Starting phenix.real_space_refine on Thu Sep 18 15:10:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6z5u_11082/09_2025/6z5u_11082.cif Found real_map, /net/cci-nas-00/data/ceres_data/6z5u_11082/09_2025/6z5u_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6z5u_11082/09_2025/6z5u_11082.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6z5u_11082/09_2025/6z5u_11082.map" model { file = "/net/cci-nas-00/data/ceres_data/6z5u_11082/09_2025/6z5u_11082.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6z5u_11082/09_2025/6z5u_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-2.0-5805/lib/python3.9/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: 3.99, per 1000 atoms: 0.22 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: 1.47 Conformation dependent library (CDL) restraints added in 748.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.69 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: 2.48 Time building geometry restraints manager: 1.98 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: 10369 18.13 - 36.27: 380 36.27 - 54.40: 135 54.40 - 72.53: 48 72.53 - 90.67: 20 Dihedral angle restraints: 10952 sinusoidal: 4322 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 10949 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: 1.090 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.790 Find NCS groups from input model: 0.330 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0301 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 : 12.689 90.668 6704 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 aren 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 covalent geometry : bond 0.02085 (18134) covalent geometry : angle 1.88133 (24544) hydrogen bonds : bond 0.19343 ( 997) hydrogen bonds : angle 7.77693 ( 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 : 0.644 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: 0.0037 (mmm) cc_final: -0.0486 (pmm) REVERT: I 5 THR cc_start: -0.4658 (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: -0.0684 (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: 0.1373 time to fit residues: 58.3032 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.5602 r_free = 0.5602 target = 0.351817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.5453 r_free = 0.5453 target = 0.329436 restraints weight = 33229.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.5497 r_free = 0.5497 target = 0.336214 restraints weight = 19723.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.5528 r_free = 0.5528 target = 0.340819 restraints weight = 12515.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.5548 r_free = 0.5548 target = 0.343753 restraints weight = 8254.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.5560 r_free = 0.5560 target = 0.345819 restraints weight = 5729.505| |-----------------------------------------------------------------------------| r_work (final): 0.5580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0686 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 18134 Z= 0.198 Angle : 0.777 11.283 24544 Z= 0.415 Chirality : 0.048 0.311 2947 Planarity : 0.005 0.066 3103 Dihedral : 8.996 69.259 2550 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.53 % Allowed : 5.01 % Favored : 93.46 % 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 aren not related in a simple way. whole: 0.22 (0.17), residues: 2310 helix: 0.85 (0.15), residues: 1081 sheet: 0.27 (0.29), residues: 256 loop : -0.62 (0.19), residues: 973 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 0.046 0.002 PHE J 22 TRP 0.013 0.002 TRP A 146 HIS 0.003 0.001 HIS L 207 Details of bonding type rmsd covalent geometry : bond 0.00389 (18134) covalent geometry : angle 0.77715 (24544) hydrogen bonds : bond 0.06580 ( 997) hydrogen bonds : angle 5.70106 ( 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 229 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 199 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 179 GLU cc_start: 0.5753 (mp0) cc_final: 0.5040 (mm-30) REVERT: B 255 PHE cc_start: 0.1033 (m-80) cc_final: -0.1511 (m-80) REVERT: E 145 TYR cc_start: 0.2457 (OUTLIER) cc_final: 0.0432 (m-80) REVERT: E 162 VAL cc_start: 0.3164 (OUTLIER) cc_final: 0.2431 (t) REVERT: G 160 LYS cc_start: -0.0222 (ttmt) cc_final: -0.0835 (ttpp) REVERT: H 183 MET cc_start: 0.0188 (mmm) cc_final: -0.0643 (pmm) REVERT: I 172 ARG cc_start: 0.2685 (mmm-85) cc_final: 0.2009 (mmp80) REVERT: J 78 ARG cc_start: 0.2292 (mtt90) cc_final: 0.2048 (mtt90) REVERT: J 160 LYS cc_start: 0.0495 (ttpt) cc_final: -0.0403 (pttt) REVERT: J 183 MET cc_start: 0.1649 (ttt) cc_final: 0.1186 (pmm) REVERT: K 153 MET cc_start: 0.1319 (tpp) cc_final: 0.0120 (mtp) REVERT: L 35 ILE cc_start: 0.3674 (mt) cc_final: 0.3365 (mt) REVERT: L 91 MET cc_start: 0.4615 (ptp) cc_final: 0.4368 (ptp) REVERT: F 172 ARG cc_start: 0.2527 (mmm-85) cc_final: 0.1910 (mmp80) outliers start: 30 outliers final: 17 residues processed: 216 average time/residue: 0.1214 time to fit residues: 41.4317 Evaluate side-chains 191 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 172 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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: 0.3980 chunk 129 optimal weight: 6.9990 chunk 180 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 209 optimal weight: 9.9990 chunk 160 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 200 optimal weight: 6.9990 chunk 187 optimal weight: 8.9990 chunk 149 optimal weight: 4.