Starting phenix.real_space_refine on Thu Jun 19 03:56:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6k0a_30036/06_2025/6k0a_30036.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k0a_30036/06_2025/6k0a_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6k0a_30036/06_2025/6k0a_30036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k0a_30036/06_2025/6k0a_30036.map" model { file = "/net/cci-nas-00/data/ceres_data/6k0a_30036/06_2025/6k0a_30036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k0a_30036/06_2025/6k0a_30036.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: "Y" Number of atoms: 5535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 5535 Classifications: {'RNA': 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, J, D, F, H, X Time building chain proxies: 19.35, per 1000 atoms: 0.87 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: 5.88 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 9.44 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: 7.33 Time building geometry restraints manager: 7.00 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=" 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=" C3' U Y 198 " pdb=" O3' U Y 198 " ideal model delta sigma weight residual 1.427 1.452 -0.025 1.50e-02 4.44e+03 2.69e+00 bond pdb=" C3' U X 198 " pdb=" O3' U X 198 " ideal model delta sigma weight residual 1.427 1.451 -0.024 1.50e-02 4.44e+03 2.59e+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: 34073 2.31 - 4.62: 385 4.62 - 6.93: 84 6.93 - 9.25: 24 9.25 - 11.56: 4 Bond angle restraints: 34570 Sorted by residual: 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' U X 198 " pdb=" O3' U X 198 " pdb=" P U X 199 " ideal model delta sigma weight residual 120.20 126.54 -6.34 1.50e+00 4.44e-01 1.78e+01 angle pdb=" C3' U Y 198 " pdb=" O3' U Y 198 " pdb=" P U Y 199 " ideal model delta sigma weight residual 120.20 126.50 -6.30 1.50e+00 4.44e-01 1.77e+01 angle pdb=" CA LYS D 50 " pdb=" C LYS D 50 " pdb=" N LEU D 51 " ideal model delta sigma weight residual 115.81 120.48 -4.67 1.15e+00 7.56e-01 1.65e+01 ... (remaining 34565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 13624 35.76 - 71.51: 1428 71.51 - 107.27: 174 107.27 - 143.03: 0 143.03 - 178.79: 6 Dihedral angle restraints: 15232 sinusoidal: 11214 harmonic: 4018 Sorted by residual: dihedral pdb=" O4' U X 207 " pdb=" C1' U X 207 " pdb=" N1 U X 207 " pdb=" C2 U X 207 " ideal model delta sinusoidal sigma weight residual 232.00 53.21 178.79 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U Y 207 " pdb=" C1' U Y 207 " pdb=" N1 U Y 207 " pdb=" C2 U Y 207 " ideal model delta sinusoidal sigma weight residual 232.00 53.24 178.76 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U X 228 " pdb=" C1' U X 228 " pdb=" N1 U X 228 " pdb=" C2 U X 228 " ideal model delta sinusoidal sigma weight residual -160.00 -98.94 -61.06 1 1.50e+01 4.44e-03 2.20e+01 ... (remaining 15229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3910 0.060 - 0.119: 302 0.119 - 0.178: 63 0.178 - 0.238: 7 0.238 - 0.297: 6 Chirality restraints: 4288 Sorted by residual: chirality pdb=" CB ILE H 80 " pdb=" CA ILE H 80 " pdb=" CG1 ILE H 80 " pdb=" CG2 ILE H 80 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CB ILE G 80 " pdb=" CA ILE G 80 " pdb=" CG1 ILE G 80 " pdb=" CG2 ILE G 80 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.14e+00 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 2.41 -2.66 -0.25 2.00e-01 2.50e+01 1.61e+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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'I' selection = chain 'J' } 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 'Y' selection = chain 'X' } 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 'I' selection = chain 'J' } 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 'Y' selection = chain 'X' } 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: 1.500 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: 0.870 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 65.560 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6014 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= 0.228 Angle : 0.785 37.092 34582 Z= 0.400 Chirality : 0.037 0.297 4288 Planarity : 0.005 0.069 2404 Dihedral : 22.494 178.786 12632 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.006 0.001 TRP D 22 HIS 0.003 0.001 HIS J 60 PHE 0.012 0.001 PHE D 152 TYR 0.019 0.002 TYR B 46 ARG 0.007 0.000 ARG B 105 Details of bonding type rmsd hydrogen bonds : bond 0.30575 ( 664) hydrogen bonds : angle 9.61124 ( 1632) metal coordination : bond 0.26123 ( 8) metal coordination : angle 18.82681 ( 12) covalent geometry : bond 0.00281 (23772) covalent geometry : angle 0.70297 (34570) *********************** 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 : 0.130 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: 0.1770 time to fit residues: 8.6425 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 : 0.125 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 : 0.097 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: 0.1693 time to fit residues: 3.6980 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 : 0.115 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 : 0.251 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: 0.2238 time to fit residues: 17.0788 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 : 0.216 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 : 0.090 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: 0.3167 time to fit residues: 9.1935 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 : 0.092 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 : 0.122 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: 0.2732 time to fit residues: 13.1566 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 : 0.124 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 : 0.156 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1974 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 : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 4.9990 chunk 136 optimal weight: 0.9980 chunk 75 optimal weight: 9.9990 chunk 46 optimal weight: 0.9990 chunk 92 optimal weight: 0.0010 chunk 72 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 85 optimal weight: 20.0000 chunk 105 optimal weight: 0.0030 chunk 163 optimal weight: 10.0000 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 79 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 91 ASN D 125 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 64 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.114366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.091088 restraints weight = 3851.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.093857 restraints weight = 2648.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.095677 restraints weight = 1980.951| |-----------------------------------------------------------------------------| r_work (final): 0.3833 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.080597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.058071 restraints weight = 4223.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.059515 restraints weight = 3519.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.060467 restraints weight = 3040.475| |-----------------------------------------------------------------------------| r_work (final): 0.3483 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.116890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.100911 restraints weight = 7623.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.103347 restraints weight = 5298.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.105126 restraints weight = 3964.653| |-----------------------------------------------------------------------------| r_work (final): 0.4046 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.097374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.085833 restraints weight = 4627.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.087446 restraints weight = 3683.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.088627 restraints weight = 2996.633| |-----------------------------------------------------------------------------| r_work (final): 0.3972 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.077584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.064822 restraints weight = 6090.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.065973 restraints weight = 4630.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.066844 restraints weight = 3713.668| |-----------------------------------------------------------------------------| r_work (final): 0.3570 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.090564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.088665 restraints weight = 1013206.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.088811 restraints weight = 746441.