Starting phenix.real_space_refine on Sun Jul 5 02:00:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9za2_73964/07_2026/9za2_73964.cif Found real_map, /net/cci-nas-00/data/ceres_data/9za2_73964/07_2026/9za2_73964.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9za2_73964/07_2026/9za2_73964.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9za2_73964/07_2026/9za2_73964.map" model { file = "/net/cci-nas-00/data/ceres_data/9za2_73964/07_2026/9za2_73964.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9za2_73964/07_2026/9za2_73964.cif" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 48 5.16 5 C 7608 2.51 5 N 2272 2.21 5 O 2248 1.98 5 H 12376 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 184 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24552 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 3069 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 8, 'TRANS': 189} Chain: "B" Number of atoms: 3069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 3069 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 8, 'TRANS': 189} Chain: "C" Number of atoms: 3069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 3069 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 8, 'TRANS': 189} Chain: "D" Number of atoms: 3069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 3069 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 8, 'TRANS': 189} Chain: "E" Number of atoms: 3069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 3069 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 8, 'TRANS': 189} Chain: "F" Number of atoms: 3069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 3069 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 8, 'TRANS': 189} Chain: "G" Number of atoms: 3069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 3069 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 8, 'TRANS': 189} Chain: "H" Number of atoms: 3069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 3069 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 8, 'TRANS': 189} Time building chain proxies: 4.72, per 1000 atoms: 0.19 Number of scatterers: 24552 At special positions: 0 Unit cell: (113.25, 113.25, 114.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 O 2248 8.00 N 2272 7.00 C 7608 6.00 H 12376 1.00 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: 2.30 Conformation dependent library (CDL) restraints added in 582.7 milliseconds 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2960 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 4 sheets defined 67.1% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 17 through 21 removed outlier: 4.004A pdb=" N ASP A 21 " --> pdb=" O ARG A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 38 Processing helix chain 'A' and resid 40 through 47 Processing helix chain 'A' and resid 47 through 55 Proline residue: A 53 - end of helix Processing helix chain 'A' and resid 60 through 75 removed outlier: 4.222A pdb=" N LEU A 73 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP A 75 " --> pdb=" O CYS A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 99 removed outlier: 4.066A pdb=" N CYS A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 114 removed outlier: 4.154A pdb=" N ALA A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP A 108 " --> pdb=" O ASP A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 120 removed outlier: 3.905A pdb=" N GLY A 119 " --> pdb=" O ASP A 116 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL A 120 " --> pdb=" O ALA A 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 116 through 120' Processing helix chain 'A' and resid 121 through 144 removed outlier: 3.999A pdb=" N TRP A 125 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N GLU A 127 " --> pdb=" O LEU A 123 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ALA A 128 " --> pdb=" O SER A 124 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 198 removed outlier: 4.192A pdb=" N GLY A 198 " --> pdb=" O PRO A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 211 Processing helix chain 'B' and resid 17 through 21 Processing helix chain 'B' and resid 26 through 38 Processing helix chain 'B' and resid 42 through 47 Processing helix chain 'B' and resid 47 through 55 Proline residue: B 53 - end of helix Processing helix chain 'B' and resid 60 through 75 Processing helix chain 'B' and resid 77 through 98 removed outlier: 4.333A pdb=" N CYS B 88 " --> pdb=" O SER B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 114 removed outlier: 4.382A pdb=" N ALA B 107 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASP B 108 " --> pdb=" O ASP B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 120 removed outlier: 3.858A pdb=" N GLY B 119 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL B 120 " --> pdb=" O ALA B 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 116 through 120' Processing helix chain 'B' and resid 121 through 142 removed outlier: 3.697A pdb=" N TRP B 125 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU B 127 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA B 128 " --> pdb=" O SER B 124 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ALA B 131 " --> pdb=" O GLU B 127 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 145 No H-bonds generated for 'chain 'B' and resid 143 through 145' Processing helix chain 'B' and resid 193 through 196 Processing helix chain 'B' and resid 197 through 211 removed outlier: 3.992A pdb=" N ASP B 205 " --> pdb=" O LYS B 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 38 Processing helix chain 'C' and resid 40 through 47 Processing helix chain 'C' and resid 47 through 55 Proline residue: C 53 - end of helix Processing helix chain 'C' and resid 60 through 74 Processing