Starting phenix.real_space_refine on Sat Sep 12 19:07:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6z5u_11082/09_2026/6z5u_11082.cif Found real_map, /net/cci-nas-00/data/ceres_data/6z5u_11082/09_2026/6z5u_11082.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6z5u_11082/09_2026/6z5u_11082.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6z5u_11082/09_2026/6z5u_11082.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6z5u_11082/09_2026/6z5u_11082.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6z5u_11082/09_2026/6z5u_11082.map" model { file = "/net/cci-nas-00/data/ceres_data/6z5u_11082/09_2026/6z5u_11082.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6z5u_11082/09_2026/6z5u_11082.cif" } resolution = 3.9 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= 0.007 sd= 0.089 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 92 5.16 5 C 11394 2.51 5 N 2967 2.21 5 O 3419 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17880 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1886 Classifications: {'peptide': 254} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 244} Chain: "B" Number of atoms: 1886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1886 Classifications: {'peptide': 254} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 245} Chain: "C" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 696 Classifications: {'peptide': 87} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 82} Chain: "D" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 696 Classifications: {'peptide': 87} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 83} Chain: "E" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1450 Classifications: {'peptide': 190} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 184} Chain: "G" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1461 Classifications: {'peptide': 191} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 3, 'TRANS': 185} Chain: "H" Number of atoms: 1443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1443 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 4, 'TRANS': 184} Chain: "I" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1476 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 4, 'TRANS': 188} Chain: "J" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1450 Classifications: {'peptide': 190} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 183} Chain: "K" Number of atoms: 1948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1948 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "L" Number of atoms: 1948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1948 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "F" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1476 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 4, 'TRANS': 188} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.24, per 1000 atoms: 0.24 Number of scatterers: 17880 At special positions: 0 Unit cell: (135.89, 144.45, 145.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 92 16.00 P 6 15.00 Mg 2 11.99 O 3419 8.00 N 2967 7.00 C 11394 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.90 Conformation dependent library (CDL) restraints added in 760.9 milliseconds 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4248 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 17 sheets defined 53.9% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 4 through 30 removed outlier: 3.556A pdb=" N GLY A 8 " --> pdb=" O ILE A 4 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 36 Processing helix chain 'A' and resid 38 through 49 removed outlier: 3.720A pdb=" N HIS A 46 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG A 47 " --> pdb=" O TYR A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 79 removed outlier: 4.986A pdb=" N ASN A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 95 removed outlier: 3.573A pdb=" N THR A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 123 removed outlier: 3.996A pdb=" N ALA A 102 " --> pdb=" O PRO A 98 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N GLY A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 133 Processing helix chain 'A' and resid 141 through 172 Proline residue: A 153 - end of helix Processing helix chain 'A' and resid 178 through 188 removed outlier: 3.840A pdb=" N PHE A 182 " --> pdb=" O ASP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 220 Processing helix chain 'A' and resid 226 through 255 removed outlier: 3.614A pdb=" N VAL A 253 " --> pdb=" O VAL A 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 31 removed outlier: 3.625A pdb=" N GLY B 8 " --> pdb=" O ILE B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 39 removed outlier: 4.048A pdb=" N GLY B 39 " --> pdb=" O GLY B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 52 through 76 Processing helix chain 'B' and resid 79 through 95 removed outlier: 5.419A pdb=" N GLY B 85 " --> pdb=" O GLU B 81 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 109 removed outlier: 4.138A pdb=" N ALA B 102 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 123 Processing helix chain 'B' and resid 126 through 133 removed outlier: 3.572A pdb=" N MET B 131 " --> pdb=" O SER B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 140 Processing helix chain 'B' and resid 141 through 172 Proline residue: B 153 - end of helix Processing helix chain 'B' and resid 178 through 190 Processing helix chain 'B' and resid 191 through 219 removed outlier: 7.257A pdb=" N VAL B 197 " --> pdb=" O GLY B 193 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 255 removed outlier: 4.172A pdb=" N ALA B 229 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 33 Processing helix chain 'C' and resid 42 through 46 Processing helix chain 'C' and resid 50 through 62 removed outlier: 3.931A pdb=" N LEU C 54 " --> pdb=" O ASN C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 86 Processing helix chain 'D' and resid 16 through 18 No H-bonds generated for 'chain 'D' and resid 16 through 18' Processing helix chain 'D' and resid 19 through 33 Processing helix chain 'D' and resid 51 through 62 Processing helix chain 'D' and resid 64 through 69 Processing helix chain 'D' and resid 76 through 84 Processing helix chain 'E' and resid 6 through 33 removed outlier: 5.188A pdb=" N ILE E 16 " --> pdb=" O ILE E 12 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE E 17 " --> pdb=" O PHE E 13 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ILE E 19 " --> pdb=" O ILE E 15 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N PHE E 22 " --> pdb=" O GLY E 18 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA E 25 " --> pdb=" O LEU E 21 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL E 28 " --> pdb=" O LEU E 24 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LEU E 31 " --> pdb=" O LYS E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 95 through 109 Processing helix chain 'E' and resid 112 through 117 Processing helix chain 'E' and resid 119 through 135 Processing helix chain 'E' and resid 184 through 191 Processing helix chain 'G' and resid 5 through 30 removed outlier: 5.060A pdb=" N VAL G 10 " --> pdb=" O SER G 6 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE G 15 " --> pdb=" O GLY G 11 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE G 22 " --> pdb=" O GLY G 18 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA G 25 " --> pdb=" O LEU G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 91 Processing helix chain 'G' and resid 94 through 113 Processing helix chain 'G' and resid 114 through 119 Processing helix chain 'G' and resid 120 through 134 Processing helix chain 'G' and resid 184 through 191 Processing helix chain 'H' and resid 7 through 33 removed outlier: 3.948A pdb=" N ILE H 19 " --> pdb=" O ILE H 15 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N PHE H 22 " --> pdb=" O GLY H 18 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU H 31 " --> pdb=" O LYS H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 92 removed outlier: 4.654A pdb=" N SER H 92 " --> pdb=" O LYS