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN B 44 GLN B 70 GLN B 77 ASN B 189 ASN K 117 HIS L 96 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5599 r_free = 0.5599 target = 0.349354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.5439 r_free = 0.5439 target = 0.324478 restraints weight = 33429.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.5486 r_free = 0.5486 target = 0.331434 restraints weight = 19596.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.5515 r_free = 0.5515 target = 0.336108 restraints weight = 12293.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.5531 r_free = 0.5531 target = 0.339136 restraints weight = 8233.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.5544 r_free = 0.5544 target = 0.341202 restraints weight = 5893.119| |-----------------------------------------------------------------------------| r_work (final): 0.5556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1254 moved from start: 0.4554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 18134 Z= 0.240 Angle : 0.862 12.480 24544 Z= 0.445 Chirality : 0.050 0.246 2947 Planarity : 0.006 0.080 3103 Dihedral : 7.671 61.042 2541 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.15 % Allowed : 7.21 % Favored : 90.64 % 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 aren not related in a simple way. whole: -0.45 (0.16), residues: 2310 helix: 0.53 (0.15), residues: 1091 sheet: -0.59 (0.32), residues: 222 loop : -1.11 (0.18), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 234 TYR 0.031 0.003 TYR A 238 PHE 0.034 0.003 PHE E 46 TRP 0.028 0.004 TRP B 183 HIS 0.004 0.001 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00511 (18134) covalent geometry : angle 0.86236 (24544) hydrogen bonds : bond 0.05481 ( 997) hydrogen bonds : angle 5.65438 ( 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 226 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 184 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ARG cc_start: 0.3671 (ptp-170) cc_final: 0.3017 (ttt180) REVERT: E 141 ASP cc_start: -0.0370 (OUTLIER) cc_final: -0.2547 (m-30) REVERT: E 146 ILE cc_start: 0.5520 (mt) cc_final: 0.4945 (tt) REVERT: E 162 VAL cc_start: 0.4173 (OUTLIER) cc_final: 0.3286 (t) REVERT: G 42 MET cc_start: 0.0915 (mpp) cc_final: 0.0432 (mpp) REVERT: G 160 LYS cc_start: -0.0832 (ttmt) cc_final: -0.1952 (pttt) REVERT: H 183 MET cc_start: 0.0106 (mmm) cc_final: -0.0936 (pmm) REVERT: J 143 ASP cc_start: 0.7377 (m-30) cc_final: 0.6840 (t0) REVERT: J 160 LYS cc_start: 0.0493 (ttpt) cc_final: -0.0445 (pttt) REVERT: J 183 MET cc_start: 0.2724 (ttt) cc_final: 0.1642 (pmm) REVERT: K 91 MET cc_start: 0.3867 (OUTLIER) cc_final: 0.2800 (mtt) REVERT: K 153 MET cc_start: 0.2089 (mpp) cc_final: 0.0568 (mtt) REVERT: L 91 MET cc_start: 0.4986 (ptp) cc_final: 0.4241 (ptp) outliers start: 42 outliers final: 25 residues processed: 207 average time/residue: 0.1218 time to fit residues: 39.4344 Evaluate side-chains 187 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 159 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 VAL 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 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 194 THR Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain H residue 178 ASN 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 91 MET Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain K residue 209 VAL Chi-restraints excluded: chain K residue 222 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 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: 4.9990 chunk 57 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 186 optimal weight: 0.5980 chunk 177 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 219 optimal weight: 9.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 ASN D 63 GLN H 94 ASN ** K 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5599 r_free = 0.5599 target = 0.349159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.5435 r_free = 0.5435 target = 0.323997 restraints weight = 33389.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.5479 r_free = 0.5479 target = 0.330749 restraints weight = 19634.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.5508 r_free = 0.5508 target = 0.335261 restraints weight = 12459.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.5527 r_free = 0.5527 target = 0.338329 restraints weight = 8470.