helix chain 'C' and resid 77 through 97 removed outlier: 3.724A pdb=" N CYS C 88 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER C 97 " --> pdb=" O SER C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 114 removed outlier: 4.300A pdb=" N ALA C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASP C 108 " --> pdb=" O ASP C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 120 removed outlier: 3.901A pdb=" N GLY C 119 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL C 120 " --> pdb=" O ALA C 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 116 through 120' Processing helix chain 'C' and resid 121 through 143 removed outlier: 3.988A pdb=" N TRP C 125 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLU C 127 " --> pdb=" O LEU C 123 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ALA C 128 " --> pdb=" O SER C 124 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA C 131 " --> pdb=" O GLU C 127 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL C 132 " --> pdb=" O ALA C 128 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE C 143 " --> pdb=" O GLU C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 198 removed outlier: 3.723A pdb=" N GLY C 198 " --> pdb=" O PRO C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 211 removed outlier: 3.569A pdb=" N GLU C 202 " --> pdb=" O GLY C 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 21 Processing helix chain 'D' and resid 26 through 38 Processing helix chain 'D' and resid 40 through 47 Processing helix chain 'D' and resid 47 through 55 Proline residue: D 53 - end of helix Processing helix chain 'D' and resid 60 through 75 Processing helix chain 'D' and resid 77 through 98 removed outlier: 3.656A pdb=" N CYS D 88 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N SER D 93 " --> pdb=" O ARG D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 114 removed outlier: 4.240A pdb=" N ALA D 107 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP D 108 " --> pdb=" O ASP D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 120 removed outlier: 3.685A pdb=" N GLY D 119 " --> pdb=" O ASP D 116 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL D 120 " --> pdb=" O ALA D 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 116 through 120' Processing helix chain 'D' and resid 121 through 144 removed outlier: 3.892A pdb=" N TRP D 125 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N GLU D 127 " --> pdb=" O LEU D 123 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ALA D 128 " --> pdb=" O SER D 124 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ALA D 131 " --> pdb=" O GLU D 127 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL D 132 " --> pdb=" O ALA D 128 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE D 142 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE D 143 " --> pdb=" O GLU D 139 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP D 144 " --> pdb=" O GLU D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 198 removed outlier: 3.834A pdb=" N GLY D 198 " --> pdb=" O PRO D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 211 removed outlier: 3.709A pdb=" N GLU D 202 " --> pdb=" O GLY D 198 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE D 211 " --> pdb=" O ILE D 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 38 Processing helix chain 'E' and resid 40 through 47 Processing helix chain 'E' and resid 47 through 55 Proline residue: E 53 - end of helix Processing helix chain 'E' and resid 60 through 75 Processing helix chain 'E' and resid 77 through 98 removed outlier: 3.690A pdb=" N CYS E 88 " --> pdb=" O SER E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 114 Processing helix chain 'E' and resid 116 through 124 removed outlier: 3.561A pdb=" N GLY E 119 " --> pdb=" O ASP E 116 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL E 120 " --> pdb=" O ALA E 117 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL E 121 " --> pdb=" O ARG E 118 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL E 122 " --> pdb=" O GLY E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 144 removed outlier: 3.631A pdb=" N ALA E 131 " --> pdb=" O GLU E 127 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL E 132 " --> pdb=" O ALA E 128 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU E 140 " --> pdb=" O GLY E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 195 No H-bonds generated for 'chain 'E' and resid 193 through 195' Processing helix chain 'E' and resid 196 through 211 removed outlier: 3.998A pdb=" N ILE E 200 " --> pdb=" O ALA E 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 21 Processing helix chain 'F' and resid 26 through 38 Processing helix chain 'F' and resid 40 through 47 Processing helix chain 'F' and resid 47 through 55 Proline residue: F 53 - end of helix Processing helix chain 'F' and resid 60 through 75 Processing helix chain 'F' and resid 77 through 98 removed outlier: 4.250A pdb=" N CYS F 88 " --> pdb=" O SER F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 114 Processing helix chain 'F' and resid 116 through 120 removed outlier: 4.158A pdb=" N GLY F 119 " --> pdb=" O ASP F 116 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL F 120 " --> pdb=" O ALA F 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 116 through 120' Processing helix chain 'F' and resid 121 through 143 removed outlier: 3.937A pdb=" N TRP F 125 " --> pdb=" O VAL F 121 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N GLU F 127 " --> pdb=" O LEU F 123 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ALA F 128 " --> pdb=" O SER F 124 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE F 142 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N PHE F 143 " --> pdb=" O GLU