERT: B 62 ASP cc_start: 0.5573 (p0) cc_final: 0.4310 (p0) REVERT: B 79 LYS cc_start: 0.9324 (ttmt) cc_final: 0.8907 (tttt) REVERT: B 104 ILE cc_start: 0.7717 (mm) cc_final: 0.7463 (pt) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0519 time to fit residues: 1.4259 Evaluate side-chains 15 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.046 Evaluate side-chains 35 residues out of total 205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 152 PHE cc_start: 0.8715 (m-80) cc_final: 0.8324 (m-80) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0841 time to fit residues: 3.3146 Evaluate side-chains 25 residues out of total 205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.074 Evaluate side-chains 16 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 21 GLU cc_start: 0.8609 (mp0) cc_final: 0.8408 (mp0) REVERT: E 36 ASP cc_start: 0.8406 (m-30) cc_final: 0.8180 (m-30) REVERT: E 82 GLU cc_start: 0.8268 (mp0) cc_final: 0.7931 (mp0) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0836 time to fit residues: 1.4379 Evaluate side-chains 9 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.026 Evaluate side-chains 30 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 33 TRP cc_start: 0.8806 (p90) cc_final: 0.8442 (p-90) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0489 time to fit residues: 1.6652 Evaluate side-chains 23 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.042 Evaluate side-chains 13 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 12 time to evaluate : 0.035 Fit side-chains REVERT: J 18 LEU cc_start: 0.9423 (tp) cc_final: 0.9182 (mt) outliers start: 1 outliers final: 0 residues processed: 12 average time/residue: 0.0220 time to fit residues: 0.3660 Evaluate side-chains 9 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.035 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.062 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0790 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.0870 chunk 178 optimal weight: 10.0000 chunk 126 optimal weight: 0.0040 chunk 47 optimal weight: 4.9990 chunk 14 optimal weight: 0.0070 chunk 73 optimal weight: 8.9990 chunk 108 optimal weight: 0.0030 chunk 57 optimal weight: 0.0170 chunk 125 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 10 optimal weight: 0.0870 overall best weight: 0.0236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 29 GLN C 180 ASN E 40 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.107771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.084635 restraints weight = 4237.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.087213 restraints weight = 2969.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.089091 restraints weight = 2240.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.090639 restraints weight = 1802.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.091661 restraints weight = 1506.008| |-----------------------------------------------------------------------------| r_work (final): 0.3765 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.105854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.088050 restraints weight = 7327.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.090649 restraints weight = 5180.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.092601 restraints weight = 3909.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.094045 restraints weight = 3093.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.095124 restraints weight = 2544.565| |-----------------------------------------------------------------------------| r_work (final): 0.3942 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.084438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.070505 restraints weight = 5913.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.072036 restraints weight = 4329.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.072926 restraints weight = 3439.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.073907 restraints weight = 2926.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.074473 restraints weight = 2547.109| |-----------------------------------------------------------------------------| r_work (final): 0.3816 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.074793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.061045 restraints weight = 6680.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.062272 restraints weight = 5287.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.063216 restraints weight = 4422.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.063958 restraints weight = 3818.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.064522 restraints weight = 3392.483| |-----------------------------------------------------------------------------| r_work (final): 0.3523 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.072811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.053437 restraints weight = 4752.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.054962 restraints weight = 3794.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.055948 restraints weight = 3202.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.057050 restraints weight = 2817.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 14)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.057722 restraints weight = 2496.003| |-----------------------------------------------------------------------------| r_work (final): 0.3291 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.084340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.080260 restraints weight = 119485.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.081318 restraints weight = 56625.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.081951 restraints weight = 32195.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.082348 restraints weight = 20463.