H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 112 removed outlier: 6.032A pdb=" N LYS H 99 " --> pdb=" O ALA H 95 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLU H 100 " --> pdb=" O GLU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 117 Processing helix chain 'H' and resid 119 through 134 removed outlier: 4.845A pdb=" N THR H 125 " --> pdb=" O ALA H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 191 Processing helix chain 'I' and resid 3 through 28 removed outlier: 4.367A pdb=" N GLU I 7 " --> pdb=" O SER I 3 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU I 8 " --> pdb=" O ARG I 4 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 31 No H-bonds generated for 'chain 'I' and resid 29 through 31' Processing helix chain 'I' and resid 87 through 92 Processing helix chain 'I' and resid 94 through 112 Processing helix chain 'I' and resid 114 through 118 Processing helix chain 'I' and resid 119 through 133 Processing helix chain 'I' and resid 184 through 193 Processing helix chain 'J' and resid 6 through 31 removed outlier: 4.236A pdb=" N VAL J 14 " --> pdb=" O VAL J 10 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ILE J 15 " --> pdb=" O GLY J 11 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE J 16 " --> pdb=" O ILE J 12 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE J 17 " --> pdb=" O PHE J 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 112 Processing helix chain 'J' and resid 113 through 116 Processing helix chain 'J' and resid 120 through 134 Processing helix chain 'J' and resid 184 through 193 Processing helix chain 'K' and resid 50 through 59 Processing helix chain 'K' and resid 77 through 79 No H-bonds generated for 'chain 'K' and resid 77 through 79' Processing helix chain 'K' and resid 80 through 89 removed outlier: 4.053A pdb=" N ALA K 89 " --> pdb=" O PHE K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 105 through 112 Processing helix chain 'K' and resid 113 through 118 removed outlier: 3.869A pdb=" N HIS K 117 " --> pdb=" O PRO K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 136 removed outlier: 3.680A pdb=" N VAL K 136 " --> pdb=" O LYS K 132 " (cutoff:3.500A) Processing helix chain 'K' and resid 137 through 142 removed outlier: 5.359A pdb=" N GLY K 140 " --> pdb=" O GLY K 137 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU K 142 " --> pdb=" O ARG K 139 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 149 Processing helix chain 'K' and resid 150 through 163 Processing helix chain 'K' and resid 175 through 178 removed outlier: 4.108A pdb=" N GLY K 178 " --> pdb=" O PRO K 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 175 through 178' Processing helix chain 'K' and resid 180 through 198 Processing helix chain 'K' and resid 208 through 212 Processing helix chain 'K' and resid 232 through 239 Processing helix chain 'K' and resid 241 through 250 Processing helix chain 'L' and resid 50 through 57 Processing helix chain 'L' and resid 80 through 88 Processing helix chain 'L' and resid 105 through 112 Processing helix chain 'L' and resid 113 through 118 removed outlier: 3.921A pdb=" N HIS L 117 " --> pdb=" O PRO L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 136 removed outlier: 3.753A pdb=" N VAL L 136 " --> pdb=" O LYS L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 149 Processing helix chain 'L' and resid 150 through 164 Processing helix chain 'L' and resid 180 through 198 removed outlier: 3.797A pdb=" N GLU L 196 " --> pdb=" O ARG L 192 " (cutoff:3.500A) Processing helix chain 'L' and resid 208 through 216 removed outlier: 4.141A pdb=" N SER L 214 " --> pdb=" O PRO L 210 " (cutoff:3.500A) Processing helix chain 'L' and resid 232 through 237 Processing helix chain 'L' and resid 241 through 248 Processing helix chain 'F' and resid 3 through 28 removed outlier: 4.367A pdb=" N GLU F 7 " --> pdb=" O SER F 3 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU F 8 " --> pdb=" O ARG F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 31 No H-bonds generated for 'chain 'F' and resid 29 through 31' Processing helix chain 'F' and resid 87 through 92 Processing helix chain 'F' and resid 94 through 112 Processing helix chain 'F' and resid 114 through 118 Processing helix chain 'F' and resid 119 through 133 Processing helix chain 'F' and resid 184 through 193 Processing sheet with id=AA1, first strand: chain 'D' and resid 40 through 42 Processing sheet with id=AA2, first strand: chain 'E' and resid 147 through 150 removed outlier: 3.635A pdb=" N LYS E 57 " --> pdb=" O LYS E 157 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL E 58 " --> pdb=" O ILE E 65 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET E 60 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE E 65 " --> pdb=" O ASP E 87 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR E 83 " --> pdb=" O ASP E 69 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ILE E 71 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR E 81 " --> pdb=" O ILE E 71 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N ILE E 176 " --> pdb=" O THR E 41 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LYS E 43 " --> pdb=" O ILE E 176 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 137 through 141 removed outlier: 5.420A pdb=" N ILE E 140 " --> pdb=" O LEU E 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 145 through 150 removed outlier: 6.498A pdb=" N LYS G 57 " --> pdb=" O LEU G 159 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ILE G 161 " --> pdb=" O LYS G 57 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N THR G 59 " --> pdb=" O ILE G 161 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL G 58 " --> pdb=" O ILE G 65 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET G 60 " --> pdb=" O VAL G 63 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N VAL G 68 " --> pdb=" O ASP G 85 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ASP G 85 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ILE G 176 " --> pdb=" O THR G 41 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N LYS G 43 " --> pdb=" O ILE G 176 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 137 through 141 removed outlier: 5.490A pdb=" N ILE G 140 " --> pdb=" O LEU G 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 175 through 176 removed outlier: 8.570A pdb=" N ILE H 176 " --> pdb=" O THR H 41 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS H 43 " --> pdb=" O ILE H 176 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N THR H 81 " --> pdb=" O ILE H 71 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ILE H 71 " --> pdb=" O THR H 81 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR H 83 " --> pdb=" O ASP H 69 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL H 63 " --> pdb=" O MET H 60 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N MET H 60 " --> pdb=" O VAL H 63 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL H 58 " --> pdb=" O ILE H 65 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE H 146 " --> pdb=" O GLN H 180 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 137 through 141 removed outlier: 5.307A pdb=" N ILE H 140 " --> pdb=" O LEU H 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 40 through 46 removed outlier: 3.564A pdb=" N SER I 70 " --> pdb=" O THR I 83 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASP I 85 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N VAL I 68 " --> pdb=" O ASP I 85 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL I 58 " --> pdb=" O ILE I 65 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LYS I 57 " --> pdb=" O LEU I 159 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ILE I 161 " --> pdb=" O LYS I 57 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N THR I 59 " --> pdb=" O ILE I 161 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE I 146 " --> pdb=" O GLN I 180 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 137 through 141 removed outlier: 5.816A pdb=" N ILE I 140 " --> pdb=" O LEU I 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 145 through 150 removed outlier: 6.869A