F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 195 No H-bonds generated for 'chain 'F' and resid 193 through 195' Processing helix chain 'F' and resid 196 through 211 removed outlier: 4.311A pdb=" N ILE F 200 " --> pdb=" O ALA F 196 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE F 211 " --> pdb=" O ILE F 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 38 Processing helix chain 'G' and resid 40 through 47 Processing helix chain 'G' and resid 47 through 55 Proline residue: G 53 - end of helix Processing helix chain 'G' and resid 60 through 75 Processing helix chain 'G' and resid 77 through 98 Processing helix chain 'G' and resid 101 through 114 removed outlier: 4.208A pdb=" N ALA G 107 " --> pdb=" O THR G 103 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP G 108 " --> pdb=" O ASP G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 120 removed outlier: 3.912A pdb=" N GLY G 119 " --> pdb=" O ASP G 116 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL G 120 " --> pdb=" O ALA G 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 116 through 120' Processing helix chain 'G' and resid 121 through 143 removed outlier: 3.729A pdb=" N TRP G 125 " --> pdb=" O VAL G 121 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLU G 127 " --> pdb=" O LEU G 123 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ALA G 128 " --> pdb=" O SER G 124 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA G 129 " --> pdb=" O TRP G 125 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N PHE G 143 " --> pdb=" O GLU G 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 193 through 195 No H-bonds generated for 'chain 'G' and resid 193 through 195' Processing helix chain 'G' and resid 196 through 211 removed outlier: 4.302A pdb=" N ILE G 200 " --> pdb=" O ALA G 196 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 21 Processing helix chain 'H' and resid 26 through 38 Processing helix chain 'H' and resid 40 through 47 Processing helix chain 'H' and resid 47 through 55 Proline residue: H 53 - end of helix Processing helix chain 'H' and resid 60 through 75 Processing helix chain 'H' and resid 77 through 98 Processing helix chain 'H' and resid 101 through 114 removed outlier: 4.230A pdb=" N ALA H 107 " --> pdb=" O THR H 103 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP H 108 " --> pdb=" O ASP H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 120 removed outlier: 3.644A pdb=" N GLY H 119 " --> pdb=" O ASP H 116 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL H 120 " --> pdb=" O ALA H 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 116 through 120' Processing helix chain 'H' and resid 121 through 144 removed outlier: 3.961A pdb=" N TRP H 125 " --> pdb=" O VAL H 121 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLU H 127 " --> pdb=" O LEU H 123 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ALA H 128 " --> pdb=" O SER H 124 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE H 143 " --> pdb=" O GLU H 139 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASP H 144 " --> pdb=" O GLU H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'H' and resid 196 through 211 removed outlier: 4.497A pdb=" N ILE H 200 " --> pdb=" O ALA H 196 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP H 205 " --> pdb=" O LYS H 201 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE H 211 " --> pdb=" O ILE H 207 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 148 through 162 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 165 through 166 current: chain 'A' and resid 184 through 192 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 184 through 192 current: chain 'C' and resid 165 through 166 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 165 through 166 current: chain 'C' and resid 184 through 192 Processing sheet with id=AA2, first strand: chain 'B' and resid 148 through 162 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 165 through 166 current: chain 'B' and resid 184 through 192 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 184 through 192 current: chain 'H' and resid 165 through 181 removed outlier: 3.795A pdb=" N ALA H 173 " --> pdb=" O VAL H 192 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 148 through 149 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 148 through 149 current: chain 'D' and resid 165 through 166 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 165 through 166 current: chain 'D' and resid 184 through 192 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 184 through 192 current: chain 'F' and resid 165 through 166 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 165 through 166 current: chain 'F' and resid 184 through 192 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'E' and resid 148 through 149 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 148 through 149 current: chain 'E' and resid 165 through 166 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 165 through 166 current: chain 'E' and resid 184 through 192 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 184 through 192 current: chain 'G' and resid 165 through 166 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 165 through 166 current: chain 'G' and resid 184 through 192 No H-bonds generated for sheet with id=AA4 629 hydrogen bonds defined for protein. 1842 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.65 Time building geometry restraints manager: 2.