Starting phenix.real_space_refine on Sun Jun 15 21:26:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6z5u_11082/06_2025/6z5u_11082.cif Found real_map, /net/cci-nas-00/data/ceres_data/6z5u_11082/06_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_11082/06_2025/6z5u_11082.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6z5u_11082/06_2025/6z5u_11082.map" model { file = "/net/cci-nas-00/data/ceres_data/6z5u_11082/06_2025/6z5u_11082.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6z5u_11082/06_2025/6z5u_11082.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.51, per 1000 atoms: 0.64 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: 4.78 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 2.48 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: 5.64 Time building geometry restraints manager: 5.53 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: 3.990 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: 0.760 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 42.490 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.100 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.430 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.021 0.006 TRP D 60 HIS 0.008 0.002 HIS A 194 PHE 0.172 0.010 PHE E 84 TYR 0.226 0.014 TYR H 158 ARG 0.008 0.001 ARG G 110 Details of bonding type rmsd hydrogen bonds : bond 0.19343 ( 997) hydrogen bonds : angle 7.77693 ( 2832) covalent geometry : bond 0.02085 (18134) covalent geometry : angle 1.88133 (24544) *********************** 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 : 2.361 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: 0.2778 (mm) REVERT: E 141 ASP cc_start: 0.0007 (OUTLIER) cc_final: -0.2894 (m-30) REVERT: E 162 VAL cc_start: 0.2953 (OUTLIER) cc_final: 0.2599 (t) REVERT: G 160 LYS cc_start: -0.0016 (ttmt) cc_final: -0.0606 (ttpp) REVERT: G 162 VAL cc_start: 0.2803 (t) cc_final: 0.2035 (p) REVERT: H 183 MET cc_start: 0.0037 (mmm) cc_final: -0.0490 (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: -0.1273 (m) REVERT: L 94 LEU cc_start: 0.0545 (mt) cc_final: -0.0686 (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: 0.3752 time to fit residues: 158.6104 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 : 2.705 ------------------------------------------------------------------------------- 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 193 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 117 optimal weight: 6.9990 chunk 92 optimal weight: 0.0060 chunk 179 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 133 optimal weight: 6.9990 chunk 207 optimal weight: 7.9990 overall best weight: 1.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 70 GLN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5602 r_free = 0.5602 target = 0.351342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5456 r_free = 0.5456 target = 0.328919 restraints weight = 33460.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.5502 r_free = 0.5502 target = 0.335687 restraints weight = 19918.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.5530 r_free = 0.5530 target = 0.340092 restraints weight = 12593.176| |-----------------------------------------------------------------------------| r_work (final): 0.5541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0809 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.139 18134 Z= 0.211 Angle : 0.806 11.084 24544 Z= 0.427 Chirality : 0.049 0.377 2947 Planarity : 0.005 0.063 3103 Dihedral : 8.865 66.866 2550 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.79 % Allowed : 5.01 % Favored : 93.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.16), residues: 2310 helix: 0.76 (0.15), residues: 1082 sheet: 0.22 (0.29), residues: 254 loop : -0.69 (0.19), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 6 HIS 0.004 0.001 HIS L 207 PHE 0.055 0.003 PHE F 192 TYR 0.022 0.002 TYR F 115 ARG 0.006 0.001 ARG K 195 Details of bonding type rmsd hydrogen bonds : bond 0.06318 ( 997) hydrogen bonds : angle 5.69828 ( 2832) covalent geometry : bond 0.00441 (18134) covalent geometry : angle 0.80584 (24544) *********************** 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 234 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 199 time to evaluate : 2.