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.088837 restraints weight = 643127.225| |-----------------------------------------------------------------------------| r_work (final): 0.4238 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3972 r_free = 0.3972 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3947 r_free = 0.3947 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3947 r_start: 0.3570 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3570 r_free = 0.3570 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3564 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5450 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23780 Z= 0.141 Angle : 0.625 9.302 34582 Z= 0.314 Chirality : 0.035 0.167 4288 Planarity : 0.006 0.090 2404 Dihedral : 23.401 179.457 9632 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.17 % Allowed : 4.48 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.20), residues: 1344 helix: -2.78 (0.16), residues: 528 sheet: 0.03 (0.38), residues: 196 loop : -1.67 (0.22), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 120 HIS 0.006 0.001 HIS E 10 PHE 0.017 0.002 PHE C 210 TYR 0.036 0.002 TYR F 95 ARG 0.010 0.001 ARG D 216 Details of bonding type rmsd hydrogen bonds : bond 0.05396 ( 664) hydrogen bonds : angle 4.18022 ( 1632) metal coordination : bond 0.00770 ( 8) metal coordination : angle 4.85072 ( 12) covalent geometry : bond 0.00283 (23772) covalent geometry : angle 0.61845 (34570) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 LEU cc_start: 0.8594 (tp) cc_final: 0.8306 (tp) REVERT: B 37 LEU cc_start: 0.9301 (pp) cc_final: 0.8678 (mp) REVERT: B 49 TRP cc_start: 0.7339 (t60) cc_final: 0.5453 (m-90) REVERT: B 62 ASP cc_start: 0.4151 (p0) cc_final: 0.3546 (p0) REVERT: B 79 LYS cc_start: 0.9365 (ttmt) cc_final: 0.8856 (tttt) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1030 time to fit residues: 4.1215 Evaluate side-chains 25 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.138 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 : 0.119 Fit side-chains revert: symmetry clash REVERT: J 45 LEU cc_start: 0.9460 (mt) cc_final: 0.9214 (mt) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.1427 time to fit residues: 2.2698 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 : 0.104 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 : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 74 PHE cc_start: 0.8966 (m-10) cc_final: 0.8666 (m-10) REVERT: D 214 LEU cc_start: 0.8980 (tp) cc_final: 0.8576 (pp) outliers start: 1 outliers final: 0 residues processed: 41 average time/residue: 0.2373 time to fit residues: 10.7379 Evaluate side-chains 31 residues out of total 205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.244 Evaluate side-chains 18 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 15 LEU cc_start: 0.7841 (mt) cc_final: 0.7172 (mp) REVERT: F 42 LEU cc_start: 0.8132 (mt) cc_final: 0.7883 (mt) REVERT: F 90 LYS cc_start: 0.7047 (tptt) cc_final: 0.6586 (tptp) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.3357 time to fit residues: 6.3216 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 : 0.090 Evaluate side-chains 36 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 15 GLU cc_start: 0.9393 (tp30) cc_final: 0.9180 (tp30) REVERT: H 100 ARG cc_start: 0.7962 (mpp80) cc_final: 0.7749 (ptt180) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1778 time to fit residues: 6.9361 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 : 0.147 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 : 0.185 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2263 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 : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 101 optimal weight: 9.9990 chunk 58 optimal weight: 0.4980 chunk 54 optimal weight: 0.5980 chunk 72 optimal weight: 9.9990 chunk 13 optimal weight: 0.0030 chunk 140 optimal weight: 0.0030 chunk 165 optimal weight: 0.7980 chunk 115 optimal weight: 0.0770 chunk 106 optimal weight: 6.9990 chunk 141 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 overall best weight: 0.2358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 180 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.117233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.095250 restraints weight = 3854.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.097661 restraints weight = 2642.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.099892 restraints weight = 2001.574| |-----------------------------------------------------------------------------| r_work (final): 0.3883 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.088193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.070568 restraints weight = 4265.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.072183 restraints weight = 3474.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.073371 restraints weight = 2917.644| |-----------------------------------------------------------------------------| r_work (final): 0.3619 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.117877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.101715 restraints weight = 7744.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.104230 restraints weight = 5392.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.106146 restraints weight = 4003.861| |-----------------------------------------------------------------------------| r_work (final): 0.4083 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.091363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.082114 restraints weight = 5460.