pdb=" N LYS J 57 " --> pdb=" O LEU J 159 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ILE J 161 " --> pdb=" O LYS J 57 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR J 59 " --> pdb=" O ILE J 161 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL J 58 " --> pdb=" O ILE J 65 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N MET J 60 " --> pdb=" O VAL J 63 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR J 83 " --> pdb=" O ASP J 69 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ILE J 71 " --> pdb=" O THR J 81 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR J 81 " --> pdb=" O ILE J 71 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N LEU J 73 " --> pdb=" O LEU J 79 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU J 79 " --> pdb=" O LEU J 73 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N ILE J 176 " --> pdb=" O THR J 41 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LYS J 43 " --> pdb=" O ILE J 176 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 137 through 141 removed outlier: 4.776A pdb=" N LEU J 170 " --> pdb=" O THR J 138 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 25 through 35 removed outlier: 6.452A pdb=" N PHE K 20 " --> pdb=" O ILE K 27 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASP K 29 " --> pdb=" O LEU K 18 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU K 18 " --> pdb=" O ASP K 29 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE K 31 " --> pdb=" O LYS K 16 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LYS K 16 " --> pdb=" O ILE K 31 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU K 33 " --> pdb=" O GLU K 14 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N GLU K 14 " --> pdb=" O LEU K 33 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 91 through 94 removed outlier: 6.834A pdb=" N GLY K 92 " --> pdb=" O MET K 171 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ASP K 173 " --> pdb=" O GLY K 92 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU K 94 " --> pdb=" O ASP K 173 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE K 40 " --> pdb=" O TYR K 218 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N TYR K 220 " --> pdb=" O ILE K 40 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ALA K 42 " --> pdb=" O TYR K 220 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N VAL K 222 " --> pdb=" O ALA K 42 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N MET K 44 " --> pdb=" O VAL K 222 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ILE K 219 " --> pdb=" O GLU K 230 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLU K 230 " --> pdb=" O ILE K 219 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL K 221 " --> pdb=" O GLN K 228 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 25 through 35 removed outlier: 6.607A pdb=" N PHE L 20 " --> pdb=" O ILE L 27 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASP L 29 " --> pdb=" O LEU L 18 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU L 18 " --> pdb=" O ASP L 29 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE L 31 " --> pdb=" O LYS L 16 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LYS L 16 " --> pdb=" O ILE L 31 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU L 33 " --> pdb=" O GLU L 14 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLU L 14 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU L 18 " --> pdb=" O GLN L 66 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLN L 66 " --> pdb=" O LEU L 18 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 91 through 94 removed outlier: 6.703A pdb=" N GLY L 92 " --> pdb=" O MET L 171 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ASP L 173 " --> pdb=" O GLY L 92 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU L 94 " --> pdb=" O ASP L 173 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE L 40 " --> pdb=" O TYR L 218 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N TYR L 220 " --> pdb=" O ILE L 40 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA L 42 " --> pdb=" O TYR L 220 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL L 222 " --> pdb=" O ALA L 42 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N MET L 44 " --> pdb=" O VAL L 222 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY L 229 " --> pdb=" O VAL L 221 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ALA L 223 " --> pdb=" O ILE L 227 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ILE L 227 " --> pdb=" O ALA L 223 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 40 through 46 removed outlier: 3.564A pdb=" N SER F 70 " --> pdb=" O THR F 83 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASP F 85 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N VAL F 68 " --> pdb=" O ASP F 85 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL F 58 " --> pdb=" O ILE F 65 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LYS F 57 " --> pdb=" O LEU F 159 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ILE F 161 " --> pdb=" O LYS F 57 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N THR F 59 " --> pdb=" O ILE F 161 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE F 146 " --> pdb=" O GLN F 180 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 137 through 141 removed outlier: 5.816A pdb=" N ILE F 140 " --> pdb=" O LEU F 170 " (cutoff:3.500A) 997 hydrogen bonds defined for protein. 2832 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: 3.01 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 3092 1.30 - 1.44: 4705 1.44 - 1.58: 10101 1.58 - 1.71: 66 1.71 - 1.85: 170 Bond restraints: 18134 Sorted by residual: bond pdb=" N3B ANP K 301 " pdb=" PG ANP K 301 " ideal model delta sigma weight residual 1.795 1.566 0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" N3B ANP L 302 " pdb=" PG ANP L 302 " ideal model delta sigma weight residual 1.795 1.568 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" O3A ANP L 302 " pdb=" PB ANP L 302 " ideal model delta sigma weight residual 1.700 1.487 0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" O3A ANP K 301 " pdb=" PB ANP K 301 " ideal model delta sigma weight residual 1.700 1.517 0.183 2.00e-02 2.50e+03 8.37e+01 bond pdb=" CB HIS L 207 " pdb=" CG HIS L 207 " ideal model delta sigma weight residual 1.497 1.379 0.118 1.40e-02 5.10e+03 7.06e+01 ... (remaining 18129 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 22307 3.12 - 6.23: 1989 6.23 - 9.35: 211 9.35 - 12.47: 33 12.47 - 15.58: 4 Bond angle restraints: 24544 Sorted by residual: angle pdb=" N SER K 206 " pdb=" CA SER K 206 " pdb=" C SER K 206 " ideal model delta sigma weight residual 108.19 122.23 -14.04 1.29e+00 6.01e-01 1.18e+02 angle pdb=" C ASP H 74 " pdb=" N PRO H 75 " pdb=" CA PRO H 75 " ideal model delta sigma weight residual 119.56 128.59 -9.03 1.02e+00 9.61e-01 7.84e+01 angle pdb=" N THR G 77 " pdb=" CA THR G 77 " pdb=" C THR G 77 " ideal model delta sigma weight residual 114.31 103.34 10.97 1.29e+00 6.01e-01 7.23e+01 angle pdb=" N ILE L 27 " pdb=" CA ILE L 27 " pdb=" C ILE L 27 " ideal model delta sigma weight residual 111.81 104.76 7.05 8.60e-01 1.35e+00 6.72e+01 angle pdb=" CA PHE H 22 " pdb=" CB PHE H 22 " pdb=" CG PHE H 22 " ideal model delta sigma weight residual 113.80 105.64 8.16 1.00e+00 1.00e+00 6.67e+01 ... (remaining 24539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.13: 10357 18.13 - 36.27: 369 36.27 - 54.40: 120 54.40 - 72.53: 39 72.53 - 90.67: 11 Dihedral angle restraints: 10896 sinusoidal: 4266 harmonic: 6630 Sorted by residual: dihedral pdb=" CA MET L 79 " pdb=" C MET L 79 " pdb=" N SER L 80 " pdb=" CA SER L 80 " ideal model delta harmonic sigma weight residual -180.00 -89.33 -90.67 0 5.00e+00 4.00e-02 3.29e+02 dihedral pdb=" C GLU K 211 " pdb=" N GLU K 211 " pdb=" CA GLU K 211 " pdb=" CB GLU K 211 " ideal model delta harmonic sigma weight residual -122.60 -141.52 18.92 0 2.50e+00 1.60e-01 5.73e+01 dihedral pdb=" N GLU K 211 " pdb=" C GLU K 211 " pdb=" CA GLU K 211 " pdb=" CB GLU K 211 " ideal model delta harmonic sigma weight residual 122.80 140.13 -17.33 0 2.50e+00 1.60e-01 4.81e+01 ... (remaining 10893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.148: 2505 0.148 - 0.297: 412 0.297 - 0.445: 22 0.445 - 0.593: 7 0.593 - 0.742: 1 Chirality restraints: 2947 Sorted by residual: chirality pdb=" CA GLU K 211 " pdb=" N GLU K 211 " pdb=" C GLU K 211 " pdb=" CB GLU K 211 " both_signs ideal model delta sigma weight residual False 2.51 1.77 0.74 2.00e-01 2.50e+01 1.37e+01 chirality pdb=" CA VAL K 209 " pdb=" N VAL K 209 " pdb=" C VAL K 209 " pdb=" CB VAL K 209 " both_signs ideal model delta sigma weight residual False 2.44 1.86 0.58 2.00e-01 2.50e+01 8.56e+00 chirality pdb=" CA LEU G 36 " pdb=" N LEU G 36 " pdb=" C LEU G 36 " pdb=" CB LEU G 36 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.51e+00 ... (remaining 2944 not shown) Planarity restraints: 3103 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ANP L 302 " -0.629 2.00e-02 2.50e+03 2.45e-01 1.65e+03 pdb=" C2 ANP L 302 " 0.071 2.00e-02 2.50e+03 pdb=" C4 ANP L 302 " 0.180 2.00e-02 2.50e+03 pdb=" C5 ANP L 302 " 0.029 2.00e-02 2.50e+03 pdb=" C6 ANP L 302 " -0.095 2.00e-02 2.50e+03 pdb=" C8 ANP L 302 " 0.221 2.00e-02 2.50e+03 pdb=" N1 ANP L 302 " -0.074 2.00e-02 2.50e+03 pdb=" N3 ANP L 302 " 0.206 2.00e-02 2.50e+03 pdb=" N6 ANP L 302 " -0.228 2.00e-02 2.50e+03 pdb=" N7 ANP L 302 " 0.063 2.00e-02 2.50e+03 pdb=" N9 ANP L 302 " 0.256 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ANP K 301 " -0.550 2.00e-02 2.50e+03 2.15e-01 1.27e+03 pdb=" C2 ANP K 301 " 0.058 2.00e-02 2.50e+03 pdb=" C4 ANP K 301 " 0.157 2.00e-02 2.50e+03 pdb=" C5 ANP K 301 " 0.034 2.00e-02 2.50e+03 pdb=" C6 ANP K 301 " -0.080 2.00e-02 2.50e+03 pdb=" C8 ANP K 301 " 0.191 2.00e-02 2.50e+03 pdb=" N1 ANP K 301 " -0.068 2.00e-02 2.50e+03 pdb=" N3 ANP K 301 " 0.174 2.00e-02 2.50e+03 pdb=" N6 ANP K 301 " -0.208 2.00e-02 2.50e+03 pdb=" N7 ANP K 301 " 0.061 2.00e-02 2.50e+03 pdb=" N9 ANP K 301 " 0.231 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 158 " 0.226 2.00e-02 2.50e+03 1.16e-01 2.70e+02 pdb=" CG TYR H 158 " -0.113 2.00e-02 2.50e+03 pdb=" CD1 TYR H 158 " -0.084 2.00e-02 2.50e+03 pdb=" CD2 TYR H 158 " -0.098 2.00e-02 2.50e+03 pdb=" CE1 TYR H 158 " -0.055 2.00e-02 2.50e+03 pdb=" CE2 TYR H 158 " -0.031 2.00e-02 2.50e+03 pdb=" CZ TYR H 158 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 158 " 0.153 2.00e-02 2.50e+03 ... (remaining 3100 not shown) Histogram of nonbonded interaction distances: 0.90 - 1.70: 20 1.70 - 2.50: 59 2.50 - 3.30: 21941 3.30 - 4.10: 42494 4.10 - 4.90: 74776 Warning: very small nonbonded interaction distances. Nonbonded interactions: 139290 Sorted by model distance: nonbonded pdb=" OG1 THR G 194 " pdb=" CD1 PHE F 192 " model vdw 0.901 3.340 nonbonded pdb=" CB THR G 194 " pdb=" CZ PHE F 192 " model vdw 0.902 3.770 nonbonded pdb=" CB THR G 194 " pdb=" CE1 PHE F 192 " model vdw 0.915 3.770 nonbonded pdb=" O THR G 194 " pdb=" CE LYS F 191 " model vdw 1.062 3.440 nonbonded pdb=" CE MET E 183 " pdb=" CD GLU F 186 " model vdw 1.065 3.690 ... (remaining 139285 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' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and resid 6 through 194) selection = (chain 'F' and resid 6 through 194) selection = (chain 'G' and resid 6 through 194) selection = chain 'H' selection = (chain 'I' and resid 6 through 194) selection = (chain 'J' and resid 6 through 194) } ncs_group { reference = (chain 'K' and resid 11 through 263) selection = (chain 'L' and resid 11 through 263) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.870 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0317 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 : 0.021 0.229 18134 Z= 1.142 Angle : 1.881 15.582 24544 Z= 1.255 Chirality : 0.107 0.742 2947 Planarity : 0.012 0.245 3103 Dihedral : 11.905 90.668 6648 Min Nonbonded Distance : 0.901 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.03 % Favored : 97.66 % Rotamer: Outliers : 1.69 % Allowed : 1.99 % Favored : 96.32 % Cbeta Deviations : 0.47 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.47 (0.16), residues: 2310 helix: -0.27 (0.14), residues: 1070 sheet: 0.88 (0.33), residues: 259 loop : -0.53 (0.18), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 110 TYR 0.226 0.014 TYR H 158 PHE 0.172 0.010 PHE E 84 TRP 0.021 0.006 TRP D 60 HIS 0.008 0.002 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.02085 / 1.14 (18134) covalent geometry : angle 1.88133 / 1.25 (24544) hydrogen bonds : bond 0.19343 / 12.94 ( 997) hydrogen bonds : angle 7.77693 / 5.74 ( 2832) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 254 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 129 MET cc_start: 0.0251 (mtp) cc_final: -0.0243 (mpp) REVERT: E 16 ILE cc_start: 0.3016 (mm) cc_final: 0.2801 (mm) REVERT: E 141 ASP cc_start: 0.0007 (OUTLIER) cc_final: -0.2898 (m-30) REVERT: E 162 VAL cc_start: 0.2953 (OUTLIER) cc_final: 0.2594 (t) REVERT: G 160 LYS cc_start: -0.0016 (ttmt) cc_final: -0.0602 (ttpp) REVERT: G 162 VAL cc_start: 0.2803 (t) cc_final: 0.2032 (p) REVERT: H 183 MET cc_start: 0.0038 (mmm) cc_final: -0.0485 (pmm) REVERT: I 5 THR cc_start: -0.4657 (OUTLIER) cc_final: -0.5424 (m) REVERT: J 160 LYS cc_start: 0.1084 (ttpt) cc_final: 0.0089 (tttt) REVERT: K 202 THR cc_start: -0.0014 (p) cc_final: -0.1270 (m) REVERT: L 94 LEU cc_start: 0.0545 (mt) cc_final: -0.0685 (mp) REVERT: L 202 THR cc_start: -0.0385 (p) cc_final: -0.1414 (m) REVERT: F 5 THR cc_start: -0.4730 (OUTLIER) cc_final: -0.5562 (m) outliers start: 33 outliers final: 8 residues processed: 280 average time/residue: 0.1436 time to fit residues: 61.2200 Evaluate side-chains 185 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 173 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain G residue 178 ASN Chi-restraints excluded: chain H residue 60 MET Chi-restraints excluded: chain H residue 178 ASN Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain J residue 193 ILE Chi-restraints excluded: chain K residue 206 SER Chi-restraints excluded: chain F residue 5 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 77 ASN C 74 ASN D 84 GLN ** K 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 207 HIS L 179 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5604 r_free = 0.5604 target = 0.351863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5450 r_free = 0.5450 target = 0.328888 restraints weight = 33184.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.5496 r_free = 0.5496 target = 0.335859 restraints weight = 19752.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.5528 r_free = 0.5528 target = 0.340635 restraints weight = 12485.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.5548 r_free = 0.5548 target = 0.343708 restraints weight = 8201.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.5561 r_free = 0.5561 target = 0.345739 restraints weight = 5652.266| |-----------------------------------------------------------------------------| r_work (final): 0.5572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0714 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 18134 Z= 0.209 Angle : 0.772 11.526 24544 Z= 0.412 Chirality : 0.048 0.399 2947 Planarity : 0.005 0.066 3103 Dihedral : 6.776 59.841 2494 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.58 % Allowed : 5.01 % Favored : 93.