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 255 PHE cc_start: 0.1336 (m-80) cc_final: -0.1341 (m-80) REVERT: E 26 MET cc_start: 0.3124 (ptm) cc_final: 0.2465 (mmm) REVERT: E 145 TYR cc_start: 0.2660 (OUTLIER) cc_final: 0.0595 (m-80) REVERT: E 162 VAL cc_start: 0.3121 (OUTLIER) cc_final: 0.2406 (t) REVERT: G 78 ARG cc_start: 0.2385 (mtt90) cc_final: 0.2163 (ttm-80) REVERT: G 160 LYS cc_start: -0.0127 (ttmt) cc_final: -0.0792 (ttpt) REVERT: G 194 THR cc_start: 0.2646 (OUTLIER) cc_final: 0.2198 (m) REVERT: H 183 MET cc_start: 0.0187 (mmm) cc_final: -0.0719 (pmm) REVERT: J 60 MET cc_start: 0.0955 (OUTLIER) cc_final: 0.0751 (ttm) REVERT: J 160 LYS cc_start: 0.0527 (ttpt) cc_final: -0.0340 (pttt) REVERT: J 183 MET cc_start: 0.2020 (ttt) cc_final: 0.1265 (pmm) REVERT: K 153 MET cc_start: 0.1536 (tpp) cc_final: -0.0043 (mtt) REVERT: L 35 ILE cc_start: 0.3820 (mt) cc_final: 0.3511 (mt) REVERT: L 91 MET cc_start: 0.4649 (ptp) cc_final: 0.4367 (ptp) outliers start: 35 outliers final: 18 residues processed: 216 average time/residue: 0.3001 time to fit residues: 103.1315 Evaluate side-chains 194 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 2.696 ------------------------------------------------------------------------------- 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 G residue 194 THR 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 J residue 60 MET 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 Chi-restraints excluded: chain F residue 77 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 78 optimal weight: 8.9990 chunk 222 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 128 optimal weight: 0.0870 chunk 149 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 215 optimal weight: 0.0370 chunk 166 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 overall best weight: 2.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN B 77 ASN B 189 ASN K 117 HIS ** K 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 96 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5600 r_free = 0.5600 target = 0.348702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.5439 r_free = 0.5439 target = 0.324556 restraints weight = 33863.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.5483 r_free = 0.5483 target = 0.330968 restraints weight = 20170.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.5511 r_free = 0.5511 target = 0.335259 restraints weight = 12829.252| |-----------------------------------------------------------------------------| r_work (final): 0.5523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1344 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 18134 Z= 0.226 Angle : 0.842 10.315 24544 Z= 0.436 Chirality : 0.049 0.242 2947 Planarity : 0.006 0.065 3103 Dihedral : 7.354 59.817 2541 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.99 % Allowed : 8.33 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.16), residues: 2310 helix: 0.56 (0.15), residues: 1091 sheet: -0.48 (0.33), residues: 218 loop : -1.14 (0.18), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP B 183 HIS 0.004 0.001 HIS B 194 PHE 0.030 0.003 PHE E 46 TYR 0.029 0.003 TYR A 238 ARG 0.014 0.001 ARG A 234 Details of bonding type rmsd hydrogen bonds : bond 0.05329 ( 997) hydrogen bonds : angle 5.58787 ( 2832) covalent geometry : bond 0.00475 (18134) covalent geometry : angle 0.84208 (24544) *********************** 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 224 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 185 time to evaluate : 2.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ARG cc_start: 0.4462 (ptp-170) cc_final: 0.3779 (mmp-170) REVERT: B 24 MET cc_start: 0.2581 (tmm) cc_final: 0.2270 (tmm) REVERT: B 131 MET cc_start: 0.0012 (OUTLIER) cc_final: -0.0264 (mmt) REVERT: E 141 ASP cc_start: 0.0050 (OUTLIER) cc_final: -0.2061 (m-30) REVERT: E 146 ILE cc_start: 0.5684 (mt) cc_final: 0.4958 (tt) REVERT: E 162 VAL cc_start: 0.4368 (OUTLIER) cc_final: 0.3404 (t) REVERT: G 42 MET cc_start: 0.0683 (OUTLIER) cc_final: 0.0392 (mpp) REVERT: G 78 ARG cc_start: 0.1811 (mtt90) cc_final: 0.0660 (mtt90) REVERT: G 160 LYS cc_start: -0.0859 (ttmt) cc_final: -0.1744 (tttt) REVERT: H 183 MET cc_start: 0.0038 (mmm) cc_final: -0.1033 (pmm) REVERT: I 160 LYS cc_start: 0.0227 (ttmt) cc_final: -0.0174 (tptp) REVERT: J 78 ARG cc_start: 0.1602 (OUTLIER) cc_final: 0.1013 (ttm-80) REVERT: J 143 ASP cc_start: 0.7374 (m-30) cc_final: 0.6848 (t0) REVERT: J 160 LYS cc_start: 0.0516 (ttpt) cc_final: -0.0497 (pttt) REVERT: J 183 MET cc_start: 0.2700 (ttt) cc_final: 0.1632 (pmm) REVERT: K 91 MET cc_start: 0.3544 (OUTLIER) cc_final: 0.3020 (mtt) REVERT: K 153 MET cc_start: 0.2235 (mpp) cc_final: 0.0753 (mtt) REVERT: L 31 ILE cc_start: 0.2636 (mm) cc_final: 0.2432 (mm) REVERT: L 91 MET cc_start: 0.4913 (ptp) cc_final: 0.3893 (ptp) outliers start: 39 outliers final: 25 residues processed: 207 average time/residue: 0.3521 time to fit residues: 113.0010 Evaluate side-chains 193 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 1.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 183 MET Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain G residue 42 MET Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain H residue 42 MET 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 150 THR Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain K residue 91 MET Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain K residue 171 MET Chi-restraints excluded: chain K residue 209 VAL Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain F residue 22 PHE Chi-restraints excluded: chain F residue 150 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 223 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 186 optimal weight: 0.3980 chunk 53 optimal weight: 0.4980 chunk 64 optimal weight: 30.0000 chunk 84 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 134 optimal weight: 6.9990 chunk 218 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 94 ASN ** 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 = 0.5593 r_free = 0.5593 target = 0.348958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.5427 r_free = 0.5427 target = 0.324101 restraints weight = 33014.