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 12344 1.13 - 1.30: 2474 1.30 - 1.48: 4252 1.48 - 1.65: 5602 1.65 - 1.82: 64 Bond restraints: 24736 Sorted by residual: bond pdb=" CE1 TYR E 191 " pdb=" HE1 TYR E 191 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N CYS A 204 " pdb=" H CYS A 204 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ALA E 58 " pdb=" H ALA E 58 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N GLY G 57 " pdb=" H GLY G 57 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N GLU D 140 " pdb=" H GLU D 140 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 24731 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 38877 2.78 - 5.57: 4524 5.57 - 8.35: 1340 8.35 - 11.14: 12 11.14 - 13.92: 31 Bond angle restraints: 44784 Sorted by residual: angle pdb=" CA ASP A 157 " pdb=" CB ASP A 157 " pdb=" CG ASP A 157 " ideal model delta sigma weight residual 112.60 121.04 -8.44 1.00e+00 1.00e+00 7.12e+01 angle pdb=" CA ASP C 157 " pdb=" CB ASP C 157 " pdb=" CG ASP C 157 " ideal model delta sigma weight residual 112.60 120.11 -7.51 1.00e+00 1.00e+00 5.64e+01 angle pdb=" CA ASP E 157 " pdb=" CB ASP E 157 " pdb=" CG ASP E 157 " ideal model delta sigma weight residual 112.60 119.86 -7.26 1.00e+00 1.00e+00 5.27e+01 angle pdb=" C ALA C 129 " pdb=" N LYS C 130 " pdb=" CA LYS C 130 " ideal model delta sigma weight residual 120.54 127.48 -6.94 1.35e+00 5.49e-01 2.64e+01 angle pdb=" CA ASP D 157 " pdb=" CB ASP D 157 " pdb=" CG ASP D 157 " ideal model delta sigma weight residual 112.60 117.69 -5.09 1.00e+00 1.00e+00 2.59e+01 ... (remaining 44779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 10410 17.83 - 35.65: 589 35.65 - 53.48: 226 53.48 - 71.30: 167 71.30 - 89.13: 8 Dihedral angle restraints: 11400 sinusoidal: 6384 harmonic: 5016 Sorted by residual: dihedral pdb=" CA ILE H 142 " pdb=" C ILE H 142 " pdb=" N PHE H 143 " pdb=" CA PHE H 143 " ideal model delta harmonic sigma weight residual -180.00 -150.31 -29.69 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA ASP C 169 " pdb=" C ASP C 169 " pdb=" N ALA C 170 " pdb=" CA ALA C 170 " ideal model delta harmonic sigma weight residual 180.00 -151.23 -28.77 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA ILE G 142 " pdb=" C ILE G 142 " pdb=" N PHE G 143 " pdb=" CA PHE G 143 " ideal model delta harmonic sigma weight residual -180.00 -151.40 -28.60 0 5.00e+00 4.00e-02 3.27e+01 ... (remaining 11397 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1189 0.070 - 0.140: 529 0.140 - 0.210: 174 0.210 - 0.281: 31 0.281 - 0.351: 5 Chirality restraints: 1928 Sorted by residual: chirality pdb=" CA ASP A 99 " pdb=" N ASP A 99 " pdb=" C ASP A 99 " pdb=" CB ASP A 99 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CA PHE D 90 " pdb=" N PHE D 90 " pdb=" C PHE D 90 " pdb=" CB PHE D 90 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CA PRO E 194 " pdb=" N PRO E 194 " pdb=" C PRO E 194 " pdb=" CB PRO E 194 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 1925 not shown) Planarity restraints: 3712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 164 " 0.229 9.50e-02 1.11e+02 1.30e-01 2.54e+02 pdb=" NE ARG H 164 " 0.089 2.00e-02 2.50e+03 pdb=" CZ ARG H 164 " 0.082 2.00e-02 2.50e+03 pdb=" NH1 ARG H 164 " 0.087 2.00e-02 2.50e+03 pdb=" NH2 ARG H 164 " 0.034 2.00e-02 2.50e+03 pdb="HH11 ARG H 164 " -0.212 2.00e-02 2.50e+03 pdb="HH12 ARG H 164 " 0.046 2.00e-02 2.50e+03 pdb="HH21 ARG H 164 " -0.167 2.00e-02 2.50e+03 pdb="HH22 ARG H 164 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 134 " -0.087 9.50e-02 1.11e+02 9.48e-02 1.84e+02 pdb=" NE ARG D 134 " -0.070 2.00e-02 2.50e+03 pdb=" CZ ARG D 134 " -0.064 2.00e-02 2.50e+03 pdb=" NH1 ARG D 134 " -0.077 2.00e-02 2.50e+03 pdb=" NH2 ARG D 134 " -0.031 2.00e-02 2.50e+03 pdb="HH11 ARG D 134 " 0.193 2.00e-02 2.50e+03 pdb="HH12 ARG D 134 " -0.080 2.00e-02 2.50e+03 pdb="HH21 ARG D 134 " 0.114 2.00e-02 2.50e+03 pdb="HH22 ARG D 134 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 164 " 0.018 9.50e-02 1.11e+02 8.09e-02 1.46e+02 pdb=" NE ARG G 164 " 0.033 2.00e-02 2.50e+03 pdb=" CZ ARG G 164 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG G 164 " -0.036 2.00e-02 2.50e+03 pdb=" NH2 ARG G 164 " 0.008 2.00e-02 2.50e+03 pdb="HH11 ARG G 164 " -0.095 2.00e-02 2.50e+03 pdb="HH12 ARG G 164 " 0.171 2.00e-02 2.50e+03 pdb="HH21 ARG G 164 " 0.048 2.00e-02 2.50e+03 pdb="HH22 ARG G 164 " -0.125 2.00e-02 2.50e+03 ... (remaining 3709 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1873 2.21 - 2.80: 45550 2.80 - 3.40: 66118 3.40 - 4.00: 82037 4.00 - 4.60: 120518 Nonbonded interactions: 316096 Sorted by model distance: nonbonded pdb=" HG SER E 77 " pdb=" OD2 ASP E 80 " model vdw 1.608 2.450 nonbonded pdb=" HG SER C 77 " pdb=" OD2 ASP C 80 " model vdw 1.611 2.450 nonbonded pdb=" HG SER G 77 " pdb=" OD2 ASP G 80 " model vdw 1.611 2.450 nonbonded pdb=" HG SER A 77 " pdb=" OD2 ASP A 80 " model vdw 1.612 2.450 nonbonded pdb=" HG SER F 77 " pdb=" OD2 ASP F 80 " model vdw 1.614 2.450 ... (remaining 316091 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 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: 0.180 Extract box with map and model: 0.530 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.820 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 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 : 0.012 0.041 12360 Z= 0.775 Angle : 1.761 8.440 16760 Z= 1.184 Chirality : 0.086 0.351 1928 Planarity : 0.019 0.163 2200 Dihedral : 12.656 89.131 4624 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 0.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.66 % Allowed : 5.24 % Favored : 92.