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.083696 restraints weight = 3924.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.084858 restraints weight = 2997.363| |-----------------------------------------------------------------------------| r_work (final): 0.3900 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.077116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.064250 restraints weight = 5485.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.065462 restraints weight = 4228.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.066406 restraints weight = 3472.547| |-----------------------------------------------------------------------------| r_work (final): 0.3560 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.090357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.088552 restraints weight = 1012931.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.088673 restraints weight = 730021.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.088698 restraints weight = 604874.659| |-----------------------------------------------------------------------------| r_work (final): 0.4230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3900 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3900 r_free = 0.3900 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3898 r_free = 0.3898 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3898 r_start: 0.3554 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3554 r_free = 0.3554 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3554 r_free = 0.3554 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3554 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5510 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23780 Z= 0.164 Angle : 0.778 20.639 34582 Z= 0.383 Chirality : 0.046 0.780 4288 Planarity : 0.009 0.161 2404 Dihedral : 23.374 179.842 9632 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 1.16 % Allowed : 6.63 % Favored : 92.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.20), residues: 1344 helix: -2.06 (0.18), residues: 508 sheet: 0.08 (0.37), residues: 196 loop : -1.78 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.007 TRP A 57 HIS 0.032 0.003 HIS C 79 PHE 0.102 0.007 PHE B 63 TYR 0.099 0.007 TYR A 45 ARG 0.088 0.003 ARG A 13 Details of bonding type rmsd hydrogen bonds : bond 0.05466 ( 664) hydrogen bonds : angle 4.65636 ( 1632) metal coordination : bond 0.00523 ( 8) metal coordination : angle 4.16021 ( 12) covalent geometry : bond 0.00358 (23772) covalent geometry : angle 0.77398 (34570) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.142 Fit side-chains revert: symmetry clash REVERT: B 8 LEU cc_start: 0.8745 (tp) cc_final: 0.8511 (tp) REVERT: B 79 LYS cc_start: 0.9212 (ttmt) cc_final: 0.8620 (tttt) REVERT: B 87 GLU cc_start: 0.8992 (tt0) cc_final: 0.8737 (tp30) outliers start: 5 outliers final: 2 residues processed: 33 average time/residue: 0.1276 time to fit residues: 4.7845 Evaluate side-chains 21 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.126 Evaluate side-chains 10 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 9 time to evaluate : 0.107 Fit side-chains revert: symmetry clash REVERT: J 45 LEU cc_start: 0.9493 (mt) cc_final: 0.9257 (mt) REVERT: J 110 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6984 (pm20) outliers start: 1 outliers final: 0 residues processed: 10 average time/residue: 0.1687 time to fit residues: 2.0803 Evaluate side-chains 8 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 7 time to evaluate : 0.218 Evaluate side-chains 48 residues out of total 205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 59 ILE cc_start: 0.5904 (tp) cc_final: 0.5624 (tt) REVERT: C 67 LEU cc_start: 0.8424 (tp) cc_final: 0.7953 (tp) REVERT: C 74 PHE cc_start: 0.8886 (m-10) cc_final: 0.8640 (m-10) REVERT: C 152 PHE cc_start: 0.8026 (m-80) cc_final: 0.7743 (m-80) REVERT: C 171 ASP cc_start: 0.7667 (t0) cc_final: 0.7433 (t0) REVERT: C 175 LYS cc_start: 0.6816 (mmtm) cc_final: 0.5537 (pttp) REVERT: C 209 ASP cc_start: 0.7874 (m-30) cc_final: 0.7278 (m-30) REVERT: C 214 LEU cc_start: 0.8972 (tp) cc_final: 0.8499 (pp) outliers start: 1 outliers final: 1 residues processed: 48 average time/residue: 0.2780 time to fit residues: 14.7744 Evaluate side-chains 43 residues out of total 205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.369 Evaluate side-chains 20 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 15 LEU cc_start: 0.8136 (mt) cc_final: 0.7284 (mp) REVERT: E 42 LEU cc_start: 0.8367 (mt) cc_final: 0.8143 (mt) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.3208 time to fit residues: 6.7482 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 : 0.090 