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.5474 r_free = 0.5474 target = 0.331134 restraints weight = 19560.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.5504 r_free = 0.5504 target = 0.335868 restraints weight = 12358.030| |-----------------------------------------------------------------------------| r_work (final): 0.5521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1275 moved from start: 0.5173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18134 Z= 0.138 Angle : 0.646 12.271 24544 Z= 0.332 Chirality : 0.043 0.214 2947 Planarity : 0.004 0.054 3103 Dihedral : 6.620 66.228 2539 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.84 % Allowed : 9.46 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.17), residues: 2310 helix: 0.99 (0.16), residues: 1086 sheet: -0.55 (0.31), residues: 239 loop : -1.03 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 6 HIS 0.001 0.000 HIS B 194 PHE 0.024 0.002 PHE I 13 TYR 0.016 0.001 TYR L 218 ARG 0.004 0.000 ARG B 40 Details of bonding type rmsd hydrogen bonds : bond 0.04275 ( 997) hydrogen bonds : angle 5.22149 ( 2832) covalent geometry : bond 0.00275 (18134) covalent geometry : angle 0.64633 (24544) *********************** 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 202 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 166 time to evaluate : 3.928 Fit side-chains REVERT: A 234 ARG cc_start: 0.3857 (ptp-170) cc_final: 0.3599 (mmp-170) REVERT: E 141 ASP cc_start: -0.0041 (OUTLIER) cc_final: -0.2482 (p0) REVERT: E 146 ILE cc_start: 0.5305 (mt) cc_final: 0.4638 (tt) REVERT: E 157 LYS cc_start: 0.2073 (ttmt) cc_final: 0.1171 (tptp) REVERT: G 78 ARG cc_start: 0.1417 (mtt90) cc_final: 0.0386 (mtt90) REVERT: G 160 LYS cc_start: -0.1176 (ttmt) cc_final: -0.2067 (tttm) REVERT: H 60 MET cc_start: 0.0520 (mtt) cc_final: 0.0313 (mmm) REVERT: H 183 MET cc_start: -0.0091 (mmm) cc_final: -0.1342 (pmm) REVERT: I 160 LYS cc_start: -0.0102 (ttmt) cc_final: -0.0590 (tppt) REVERT: J 143 ASP cc_start: 0.7302 (m-30) cc_final: 0.6697 (t0) REVERT: J 183 MET cc_start: 0.1816 (ttt) cc_final: 0.1138 (pmm) REVERT: K 153 MET cc_start: 0.2230 (mpp) cc_final: 0.0763 (mtt) REVERT: K 182 ILE cc_start: 0.2334 (mp) cc_final: 0.1913 (mm) REVERT: L 91 MET cc_start: 0.4718 (ptp) cc_final: 0.3942 (ptp) outliers start: 36 outliers final: 29 residues processed: 189 average time/residue: 0.3630 time to fit residues: 111.5900 Evaluate side-chains 188 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 2.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 42 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 26 MET Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain 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 72 THR Chi-restraints excluded: chain H residue 176 ILE Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain K residue 52 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 256 VAL Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 159 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 77 optimal weight: 40.0000 chunk 182 optimal weight: 9.9990 chunk 216 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 129 optimal weight: 0.6980 chunk 172 optimal weight: 10.0000 chunk 203 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 GLN ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN D 63 GLN G 45 GLN I 151 ASN ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 151 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5567 r_free = 0.5567 target = 0.343675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.5387 r_free = 0.5387 target = 0.318185 restraints weight = 34739.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.5414 r_free = 0.5414 target = 0.322595 restraints weight = 21330.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.5446 r_free = 0.5446 target = 0.326335 restraints weight = 15466.685| |-----------------------------------------------------------------------------| r_work (final): 0.5458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1961 moved from start: 0.6976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.125 18134 Z= 0.288 Angle : 0.990 13.439 24544 Z= 0.505 Chirality : 0.053 0.273 2947 Planarity : 0.007 0.065 3103 Dihedral : 7.995 81.523 2537 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 19.