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.5541 r_free = 0.5541 target = 0.340435 restraints weight = 6140.474| |-----------------------------------------------------------------------------| r_work (final): 0.5538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1260 moved from start: 0.5231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18134 Z= 0.145 Angle : 0.670 13.158 24544 Z= 0.343 Chirality : 0.044 0.216 2947 Planarity : 0.004 0.058 3103 Dihedral : 6.608 68.380 2539 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.10 % Allowed : 9.10 % Favored : 88.80 % 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 aren not related in a simple way. whole: -0.10 (0.17), residues: 2310 helix: 0.97 (0.16), residues: 1086 sheet: -0.70 (0.30), residues: 236 loop : -1.04 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 78 TYR 0.017 0.002 TYR L 218 PHE 0.024 0.002 PHE I 13 TRP 0.018 0.002 TRP A 6 HIS 0.003 0.001 HIS B 46 Details of bonding type rmsd covalent geometry : bond 0.00295 (18134) covalent geometry : angle 0.67008 (24544) hydrogen bonds : bond 0.04291 ( 997) hydrogen bonds : angle 5.24848 ( 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 213 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 172 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ARG cc_start: 0.3401 (ptp-170) cc_final: 0.2660 (ttt180) REVERT: B 255 PHE cc_start: 0.2166 (m-80) cc_final: 0.1929 (m-10) REVERT: E 141 ASP cc_start: -0.0057 (OUTLIER) cc_final: -0.1818 (m-30) REVERT: E 157 LYS cc_start: 0.1364 (ttmt) cc_final: 0.0647 (tptp) REVERT: G 42 MET cc_start: 0.0298 (mpp) cc_final: 0.0061 (mpp) REVERT: H 60 MET cc_start: 0.0434 (mtt) cc_final: 0.0029 (mmm) REVERT: H 65 ILE cc_start: 0.2461 (pt) cc_final: 0.0397 (mt) REVERT: H 183 MET cc_start: -0.0025 (mmm) cc_final: -0.1294 (pmm) REVERT: I 160 LYS cc_start: -0.0150 (ttmt) cc_final: -0.0612 (tppt) REVERT: J 78 ARG cc_start: 0.2197 (OUTLIER) cc_final: 0.1943 (ttm-80) REVERT: J 143 ASP cc_start: 0.7073 (m-30) cc_final: 0.6598 (t0) REVERT: J 183 MET cc_start: 0.2046 (ttt) cc_final: 0.1287 (pmm) REVERT: K 91 MET cc_start: 0.4944 (ptt) cc_final: 0.2601 (mtt) REVERT: K 153 MET cc_start: 0.2136 (mpp) cc_final: 0.0743 (mtt) REVERT: K 168 ASP cc_start: 0.6794 (t0) cc_final: 0.6593 (t0) REVERT: L 91 MET cc_start: 0.4995 (ptp) cc_final: 0.4110 (ptp) outliers start: 41 outliers final: 27 residues processed: 196 average time/residue: 0.1104 time to fit residues: 34.6806 Evaluate side-chains 190 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 48 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 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 194 THR Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 176 ILE Chi-restraints excluded: chain I residue 146 ILE Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain J residue 78 ARG 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 K residue 209 VAL Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 256 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 115 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 chunk 103 optimal weight: 0.5980 chunk 208 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 45 GLN ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 179 GLN ** 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 = 0.5600 r_free = 0.5600 target = 0.349370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.5432 r_free = 0.5432 target = 0.323719 restraints weight = 32911.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.5477 r_free = 0.5477 target = 0.330743 restraints weight = 19011.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.5508 r_free = 0.5508 target = 0.335547 restraints weight = 11954.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.5527 r_free = 0.5527 target = 0.338562 restraints weight = 8021.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.5538 r_free = 0.5538 target = 0.340489 restraints weight = 5771.317| |-----------------------------------------------------------------------------| r_work (final): 0.5536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1320 moved from start: 0.5667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18134 Z= 0.135 Angle : 0.632 12.524 24544 Z= 0.322 Chirality : 0.043 0.215 2947 Planarity : 0.004 0.050 3103 Dihedral : 6.263 61.572 2537 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.15 % Allowed : 10.07 % 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 aren not related in a simple way. whole: -0.01 (0.17), residues: 2310 helix: 1.14 (0.16), residues: 1092 sheet: -0.79 (0.30), residues: 239 loop : -1.10 (0.19), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 40 TYR 0.015 0.001 TYR H 158 PHE 0.021 0.002 PHE E 13 TRP 0.023 0.002 TRP B 212 HIS 0.001 0.000 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00275 (18134) covalent geometry : angle 0.63199 (24544) hydrogen bonds : bond 0.03952 ( 997) hydrogen bonds : angle 5.13652 ( 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 210 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 