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.19), residues: 1568 helix: -1.07 (0.15), residues: 912 sheet: -1.34 (0.29), residues: 200 loop : -0.42 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 187 TYR 0.107 0.014 TYR D 126 PHE 0.047 0.012 PHE C 70 TRP 0.051 0.012 TRP C 33 HIS 0.005 0.001 HIS B 167 Details of bonding type rmsd/Z covalent geometry : bond 0.01229 / 0.78 (12360) covalent geometry : angle 1.76118 / 1.18 (16760) hydrogen bonds : bond 0.14445 / 9.61 ( 629) hydrogen bonds : angle 6.94319 / 4.93 ( 1842) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8380 (mm-40) cc_final: 0.8145 (tm-30) REVERT: A 66 ARG cc_start: 0.9196 (mmt90) cc_final: 0.8839 (mmt180) REVERT: A 90 PHE cc_start: 0.9092 (t80) cc_final: 0.8771 (t80) REVERT: A 134 ARG cc_start: 0.9198 (ttp-170) cc_final: 0.8912 (ttt-90) REVERT: A 135 ARG cc_start: 0.9101 (ttm170) cc_final: 0.8585 (ttt90) REVERT: A 139 GLU cc_start: 0.9115 (pt0) cc_final: 0.8724 (pp20) REVERT: A 140 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8655 (tt0) REVERT: A 142 ILE cc_start: 0.9546 (mt) cc_final: 0.9336 (mt) outliers start: 5 outliers final: 2 residues processed: 49 average time/residue: 0.1410 time to fit residues: 7.6670 Evaluate side-chains 40 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.0770 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.3980 chunk 149 optimal weight: 0.0030 overall best weight: 0.4148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.174940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.136426 restraints weight = 13363.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.143212 restraints weight = 6162.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.147354 restraints weight = 3565.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.149756 restraints weight = 2458.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.151214 restraints weight = 1958.738| |-----------------------------------------------------------------------------| r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.7537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 12360 Z= 0.317 Angle : 0.709 4.997 16760 Z= 0.433 Chirality : 0.038 0.132 1928 Planarity : 0.007 0.049 2200 Dihedral : 5.680 23.328 1784 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.21), residues: 1568 helix: 0.58 (0.16), residues: 952 sheet: -2.28 (0.29), residues: 200 loop : -0.42 (0.33), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 44 TYR 0.012 0.002 TYR C 74 PHE 0.016 0.002 PHE D 90 TRP 0.005 0.001 TRP F 48 HIS 0.074 0.027 HIS C 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.32 (12360) covalent geometry : angle 0.70873 / 0.43 (16760) hydrogen bonds : bond 0.09579 / 6.39 ( 629) hydrogen bonds : angle 5.18539 / 3.80 ( 1842) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 134 ARG cc_start: 0.9344 (ttp-170) cc_final: 0.9113 (tpt170) REVERT: H 135 ARG cc_start: 0.8933 (ttm170) cc_final: 0.8391 (ttt90) REVERT: H 139 GLU cc_start: 0.9255 (pt0) cc_final: 0.8794 (mm-30) REVERT: H 190 ILE cc_start: 0.8929 (tp) cc_final: 0.8712 (tt) REVERT: H 208 GLU cc_start: 0.8442 (tp30) cc_final: 0.8108 (tp30) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1525 time to fit residues: 7.8596 Evaluate side-chains 37 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 3 optimal weight: 0.1980 chunk 35 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 123 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 21 optimal weight: 0.5980 chunk 100 optimal weight: 9.9990 chunk 148 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.170159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.131047 restraints weight = 13749.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.137691 restraints weight = 6250.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.142283 restraints weight = 3552.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.144889 restraints weight = 2351.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.146809 restraints weight = 1810.168| |-----------------------------------------------------------------------------| r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.7970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 12360 Z= 0.333 Angle : 0.691 4.681 16760 Z= 0.419 Chirality : 0.037 0.110 1928 Planarity : 0.006 0.049 2200 Dihedral : 4.978 18.592 1784 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.22), residues: 1568 helix: 0.61 (0.17), residues: 960 sheet: -2.12 (0.32), residues: 200 loop : -0.27 (0.37), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 187 TYR 0.011 0.002 TYR C 74 PHE 0.007 0.002 PHE H 143 TRP 0.008 0.002 TRP F 125 HIS 0.076 0.027 HIS C 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.33 (12360) covalent geometry : angle 0.69127 / 0.42 (16760) hydrogen bonds : bond 0.07825 / 5.23 ( 629) hydrogen bonds : angle 4.91941 / 3.64 ( 1842) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 ARG cc_start: 0.9084 (ttp-170) cc_final: 0.8882 (ttp-170) REVERT: H 134 ARG cc_start: 0.9463 (ttp-170) cc_final: 0.9192 (tpt170) REVERT: H 135 ARG cc_start: 0.8950 (ttm170) cc_final: 0.8400 (ttt90) REVERT: H 139 GLU cc_start: 0.9193 (pt0) cc_final: 0.8810 (tm-30) REVERT: H 163 ASP cc_start: 0.6379 (m-30) cc_final: 0.5514 (t0) REVERT: H 190 ILE cc_start: 0.8822 (tp) cc_final: 0.8535 (tt) REVERT: H 208 GLU cc_start: 0.8400 (tp30) cc_final: 0.8071 (tp30) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.1728 time to fit residues: 7.7264 Evaluate side-chains 35 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 2 optimal weight: 0.3980 chunk 133 optimal weight: 20.0000 chunk 71 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 55 optimal weight: 0.0670 chunk 130 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 85 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 overall best weight: 2.0924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.170101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.132045 restraints weight = 15305.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.138845 restraints weight = 7185.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.143032 restraints weight = 4179.