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 3.53 % Allowed : 10.28 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.16), residues: 2310 helix: 0.11 (0.15), residues: 1098 sheet: -1.21 (0.31), residues: 240 loop : -1.60 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.005 TRP A 212 HIS 0.007 0.001 HIS B 194 PHE 0.041 0.004 PHE K 176 TYR 0.040 0.003 TYR A 238 ARG 0.011 0.001 ARG A 234 Details of bonding type rmsd hydrogen bonds : bond 0.05582 ( 997) hydrogen bonds : angle 6.17176 ( 2832) covalent geometry : bond 0.00642 (18134) covalent geometry : angle 0.99031 (24544) *********************** 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 237 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 168 time to evaluate : 1.990 Fit side-chains revert: symmetry clash REVERT: A 234 ARG cc_start: 0.5114 (ptp-170) cc_final: 0.3554 (mmp-170) REVERT: B 40 ARG cc_start: 0.4600 (OUTLIER) cc_final: 0.4333 (ptt90) REVERT: B 131 MET cc_start: 0.1241 (OUTLIER) cc_final: 0.1003 (tpp) REVERT: B 232 MET cc_start: 0.2783 (ttp) cc_final: 0.0698 (pmm) REVERT: B 255 PHE cc_start: 0.2773 (m-10) cc_final: 0.2503 (m-10) REVERT: E 134 MET cc_start: 0.1500 (mmt) cc_final: 0.0786 (mpp) REVERT: E 141 ASP cc_start: 0.0250 (OUTLIER) cc_final: -0.1747 (m-30) REVERT: E 157 LYS cc_start: 0.1887 (ttmt) cc_final: 0.0771 (tptp) REVERT: G 79 LEU cc_start: 0.0207 (OUTLIER) cc_final: -0.0447 (mt) REVERT: G 153 LEU cc_start: 0.5046 (OUTLIER) cc_final: 0.3392 (pp) REVERT: H 78 ARG cc_start: 0.3269 (tmm160) cc_final: 0.2572 (tpm170) REVERT: J 60 MET cc_start: 0.2388 (mtt) cc_final: 0.1859 (mtm) REVERT: J 183 MET cc_start: 0.2434 (ttt) cc_final: 0.1521 (pmm) REVERT: K 153 MET cc_start: 0.2307 (tpp) cc_final: 0.0721 (mtt) REVERT: K 168 ASP cc_start: 0.7213 (t0) cc_final: 0.6852 (t0) REVERT: L 44 MET cc_start: 0.1728 (ptt) cc_final: 0.1410 (ptt) REVERT: L 91 MET cc_start: 0.5144 (ptp) cc_final: 0.4874 (ptp) REVERT: F 26 MET cc_start: -0.2945 (tpt) cc_final: -0.3274 (mmt) outliers start: 69 outliers final: 40 residues processed: 218 average time/residue: 0.3102 time to fit residues: 106.6288 Evaluate side-chains 202 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 157 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 131 MET 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 72 THR Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 84 PHE Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain 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 140 ILE Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain H residue 176 ILE Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 159 LEU Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 219 ILE Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 159 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 20 optimal weight: 0.7980 chunk 164 optimal weight: 0.9990 chunk 119 optimal weight: 0.3980 chunk 138 optimal weight: 0.0020 chunk 211 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 222 optimal weight: 7.9990 chunk 114 optimal weight: 50.0000 chunk 147 optimal weight: 2.9990 chunk 208 optimal weight: 0.8980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5605 r_free = 0.5605 target = 0.347153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.5441 r_free = 0.5441 target = 0.323374 restraints weight = 35704.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.5485 r_free = 0.5485 target = 0.329650 restraints weight = 21025.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.5513 r_free = 0.5513 target = 0.333681 restraints weight = 13409.318| |-----------------------------------------------------------------------------| r_work (final): 0.5492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1633 moved from start: 0.6919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18134 Z= 0.132 Angle : 0.655 12.854 24544 Z= 0.335 Chirality : 0.043 0.171 2947 Planarity : 0.004 0.053 3103 Dihedral : 6.680 76.549 2537 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.94 % Allowed : 12.58 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.17), residues: 2310 helix: 0.84 (0.16), residues: 1095 sheet: -0.93 (0.30), residues: 259 loop : -1.35 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 6 HIS 0.003 0.001 HIS L 207 PHE 0.024 0.002 PHE I 13 TYR 0.018 0.001 TYR K 218 ARG 0.014 0.001 ARG G 78 Details of bonding type rmsd hydrogen bonds : bond 0.03962 ( 997) hydrogen bonds : angle 5.34053 ( 2832) covalent geometry : bond 0.00264 (18134) covalent geometry : angle 0.65548 (24544) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 1.929 Fit side-chains revert: symmetry clash REVERT: A 24 MET cc_start: 0.2932 (tmm) cc_final: 0.2722 (tmm) REVERT: A 234 ARG cc_start: 0.4278 (ptp-170) cc_final: 0.3422 (mmp-170) REVERT: B 129 MET cc_start: -0.1671 (mtt) cc_final: -0.1932 (mtm) REVERT: E 126 MET cc_start: -0.1614 (mtt) cc_final: -0.1925 (mtt) REVERT: E 134 MET cc_start: 0.1597 (mmt) cc_final: 0.0711 (mpp) REVERT: E 141 ASP cc_start: 0.0487 (OUTLIER) cc_final: -0.1783 (m-30) REVERT: E 157 LYS cc_start: 0.1505 (ttmt) cc_final: 0.0459 (tptp) REVERT: E 183 MET cc_start: 0.2765 (mmm) cc_final: 