168 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ARG cc_start: 0.3507 (ptp-170) cc_final: 0.2798 (ttt180) REVERT: B 129 MET cc_start: -0.1109 (mtt) cc_final: -0.1462 (mtm) REVERT: E 141 ASP cc_start: 0.0144 (OUTLIER) cc_final: -0.1909 (p0) REVERT: E 157 LYS cc_start: 0.1608 (ttmt) cc_final: 0.0557 (tptp) REVERT: G 60 MET cc_start: -0.0934 (ttt) cc_final: -0.1304 (mtt) REVERT: G 78 ARG cc_start: 0.1519 (mtt90) cc_final: 0.1253 (mtt90) REVERT: G 79 LEU cc_start: 0.1000 (OUTLIER) cc_final: 0.0586 (mt) REVERT: H 65 ILE cc_start: 0.2756 (pt) cc_final: 0.1247 (mt) REVERT: H 183 MET cc_start: 0.0532 (mmm) cc_final: -0.0783 (pmm) REVERT: I 160 LYS cc_start: 0.0319 (ttmt) cc_final: -0.0024 (ttmt) REVERT: J 60 MET cc_start: 0.1509 (OUTLIER) cc_final: 0.0967 (mtm) REVERT: J 143 ASP cc_start: 0.7098 (m-30) cc_final: 0.6555 (t0) REVERT: J 183 MET cc_start: 0.1511 (ttt) cc_final: 0.1295 (pmm) REVERT: K 91 MET cc_start: 0.4794 (ptt) cc_final: 0.3138 (mtt) REVERT: K 153 MET cc_start: 0.2216 (mpp) cc_final: 0.0796 (mtt) REVERT: L 91 MET cc_start: 0.4797 (ptp) cc_final: 0.4014 (ptp) REVERT: L 171 MET cc_start: 0.0073 (mtp) cc_final: -0.0150 (mtp) outliers start: 42 outliers final: 28 residues processed: 195 average time/residue: 0.1239 time to fit residues: 38.3131 Evaluate side-chains 190 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 159 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 237 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 26 MET Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 178 ASN 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 162 VAL 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 H residue 140 ILE Chi-restraints excluded: chain H residue 176 ILE Chi-restraints excluded: chain I 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 153 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 98 optimal weight: 0.0060 chunk 220 optimal weight: 20.0000 chunk 219 optimal weight: 7.9990 chunk 173 optimal weight: 0.8980 chunk 133 optimal weight: 0.6980 chunk 204 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 ASN B 198 ASN ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5599 r_free = 0.5599 target = 0.348685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.5428 r_free = 0.5428 target = 0.323352 restraints weight = 32358.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.5475 r_free = 0.5475 target = 0.330621 restraints weight = 19215.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.5507 r_free = 0.5507 target = 0.335060 restraints weight = 12522.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.5519 r_free = 0.5519 target = 0.337442 restraints weight = 8651.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.5537 r_free = 0.5537 target = 0.340471 restraints weight = 6528.687| |-----------------------------------------------------------------------------| r_work (final): 0.5541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1301 moved from start: 0.5979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18134 Z= 0.116 Angle : 0.595 12.455 24544 Z= 0.302 Chirality : 0.042 0.167 2947 Planarity : 0.004 0.044 3103 Dihedral : 5.820 61.676 2535 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.84 % Allowed : 10.48 % Favored : 87.68 % 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 aren not related in a simple way. whole: 0.16 (0.17), residues: 2310 helix: 1.32 (0.16), residues: 1092 sheet: -0.77 (0.31), residues: 224 loop : -1.05 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 36 TYR 0.013 0.001 TYR H 158 PHE 0.020 0.002 PHE I 13 TRP 0.020 0.002 TRP B 212 HIS 0.002 0.000 HIS K 207 Details of bonding type rmsd covalent geometry : bond 0.00230 (18134) covalent geometry : angle 0.59548 (24544) hydrogen bonds : bond 0.03611 ( 997) hydrogen bonds : angle 4.98732 ( 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 202 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 166 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 ARG cc_start: 0.3641 (ptp-170) cc_final: 0.2960 (ttt180) REVERT: B 129 MET cc_start: -0.1317 (mtt) cc_final: -0.1520 (mtm) REVERT: E 134 MET cc_start: 0.1822 (mmt) cc_final: 0.1517 (mpp) REVERT: E 141 ASP cc_start: 0.0331 (OUTLIER) cc_final: -0.1841 (m-30) REVERT: E 157 LYS cc_start: 0.1668 (ttmt) cc_final: 0.0567 (tptp) REVERT: G 60 MET cc_start: -0.0940 (ttt) cc_final: -0.1154 (mtp) REVERT: H 65 ILE cc_start: 0.3028 (pt) cc_final: 0.0628 (mt) REVERT: H 183 MET cc_start: 0.0225 (mmm) cc_final: -0.0982 (pmm) REVERT: I 26 MET cc_start: -0.2979 (tpt) cc_final: -0.3198 (mmt) REVERT: I 160 LYS cc_start: 0.0293 (ttmt) cc_final: -0.0507 (tppt) REVERT: J 60 MET cc_start: 0.1414 (OUTLIER) cc_final: 0.0866 (mtm) REVERT: J 78 ARG cc_start: 0.0610 (ttm-80) cc_final: -0.0655 (mtt90) REVERT: J 143 ASP cc_start: 0.7025 (m-30) cc_final: 0.6456 (t0) REVERT: J 183 MET cc_start: 0.2902 (ttt) cc_final: 0.2180 (pmm) REVERT: K 91 MET cc_start: 0.4998 (ptt) cc_final: 