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.146189 restraints weight = 2889.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.147696 restraints weight = 2207.432| |-----------------------------------------------------------------------------| r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.8140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 12360 Z= 0.321 Angle : 0.659 4.698 16760 Z= 0.405 Chirality : 0.037 0.113 1928 Planarity : 0.006 0.049 2200 Dihedral : 4.895 17.147 1784 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.21), residues: 1568 helix: 0.60 (0.17), residues: 968 sheet: -2.42 (0.31), residues: 200 loop : -1.27 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 31 TYR 0.008 0.001 TYR F 74 PHE 0.006 0.001 PHE B 143 TRP 0.023 0.002 TRP A 125 HIS 0.075 0.026 HIS C 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.32 (12360) covalent geometry : angle 0.65876 / 0.40 (16760) hydrogen bonds : bond 0.07135 / 4.77 ( 629) hydrogen bonds : angle 4.83432 / 3.57 ( 1842) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 ARG cc_start: 0.9078 (ttp-170) cc_final: 0.8851 (ttp-170) REVERT: H 134 ARG cc_start: 0.9474 (ttp-170) cc_final: 0.9137 (tpt90) REVERT: H 135 ARG cc_start: 0.8913 (ttm170) cc_final: 0.8304 (ttt90) REVERT: H 139 GLU cc_start: 0.9206 (pt0) cc_final: 0.8816 (mm-30) REVERT: H 144 ASP cc_start: 0.7725 (m-30) cc_final: 0.7489 (m-30) REVERT: H 190 ILE cc_start: 0.8748 (tp) cc_final: 0.8453 (tt) REVERT: H 208 GLU cc_start: 0.8383 (tp30) cc_final: 0.8039 (tp30) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.2079 time to fit residues: 8.7554 Evaluate side-chains 35 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 9 optimal weight: 9.9990 chunk 83 optimal weight: 0.3980 chunk 86 optimal weight: 9.9990 chunk 123 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 135 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 17 optimal weight: 0.0030 chunk 75 optimal weight: 3.9990 overall best weight: 1.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.170297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.132210 restraints weight = 15266.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.139179 restraints weight = 7255.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.143519 restraints weight = 4193.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.146627 restraints weight = 2855.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.148224 restraints weight = 2148.214| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.8279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 12360 Z= 0.314 Angle : 0.629 4.685 16760 Z= 0.386 Chirality : 0.036 0.111 1928 Planarity : 0.006 0.049 2200 Dihedral : 4.896 29.566 1784 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.22), residues: 1568 helix: 0.76 (0.17), residues: 968 sheet: -2.07 (0.33), residues: 192 loop : -1.18 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 209 TYR 0.007 0.001 TYR B 74 PHE 0.005 0.001 PHE B 143 TRP 0.016 0.002 TRP F 125 HIS 0.076 0.026 HIS C 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.31 (12360) covalent geometry : angle 0.62907 / 0.39 (16760) hydrogen bonds : bond 0.06525 / 4.34 ( 629) hydrogen bonds : angle 4.71714 / 3.48 ( 1842) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 66 ARG cc_start: 0.9154 (mmt90) cc_final: 0.8812 (mmm160) REVERT: H 86 ARG cc_start: 0.9030 (ttp-170) cc_final: 0.8828 (ttp-170) REVERT: H 134 ARG cc_start: 0.9508 (ttp-170) cc_final: 0.9123 (tpt90) REVERT: H 135 ARG cc_start: 0.8886 (ttm170) cc_final: 0.8377 (ttt90) REVERT: H 139 GLU cc_start: 0.9216 (pt0) cc_final: 0.8827 (tm-30) REVERT: H 144 ASP cc_start: 0.7655 (m-30) cc_final: 0.7394 (m-30) REVERT: H 157 ASP cc_start: 0.7144 (t70) cc_final: 0.6866 (t70) REVERT: H 190 ILE cc_start: 0.8614 (tp) cc_final: 0.8292 (tt) REVERT: H 208 GLU cc_start: 0.8480 (tp30) cc_final: 0.8085 (tp30) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1831 time to fit residues: 7.5656 Evaluate side-chains 35 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 61 optimal weight: 7.9990 chunk 99 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 25 optimal weight: 20.0000 chunk 72 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 143 optimal weight: 20.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.168162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.131598 restraints weight = 16586.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.138432 restraints weight = 7977.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.142643 restraints weight = 4675.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.145771 restraints weight = 3226.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.147760 restraints weight = 2447.380| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.8443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 12360 Z= 0.348 Angle : 0.682 5.726 16760 Z= 0.409 Chirality : 0.036 0.109 1928 Planarity : 0.006 0.049 2200 Dihedral : 4.876 21.966 1784 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.22), residues: 1568 helix: 0.62 (0.17), residues: 968 sheet: -2.29 (0.33), residues: 192 loop : -1.25 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 209 TYR 0.006 0.001 TYR F 74 PHE 0.008 0.002 PHE B 143 TRP 0.014 0.002 TRP F 125 HIS 0.076 0.026 HIS C 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.35 (12360) covalent geometry : angle 0.68159 / 0.41 (16760) hydrogen bonds : bond 0.06327 / 4.21 ( 629) hydrogen bonds : angle 4.79999 / 3.55 ( 1842) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 66 ARG cc_start: 0.9143 (mmt90) cc_final: 0.8804 (mmm160) REVERT: H 86 ARG cc_start: 0.9024 (ttp-170) cc_final: 0.8805 (ttp-170) REVERT: H 134 ARG cc_start: 0.9532 (ttp-170) cc_final: 0.9225 (tpt170) REVERT: H 