0.1926 (mmt) REVERT: G 78 ARG cc_start: 0.1243 (mmt-90) cc_final: 0.0932 (mmp80) REVERT: H 60 MET cc_start: 0.1001 (mmt) cc_final: -0.0798 (mmt) REVERT: H 65 ILE cc_start: 0.3459 (pt) cc_final: 0.0966 (mt) REVERT: I 160 LYS cc_start: 0.1052 (ttmt) cc_final: 0.0683 (ttmt) REVERT: I 192 PHE cc_start: -0.1467 (m-10) cc_final: -0.1693 (m-10) REVERT: J 42 MET cc_start: 0.1998 (mmm) cc_final: 0.1520 (mpp) REVERT: J 60 MET cc_start: 0.2448 (OUTLIER) cc_final: 0.1666 (mtm) REVERT: J 183 MET cc_start: 0.2421 (ttt) cc_final: 0.1962 (pmm) REVERT: K 153 MET cc_start: 0.2475 (tpp) cc_final: 0.1163 (mtt) REVERT: K 168 ASP cc_start: 0.6941 (t0) cc_final: 0.6628 (t0) REVERT: L 31 ILE cc_start: 0.2679 (mm) cc_final: 0.2269 (mm) REVERT: L 91 MET cc_start: 0.4951 (ptp) cc_final: 0.4328 (ptp) REVERT: F 26 MET cc_start: -0.3023 (tpt) cc_final: -0.3253 (mmt) outliers start: 38 outliers final: 27 residues processed: 189 average time/residue: 0.2761 time to fit residues: 82.8167 Evaluate side-chains 189 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 2.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 41 PHE 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 162 VAL Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 84 PHE Chi-restraints excluded: chain G residue 183 MET Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain I residue 159 LEU Chi-restraints excluded: chain J residue 13 PHE Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain J residue 60 MET Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain L residue 74 LYS Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain F residue 159 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 179 optimal weight: 6.9990 chunk 135 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 146 optimal weight: 3.9990 chunk 205 optimal weight: 0.9990 chunk 209 optimal weight: 10.0000 chunk 175 optimal weight: 0.0470 chunk 84 optimal weight: 0.7980 chunk 224 optimal weight: 0.9990 chunk 104 optimal weight: 0.0000 overall best weight: 0.5686 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5595 r_free = 0.5595 target = 0.346540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.5434 r_free = 0.5434 target = 0.322967 restraints weight = 35304.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.5461 r_free = 0.5461 target = 0.328210 restraints weight = 21302.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.5502 r_free = 0.5502 target = 0.332357 restraints weight = 15305.158| |-----------------------------------------------------------------------------| r_work (final): 0.5498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1624 moved from start: 0.7035 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= 0.121 Angle : 0.621 15.536 24544 Z= 0.314 Chirality : 0.043 0.192 2947 Planarity : 0.004 0.049 3103 Dihedral : 6.209 72.592 2537 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.15 % Allowed : 12.78 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.17), residues: 2310 helix: 1.11 (0.16), residues: 1104 sheet: -1.02 (0.30), residues: 245 loop : -1.28 (0.19), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 212 HIS 0.001 0.000 HIS B 194 PHE 0.020 0.002 PHE I 13 TYR 0.017 0.001 TYR K 218 ARG 0.008 0.000 ARG L 36 Details of bonding type rmsd hydrogen bonds : bond 0.03646 ( 997) hydrogen bonds : angle 5.15781 ( 2832) covalent geometry : bond 0.00244 (18134) covalent geometry : angle 0.62148 (24544) *********************** 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 203 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 161 time to evaluate : 2.001 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.2644 (tmm) cc_final: 0.2386 (tmm) REVERT: A 234 ARG cc_start: 0.4124 (ptp-170) cc_final: 0.3491 (mmp-170) REVERT: E 126 MET cc_start: -0.1734 (mtt) cc_final: -0.1955 (mtt) REVERT: E 141 ASP cc_start: -0.0211 (OUTLIER) cc_final: -0.2502 (m-30) REVERT: E 157 LYS cc_start: 0.1398 (ttmt) cc_final: 0.0473 (tptp) REVERT: E 183 MET cc_start: 0.2549 (mmm) cc_final: 0.2051 (mmp) REVERT: G 60 MET cc_start: 0.1011 (mtt) cc_final: 0.0307 (mtt) REVERT: H 60 MET cc_start: 0.0967 (mmt) cc_final: -0.1001 (mmt) REVERT: H 65 ILE cc_start: 0.3512 (pt) cc_final: 0.1169 (mt) REVERT: H 78 ARG cc_start: 0.2501 (tmm160) cc_final: 0.1579 (tpp-160) REVERT: I 160 LYS cc_start: 0.1181 (ttmt) cc_final: 0.0841 (ttmt) REVERT: J 60 MET cc_start: 0.2566 (OUTLIER) cc_final: 0.1704 (mtm) REVERT: J 183 MET cc_start: 0.2134 (ttt) cc_final: 0.1867 (pmm) REVERT: K 153 MET cc_start: 0.2308 (tpp) cc_final: 0.1024 (mtt) REVERT: K 168 ASP cc_start: 0.7103 (t0) cc_final: 0.6760 (t0) REVERT: L 31 ILE cc_start: 0.2702 (mm) cc_final: 0.2305 (mm) REVERT: L 91 MET cc_start: 0.5075 (ptp) cc_final: 0.4720 (ptp) REVERT: L 171 MET cc_start: -0.1326 (mtp) cc_final: -0.1696 (mtp) REVERT: F 48 ASN cc_start: 0.4059 (t0) cc_final: 0.3796 (t0) outliers start: 42 outliers final: 33 residues processed: 188 average time/residue: 0.2725 time to fit residues: 80.9364 Evaluate side-chains 193 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 158 time to evaluate : 2.