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.082626 restraints weight = 14021.740| |-----------------------------------------------------------------------------| r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5554 moved from start: 0.6940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23780 Z= 0.125 Angle : 0.861 9.936 34582 Z= 0.359 Chirality : 0.064 0.489 4288 Planarity : 0.004 0.049 2404 Dihedral : 17.850 164.033 7708 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.17 % Allowed : 3.65 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.78 (0.22), residues: 1344 helix: 0.28 (0.22), residues: 528 sheet: -0.30 (0.33), residues: 248 loop : -1.32 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 38 TYR 0.021 0.002 TYR D 205 PHE 0.020 0.002 PHE A 121 TRP 0.014 0.002 TRP G 58 HIS 0.002 0.001 HIS C 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.13 (23772) covalent geometry : angle 0.86023 / 0.36 (34570) hydrogen bonds : bond 0.04322 / 2.74 ( 664) hydrogen bonds : angle 3.72628 / 2.49 ( 1632) metal coordination : bond 0.00182 / 0.08 ( 8) metal coordination : angle 2.10705 / 1.14 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 39 ARG cc_start: 0.9187 (ptt90) cc_final: 0.8826 (ptt90) REVERT: B 63 PHE cc_start: 0.7765 (m-80) cc_final: 0.7330 (m-10) REVERT: B 79 LYS cc_start: 0.9330 (ttmt) cc_final: 0.8851 (tttt) REVERT: B 103 THR cc_start: 0.5788 (m) cc_final: 0.5569 (t) REVERT: B 104 ILE cc_start: 0.7957 (mm) cc_final: 0.7297 (pt) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0678 time to fit residues: 2.0120 Evaluate side-chains 20 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.045 Evaluate side-chains 38 residues out of total 205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 112 ASP cc_start: 0.8636 (t0) cc_final: 0.8295 (t0) REVERT: C 152 PHE cc_start: 0.8308 (m-10) cc_final: 0.8017 (m-80) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0966 time to fit residues: 4.0807 Evaluate side-chains 33 residues out of total 205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.078 Evaluate side-chains 15 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.032 Fit side-chains revert: symmetry clash REVERT: F 36 ASP cc_start: 0.6961 (m-30) cc_final: 0.6716 (m-30) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0779 time to fit residues: 1.2693 Evaluate side-chains 7 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.034 Evaluate side-chains 32 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.026 Fit side-chains revert: symmetry clash REVERT: G 33 TRP cc_start: 0.8537 (p90) cc_final: 0.8311 (p-90) REVERT: G 109 GLU cc_start: 0.9446 (tm-30) cc_final: 0.9238 (tm-30) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0795 time to fit residues: 2.7419 Evaluate side-chains 21 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.045 Evaluate side-chains 17 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.037 Fit side-chains revert: symmetry clash REVERT: I 18 LEU cc_start: 0.9389 (tp) cc_final: 0.9112 (mt) REVERT: I 45 LEU cc_start: 0.9025 (mt) cc_final: 0.8721 (mt) REVERT: I 61 LEU cc_start: 0.7978 (mm) cc_final: 0.7748 (mm) REVERT: I 65 CYS cc_start: 0.9446 (m) cc_final: 0.9227 (m) outliers start: 1 outliers final: 0 residues processed: 17 average time/residue: 0.0387 time to fit residues: 0.7795 Evaluate side-chains 11 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.034 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.062 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0766 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 159 optimal weight: 10.0000 chunk 60 optimal weight: 0.0050 chunk 8 optimal weight: 0.2980 chunk 79 optimal weight: 10.0000 chunk 123 optimal weight: 0.0010 chunk 92 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 50 optimal weight: 9.9990 chunk 35 optimal weight: 0.0030 chunk 109 optimal weight: 0.0070 chunk 37 optimal weight: 6.9990 overall best weight: 0.0628 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 40 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.106657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.085738 restraints weight = 4178.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.087999 restraints weight = 2907.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.089613 restraints weight = 2207.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.090261 restraints weight = 1784.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.091360 restraints weight = 1580.249| |-----------------------------------------------------------------------------| r_work (final): 0.3780 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.108256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.093154 restraints weight = 7844.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.095324 restraints weight = 5704.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.096928 restraints weight = 4369.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.098211 restraints weight = 3518.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.099222 restraints weight = 2922.624| |-----------------------------------------------------------------------------| r_work (final): 0.3986 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.085398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.073512 restraints weight = 5893.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.075200 restraints weight = 3910.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.076309 restraints weight = 2933.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.077059 restraints weight = 2394.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.077634 restraints weight = 2040.507| |-----------------------------------------------------------------------------| r_work (final): 0.3846 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.074114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.060214 restraints weight = 6648.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.061476 restraints weight = 5259.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.062416 restraints weight = 4391.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.063150 restraints weight = 3793.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.063728 restraints weight = 3373.021| |-----------------------------------------------------------------------------| r_work (final): 0.3508 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.074881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.055165 restraints weight = 4536.