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 : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 21 MET cc_start: 0.9083 (tmm) cc_final: 0.8781 (tmm) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.2574 time to fit residues: 8.2864 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 : 0.151 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 : 0.178 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2299 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 : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 131 optimal weight: 7.9990 chunk 120 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 151 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 175 optimal weight: 8.9990 chunk 138 optimal weight: 0.1980 chunk 66 optimal weight: 4.9990 chunk 177 optimal weight: 9.9990 chunk 174 optimal weight: 10.0000 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.113782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.092554 restraints weight = 4078.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.095255 restraints weight = 2766.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.097094 restraints weight = 2061.250| |-----------------------------------------------------------------------------| r_work (final): 0.3843 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.081173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.054067 restraints weight = 3843.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.055082 restraints weight = 3382.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.056099 restraints weight = 3043.710| |-----------------------------------------------------------------------------| r_work (final): 0.3511 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.112847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.096531 restraints weight = 8138.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.098972 restraints weight = 5763.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.100755 restraints weight = 4389.060| |-----------------------------------------------------------------------------| r_work (final): 0.4008 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.087683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.078182 restraints weight = 5815.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.079745 restraints weight = 4285.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.080922 restraints weight = 3309.965| |-----------------------------------------------------------------------------| r_work (final): 0.3811 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.073444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.060997 restraints weight = 5817.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.062079 restraints weight = 4514.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.062767 restraints weight = 3714.337| |-----------------------------------------------------------------------------| r_work (final): 0.3479 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.089215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.087460 restraints weight = 1005423.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.087625 restraints weight = 701273.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.087619 restraints weight = 621453.305| |-----------------------------------------------------------------------------| r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3480 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3480 r_free = 0.3480 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3478 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5696 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 23780 Z= 0.163 Angle : 0.771 15.907 34582 Z= 0.384 Chirality : 0.051 1.028 4288 Planarity : 0.009 0.095 2404 Dihedral : 23.324 178.744 9632 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.59 % Favored : 91.96 % Rotamer: Outliers : 0.50 % Allowed : 5.14 % Favored : 94.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.20), residues: 1344 helix: -1.81 (0.19), residues: 508 sheet: -0.78 (0.35), residues: 202 loop : -2.05 (0.22), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.008 TRP B 120 HIS 0.016 0.003 HIS D 79 PHE 0.170 0.009 PHE A 63 TYR 0.102 0.007 TYR A 45 ARG 0.101 0.003 ARG A 13 Details of bonding type rmsd hydrogen bonds : bond 0.05144 ( 664) hydrogen bonds : angle 4.68923 ( 1632) metal coordination : bond 0.00794 ( 8) metal coordination : angle 3.61841 ( 12) covalent geometry : bond 0.00349 (23772) covalent geometry : angle 0.76808 (34570) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 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: 3 poor density : 31 time to evaluate : 0.138 Fit side-chains revert: symmetry clash REVERT: A 5 LEU cc_start: 0.8710 (mt) cc_final: 