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.17), residues: 2310 helix: 0.81 (0.15), residues: 1082 sheet: 0.27 (0.29), residues: 256 loop : -0.63 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 195 TYR 0.023 0.002 TYR F 115 PHE 0.045 0.003 PHE J 22 TRP 0.012 0.002 TRP A 146 HIS 0.003 0.001 HIS A 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.21 (18134) covalent geometry : angle 0.77247 / 0.41 (24544) hydrogen bonds : bond 0.06506 / 4.25 ( 997) hydrogen bonds : angle 5.69975 / 4.18 ( 2832) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 199 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 179 GLU cc_start: 0.5761 (mp0) cc_final: 0.5047 (mm-30) REVERT: B 255 PHE cc_start: 0.1032 (m-80) cc_final: -0.1508 (m-80) REVERT: E 60 MET cc_start: -0.3142 (ttt) cc_final: -0.4203 (mmt) REVERT: E 145 TYR cc_start: 0.2453 (OUTLIER) cc_final: 0.0418 (m-80) REVERT: E 162 VAL cc_start: 0.2975 (OUTLIER) cc_final: 0.2262 (t) REVERT: G 160 LYS cc_start: -0.0122 (ttmt) cc_final: -0.0821 (ttpp) REVERT: G 162 VAL cc_start: 0.3230 (t) cc_final: 0.3026 (p) REVERT: H 183 MET cc_start: 0.0200 (mmm) cc_final: -0.0640 (pmm) REVERT: I 172 ARG cc_start: 0.2674 (mmm-85) cc_final: 0.2003 (mmp80) REVERT: J 160 LYS cc_start: 0.0523 (ttpt) cc_final: -0.0387 (pttt) REVERT: J 183 MET cc_start: 0.1652 (ttt) cc_final: 0.1188 (pmm) REVERT: K 153 MET cc_start: 0.1325 (tpp) cc_final: 0.0146 (mtp) REVERT: L 35 ILE cc_start: 0.3681 (mt) cc_final: 0.3374 (mt) REVERT: L 91 MET cc_start: 0.4615 (ptp) cc_final: 0.4374 (ptp) REVERT: F 172 ARG cc_start: 0.2512 (mmm-85) cc_final: 0.1889 (mmp80) outliers start: 31 outliers final: 17 residues processed: 217 average time/residue: 0.1259 time to fit residues: 43.4090 Evaluate side-chains 190 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 178 ASN Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain H residue 178 ASN Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain K residue 209 VAL Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain F residue 42 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 161 optimal weight: 0.0170 chunk 129 optimal weight: 0.1980 chunk 180 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 209 optimal weight: 8.9990 chunk 160 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 200 optimal weight: 7.9990 chunk 187 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 70 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5599 r_free = 0.5599 target = 0.351325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5459 r_free = 0.5459 target = 0.329312 restraints weight = 33597.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.5503 r_free = 0.5503 target = 0.335777 restraints weight = 19932.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.5529 r_free = 0.5529 target = 0.339803 restraints weight = 12468.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.5546 r_free = 0.5546 target = 0.342825 restraints weight = 8405.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.5557 r_free = 0.5557 target = 0.344857 restraints weight = 5949.175| |-----------------------------------------------------------------------------| r_work (final): 0.5573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0775 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18134 Z= 0.139 Angle : 0.651 11.666 24544 Z= 0.340 Chirality : 0.043 0.255 2947 Planarity : 0.004 0.062 3103 Dihedral : 5.817 57.976 2485 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.53 % Allowed : 6.60 % Favored : 91.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.35 (0.17), residues: 2310 helix: 1.13 (0.16), residues: 1089 sheet: 0.10 (0.31), residues: 251 loop : -0.71 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 234 TYR 0.013 0.002 TYR C 24 PHE 0.032 0.002 PHE J 22 TRP 0.013 0.002 TRP B 183 HIS 0.002 0.000 HIS D 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.14 (18134) covalent geometry : angle 0.65082 / 0.34 (24544) hydrogen bonds : bond 0.04988 / 3.27 ( 997) hydrogen bonds : angle 5.21446 / 3.81 ( 2832) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 186 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 PHE cc_start: 0.4188 (t80) cc_final: 0.3728 (t80) REVERT: A 234 ARG cc_start: 0.3352 (ptp-170) cc_final: 0.3117 (ttm170) REVERT: B 40 ARG cc_start: 0.4515 (OUTLIER) cc_final: 0.3977 (ppt90) REVERT: B 255 PHE cc_start: 0.1243 (m-80) cc_final: -0.1134 (m-80) REVERT: E 26 MET cc_start: 0.1338 (OUTLIER) cc_final: -0.0118 (mtp) REVERT: E 60 MET cc_start: -0.3660 (ttt) cc_final: -0.5105 (mtt) REVERT: E 145 TYR cc_start: 0.2626 (OUTLIER) cc_final: 0.0562 (m-80) REVERT: E 162 VAL cc_start: 0.3285 (OUTLIER) cc_final: 0.2618 (t) REVERT: G 42 MET cc_start: 0.0705 (mpp) cc_final: -0.0060 (mpp) REVERT: G 160 LYS cc_start: -0.0467 (ttmt) cc_final: -0.0849 (ttpt) REVERT: G 162 VAL cc_start: 0.3329 (t) cc_final: 0.2966 (p) REVERT: H 65 ILE cc_start: 0.1972 (pt) cc_final: 0.1658 (mm) REVERT: H 183 MET cc_start: 0.0072 (mmm) cc_final: -0.0718 (pmm) REVERT: J 78 ARG cc_start: 0.2186 (mtt90) cc_final: 0.1635 (ttp80) REVERT: J 160 LYS cc_start: 0.0375 (ttpt) cc_final: -0.0398 (pttt) REVERT: J 183 MET cc_start: 0.1427 (ttt) cc_final: 0.0906 (pmm) REVERT: K 153 MET cc_start: 0.1691 (mpp) cc_final: 0.0618 (mtt) REVERT: L 91 MET cc_start: 0.4512 (ptp) cc_final: 0.4218 (ptp) outliers start: 30 outliers final: 21 residues processed: 201 average time/residue: 0.1216 time to fit residues: 39.1908 Evaluate side-chains 198 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 173 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain I residue 22 PHE Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain K residue 209 VAL Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain F residue 150 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 224 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 219 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 GLN A 187 GLN B 44 GLN B 77 ASN B 189 ASN D 63 GLN H 94 ASN ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 117 HIS L 96 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5588 r_free = 0.5588 target = 0.346738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.5413 r_free = 0.5413 target = 0.321556 restraints weight = 34020.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.5457 r_free = 0.5457 target = 0.327686 restraints weight = 20541.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.5485 r_free = 0.5485 target = 0.331616 restraints weight = 13441.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.5503 r_free = 0.5503 target = 0.334326 restraints weight = 9520.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.5518 r_free = 0.5518 target = 0.336334 restraints weight = 7202.241| |-----------------------------------------------------------------------------| r_work (final): 0.5523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1702 moved from start: 0.5868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.128 18134 Z= 0.307 Angle : 1.043 13.445 24544 Z= 0.534 Chirality : 0.056 0.255 2947 Planarity : 0.007 0.080 3103 Dihedral : 6.796 59.129 2481 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.02 % Allowed : 8.49 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.12 (0.16), residues: 2310 helix: 0.09 (0.15), residues: 1091 sheet: -1.34 (0.35), residues: 176 loop : -1.49 (0.17), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 78 TYR 0.045 0.004 TYR A 238 PHE 0.048 0.004 PHE H 84 TRP 0.039 0.005 TRP B 146 HIS 0.008 0.002 HIS B 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00672 / 0.31 (18134) covalent geometry : angle 1.04323 / 0.53 (24544) hydrogen bonds : bond 0.05839 / 3.91 ( 997) hydrogen bonds : angle 6.21943 / 4.54 ( 2832) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 175 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.3036 (tmm) cc_final: 0.2809 (tmm) REVERT: A 234 ARG cc_start: 0.4450 (ptp-170) cc_final: 0.3337 (mmp-170) REVERT: B 131 MET cc_start: 0.0313 (mmt) cc_final: -0.0588 (mmt) REVERT: E 134 MET cc_start: 0.1027 (mmt) cc_final: 0.0424 (mpp) REVERT: E 141 ASP cc_start: -0.0049 (OUTLIER) cc_final: -0.2169 (p0) REVERT: G 42 MET cc_start: 0.0829 (mpp) cc_final: 0.0424 (mpp) REVERT: G 79 LEU cc_start: 0.0417 (OUTLIER) cc_final: -0.0332 (mt) REVERT: G 160 LYS cc_start: -0.0328 (ttmt) cc_final: -0.1717 (tttt) REVERT: G 162 VAL cc_start: 0.2555 (t) cc_final: 0.1946 (p) REVERT: H 78 ARG cc_start: 0.2285 (tmm160) cc_final: 0.1299 (mmm160) REVERT: I 60 MET cc_start: 0.1113 (ttm) cc_final: 0.0894 (ttm) REVERT: J 78 ARG cc_start: 0.1697 (mtt90) cc_final: 0.0911 (mtt90) REVERT: J 183 MET cc_start: 0.2391 (ttt) cc_final: 0.1377 (pmm) REVERT: K 43 ILE cc_start: 0.0093 (mt) cc_final: -0.1148 (mm) REVERT: K 44 MET cc_start: 0.0534 (ptt) cc_final: 0.0280 (ptt) REVERT: K 153 MET cc_start: 0.2436 (mpp) cc_final: 0.0897 (mtt) REVERT: K 168 ASP cc_start: 0.7110 (t0) cc_final: 0.6780 (t0) REVERT: L 44 MET cc_start: 0.0687 (ptt) cc_final: 0.0432 (ptp) outliers start: 59 outliers final: 35 residues processed: 219 average time/residue: 0.1365 time to fit residues: 45.7861 Evaluate side-chains 189 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 152 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain H residue 176 ILE Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain K residue 171 MET Chi-restraints excluded: chain K residue 209 VAL Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain F residue 22 PHE Chi-restraints excluded: chain F residue 150 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 115 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 208 optimal weight: 0.0030 chunk 88 optimal weight: 5.9990 chunk 59 optimal weight: 30.0000 chunk 26 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 94 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 198 ASN B 198 ASN ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5600 r_free = 0.5600 target = 0.348445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.5434 r_free = 0.5434 target = 0.323019 restraints weight = 34535.