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.056787 restraints weight = 3546.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.058205 restraints weight = 2947.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.059191 restraints weight = 2509.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.060154 restraints weight = 2221.635| |-----------------------------------------------------------------------------| r_work (final): 0.3532 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.085043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.080878 restraints weight = 120597.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.081951 restraints weight = 57929.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.082597 restraints weight = 33282.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.083001 restraints weight = 21258.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.083269 restraints weight = 14746.118| |-----------------------------------------------------------------------------| r_work (final): 0.4309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.7165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23780 Z= 0.125 Angle : 0.845 10.076 34582 Z= 0.353 Chirality : 0.063 0.489 4288 Planarity : 0.004 0.059 2404 Dihedral : 17.645 169.906 7708 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.72 (0.22), residues: 1344 helix: 0.43 (0.23), residues: 534 sheet: -0.46 (0.32), residues: 244 loop : -1.30 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 80 TYR 0.021 0.001 TYR C 205 PHE 0.012 0.001 PHE D 152 TRP 0.009 0.001 TRP H 58 HIS 0.001 0.000 HIS D 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (23772) covalent geometry : angle 0.84438 / 0.35 (34570) hydrogen bonds : bond 0.04270 / 2.69 ( 664) hydrogen bonds : angle 3.80901 / 2.53 ( 1632) metal coordination : bond 0.00283 / 0.13 ( 8) metal coordination : angle 2.00286 / 1.13 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.026 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 TYR cc_start: 0.7886 (m-10) cc_final: 0.7379 (m-10) REVERT: A 63 PHE cc_start: 0.7668 (m-80) cc_final: 0.7235 (m-10) REVERT: A 79 LYS cc_start: 0.9124 (ttmt) cc_final: 0.8545 (tttt) REVERT: A 100 VAL cc_start: 0.6425 (m) cc_final: 0.5973 (p) REVERT: A 121 PHE cc_start: 0.4166 (t80) cc_final: 0.3966 (t80) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0334 time to fit residues: 0.9154 Evaluate side-chains 16 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.043 Evaluate side-chains 39 residues out of total 205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 152 PHE cc_start: 0.8052 (m-10) cc_final: 0.7786 (m-80) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0949 time to fit residues: 4.0893 Evaluate side-chains 34 residues out of total 205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.091 Evaluate side-chains 13 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.044 Fit side-chains REVERT: F 82 GLU cc_start: 0.7852 (mp0) cc_final: 0.7411 (mp0) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0633 time to fit residues: 0.9149 Evaluate side-chains 8 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.034 Evaluate side-chains 28 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 85 TYR cc_start: 0.6535 (m-80) cc_final: 0.6309 (m-80) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0513 time to fit residues: 1.6240 Evaluate side-chains 22 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.045 Evaluate side-chains 18 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.037 Fit side-chains REVERT: I 18 LEU cc_start: 0.9422 (tp) cc_final: 0.9178 (mt) REVERT: I 45 LEU cc_start: 0.9326 (mt) cc_final: 0.9088 (mt) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0623 time to fit residues: 1.2474 Evaluate side-chains 10 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.039 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.036 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0777 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 44 optimal weight: 0.3980 chunk 113 optimal weight: 0.0980 chunk 174 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 149 optimal weight: 9.9990 chunk 133 optimal weight: 3.9990 chunk 29 optimal weight: 0.0000 chunk 2 optimal weight: 0.5980 chunk 179 optimal weight: 9.9990 chunk 142 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 87 HIS ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.108187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.087231 restraints weight = 4547.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.089495 restraints weight = 3156.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.091118 restraints weight = 2391.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.092317 restraints weight = 1939.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.093134 restraints weight = 1657.728| |-----------------------------------------------------------------------------| r_work (final): 0.3778 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.107075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.092482 restraints weight = 7789.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.094738 restraints weight = 5492.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.096396 restraints weight = 4128.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.097614 restraints weight = 3271.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.098486 restraints weight = 2705.409| |-----------------------------------------------------------------------------| r_work (final): 0.3973 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.081880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.070551 restraints weight = 5376.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.071733 restraints weight = 4079.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.072815 restraints weight = 3287.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.073453 restraints weight = 2729.