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 42 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 26 MET Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 84 PHE Chi-restraints excluded: chain G residue 183 MET 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 141 ASP Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 159 LEU Chi-restraints excluded: chain J residue 13 PHE Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain J residue 60 MET Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 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 Chi-restraints excluded: chain F residue 159 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 133 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 192 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 206 optimal weight: 0.6980 chunk 160 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN A 70 GLN ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 HIS B 125 GLN ** I 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5552 r_free = 0.5552 target = 0.341790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.5373 r_free = 0.5373 target = 0.316122 restraints weight = 34803.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.5417 r_free = 0.5417 target = 0.322118 restraints weight = 21096.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.5446 r_free = 0.5446 target = 0.326158 restraints weight = 14009.781| |-----------------------------------------------------------------------------| r_work (final): 0.5458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2069 moved from start: 0.7929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 18134 Z= 0.200 Angle : 0.788 10.744 24544 Z= 0.400 Chirality : 0.048 0.298 2947 Planarity : 0.005 0.100 3103 Dihedral : 6.791 71.197 2537 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.76 % Allowed : 12.22 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.17), residues: 2310 helix: 0.72 (0.15), residues: 1105 sheet: -1.27 (0.31), residues: 239 loop : -1.48 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 146 HIS 0.004 0.001 HIS A 194 PHE 0.029 0.003 PHE B 41 TYR 0.030 0.002 TYR J 158 ARG 0.012 0.001 ARG G 78 Details of bonding type rmsd hydrogen bonds : bond 0.04450 ( 997) hydrogen bonds : angle 5.51462 ( 2832) covalent geometry : bond 0.00431 (18134) covalent geometry : angle 0.78832 (24544) *********************** 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 210 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 156 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 ARG cc_start: 0.4598 (ptp-170) cc_final: 0.3860 (mmp-170) REVERT: B 129 MET cc_start: -0.0391 (mpp) cc_final: -0.0760 (mpp) REVERT: B 232 MET cc_start: 0.2095 (ttp) cc_final: 0.1262 (pmm) REVERT: B 255 PHE cc_start: 0.1848 (m-10) cc_final: 0.0662 (t80) REVERT: E 42 MET cc_start: 0.3567 (ptp) cc_final: 0.3015 (ptp) REVERT: E 126 MET cc_start: -0.1604 (mtt) cc_final: -0.1828 (mtt) REVERT: E 134 MET cc_start: 0.1469 (mmt) cc_final: 0.0993 (mpp) REVERT: E 141 ASP cc_start: 0.1201 (OUTLIER) cc_final: -0.1503 (m-30) REVERT: E 157 LYS cc_start: 0.1316 (ttmt) cc_final: -0.0004 (ttmt) REVERT: E 183 MET cc_start: 0.3644 (mmm) cc_final: 0.3060 (mmp) REVERT: H 60 MET cc_start: 0.2675 (mmt) cc_final: -0.0262 (mmt) REVERT: H 65 ILE cc_start: 0.4395 (pt) cc_final: 0.2312 (mt) REVERT: I 160 LYS cc_start: 0.1818 (ttmt) cc_final: 0.0464 (tttm) REVERT: J 60 MET cc_start: 0.3117 (OUTLIER) cc_final: 0.1516 (mtt) REVERT: J 183 MET cc_start: 0.3051 (ttt) cc_final: 0.2108 (pmm) REVERT: K 153 MET cc_start: 0.2474 (tpp) cc_final: 0.1051 (mtt) REVERT: K 168 ASP cc_start: 0.7606 (t0) cc_final: 0.7336 (t0) REVERT: L 31 ILE cc_start: 0.2795 (mm) cc_final: 0.2460 (mm) REVERT: L 91 MET cc_start: 0.5345 (ptp) cc_final: 0.5059 (ptp) REVERT: L 171 MET cc_start: -0.0564 (mtp) cc_final: -0.1136 (mtp) outliers start: 54 outliers final: 39 residues processed: 193 average time/residue: 0.2594 time to fit residues: 80.3152 Evaluate side-chains 191 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 150 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 215 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 26 MET Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 84 PHE Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 183 MET Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 176 ILE Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 159 LEU 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 84 PHE Chi-restraints excluded: chain J residue 148 VAL 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 L residue 258 TYR Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 159 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 205 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 172 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 58 optimal weight: 0.0000 chunk 48 optimal weight: 0.8980 chunk 117 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 103 optimal weight: 0.0770 chunk 25 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 overall best weight: 0.5342 ------------------------------------------------------------------------------- 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 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 123 ASN F 102 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5582 r_free = 0.5582 target = 0.345304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.5408 r_free = 0.5408 target = 0.319394 restraints weight = 34709.