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.5477 r_free = 0.5477 target = 0.329646 restraints weight = 20354.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.5506 r_free = 0.5506 target = 0.334228 restraints weight = 13075.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.5526 r_free = 0.5526 target = 0.337390 restraints weight = 8938.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.5540 r_free = 0.5540 target = 0.339466 restraints weight = 6435.462| |-----------------------------------------------------------------------------| r_work (final): 0.5524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1475 moved from start: 0.6002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18134 Z= 0.137 Angle : 0.668 12.885 24544 Z= 0.343 Chirality : 0.044 0.211 2947 Planarity : 0.004 0.052 3103 Dihedral : 5.828 56.985 2481 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.89 % Allowed : 10.33 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.40 (0.17), residues: 2310 helix: 0.72 (0.15), residues: 1097 sheet: -0.88 (0.32), residues: 225 loop : -1.21 (0.18), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 78 TYR 0.014 0.001 TYR H 145 PHE 0.024 0.002 PHE I 13 TRP 0.021 0.002 TRP A 6 HIS 0.002 0.001 HIS L 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 (18134) covalent geometry : angle 0.66760 / 0.34 (24544) hydrogen bonds : bond 0.04180 / 2.77 ( 997) hydrogen bonds : angle 5.34282 / 3.91 ( 2832) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 163 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 MET cc_start: 0.0925 (ttm) cc_final: 0.0677 (ttp) REVERT: A 234 ARG cc_start: 0.4337 (ptp-170) cc_final: 0.3205 (ttt180) REVERT: B 129 MET cc_start: -0.1313 (mtt) cc_final: -0.1598 (mtm) REVERT: B 131 MET cc_start: 0.0010 (mmt) cc_final: -0.0746 (mmt) REVERT: B 186 MET cc_start: -0.2829 (ttt) cc_final: -0.3439 (ptm) REVERT: B 232 MET cc_start: 0.0610 (ttm) cc_final: -0.0558 (pmm) REVERT: E 141 ASP cc_start: 0.0503 (OUTLIER) cc_final: -0.1913 (m-30) REVERT: E 157 LYS cc_start: 0.2063 (ttmt) cc_final: 0.1249 (tptp) REVERT: E 183 MET cc_start: 0.1201 (mmm) cc_final: 0.0367 (mtp) REVERT: G 60 MET cc_start: 0.1996 (mtt) cc_final: 0.1685 (mtt) REVERT: G 78 ARG cc_start: 0.0565 (mtm-85) cc_final: -0.0018 (mtm-85) REVERT: J 60 MET cc_start: 0.1285 (OUTLIER) cc_final: 0.0862 (mtm) REVERT: J 78 ARG cc_start: 0.1494 (mtt90) cc_final: 0.0891 (mtt90) REVERT: J 183 MET cc_start: 0.2187 (ttt) cc_final: 0.1424 (pmm) REVERT: K 153 MET cc_start: 0.2607 (mpp) cc_final: 0.1049 (mtt) REVERT: K 168 ASP cc_start: 0.6782 (t0) cc_final: 0.6479 (t0) outliers start: 37 outliers final: 26 residues processed: 186 average time/residue: 0.1244 time to fit residues: 36.8654 Evaluate side-chains 181 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 178 ASN Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain J residue 13 PHE Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain J residue 60 MET Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain K residue 209 VAL Chi-restraints excluded: chain K residue 232 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 209 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 30 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 98 optimal weight: 6.9990 chunk 220 optimal weight: 40.0000 chunk 219 optimal weight: 8.9990 chunk 173 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 204 optimal weight: 0.0870 chunk 3 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 45 GLN ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5595 r_free = 0.5595 target = 0.346825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.5429 r_free = 0.5429 target = 0.322310 restraints weight = 33977.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.5473 r_free = 0.5473 target = 0.328656 restraints weight = 19915.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.5501 r_free = 0.5501 target = 0.332926 restraints weight = 12750.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.5522 r_free = 0.5522 target = 0.335889 restraints weight = 8784.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.5535 r_free = 0.5535 target = 0.337843 restraints weight = 6405.498| |-----------------------------------------------------------------------------| r_work (final): 0.5537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1616 moved from start: 0.6554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18134 Z= 0.157 Angle : 0.689 12.047 24544 Z= 0.350 Chirality : 0.044 0.204 2947 Planarity : 0.005 0.050 3103 Dihedral : 5.470 54.543 2480 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.15 % Allowed : 11.91 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.17), residues: 2310 helix: 0.92 (0.16), residues: 1088 sheet: -1.37 (0.30), residues: 242 loop : -1.28 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 78 TYR 0.018 0.002 TYR F 158 PHE 0.036 0.002 PHE A 255 TRP 0.023 0.003 TRP A 212 HIS 0.002 0.001 HIS B 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.16 (18134) covalent geometry : angle 0.68941 / 0.35 (24544) hydrogen bonds : bond 0.04071 / 2.71 ( 997) hydrogen bonds : angle 5.36221 / 3.92 ( 2832) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 163 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ARG cc_start: 0.4285 (ptp-170) cc_final: 0.3188 (ttt180) REVERT: B 129 MET cc_start: -0.0863 (mtt) cc_final: -0.1166 (mtm) REVERT: B 186 MET cc_start: -0.2643 (ttt) cc_final: -0.3535 (ptm) REVERT: B 254 MET cc_start: -0.0272 (ptp) cc_final: -0.0507 (ptp) REVERT: E 141 ASP cc_start: 0.0225 (OUTLIER) cc_final: -0.2849 (m-30) REVERT: G 147 MET cc_start: 0.4470 (ttm) cc_final: 0.4260 (ttp) REVERT: H 65 ILE cc_start: 0.3560 (pt) cc_final: 0.2568 (mt) REVERT: J 42 MET cc_start: 0.1850 (mpp) cc_final: 0.1608 (mpp) REVERT: J 60 MET cc_start: 0.2148 (OUTLIER) cc_final: 0.1428 (mtm) REVERT: J 183 MET cc_start: 0.2652 (ttt) cc_final: 0.1919 (pmm) REVERT: K 36 ARG cc_start: 0.3706 (mpt180) cc_final: 0.2242 (mtm180) REVERT: K 153 MET cc_start: 0.2702 (tpp) cc_final: 0.1085 (mtt) REVERT: K 218 TYR cc_start: 0.4349 (t80) cc_final: 0.3957 (t80) REVERT: L 31 ILE cc_start: 0.2872 (mm) cc_final: 0.2476 (mm) REVERT: F 26 MET cc_start: -0.3012 (tpt) cc_final: -0.3236 (mmt) REVERT: F 160 LYS cc_start: 0.0639 (ttmt) cc_final: 0.0046 (tppt) outliers start: 42 outliers final: 34 residues processed: 193 average time/residue: 0.1286 time to fit residues: 39.6385 Evaluate side-chains 188 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 42 MET Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 84 PHE Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain J residue 13 PHE Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain J residue 60 MET Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain F residue 150 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 98 optimal weight: 0.9990 chunk 141 optimal weight: 0.0470 chunk 68 optimal weight: 5.9990 chunk 225 optimal weight: 0.0770 chunk 96 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 127 optimal weight: 0.2980 chunk 105 optimal weight: 0.0980 chunk 181 optimal weight: 0.0970 overall best weight: 0.1234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 198 ASN B 198 ASN ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5598 r_free = 0.5598 target = 0.348256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.5429 r_free = 0.5429 target = 0.323097 restraints weight = 34176.