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.074047 restraints weight = 2380.682| |-----------------------------------------------------------------------------| r_work (final): 0.3763 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.073859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.059702 restraints weight = 6640.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.060779 restraints weight = 5459.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.061489 restraints weight = 4664.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.062189 restraints weight = 4155.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.062735 restraints weight = 3748.203| |-----------------------------------------------------------------------------| r_work (final): 0.3477 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.075788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.057710 restraints weight = 5360.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.059235 restraints weight = 4313.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.060459 restraints weight = 3620.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.061408 restraints weight = 3121.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.061995 restraints weight = 2755.672| |-----------------------------------------------------------------------------| r_work (final): 0.3539 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.085070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.083558 restraints weight = 1051215.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.083636 restraints weight = 763497.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.083607 restraints weight = 691369.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.083595 restraints weight = 680115.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.083601 restraints weight = 666885.618| |-----------------------------------------------------------------------------| r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5923 moved from start: 0.7470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23780 Z= 0.121 Angle : 0.840 10.026 34582 Z= 0.352 Chirality : 0.062 0.482 4288 Planarity : 0.004 0.051 2404 Dihedral : 17.561 172.017 7708 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.63 (0.22), residues: 1344 helix: 0.47 (0.23), residues: 528 sheet: -0.40 (0.33), residues: 240 loop : -1.19 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 80 TYR 0.027 0.002 TYR D 49 PHE 0.013 0.001 PHE D 152 TRP 0.007 0.001 TRP A 120 HIS 0.002 0.001 HIS I 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (23772) covalent geometry : angle 0.83892 / 0.35 (34570) hydrogen bonds : bond 0.04197 / 2.61 ( 664) hydrogen bonds : angle 3.90789 / 2.61 ( 1632) metal coordination : bond 0.00321 / 0.14 ( 8) metal coordination : angle 2.41317 / 1.36 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 4 MET cc_start: 0.8587 (ppp) cc_final: 0.7913 (tpt) REVERT: B 63 PHE cc_start: 0.7587 (m-80) cc_final: 0.7316 (m-10) REVERT: B 79 LYS cc_start: 0.9122 (ttmt) cc_final: 0.8545 (tttt) REVERT: B 83 ILE cc_start: 0.9143 (pt) cc_final: 0.8884 (mt) REVERT: B 121 PHE cc_start: 0.4578 (t80) cc_final: 0.4363 (t80) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0848 time to fit residues: 1.9465 Evaluate side-chains 17 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.043 Evaluate side-chains 37 residues out of total 205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0941 time to fit residues: 3.8718 Evaluate side-chains 34 residues out of total 205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.073 Evaluate side-chains 14 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.033 Fit side-chains REVERT: E 73 ASP cc_start: 0.5319 (p0) cc_final: 0.5110 (p0) REVERT: E 82 GLU cc_start: 0.7557 (mp0) cc_final: 0.7192 (mp0) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0283 time to fit residues: 0.4891 Evaluate side-chains 8 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.034 Evaluate side-chains 31 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0620 time to fit residues: 2.1170 Evaluate side-chains 25 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.045 Evaluate side-chains 17 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.035 Fit side-chains REVERT: I 18 LEU cc_start: 0.9460 (tp) cc_final: 0.9239 (mt) REVERT: I 45 LEU cc_start: 0.9415 (mt) cc_final: 0.9187 (mt) REVERT: I 115 LEU cc_start: 0.8085 (mt) cc_final: 0.7621 (tp) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0505 time to fit residues: 0.9759 Evaluate side-chains 10 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.021 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.050 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0512 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 49 optimal weight: 10.0000 chunk 134 optimal weight: 1.9990 chunk 124 optimal weight: 0.0270 chunk 36 optimal weight: 4.9990 chunk 24 optimal weight: 0.0980 chunk 179 optimal weight: 10.0000 chunk 106 optimal weight: 0.9980 chunk 158 optimal weight: 8.9990 chunk 131 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 overall best weight: 1.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 HIS ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.106963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.085942 restraints weight = 4321.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.088043 restraints weight = 3085.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.089649 restraints weight = 2395.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.090833 restraints weight = 1969.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.091403 restraints weight = 1688.952| |-----------------------------------------------------------------------------| r_work (final): 0.3749 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.103202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.087931 restraints weight = 7501.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.090360 restraints weight = 5215.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.092145 restraints weight = 3883.