0.3669 (mtt) REVERT: K 153 MET cc_start: 0.2172 (mpp) cc_final: 0.0731 (mtt) REVERT: L 91 MET cc_start: 0.4699 (ptp) cc_final: 0.4350 (ptm) REVERT: L 171 MET cc_start: 0.0104 (mtp) cc_final: -0.0260 (mtp) REVERT: F 26 MET cc_start: -0.3202 (tpt) cc_final: -0.3420 (mmt) outliers start: 36 outliers final: 29 residues processed: 189 average time/residue: 0.1126 time to fit residues: 34.0847 Evaluate side-chains 192 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 161 time to evaluate : 0.664 ------------------------------------------------------------------------------- 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 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 176 ILE Chi-restraints excluded: chain E residue 178 ASN Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain I 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 153 LEU 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 L residue 256 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: 0.7980 chunk 141 optimal weight: 0.0270 chunk 68 optimal weight: 8.9990 chunk 225 optimal weight: 0.7980 chunk 96 optimal weight: 0.1980 chunk 78 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 127 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 181 optimal weight: 0.7980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 198 ASN ** 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 = 0.5598 r_free = 0.5598 target = 0.348261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.5429 r_free = 0.5429 target = 0.323485 restraints weight = 32602.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.5473 r_free = 0.5473 target = 0.330407 restraints weight = 19387.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.5506 r_free = 0.5506 target = 0.334603 restraints weight = 12647.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.5517 r_free = 0.5517 target = 0.336655 restraints weight = 8622.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.5534 r_free = 0.5534 target = 0.339767 restraints weight = 6758.263| |-----------------------------------------------------------------------------| r_work (final): 0.5540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1310 moved from start: 0.6194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 18134 Z= 0.109 Angle : 0.578 11.815 24544 Z= 0.292 Chirality : 0.041 0.161 2947 Planarity : 0.004 0.046 3103 Dihedral : 5.578 60.481 2535 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.99 % Allowed : 10.84 % Favored : 87.17 % 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 aren not related in a simple way. whole: 0.31 (0.17), residues: 2310 helix: 1.47 (0.16), residues: 1097 sheet: -0.75 (0.31), residues: 228 loop : -0.99 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 78 TYR 0.014 0.001 TYR L 218 PHE 0.023 0.002 PHE J 22 TRP 0.027 0.002 TRP B 212 HIS 0.001 0.000 HIS L 207 Details of bonding type rmsd covalent geometry : bond 0.00216 (18134) covalent geometry : angle 0.57806 (24544) hydrogen bonds : bond 0.03452 ( 997) hydrogen bonds : angle 4.89335 ( 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 206 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 167 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.2510 (tmm) cc_final: 0.2291 (tmm) REVERT: A 26 LEU cc_start: 0.6123 (mt) cc_final: 0.5644 (pp) REVERT: A 234 ARG cc_start: 0.3707 (ptp-170) cc_final: 0.3145 (ttt180) REVERT: E 141 ASP cc_start: 0.0145 (OUTLIER) cc_final: -0.2369 (m-30) REVERT: E 157 LYS cc_start: 0.2022 (ttmt) cc_final: 0.0721 (tptp) REVERT: G 60 MET cc_start: -0.1063 (ttt) cc_final: -0.1461 (mtt) REVERT: H 65 ILE cc_start: 0.3117 (pt) cc_final: 0.1175 (mt) REVERT: H 78 ARG cc_start: 0.2788 (tmm160) cc_final: 0.0467 (ptp-170) REVERT: H 183 MET cc_start: 0.0507 (mmm) cc_final: -0.0747 (pmm) REVERT: I 160 LYS cc_start: 0.0550 (ttmt) cc_final: 0.0174 (ttmt) REVERT: J 60 MET cc_start: 0.1570 (OUTLIER) cc_final: 0.1017 (mtm) REVERT: J 143 ASP cc_start: 0.7024 (m-30) cc_final: 0.6478 (t0) REVERT: J 183 MET cc_start: 0.2403 (ttt) cc_final: 0.1931 (pmm) REVERT: K 91 MET cc_start: 0.4931 (ptt) cc_final: 0.3590 (mtt) REVERT: K 153 MET cc_start: 0.2149 (mpp) cc_final: 0.0739 (mtt) REVERT: L 35 ILE cc_start: 0.4144 (mp) cc_final: 0.3416 (mt) REVERT: L 91 MET cc_start: 0.4731 (ptp) cc_final: 0.4341 (ptm) REVERT: L 171 MET cc_start: 0.0015 (mtp) cc_final: -0.0293 (mtp) REVERT: F 26 MET cc_start: -0.3193 (tpt) cc_final: -0.3411 (mmt) outliers start: 39 outliers final: 32 residues processed: 189 average time/residue: 0.1143 time to fit residues: 34.4417 Evaluate side-chains 196 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 162 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL 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 49 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 145 TYR 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 162 VAL 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 H residue 91 THR Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 