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.5478 r_free = 0.5478 target = 0.330302 restraints weight = 20040.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.5507 r_free = 0.5507 target = 0.334877 restraints weight = 12592.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.5528 r_free = 0.5528 target = 0.337852 restraints weight = 8500.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.5542 r_free = 0.5542 target = 0.340063 restraints weight = 6143.127| |-----------------------------------------------------------------------------| r_work (final): 0.5528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1438 moved from start: 0.6569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18134 Z= 0.111 Angle : 0.600 12.479 24544 Z= 0.305 Chirality : 0.042 0.190 2947 Planarity : 0.004 0.051 3103 Dihedral : 5.095 51.949 2480 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.69 % Allowed : 12.42 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.02 (0.17), residues: 2310 helix: 1.22 (0.16), residues: 1101 sheet: -1.04 (0.31), residues: 226 loop : -1.16 (0.19), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 40 TYR 0.025 0.001 TYR H 145 PHE 0.022 0.002 PHE I 13 TRP 0.023 0.001 TRP B 212 HIS 0.001 0.000 HIS L 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.11 (18134) covalent geometry : angle 0.60049 / 0.30 (24544) hydrogen bonds : bond 0.03557 / 2.35 ( 997) hydrogen bonds : angle 5.01193 / 3.68 ( 2832) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ARG cc_start: 0.3674 (ptp-170) cc_final: 0.3399 (mmp-170) REVERT: B 131 MET cc_start: 0.0462 (tpp) cc_final: -0.0058 (mpp) REVERT: B 186 MET cc_start: -0.2789 (ttt) cc_final: -0.3542 (ptm) REVERT: E 141 ASP cc_start: 0.0143 (OUTLIER) cc_final: -0.2126 (p0) REVERT: E 157 LYS cc_start: 0.1928 (ttmt) cc_final: 0.0986 (tptp) REVERT: E 183 MET cc_start: 0.2350 (mmm) cc_final: 0.1681 (mmm) REVERT: H 183 MET cc_start: -0.0595 (tpt) cc_final: -0.1201 (pmm) REVERT: J 60 MET cc_start: 0.1625 (OUTLIER) cc_final: 0.0912 (mtm) REVERT: J 183 MET cc_start: 0.2113 (ttt) cc_final: 0.1709 (pmm) REVERT: K 153 MET cc_start: 0.2645 (tpp) cc_final: 0.1159 (mtt) REVERT: L 31 ILE cc_start: 0.2491 (mm) cc_final: 0.2090 (mm) REVERT: F 160 LYS cc_start: 0.0699 (ttmt) cc_final: 0.0007 (tppt) outliers start: 33 outliers final: 26 residues processed: 177 average time/residue: 0.1190 time to fit residues: 33.9631 Evaluate side-chains 181 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 42 MET Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 178 ASN Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain J residue 13 PHE Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain J residue 60 MET Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain F residue 150 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 22 optimal weight: 6.9990 chunk 227 optimal weight: 0.0570 chunk 37 optimal weight: 0.9990 chunk 139 optimal weight: 0.7980 chunk 95 optimal weight: 20.0000 chunk 36 optimal weight: 0.9990 chunk 216 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 166 optimal weight: 0.7980 chunk 149 optimal weight: 0.5980 chunk 123 optimal weight: 4.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 GLN ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5593 r_free = 0.5593 target = 0.347456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.5426 r_free = 0.5426 target = 0.321990 restraints weight = 34298.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.5473 r_free = 0.5473 target = 0.329062 restraints weight = 20011.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.5501 r_free = 0.5501 target = 0.333702 restraints weight = 12706.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.5522 r_free = 0.5522 target = 0.336772 restraints weight = 8673.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.5536 r_free = 0.5536 target = 0.338887 restraints weight = 6311.158| |-----------------------------------------------------------------------------| r_work (final): 0.5521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1501 moved from start: 0.6803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 18134 Z= 0.116 Angle : 0.593 10.769 24544 Z= 0.301 Chirality : 0.042 0.162 2947 Planarity : 0.004 0.050 3103 Dihedral : 4.892 48.156 2480 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.74 % Allowed : 12.58 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % 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: 0.09 (0.17), residues: 2310 helix: 1.36 (0.16), residues: 1095 sheet: -0.99 (0.31), residues: 228 loop : -1.16 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 40 TYR 0.012 0.001 TYR F 158 PHE 0.017 0.002 PHE E 23 TRP 0.035 0.002 TRP B 212 HIS 0.001 0.000 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.12 (18134) covalent geometry : angle 0.59277 / 0.30 (24544) hydrogen bonds : bond 0.03473 / 2.32 ( 997) hydrogen bonds : angle 4.96538 / 3.64 ( 2832) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 ARG cc_start: 0.3668 (ptp-170) cc_final: 0.3404 (mmt180) REVERT: B 186 MET cc_start: -0.2700 (ttt) cc_final: -0.3502 (ptm) REVERT: E 134 MET cc_start: 0.1824 (mmt) cc_final: 0.1404 (mpp) REVERT: E 141 ASP cc_start: 0.0048 (OUTLIER) cc_final: -0.3440 (m-30) REVERT: E 157 LYS cc_start: 0.1762 (ttmt) cc_final: 0.0641 (tptp) REVERT: E 183 MET cc_start: 0.2471 (mmm) cc_final: 0.1726 (mmm) REVERT: H 60 MET cc_start: -0.0736 (mpt) cc_final: -0.0951 (mpt) REVERT: H 183 MET cc_start: -0.0357 (tpt) cc_final: -0.1178 (pmm) REVERT: J 60 MET cc_start: 0.1870 (OUTLIER) cc_final: 0.1172 (mtm) REVERT: J 183 MET cc_start: 0.2188 (ttt) cc_final: 0.1780 (pmm) REVERT: K 153 MET cc_start: 0.2655 (tpp) cc_final: 0.1180 (mtt) REVERT: L 31 ILE cc_start: 0.2611 (mm) cc_final: 0.2247 (mm) REVERT: F 160 LYS cc_start: 0.1222 (ttmt) cc_final: 0.0813 (ttmt) outliers start: 34 outliers final: 24 residues processed: 178 average time/residue: 0.1213 time to fit residues: 34.9707 Evaluate side-chains 175 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 42 MET Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain J residue 13 PHE Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain J residue 60 MET Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain F residue 150 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 37 optimal weight: 0.2980 chunk 25 optimal weight: 10.0000 chunk 144 optimal weight: 1.9990 chunk 184 optimal weight: 0.0670 chunk 79 optimal weight: 0.0050 chunk 88 optimal weight: 3.9990 chunk 70 optimal weight: 0.0970 chunk 164 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 overall best weight: 0.2530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5609 r_free = 0.5609 target = 0.348074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.5451 r_free = 0.5451 target = 0.324394 restraints weight = 34407.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.5497 r_free = 0.5497 target = 0.331332 restraints weight = 19773.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.5525 r_free = 0.5525 target = 0.335841 restraints weight = 12382.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.5545 r_free = 0.5545 target = 0.338714 restraints weight = 8309.