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.093461 restraints weight = 3059.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.094471 restraints weight = 2515.876| |-----------------------------------------------------------------------------| r_work (final): 0.3915 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.081654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.067837 restraints weight = 5913.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.069531 restraints weight = 4323.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.070761 restraints weight = 3326.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.071731 restraints weight = 2724.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.072435 restraints weight = 2331.089| |-----------------------------------------------------------------------------| r_work (final): 0.3954 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.072792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.057902 restraints weight = 6823.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.058943 restraints weight = 5613.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.059729 restraints weight = 4857.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.060218 restraints weight = 4331.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.060736 restraints weight = 3994.076| |-----------------------------------------------------------------------------| r_work (final): 0.3408 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.120126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.103771 restraints weight = 5619.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.105904 restraints weight = 3825.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.107541 restraints weight = 2846.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.108764 restraints weight = 2209.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.109664 restraints weight = 1779.586| |-----------------------------------------------------------------------------| r_work (final): 0.3691 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.084409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.083012 restraints weight = 1060422.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.083034 restraints weight = 761523.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.083070 restraints weight = 663043.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.083063 restraints weight = 671821.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.083031 restraints weight = 660377.820| |-----------------------------------------------------------------------------| r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5855 moved from start: 0.7816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23780 Z= 0.123 Angle : 0.843 10.123 34582 Z= 0.353 Chirality : 0.061 0.485 4288 Planarity : 0.005 0.051 2404 Dihedral : 17.538 173.746 7708 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.51 (0.23), residues: 1344 helix: 0.60 (0.23), residues: 548 sheet: -0.44 (0.35), residues: 216 loop : -1.15 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 45 TYR 0.016 0.002 TYR D 205 PHE 0.049 0.002 PHE C 152 TRP 0.009 0.001 TRP G 58 HIS 0.003 0.001 HIS C 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (23772) covalent geometry : angle 0.84124 / 0.35 (34570) hydrogen bonds : bond 0.04143 / 2.60 ( 664) hydrogen bonds : angle 3.80290 / 2.51 ( 1632) metal coordination : bond 0.00565 / 0.24 ( 8) metal coordination : angle 3.13243 / 1.77 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 4 MET cc_start: 0.8537 (ppp) cc_final: 0.7854 (tpt) REVERT: B 21 PHE cc_start: 0.8478 (p90) cc_final: 0.8233 (p90) REVERT: B 63 PHE cc_start: 0.7721 (m-80) cc_final: 0.7295 (m-10) REVERT: B 79 LYS cc_start: 0.9141 (ttmt) cc_final: 0.8541 (tttt) REVERT: B 83 ILE cc_start: 0.9164 (pt) cc_final: 0.8928 (mt) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0587 time to fit residues: 1.2694 Evaluate side-chains 15 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.040 Evaluate side-chains 38 residues out of total 205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 160 LYS cc_start: 0.7095 (tttt) cc_final: 0.6435 (mmtt) REVERT: D 175 LYS cc_start: 0.8277 (mmtm) cc_final: 0.7216 (pptt) REVERT: D 180 ASN cc_start: 0.7538 (m-40) cc_final: 0.7124 (m-40) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0876 time to fit residues: 3.7170 Evaluate side-chains 29 residues out of total 205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.056 Evaluate side-chains 12 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.035 Fit side-chains REVERT: E 82 GLU cc_start: 0.8541 (mp0) cc_final: 0.8301 (mp0) outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0340 time to fit residues: 0.5067 Evaluate side-chains 7 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.032 Evaluate side-chains 26 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.044 Fit side-chains revert: symmetry clash REVERT: G 85 TYR cc_start: 0.7055 (m-80) cc_final: 0.6597 (m-80) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0400 time to fit residues: 1.2186 Evaluate side-chains 21 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.044 Evaluate side-chains 16 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.034 Fit side-chains REVERT: I 18 LEU cc_start: 0.9523 (tp) cc_final: 0.9310 (mt) REVERT: I 63 TYR cc_start: 0.9430 (m-10) cc_final: 0.9168 (m-80) REVERT: I 115 LEU cc_start: 0.8086 (mt) cc_final: 0.7645 (tp) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0374 time to fit residues: 0.7143 Evaluate side-chains 12 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.035 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.036 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0486 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 172 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 179 optimal weight: 9.9990 chunk 40 optimal weight: 0.9990 chunk 135 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 147 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.094538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.074818 restraints weight = 4654.