176 ILE Chi-restraints excluded: chain I 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 153 LEU Chi-restraints excluded: chain J residue 179 THR 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 L residue 256 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: 0.9990 chunk 227 optimal weight: 0.0870 chunk 37 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 95 optimal weight: 20.0000 chunk 36 optimal weight: 0.9980 chunk 216 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 166 optimal weight: 7.9990 chunk 149 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 HIS ** 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 = 0.5601 r_free = 0.5601 target = 0.347806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.5422 r_free = 0.5422 target = 0.321618 restraints weight = 30305.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.5472 r_free = 0.5472 target = 0.328820 restraints weight = 17449.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.5504 r_free = 0.5504 target = 0.333330 restraints weight = 10916.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.5525 r_free = 0.5525 target = 0.336567 restraints weight = 7435.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.5540 r_free = 0.5540 target = 0.338726 restraints weight = 5380.286| |-----------------------------------------------------------------------------| r_work (final): 0.5543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1528 moved from start: 0.6794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18134 Z= 0.146 Angle : 0.647 11.696 24544 Z= 0.329 Chirality : 0.043 0.176 2947 Planarity : 0.004 0.044 3103 Dihedral : 5.822 61.645 2535 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.45 % Allowed : 10.74 % Favored : 86.81 % 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 aren not related in a simple way. whole: 0.08 (0.17), residues: 2310 helix: 1.26 (0.16), residues: 1102 sheet: -0.99 (0.34), residues: 200 loop : -1.08 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 94 TYR 0.027 0.002 TYR H 145 PHE 0.020 0.002 PHE J 84 TRP 0.032 0.003 TRP A 212 HIS 0.003 0.001 HIS K 207 Details of bonding type rmsd covalent geometry : bond 0.00313 (18134) covalent geometry : angle 0.64680 (24544) hydrogen bonds : bond 0.03667 ( 997) hydrogen bonds : angle 5.05475 ( 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 214 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 166 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ARG cc_start: 0.4266 (ptp-170) cc_final: 0.4057 (mmt180) REVERT: B 40 ARG cc_start: 0.4997 (OUTLIER) cc_final: 0.4794 (ptt90) REVERT: E 141 ASP cc_start: 0.0024 (OUTLIER) cc_final: -0.2904 (m-30) REVERT: E 157 LYS cc_start: 0.2040 (ttmt) cc_final: 0.0898 (tptp) REVERT: H 65 ILE cc_start: 0.3159 (pt) cc_final: 0.1772 (mt) REVERT: H 183 MET cc_start: 0.0585 (mmm) cc_final: -0.0329 (pmm) REVERT: I 160 LYS cc_start: 0.1197 (ttmt) cc_final: 0.0717 (ttmt) REVERT: J 60 MET cc_start: 0.2503 (OUTLIER) cc_final: 0.1780 (mtm) REVERT: J 143 ASP cc_start: 0.6924 (m-30) cc_final: 0.6352 (t0) REVERT: J 183 MET cc_start: 0.2820 (ttt) cc_final: 0.2259 (pmm) REVERT: K 91 MET cc_start: 0.4964 (ptt) cc_final: 0.3641 (mtt) REVERT: K 153 MET cc_start: 0.2553 (mpp) cc_final: 0.0850 (mtt) REVERT: L 31 ILE cc_start: 0.2849 (mm) cc_final: 0.2451 (mm) REVERT: L 36 ARG cc_start: 0.1940 (mmt90) cc_final: 0.1053 (mtm180) REVERT: L 91 MET cc_start: 0.4723 (ptp) cc_final: 0.4234 (ptp) REVERT: F 26 MET cc_start: -0.2843 (tpt) cc_final: -0.3060 (mmt) outliers start: 48 outliers final: 37 residues processed: 198 average time/residue: 0.1343 time to fit residues: 41.6688 Evaluate side-chains 197 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 157 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain B residue 40 ARG 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 49 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 162 VAL 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 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 170 LEU Chi-restraints excluded: chain H residue 176 ILE Chi-restraints excluded: chain I 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 153 LEU Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain K residue 52 THR 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: 1.9990 chunk 25 optimal weight: 9.9990 chunk 144 optimal weight: 5.9990 chunk 184 optimal weight: 0.6980 chunk 79 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 164 optimal weight: 0.8980 chunk 29 optimal weight: 0.4980 chunk 75 optimal weight: 7.9990 chunk 72 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.5592 r_free = 0.5592 target = 0.346643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.5424 r_free = 0.5424 target = 0.322154 restraints weight = 32867.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.5471 r_free = 0.5471 target = 0.328792 restraints weight = 19271.