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.5454 r_free = 0.5454 target = 0.326098 restraints weight = 20425.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.5485 r_free = 0.5485 target = 0.330547 restraints weight = 13162.784| |-----------------------------------------------------------------------------| r_work (final): 0.5485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1726 moved from start: 0.7907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 18134 Z= 0.121 Angle : 0.634 12.446 24544 Z= 0.321 Chirality : 0.043 0.200 2947 Planarity : 0.004 0.057 3103 Dihedral : 6.145 63.739 2537 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.89 % Allowed : 13.19 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.17), residues: 2310 helix: 1.11 (0.16), residues: 1097 sheet: -1.02 (0.30), residues: 250 loop : -1.34 (0.19), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 212 HIS 0.002 0.000 HIS L 207 PHE 0.020 0.002 PHE I 13 TYR 0.019 0.001 TYR K 218 ARG 0.005 0.000 ARG G 78 Details of bonding type rmsd hydrogen bonds : bond 0.03620 ( 997) hydrogen bonds : angle 5.10306 ( 2832) covalent geometry : bond 0.00248 (18134) covalent geometry : angle 0.63424 (24544) *********************** 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 192 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 155 time to evaluate : 1.848 Fit side-chains revert: symmetry clash REVERT: A 234 ARG cc_start: 0.4392 (ptp-170) cc_final: 0.4081 (mmp-170) REVERT: B 129 MET cc_start: -0.1228 (mpp) cc_final: -0.1469 (mpp) REVERT: B 131 MET cc_start: 0.1056 (tpp) cc_final: 0.0261 (tpp) REVERT: B 232 MET cc_start: 0.2221 (ttp) cc_final: 0.1040 (pmm) REVERT: E 42 MET cc_start: 0.3435 (ptp) cc_final: 0.2767 (ptp) REVERT: E 141 ASP cc_start: 0.0085 (OUTLIER) cc_final: -0.2528 (m-30) REVERT: E 157 LYS cc_start: 0.1732 (ttmt) cc_final: 0.0678 (tptp) REVERT: E 183 MET cc_start: 0.3080 (mmm) cc_final: 0.2780 (mmp) REVERT: H 60 MET cc_start: 0.1680 (mmt) cc_final: 0.0299 (mmt) REVERT: H 65 ILE cc_start: 0.4246 (pt) cc_final: 0.2314 (mt) REVERT: H 183 MET cc_start: 0.0197 (tpt) cc_final: -0.0586 (pmm) REVERT: I 160 LYS cc_start: 0.1288 (ttmt) cc_final: 0.0047 (tttm) REVERT: J 60 MET cc_start: 0.2838 (OUTLIER) cc_final: 0.1310 (mtt) REVERT: J 183 MET cc_start: 0.1901 (ttt) cc_final: 0.1501 (pmm) REVERT: K 91 MET cc_start: 0.5390 (ptt) cc_final: 0.2892 (mtt) REVERT: K 153 MET cc_start: 0.2534 (tpp) cc_final: 0.1258 (mtt) REVERT: K 168 ASP cc_start: 0.7452 (t0) cc_final: 0.7147 (t0) REVERT: L 171 MET cc_start: -0.1157 (mtp) cc_final: -0.1642 (mtp) outliers start: 37 outliers final: 32 residues processed: 180 average time/residue: 0.2842 time to fit residues: 82.0152 Evaluate side-chains 187 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 42 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 49 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 84 PHE Chi-restraints excluded: chain G residue 183 MET Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 159 LEU Chi-restraints excluded: chain J residue 13 PHE Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain J residue 60 MET Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 258 TYR Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 159 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 145 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 104 optimal weight: 0.0770 chunk 200 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 184 optimal weight: 10.0000 chunk 177 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 215 optimal weight: 0.9990 chunk 212 optimal weight: 0.5980 overall best weight: 0.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 61 GLN ** 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 = 0.5581 r_free = 0.5581 target = 0.344732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.5415 r_free = 0.5415 target = 0.320877 restraints weight = 35236.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.5450 r_free = 0.5450 target = 0.326724 restraints weight = 21524.