0.8446 (mt) REVERT: A 8 LEU cc_start: 0.8633 (tp) cc_final: 0.7738 (tp) REVERT: A 63 PHE cc_start: 0.7590 (m-80) cc_final: 0.7376 (m-80) REVERT: A 79 LYS cc_start: 0.9187 (ttmt) cc_final: 0.8622 (tttt) REVERT: A 87 GLU cc_start: 0.8924 (tt0) cc_final: 0.8357 (mm-30) REVERT: A 104 ILE cc_start: 0.8038 (mm) cc_final: 0.7627 (pt) REVERT: A 112 LEU cc_start: 0.8424 (mm) cc_final: 0.7975 (mt) outliers start: 3 outliers final: 0 residues processed: 34 average time/residue: 0.1392 time to fit residues: 5.2791 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 : 0.141 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 : 0.115 Fit side-chains revert: symmetry clash REVERT: J 45 LEU cc_start: 0.9064 (mt) cc_final: 0.8777 (mt) outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.1327 time to fit residues: 1.3120 Evaluate side-chains 7 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.113 Evaluate side-chains 45 residues out of total 205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.249 Fit side-chains REVERT: C 74 PHE cc_start: 0.8886 (m-10) cc_final: 0.8616 (m-10) REVERT: C 152 PHE cc_start: 0.8216 (m-80) cc_final: 0.7977 (m-80) REVERT: C 171 ASP cc_start: 0.8164 (t0) cc_final: 0.7885 (t0) REVERT: C 175 LYS cc_start: 0.6962 (mmtm) cc_final: 0.5524 (pttp) REVERT: C 209 ASP cc_start: 0.8037 (m-30) cc_final: 0.7435 (m-30) REVERT: C 214 LEU cc_start: 0.9070 (tp) cc_final: 0.8613 (pp) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.2104 time to fit residues: 10.6361 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 : 0.221 Evaluate side-chains 17 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 15 LEU cc_start: 0.8116 (mt) cc_final: 0.7206 (mp) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.2218 time to fit residues: 4.0585 Evaluate side-chains 10 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.092 Evaluate side-chains 27 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 15 GLU cc_start: 0.8514 (pt0) cc_final: 0.8191 (pm20) REVERT: H 109 GLU cc_start: 0.9404 (tm-30) cc_final: 0.9201 (tm-30) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.1138 time to fit residues: 3.5594 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 : 0.142 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 : 0.153 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1959 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 : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 801, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.0445 > 50: distance: 0 - 1: 6.163 distance: 1 - 2: 18.540 distance: 1 - 4: 12.847 distance: 2 - 3: 21.036 distance: 2 - 12: 17.841 distance: 4 - 5: 10.022 distance: 5 - 6: 4.739 distance: 5 - 7: 3.851 distance: 7 - 9: 9.988 distance: 8 - 10: 5.062 distance: 9 - 10: 9.794 distance: 10 - 11: 5.253 distance: 12 - 13: 26.724 distance: 13 - 14: 50.198 distance: 13 - 16: 12.857 distance: 14 - 15: 25.479 distance: 14 - 20: 43.654 distance: 16 - 17: 22.132 distance: 17 - 18: 15.798 distance: 17 - 19: 20.680 distance: 20 - 21: 15.632 distance: 21 - 22: 45.089 distance: 21 - 24: 42.767 distance: 22 - 23: 41.065 distance: 22 - 31: 56.873 distance: 24 - 25: 38.152 distance: 25 - 26: 42.688 distance: 25 - 27: 45.082 distance: 26 - 28: 26.320 distance: 27 - 29: 34.753 distance: 28 - 30: 9.892 distance: 29 - 30: 20.417 distance: 31 - 32: 55.689 distance: 31 - 37: 53.933 distance: 32 - 33: 52.316 distance: 32 - 35: 44.535 distance: 33 - 34: 26.423 distance: 33 - 38: 49.718 distance: 35 - 36: 24.468 distance: 36 - 37: 32.279 distance: 38 - 39: 18.071 distance: 39 - 40: 33.785 distance: 39 - 42: 41.764 distance: 40 - 41: 20.836 distance: 40 - 50: 33.716 distance: 42 - 43: 16.154 distance: 43 - 44: 32.122 distance: 43 - 45: 22.348 distance: 44 - 46: 33.994 distance: 45 - 47: 27.362 distance: 46 - 48: 28.090 distance: 47 - 48: 38.335 distance: 48 - 49: 59.044 distance: 50 - 51: 35.873 distance: 51 - 52: 47.092 distance: 52 - 53: 47.159 distance: 52 - 54: 39.519 distance: 54 - 55: 20.239 distance: 55 - 56: 20.064 distance: 55 - 58: 27.888 distance: 56 - 57: 38.965 distance: 56 - 62: 46.961 distance: 58 - 59: 23.233 distance: 58 - 60: 24.750 distance: 59 - 61: 13.542 distance: 62 - 63: 34.126 distance: 63 - 64: 31.023 distance: 63 - 66: 12.052 distance: 64 - 65: 32.891 distance: 64 - 70: 12.213 distance: 66 - 67: 11.489 distance: 67 - 68: 29.175 distance: 67 - 69: 37.804 distance: 70 - 71: 30.107 distance: 71 - 72: 40.845 distance: 71 - 74: 13.205 distance: 72 - 73: 24.210 distance: 72 - 81: 20.646 distance: 74 - 75: 23.207 distance: 75 - 76: 27.139 distance: 76 - 77: 23.699 distance: 77 - 78: 51.452 distance: 78 - 79: 30.016 distance: 78 - 80: 40.474 distance: 81 - 82: 11.331 distance: 82 - 83: 5.128 distance: 82 - 85: 5.122 distance: 83 - 84: 10.305 distance: 85 - 86: 3.832