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.5501 r_free = 0.5501 target = 0.333201 restraints weight = 12186.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.5521 r_free = 0.5521 target = 0.336045 restraints weight = 8304.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.5534 r_free = 0.5534 target = 0.338078 restraints weight = 6074.448| |-----------------------------------------------------------------------------| r_work (final): 0.5546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1461 moved from start: 0.6941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18134 Z= 0.117 Angle : 0.619 12.908 24544 Z= 0.311 Chirality : 0.042 0.164 2947 Planarity : 0.004 0.046 3103 Dihedral : 5.631 59.450 2535 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.94 % Allowed : 11.50 % Favored : 86.55 % 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 aren not related in a simple way. whole: 0.23 (0.17), residues: 2310 helix: 1.40 (0.16), residues: 1106 sheet: -0.80 (0.34), residues: 194 loop : -1.04 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 78 TYR 0.012 0.001 TYR I 158 PHE 0.023 0.002 PHE J 22 TRP 0.028 0.002 TRP B 212 HIS 0.001 0.000 HIS K 207 Details of bonding type rmsd covalent geometry : bond 0.00241 (18134) covalent geometry : angle 0.61869 (24544) hydrogen bonds : bond 0.03430 ( 997) hydrogen bonds : angle 4.93996 ( 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 193 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 155 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.5980 (mt) cc_final: 0.5543 (pp) REVERT: A 129 MET cc_start: -0.2607 (mtt) cc_final: -0.2831 (mtm) REVERT: A 131 MET cc_start: -0.0449 (tpp) cc_final: -0.0777 (tpt) REVERT: B 84 LEU cc_start: 0.3863 (mm) cc_final: 0.3649 (mm) REVERT: B 129 MET cc_start: -0.0354 (mpp) cc_final: -0.0820 (mpp) REVERT: E 141 ASP cc_start: 0.0134 (OUTLIER) cc_final: -0.2883 (m-30) REVERT: E 157 LYS cc_start: 0.1289 (ttmt) cc_final: 0.0189 (tptp) REVERT: G 171 LYS cc_start: 0.0730 (tmtt) cc_final: 0.0496 (tmmt) REVERT: H 65 ILE cc_start: 0.3205 (pt) cc_final: 0.1224 (mt) REVERT: H 78 ARG cc_start: 0.2679 (tmm160) cc_final: -0.0772 (ptp-170) REVERT: H 183 MET cc_start: 0.0498 (mmm) cc_final: -0.0438 (pmm) REVERT: I 160 LYS cc_start: 0.1105 (ttmt) cc_final: 0.0572 (ttmt) REVERT: J 60 MET cc_start: 0.1938 (OUTLIER) cc_final: 0.1376 (mtm) REVERT: J 143 ASP cc_start: 0.6696 (m-30) cc_final: 0.6214 (t0) REVERT: J 183 MET cc_start: 0.2616 (ttt) cc_final: 0.1953 (pmm) REVERT: K 91 MET cc_start: 0.4873 (ptt) cc_final: 0.3594 (mtt) REVERT: K 153 MET cc_start: 0.2481 (mpp) cc_final: 0.0947 (mtt) REVERT: L 31 ILE cc_start: 0.3019 (mm) cc_final: 0.2687 (mm) REVERT: L 36 ARG cc_start: 0.1732 (mmt90) cc_final: 0.1044 (mtm180) REVERT: F 147 MET cc_start: 0.5666 (tpp) cc_final: 0.5319 (tpp) REVERT: F 160 LYS cc_start: 0.2889 (tppt) cc_final: 0.2166 (ttpt) outliers start: 38 outliers final: 32 residues processed: 180 average time/residue: 0.1338 time to fit residues: 37.5304 Evaluate side-chains 183 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 149 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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 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 176 ILE Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 162 VAL 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 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 42 MET Chi-restraints excluded: chain I 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 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 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: 0.7980 chunk 189 optimal weight: 0.0980 chunk 127 optimal weight: 0.9990 chunk 213 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 222 optimal weight: 4.9990 chunk 209 optimal weight: 0.8980 chunk 206 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 137 optimal weight: 0.0050 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.5592 r_free = 0.5592 target = 0.346946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.5423 r_free = 0.5423 target = 0.322078 restraints weight = 32356.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.5472 r_free = 0.5472 target = 0.329069 restraints weight = 18647.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.5502 r_free = 0.5502 target = 0.333530 restraints weight = 11588.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.5524 r_free = 0.5524 target = 0.336518 restraints weight = 7815.