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.5477 r_free = 0.5477 target = 0.330678 restraints weight = 14373.101| |-----------------------------------------------------------------------------| r_work (final): 0.5495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1823 moved from start: 0.8054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 18134 Z= 0.120 Angle : 0.625 11.786 24544 Z= 0.315 Chirality : 0.042 0.173 2947 Planarity : 0.004 0.051 3103 Dihedral : 5.922 59.119 2537 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.79 % Allowed : 13.14 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.17), residues: 2310 helix: 1.23 (0.16), residues: 1105 sheet: -0.86 (0.33), residues: 209 loop : -1.37 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 212 HIS 0.002 0.000 HIS A 194 PHE 0.019 0.002 PHE J 13 TYR 0.014 0.001 TYR K 218 ARG 0.004 0.000 ARG A 234 Details of bonding type rmsd hydrogen bonds : bond 0.03494 ( 997) hydrogen bonds : angle 5.02719 ( 2832) covalent geometry : bond 0.00248 (18134) covalent geometry : angle 0.62535 (24544) ********************** 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 194 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 159 time to evaluate : 2.080 Fit side-chains revert: symmetry clash REVERT: A 234 ARG cc_start: 0.4348 (ptp-170) cc_final: 0.4085 (mmp-170) REVERT: B 129 MET cc_start: -0.1159 (mpp) cc_final: -0.1472 (mpp) REVERT: B 131 MET cc_start: 0.1013 (tpp) cc_final: 0.0251 (tpp) REVERT: B 232 MET cc_start: 0.2275 (ttp) cc_final: 0.0928 (pmm) REVERT: E 42 MET cc_start: 0.3408 (ptp) cc_final: 0.2786 (ptp) REVERT: E 126 MET cc_start: -0.2329 (mtt) cc_final: -0.3039 (mtt) REVERT: E 141 ASP cc_start: 0.0353 (OUTLIER) cc_final: -0.2277 (m-30) REVERT: E 157 LYS cc_start: 0.1290 (ttmt) cc_final: 0.0583 (tptp) REVERT: E 183 MET cc_start: 0.3672 (mmm) cc_final: 0.3372 (mmp) REVERT: H 60 MET cc_start: 0.2247 (mmt) cc_final: 0.0906 (mmt) REVERT: H 65 ILE cc_start: 0.4038 (pt) cc_final: 0.2217 (mt) REVERT: H 183 MET cc_start: 0.0614 (tpt) cc_final: -0.0217 (pmm) REVERT: I 160 LYS cc_start: 0.1176 (ttmt) cc_final: -0.0076 (tttm) REVERT: J 60 MET cc_start: 0.2549 (OUTLIER) cc_final: 0.1686 (mtm) REVERT: J 183 MET cc_start: 0.1945 (ttt) cc_final: 0.1713 (pmm) REVERT: K 91 MET cc_start: 0.5190 (ptt) cc_final: 0.2550 (mtt) REVERT: K 153 MET cc_start: 0.2655 (tpp) cc_final: 0.1269 (mtt) REVERT: K 168 ASP cc_start: 0.7578 (t0) cc_final: 0.7348 (t0) REVERT: L 171 MET cc_start: -0.0647 (mtp) cc_final: -0.1091 (mtp) REVERT: L 258 TYR cc_start: 0.3158 (OUTLIER) cc_final: 0.1164 (t80) outliers start: 35 outliers final: 31 residues processed: 182 average time/residue: 0.2877 time to fit residues: 82.1663 Evaluate side-chains 190 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 156 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 42 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 49 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 84 PHE Chi-restraints excluded: chain G residue 183 MET Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 176 ILE Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 159 LEU Chi-restraints excluded: chain J residue 13 PHE Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain J residue 60 MET Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 258 TYR Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 159 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 2 optimal weight: 1.9990 chunk 157 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 193 optimal weight: 0.0470 chunk 120 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 191 optimal weight: 7.9990 chunk 190 optimal weight: 4.9990 chunk 211 optimal weight: 0.8980 overall best weight: 0.9480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 61 GLN ** 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 = 0.5579 r_free = 0.5579 target = 0.344760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.5407 r_free = 0.5407 target = 0.319217 restraints weight = 34960.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.5447 r_free = 0.5447 target = 0.325727 restraints weight = 20677.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.5485 r_free = 0.5485 target = 0.330484 restraints weight = 13722.861| |-----------------------------------------------------------------------------| r_work (final): 0.5486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1828 moved from start: 0.8331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18134 Z= 0.124 Angle : 0.633 11.568 24544 Z= 0.318 Chirality : 0.043 0.220 2947 Planarity : 0.004 0.047 3103 Dihedral : 5.853 57.738 2537 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.84 % Allowed : 13.29 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.17), residues: 2310 helix: 1.26 (0.16), residues: 1106 sheet: -0.93 (0.32), residues: 214 loop : -1.35 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 212 HIS 0.002 0.000 HIS A 194 PHE 0.020 0.002 PHE J 84 TYR 0.030 0.001 TYR L 218 ARG 0.004 0.000 ARG F 172 Details of bonding type rmsd hydrogen bonds : bond 0.03424 ( 997) hydrogen bonds : angle 4.97442 ( 2832) covalent geometry : bond 0.00260 (18134) covalent geometry : angle 0.63331 (24544) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6834.03 seconds wall clock time: 122 minutes 46.04 seconds (7366.04 seconds total)