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.076742 restraints weight = 3225.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.078037 restraints weight = 2435.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.078590 restraints weight = 1987.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.079523 restraints weight = 1737.515| |-----------------------------------------------------------------------------| r_work (final): 0.3529 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.093288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.080054 restraints weight = 8642.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.082076 restraints weight = 6012.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.083552 restraints weight = 4490.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.084692 restraints weight = 3531.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.085538 restraints weight = 2906.840| |-----------------------------------------------------------------------------| r_work (final): 0.3737 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.075817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.063463 restraints weight = 6558.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.064741 restraints weight = 4835.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.065647 restraints weight = 3843.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.066378 restraints weight = 3215.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.066926 restraints weight = 2791.405| |-----------------------------------------------------------------------------| r_work (final): 0.3609 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.066948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.054396 restraints weight = 7511.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.055598 restraints weight = 5804.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.056440 restraints weight = 4809.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.056977 restraints weight = 4141.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.057511 restraints weight = 3728.162| |-----------------------------------------------------------------------------| r_work (final): 0.3351 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.067797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.050419 restraints weight = 5296.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.051799 restraints weight = 4195.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.052870 restraints weight = 3500.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.053885 restraints weight = 3005.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.054680 restraints weight = 2636.539| |-----------------------------------------------------------------------------| r_work (final): 0.3375 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.079965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.072764 restraints weight = 77195.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.072921 restraints weight = 50034.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.073224 restraints weight = 41527.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.073259 restraints weight = 31921.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.073356 restraints weight = 32034.989| |-----------------------------------------------------------------------------| r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 0.8905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 23780 Z= 0.193 Angle : 0.955 10.708 34582 Z= 0.409 Chirality : 0.065 0.503 4288 Planarity : 0.006 0.063 2404 Dihedral : 17.787 179.391 7708 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 20.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.69 (0.23), residues: 1344 helix: 0.50 (0.22), residues: 536 sheet: -0.62 (0.32), residues: 240 loop : -1.24 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 105 TYR 0.021 0.002 TYR C 182 PHE 0.026 0.003 PHE C 152 TRP 0.025 0.003 TRP G 58 HIS 0.007 0.002 HIS H 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.19 (23772) covalent geometry : angle 0.94877 / 0.41 (34570) hydrogen bonds : bond 0.05532 / 3.46 ( 664) hydrogen bonds : angle 4.38442 / 2.87 ( 1632) metal coordination : bond 0.01489 / 0.66 ( 8) metal coordination : angle 5.74251 / 3.36 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.045 Fit side-chains REVERT: A 18 TYR cc_start: 0.7909 (m-10) cc_final: 0.7649 (m-10) REVERT: A 31 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7568 (mm-30) REVERT: A 63 PHE cc_start: 0.7815 (m-80) cc_final: 0.7394 (m-10) REVERT: A 79 LYS cc_start: 0.9240 (ttmt) cc_final: 0.8679 (tttt) REVERT: A 100 VAL cc_start: 0.6814 (m) cc_final: 0.6394 (p) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0354 time to fit residues: 0.8216 Evaluate side-chains 16 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.046 Evaluate side-chains 32 residues out of total 205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 152 PHE cc_start: 0.8623 (m-80) cc_final: 0.8094 (m-80) REVERT: D 160 LYS cc_start: 0.7795 (tttt) cc_final: 0.7080 (mmtt) REVERT: D 175 LYS cc_start: 0.7848 (mmtm) cc_final: 0.6967 (pptt) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0825 time to fit residues: 2.9398 Evaluate side-chains 23 residues out of total 205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.075 Evaluate side-chains 12 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.032 Fit side-chains REVERT: E 27 MET cc_start: 0.4988 (mpp) cc_final: 0.4787 (pmm) outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0283 time to fit residues: 0.4233 Evaluate side-chains 7 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.033 Evaluate side-chains 26 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.042 Fit side-chains revert: symmetry clash REVERT: G 45 ARG cc_start: 0.8959 (mmm160) cc_final: 0.8703 (tpm170) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0495 time to fit residues: 1.4439 Evaluate side-chains 20 