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.5537 r_free = 0.5537 target = 0.338597 restraints weight = 5617.287| |-----------------------------------------------------------------------------| r_work (final): 0.5547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1450 moved from start: 0.7150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18134 Z= 0.111 Angle : 0.603 12.863 24544 Z= 0.301 Chirality : 0.042 0.174 2947 Planarity : 0.004 0.046 3103 Dihedral : 5.433 59.471 2535 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.79 % Allowed : 11.81 % Favored : 86.40 % 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 aren not related in a simple way. whole: 0.34 (0.17), residues: 2310 helix: 1.52 (0.16), residues: 1106 sheet: -0.80 (0.34), residues: 194 loop : -1.02 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 40 TYR 0.012 0.001 TYR K 218 PHE 0.020 0.001 PHE G 84 TRP 0.026 0.002 TRP B 212 HIS 0.001 0.000 HIS A 194 Details of bonding type rmsd covalent geometry : bond 0.00229 (18134) covalent geometry : angle 0.60332 (24544) hydrogen bonds : bond 0.03274 ( 997) hydrogen bonds : angle 4.86302 ( 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 188 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 153 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.5999 (mt) cc_final: 0.5560 (pp) REVERT: B 84 LEU cc_start: 0.3894 (mm) cc_final: 0.3385 (mm) REVERT: B 87 MET cc_start: -0.2066 (ppp) cc_final: -0.2651 (ppp) REVERT: B 129 MET cc_start: -0.0308 (mpp) cc_final: -0.0633 (mpp) REVERT: E 141 ASP cc_start: 0.0242 (OUTLIER) cc_final: -0.2673 (m-30) REVERT: E 157 LYS cc_start: 0.1081 (ttmt) cc_final: 0.0089 (tptp) REVERT: G 171 LYS cc_start: 0.0606 (tmtt) cc_final: 0.0332 (tmmt) REVERT: H 65 ILE cc_start: 0.3332 (pt) cc_final: 0.1318 (mt) REVERT: H 78 ARG cc_start: 0.2718 (tmm160) cc_final: -0.0878 (ptp-170) REVERT: H 183 MET cc_start: 0.0363 (mmm) cc_final: -0.0431 (pmm) REVERT: I 160 LYS cc_start: 0.1108 (ttmt) cc_final: 0.0637 (ttmt) REVERT: J 60 MET cc_start: 0.2243 (OUTLIER) cc_final: 0.1481 (mtm) REVERT: J 143 ASP cc_start: 0.6609 (m-30) cc_final: 0.6155 (t0) REVERT: K 91 MET cc_start: 0.4921 (ptt) cc_final: 0.3504 (mtt) REVERT: K 153 MET cc_start: 0.2394 (mpp) cc_final: 0.0912 (mtt) REVERT: L 36 ARG cc_start: 0.2016 (mmt90) cc_final: 0.1341 (mtm180) REVERT: F 147 MET cc_start: 0.5678 (tpp) cc_final: 0.5422 (tpp) REVERT: F 160 LYS cc_start: 0.3250 (tppt) cc_final: 0.1688 (tttp) outliers start: 35 outliers final: 31 residues processed: 175 average time/residue: 0.1182 time to fit residues: 33.1522 Evaluate side-chains 182 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 0.679 ------------------------------------------------------------------------------- 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 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 176 ILE Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 162 VAL 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 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 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 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 42 MET 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: 7.9990 chunk 154 optimal weight: 0.7980 chunk 132 optimal weight: 40.0000 chunk 69 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 200 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 215 optimal weight: 0.0470 chunk 17 optimal weight: 0.9980 chunk 188 optimal weight: 0.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 GLN J 178 ASN ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 123 ASN ** K 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5598 r_free = 0.5598 target = 0.347276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5433 r_free = 0.5433 target = 0.323399 restraints weight = 32840.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.5473 r_free = 0.5473 target = 0.329156 restraints weight = 19634.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.5513 r_free = 0.5513 target = 0.333703 restraints weight = 13266.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.5519 r_free = 0.5519 target = 0.335771 restraints weight = 8929.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.5538 r_free = 0.5538 target = 0.338377 restraints weight = 6804.166| |-----------------------------------------------------------------------------| r_work (final): 0.5540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1486 moved from start: 0.7405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18134 Z= 0.113 Angle : 0.601 12.525 24544 Z= 0.301 Chirality : 0.042 0.172 2947 Planarity : 0.004 0.045 3103 Dihedral : 5.403 58.240 2535 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.98 % Favored : 95.97 % Rotamer: Outliers : 1.99 % Allowed : 11.66 % Favored : 86.35 % 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 aren not related in a simple way. whole: 0.32 (0.17), residues: 2310 helix: 1.51 (0.16), residues: 1107 sheet: -0.75 (0.33), residues: 204 loop : -1.06 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 40 TYR 0.012 0.001 TYR J 158 PHE 0.025 0.002 PHE B 255 TRP 0.021 0.002 TRP B 212 HIS 0.002 0.000 HIS A 46 Details of bonding type rmsd covalent geometry : bond 0.00233 (18134) covalent geometry : angle 0.60118 (24544) hydrogen bonds : bond 0.03240 ( 997) hydrogen bonds : angle 4.83989 ( 2832) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3363.53 seconds wall clock time: 58 minutes 39.30 seconds (3519.30 seconds total)