135 ARG cc_start: 0.8818 (ttm170) cc_final: 0.8345 (ttt90) REVERT: H 139 GLU cc_start: 0.9228 (pt0) cc_final: 0.8802 (tm-30) REVERT: H 144 ASP cc_start: 0.7867 (m-30) cc_final: 0.7604 (m-30) REVERT: H 157 ASP cc_start: 0.7003 (t70) cc_final: 0.6683 (t70) REVERT: H 208 GLU cc_start: 0.8505 (tp30) cc_final: 0.8066 (tp30) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.1753 time to fit residues: 7.1025 Evaluate side-chains 37 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 119 optimal weight: 8.9990 chunk 113 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 98 optimal weight: 0.0020 chunk 31 optimal weight: 3.9990 chunk 114 optimal weight: 20.0000 chunk 17 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 104 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.171376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.132917 restraints weight = 16075.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.140439 restraints weight = 7659.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.145280 restraints weight = 4450.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.148366 restraints weight = 2982.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.150100 restraints weight = 2246.235| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.8576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 12360 Z= 0.304 Angle : 0.592 4.644 16760 Z= 0.369 Chirality : 0.036 0.113 1928 Planarity : 0.006 0.049 2200 Dihedral : 4.499 19.752 1784 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.23), residues: 1568 helix: 1.12 (0.17), residues: 960 sheet: -2.08 (0.33), residues: 192 loop : 0.32 (0.38), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 187 TYR 0.005 0.001 TYR F 74 PHE 0.002 0.001 PHE E 90 TRP 0.013 0.002 TRP F 125 HIS 0.076 0.025 HIS B 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.30 (12360) covalent geometry : angle 0.59246 / 0.37 (16760) hydrogen bonds : bond 0.05845 / 3.87 ( 629) hydrogen bonds : angle 4.56380 / 3.37 ( 1842) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 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: symmetry clash revert: symmetry clash REVERT: H 66 ARG cc_start: 0.9130 (mmt90) cc_final: 0.8788 (mmm160) REVERT: H 86 ARG cc_start: 0.8999 (ttp-170) cc_final: 0.8784 (ttp-170) REVERT: H 134 ARG cc_start: 0.9521 (ttp-170) cc_final: 0.9176 (tpt90) REVERT: H 135 ARG cc_start: 0.8805 (ttm170) cc_final: 0.8313 (ttt90) REVERT: H 139 GLU cc_start: 0.9211 (pt0) cc_final: 0.8788 (tm-30) REVERT: H 144 ASP cc_start: 0.7743 (m-30) cc_final: 0.7475 (m-30) REVERT: H 190 ILE cc_start: 0.8659 (tp) cc_final: 0.8370 (tt) REVERT: H 208 GLU cc_start: 0.8382 (tp30) cc_final: 0.7939 (tp30) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1889 time to fit residues: 7.4146 Evaluate side-chains 35 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 0 optimal weight: 20.0000 chunk 142 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 13 optimal weight: 0.0050 chunk 6 optimal weight: 7.9990 chunk 76 optimal weight: 20.0000 chunk 141 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 110 optimal weight: 4.9990 chunk 143 optimal weight: 20.0000 overall best weight: 2.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.169136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.129186 restraints weight = 15379.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.136160 restraints weight = 7152.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.140803 restraints weight = 4136.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.143879 restraints weight = 2809.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.145892 restraints weight = 2131.962| |-----------------------------------------------------------------------------| r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.8661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 12360 Z= 0.336 Angle : 0.657 5.680 16760 Z= 0.399 Chirality : 0.036 0.109 1928 Planarity : 0.006 0.050 2200 Dihedral : 4.586 15.644 1784 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.23), residues: 1568 helix: 1.04 (0.17), residues: 960 sheet: -2.18 (0.34), residues: 192 loop : 0.08 (0.38), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 184 TYR 0.005 0.001 TYR C 74 PHE 0.008 0.002 PHE H 143 TRP 0.012 0.002 TRP F 125 HIS 0.077 0.026 HIS B 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.34 (12360) covalent geometry : angle 0.65671 / 0.40 (16760) hydrogen bonds : bond 0.05851 / 3.90 ( 629) hydrogen bonds : angle 4.58811 / 3.39 ( 1842) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 66 ARG cc_start: 0.9142 (mmt90) cc_final: 0.8800 (mmm160) REVERT: H 86 ARG cc_start: 0.9028 (ttp-170) cc_final: 0.8775 (ttp-170) REVERT: H 134 ARG cc_start: 0.9511 (ttp-170) cc_final: 0.9181 (tpt90) REVERT: H 135 ARG cc_start: 0.8814 (ttm170) cc_final: 0.8314 (ttt90) REVERT: H 139 GLU cc_start: 0.9195 (pt0) cc_final: 0.8756 (tm-30) REVERT: H 144 ASP cc_start: 0.7834 (m-30) cc_final: 0.7553 (m-30) REVERT: H 190 ILE cc_start: 0.8595 (tp) cc_final: 0.8301 (tt) REVERT: H 208 GLU cc_start: 0.8343 (tp30) cc_final: 0.7879 (tp30) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1924 time to fit residues: 7.3248 Evaluate side-chains 34 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 111 optimal weight: 0.0770 chunk 144 optimal weight: 8.9990 chunk 71 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 109 optimal weight: 0.5980 overall best weight: 1.3344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.171854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.132688 restraints weight = 16486.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.140249 restraints weight = 7819.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.145245 restraints weight = 4536.