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.026 Evaluate side-chains 12 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.022 Fit side-chains REVERT: I 115 LEU cc_start: 0.8361 (mt) cc_final: 0.7973 (tp) outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0316 time to fit residues: 0.4556 Evaluate side-chains 10 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.021 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.047 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0547 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 153 optimal weight: 8.9990 chunk 131 optimal weight: 0.0070 chunk 106 optimal weight: 0.0870 chunk 111 optimal weight: 0.9990 chunk 90 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 39 optimal weight: 0.0070 chunk 82 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.101432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.081229 restraints weight = 4417.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.083245 restraints weight = 3084.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.084480 restraints weight = 2365.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.085091 restraints weight = 1962.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.086150 restraints weight = 1727.495| |-----------------------------------------------------------------------------| r_work (final): 0.3664 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.099715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.085987 restraints weight = 8313.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.088073 restraints weight = 5960.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.089684 restraints weight = 4490.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.090847 restraints weight = 3532.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.091551 restraints weight = 2883.862| |-----------------------------------------------------------------------------| r_work (final): 0.3832 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.079240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.066942 restraints weight = 6257.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.068330 restraints weight = 4579.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.069374 restraints weight = 3612.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.070069 restraints weight = 2989.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.070828 restraints weight = 2601.612| |-----------------------------------------------------------------------------| r_work (final): 0.3703 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.069299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.055799 restraints weight = 6774.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.056926 restraints weight = 5384.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.057757 restraints weight = 4505.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.058375 restraints weight = 3926.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.058890 restraints weight = 3534.427| |-----------------------------------------------------------------------------| r_work (final): 0.3421 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.072282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.053407 restraints weight = 4815.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.055074 restraints weight = 3705.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.056384 restraints weight = 3008.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.057490 restraints weight = 2550.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.058341 restraints weight = 2216.438| |-----------------------------------------------------------------------------| r_work (final): 0.3503 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.081696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.077670 restraints weight = 116633.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.078823 restraints weight = 52698.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.079488 restraints weight = 28805.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.079902 restraints weight = 17786.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.080184 restraints weight = 12053.559| |-----------------------------------------------------------------------------| r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5789 moved from start: 0.8876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23780 Z= 0.130 Angle : 0.874 10.449 34582 Z= 0.366 Chirality : 0.063 0.515 4288 Planarity : 0.005 0.062 2404 Dihedral : 17.641 177.470 7708 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.39 (0.23), residues: 1344 helix: 0.70 (0.23), residues: 534 sheet: -0.73 (0.32), residues: 220 loop : -0.88 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 45 TYR 0.027 0.001 TYR G 14 PHE 0.034 0.002 PHE D 152 TRP 0.009 0.001 TRP B 120 HIS 0.006 0.001 HIS D 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (23772) covalent geometry : angle 0.87262 / 0.37 (34570) hydrogen bonds : bond 0.04529 / 2.82 ( 664) hydrogen bonds : angle 4.12968 / 2.73 ( 1632) metal coordination : bond 0.00388 / 0.18 ( 8) metal coordination : angle 2.42120 / 1.39 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.037 Fit side-chains revert: symmetry clash REVERT: B 4 MET cc_start: 0.8312 (ppp) cc_final: 0.7747 (tpp) REVERT: B 63 PHE cc_start: 0.7762 (m-80) cc_final: 0.7282 (m-10) REVERT: B 79 LYS cc_start: 0.9125 (ttmt) cc_final: 0.8591 (tttt) REVERT: B 121 PHE cc_start: 0.5568 (t80) cc_final: 0.5318 (t80) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0379 time to fit residues: 0.7241 Evaluate side-chains 13 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.044 Evaluate side-chains 37 residues out of total 205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 152 PHE cc_start: 0.8545 (m-80) cc_final: 0.8148 (m-80) REVERT: D 175 LYS cc_start: 0.7963 (mmtm) cc_final: 0.7010 (pptt) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0951 time to fit residues: 3.8913 Evaluate side-chains 27 residues out of total 