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.5558 r_free = 0.5558 target = 0.340756 restraints weight = 5914.000| |-----------------------------------------------------------------------------| r_work (final): 0.5548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1432 moved from start: 0.6914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 18134 Z= 0.106 Angle : 0.587 15.542 24544 Z= 0.294 Chirality : 0.041 0.163 2947 Planarity : 0.004 0.049 3103 Dihedral : 4.704 44.177 2480 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.74 % Allowed : 12.63 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 (0.17), residues: 2310 helix: 1.51 (0.16), residues: 1096 sheet: -0.89 (0.31), residues: 226 loop : -1.13 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 78 TYR 0.010 0.001 TYR H 145 PHE 0.018 0.001 PHE L 95 TRP 0.038 0.002 TRP B 212 HIS 0.001 0.000 HIS A 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.11 (18134) covalent geometry : angle 0.58724 / 0.29 (24544) hydrogen bonds : bond 0.03294 / 2.18 ( 997) hydrogen bonds : angle 4.83204 / 3.56 ( 2832) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 150 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 ARG cc_start: 0.3653 (ptp-170) cc_final: 0.3084 (ttt180) REVERT: B 129 MET cc_start: -0.0851 (mpp) cc_final: -0.1100 (mpp) REVERT: B 186 MET cc_start: -0.2601 (ttt) cc_final: -0.3458 (ptm) REVERT: E 134 MET cc_start: 0.1773 (mmt) cc_final: 0.1043 (mpp) REVERT: E 141 ASP cc_start: 0.0235 (OUTLIER) cc_final: -0.2147 (p0) REVERT: E 157 LYS cc_start: 0.1648 (ttmt) cc_final: 0.0626 (tptp) REVERT: H 183 MET cc_start: -0.0446 (tpt) cc_final: -0.1145 (pmm) REVERT: J 60 MET cc_start: 0.1650 (OUTLIER) cc_final: 0.0951 (mtm) REVERT: K 153 MET cc_start: 0.3020 (tpp) cc_final: 0.1540 (mtt) REVERT: L 31 ILE cc_start: 0.2410 (mm) cc_final: 0.2063 (mm) REVERT: F 160 LYS cc_start: 0.1404 (ttmt) cc_final: 0.0042 (tppt) outliers start: 34 outliers final: 27 residues processed: 172 average time/residue: 0.1264 time to fit residues: 34.9949 Evaluate side-chains 175 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 42 MET Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 178 ASN Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain J residue 13 PHE Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain J residue 60 MET Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain F residue 150 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 228 optimal weight: 0.3980 chunk 189 optimal weight: 0.0060 chunk 127 optimal weight: 1.9990 chunk 213 optimal weight: 0.0970 chunk 121 optimal weight: 0.2980 chunk 222 optimal weight: 10.0000 chunk 209 optimal weight: 0.0020 chunk 206 optimal weight: 0.0870 chunk 42 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 chunk 137 optimal weight: 0.6980 overall best weight: 0.0980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5613 r_free = 0.5613 target = 0.348630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.5457 r_free = 0.5457 target = 0.325012 restraints weight = 34375.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.5503 r_free = 0.5503 target = 0.332002 restraints weight = 19724.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.5532 r_free = 0.5532 target = 0.336522 restraints weight = 12300.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.5551 r_free = 0.5551 target = 0.339377 restraints weight = 8248.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.5566 r_free = 0.5566 target = 0.341587 restraints weight = 5903.275| |-----------------------------------------------------------------------------| r_work (final): 0.5555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1380 moved from start: 0.7005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 18134 Z= 0.104 Angle : 0.590 14.169 24544 Z= 0.294 Chirality : 0.041 0.190 2947 Planarity : 0.004 0.049 3103 Dihedral : 4.534 39.276 2480 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.43 % Allowed : 13.14 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % 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 (0.17), residues: 2310 helix: 1.61 (0.16), residues: 1104 sheet: -0.70 (0.32), residues: 211 loop : -0.99 (0.19), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 78 TYR 0.010 0.001 TYR L 28 PHE 0.021 0.001 PHE G 84 TRP 0.040 0.002 TRP B 212 HIS 0.001 0.000 HIS B 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.10 (18134) covalent geometry : angle 0.58968 / 0.29 (24544) hydrogen bonds : bond 0.03259 / 2.16 ( 997) hydrogen bonds : angle 4.72970 / 3.49 ( 2832) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 ARG cc_start: 0.3592 (ptp-170) cc_final: 0.3313 (mtt-85) REVERT: B 40 ARG cc_start: 0.4091 (OUTLIER) cc_final: 0.1659 (mpt180) REVERT: B 84 LEU cc_start: 0.4014 (mm) cc_final: 0.3452 (mm) REVERT: B 87 MET cc_start: -0.1715 (ppp) cc_final: -0.2467 (ppp) REVERT: B 131 MET cc_start: 0.0114 (tpp) cc_final: -0.0531 (tpp) REVERT: B 186 MET cc_start: -0.2508 (ttt) cc_final: -0.3351 (ptm) REVERT: B 232 MET cc_start: 0.0027 (ttm) cc_final: -0.1010 (pmm) REVERT: B 255 PHE cc_start: 0.0998 (m-10) cc_final: 0.0707 (m-10) REVERT: E 134 MET cc_start: 0.1726 (mmt) cc_final: 0.0963 (mpp) REVERT: E 141 ASP cc_start: -0.0002 (OUTLIER) cc_final: -0.2310 (p0) REVERT: E 157 LYS cc_start: 0.1602 (ttmt) cc_final: 0.0680 (tptp) REVERT: E 183 MET cc_start: 0.2173 (mmm) cc_final: 0.1712 (mmm) REVERT: H 183 MET cc_start: -0.0096 (tpt) cc_final: -0.0638 (pmm) REVERT: J 60 MET cc_start: 0.1332 (OUTLIER) cc_final: 0.0880 (mtm) REVERT: K 44 MET cc_start: -0.0929 (ptt) cc_final: -0.2796 (tpt) REVERT: K 153 MET cc_start: 0.2993 (tpp) cc_final: 0.1487 (mtt) REVERT: L 31 ILE cc_start: 0.2285 (mm) cc_final: 0.1982 (mm) REVERT: L 258 TYR cc_start: 0.3769 (OUTLIER) cc_final: 0.1789 (t80) REVERT: F 160 LYS cc_start: 0.1165 (ttmt) cc_final: 0.0784 (ttmt) outliers start: 28 outliers final: 23 residues processed: 168 average time/residue: 0.1245 time to fit residues: 33.6807 Evaluate side-chains 174 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 42 MET Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 178 ASN Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain J residue 13 PHE Chi-restraints excluded: chain J residue 60 MET Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 258 TYR Chi-restraints excluded: chain F residue 150 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 120 optimal weight: 0.4980 chunk 154 optimal weight: 4.9990 chunk 132 optimal weight: 8.9990 chunk 69 optimal weight: 0.0470 chunk 125 optimal weight: 0.9980 chunk 200 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 215 optimal weight: 0.7980 chunk 17 optimal weight: 9.9990 chunk 188 optimal weight: 0.8980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 59 GLN J 178 ASN ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 123 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5591 r_free = 0.5591 target = 0.347333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.5426 r_free = 0.5426 target = 0.322449 restraints weight = 33823.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.5470 r_free = 0.5470 target = 0.329002 restraints weight = 19656.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.5503 r_free = 0.5503 target = 0.333959 restraints weight = 12723.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.5524 r_free = 0.5524 target = 0.337002 restraints weight = 8630.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.5538 r_free = 0.5538 target = 0.339178 restraints weight = 6209.632| |-----------------------------------------------------------------------------| r_work (final): 0.5561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1472 moved from start: 0.7232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 18134 Z= 0.108 Angle : 0.594 14.309 24544 Z= 0.295 Chirality : 0.041 0.223 2947 Planarity : 0.004 0.049 3103 Dihedral : 4.425 33.983 2480 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.43 % Allowed : 13.14 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % 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 (0.17), residues: 2310 helix: 1.62 (0.16), residues: 1105 sheet: -0.52 (0.31), residues: 235 loop : -1.05 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 78 TYR 0.011 0.001 TYR I 158 PHE 0.022 0.001 PHE J 22 TRP 0.027 0.002 TRP B 212 HIS 0.001 0.000 HIS B 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 (18134) covalent geometry : angle 0.59409 / 0.29 (24544) hydrogen bonds : bond 0.03178 / 2.12 ( 997) hydrogen bonds : angle 4.67739 / 3.44 ( 2832) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3574.45 seconds wall clock time: 62 minutes 18.92 seconds (3738.92 seconds total)