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.148366 restraints weight = 3047.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.150303 restraints weight = 2288.236| |-----------------------------------------------------------------------------| r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.8766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 12360 Z= 0.302 Angle : 0.585 4.673 16760 Z= 0.365 Chirality : 0.035 0.113 1928 Planarity : 0.006 0.050 2200 Dihedral : 4.342 15.698 1784 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.23), residues: 1568 helix: 1.40 (0.17), residues: 960 sheet: -2.24 (0.32), residues: 200 loop : 0.01 (0.38), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 187 TYR 0.004 0.001 TYR F 74 PHE 0.004 0.001 PHE G 143 TRP 0.011 0.002 TRP F 125 HIS 0.076 0.026 HIS F 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.30 (12360) covalent geometry : angle 0.58529 / 0.36 (16760) hydrogen bonds : bond 0.05554 / 3.66 ( 629) hydrogen bonds : angle 4.44208 / 3.29 ( 1842) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 66 ARG cc_start: 0.9126 (mmt90) cc_final: 0.8780 (mmm160) REVERT: H 86 ARG cc_start: 0.8984 (ttp-170) cc_final: 0.8754 (ttp-170) REVERT: H 134 ARG cc_start: 0.9526 (ttp-170) cc_final: 0.9180 (tpt90) REVERT: H 135 ARG cc_start: 0.8760 (ttm170) cc_final: 0.8275 (ttt90) REVERT: H 139 GLU cc_start: 0.9175 (pt0) cc_final: 0.8758 (tm-30) REVERT: H 144 ASP cc_start: 0.7732 (m-30) cc_final: 0.7450 (m-30) REVERT: H 190 ILE cc_start: 0.8597 (tp) cc_final: 0.8362 (tt) REVERT: H 208 GLU cc_start: 0.8378 (tp30) cc_final: 0.7884 (tp30) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1908 time to fit residues: 7.2824 Evaluate side-chains 33 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 20 optimal weight: 1.9990 chunk 124 optimal weight: 20.0000 chunk 129 optimal weight: 4.9990 chunk 141 optimal weight: 0.2980 chunk 45 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 134 optimal weight: 0.9990 chunk 5 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 41 optimal weight: 0.0970 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.171572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.132917 restraints weight = 14341.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.140457 restraints weight = 6912.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.145277 restraints weight = 4000.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.148131 restraints weight = 2676.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.150448 restraints weight = 2038.562| |-----------------------------------------------------------------------------| r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.8892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 12360 Z= 0.297 Angle : 0.602 4.686 16760 Z= 0.367 Chirality : 0.036 0.113 1928 Planarity : 0.006 0.049 2200 Dihedral : 4.140 15.769 1784 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.23), residues: 1568 helix: 1.60 (0.17), residues: 960 sheet: -2.17 (0.31), residues: 200 loop : 0.22 (0.38), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 187 TYR 0.004 0.001 TYR F 191 PHE 0.003 0.001 PHE F 143 TRP 0.013 0.002 TRP G 33 HIS 0.076 0.025 HIS B 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.30 (12360) covalent geometry : angle 0.60152 / 0.37 (16760) hydrogen bonds : bond 0.05415 / 3.57 ( 629) hydrogen bonds : angle 4.38639 / 3.23 ( 1842) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 66 ARG cc_start: 0.9140 (mmt90) cc_final: 0.8786 (mmm160) REVERT: H 86 ARG cc_start: 0.8991 (ttp-170) cc_final: 0.8735 (ttp-170) REVERT: H 134 ARG cc_start: 0.9497 (ttp-170) cc_final: 0.9196 (tpt-90) REVERT: H 135 ARG cc_start: 0.8750 (ttm170) cc_final: 0.8272 (ttt90) REVERT: H 139 GLU cc_start: 0.9142 (pt0) cc_final: 0.8747 (tm-30) REVERT: H 144 ASP cc_start: 0.7686 (m-30) cc_final: 0.7405 (m-30) REVERT: H 190 ILE cc_start: 0.8608 (tp) cc_final: 0.8368 (tt) REVERT: H 208 GLU cc_start: 0.8361 (tp30) cc_final: 0.7801 (tp30) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.1962 time to fit residues: 7.1651 Evaluate side-chains 33 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 99 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 106 optimal weight: 3.9990 chunk 139 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.168850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.130766 restraints weight = 15109.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.138182 restraints weight = 7191.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.142417 restraints weight = 4194.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.145608 restraints weight = 2902.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.147765 restraints weight = 2202.069| |-----------------------------------------------------------------------------| r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.8968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 12360 Z= 0.345 Angle : 0.661 5.876 16760 Z= 0.401 Chirality : 0.037 0.109 1928 Planarity : 0.006 0.050 2200 Dihedral : 4.349 15.559 1784 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.23), residues: 1568 helix: 1.41 (0.17), residues: 960 sheet: -2.43 (0.32), residues: 200 loop : -0.11 (0.38), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 184 TYR 0.005 0.001 TYR C 191 PHE 0.007 0.002 PHE D 143 TRP 0.014 0.002 TRP H 33 HIS 0.077 0.027 HIS B 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.35 (12360) covalent geometry : angle 0.66068 / 0.40 (16760) hydrogen bonds : bond 0.05558 / 3.70 ( 629) hydrogen bonds : angle 4.53871 / 3.35 ( 1842) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1794.77 seconds wall clock time: 31 minutes 41.11 seconds (1901.11 seconds total)