205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.077 Evaluate side-chains 11 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.034 Fit side-chains REVERT: E 36 ASP cc_start: 0.7533 (m-30) cc_final: 0.7147 (m-30) REVERT: E 73 ASP cc_start: 0.5559 (p0) cc_final: 0.5224 (p0) outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0317 time to fit residues: 0.4366 Evaluate side-chains 9 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.033 Evaluate side-chains 26 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.045 Fit side-chains REVERT: G 45 ARG cc_start: 0.9020 (mmm160) cc_final: 0.8696 (tpm170) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0766 time to fit residues: 2.1636 Evaluate side-chains 22 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.026 Evaluate side-chains 13 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.036 Fit side-chains REVERT: I 45 LEU cc_start: 0.9380 (mt) cc_final: 0.9162 (mt) REVERT: I 115 LEU cc_start: 0.8298 (mt) cc_final: 0.7932 (tp) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0611 time to fit residues: 0.8983 Evaluate side-chains 8 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.021 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.060 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0763 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 76 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 156 optimal weight: 10.0000 chunk 125 optimal weight: 0.8980 chunk 146 optimal weight: 8.9990 chunk 176 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 172 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.097504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.077357 restraints weight = 4690.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.079197 restraints weight = 3293.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.080556 restraints weight = 2569.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.081602 restraints weight = 2123.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.082440 restraints weight = 1827.054| |-----------------------------------------------------------------------------| r_work (final): 0.3578 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.093077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.079964 restraints weight = 8695.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.081897 restraints weight = 6150.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.083343 restraints weight = 4630.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.084313 restraints weight = 3658.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.085241 restraints weight = 3039.900| |-----------------------------------------------------------------------------| r_work (final): 0.3724 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.075197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.062930 restraints weight = 6564.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.064146 restraints weight = 4681.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.065037 restraints weight = 3687.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.065768 restraints weight = 3068.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.066248 restraints weight = 2653.627| |-----------------------------------------------------------------------------| r_work (final): 0.3613 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.067505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.055205 restraints weight = 7296.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.056233 restraints weight = 5828.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.056997 restraints weight = 4878.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.057437 restraints weight = 4249.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.058037 restraints weight = 3871.015| |-----------------------------------------------------------------------------| r_work (final): 0.3375 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.068689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.048139 restraints weight = 4884.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.049438 restraints weight = 3943.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.050487 restraints weight = 3372.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.051195 restraints weight = 2958.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.051793 restraints weight = 2684.657| |-----------------------------------------------------------------------------| r_work (final): 0.3331 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.079882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.074954 restraints weight = 114191.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.075984 restraints weight = 53860.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.076591 restraints weight = 30514.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.076980 restraints weight = 19347.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.077244 restraints weight = 13399.160| |-----------------------------------------------------------------------------| r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.9487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 23780 Z= 0.189 Angle : 0.937 10.599 34582 Z= 0.398 Chirality : 0.064 0.525 4288 Planarity : 0.006 0.069 2404 Dihedral : 17.790 179.958 7708 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.77 (0.23), residues: 1344 helix: 0.53 (0.22), residues: 536 sheet: -0.99 (0.31), residues: 242 loop : -1.22 (0.27), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG G 100 TYR 0.033 0.002 TYR H 14 PHE 0.028 0.002 PHE C 152 TRP 0.014 0.002 TRP B 120 HIS 0.007 0.002 HIS E 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.19 (23772) covalent geometry : angle 0.93171 / 0.40 (34570) hydrogen bonds : bond 0.05422 / 3.37 ( 664) hydrogen bonds : angle 4.47218 / 2.94 ( 1632) metal coordination : bond 0.01441 / 0.63 ( 8) metal coordination : angle 5.47890 / 3.24 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2172.59 seconds wall clock time: 39 minutes 2.88 seconds (2342.88 seconds total)