Starting phenix.real_space_refine on Sat Sep 28 01:37:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z5u_11082/09_2024/6z5u_11082.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z5u_11082/09_2024/6z5u_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z5u_11082/09_2024/6z5u_11082.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z5u_11082/09_2024/6z5u_11082.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z5u_11082/09_2024/6z5u_11082.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z5u_11082/09_2024/6z5u_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 10.46, per 1000 atoms: 0.59 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: 4.38 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: 1.92 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: 5.30 Time building geometry restraints manager: 5.10 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: 7.760 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 39.040 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.140 ------------------------------------------------------------------------------- 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= 1.372 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 *********************** 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 fitting. rotamer outliers: 33 poor density : 254 time to evaluate : 1.923 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: 0.3188 time to fit residues: 133.8270 Evaluate side-chains 185 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 173 time to evaluate : 1.816 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0732 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= 0.295 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 *********************** 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 fitting. rotamer outliers: 35 poor density : 199 time to evaluate : 2.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 255 PHE cc_start: 0.1911 (m-80) cc_final: -0.0961 (m-80) REVERT: E 26 MET cc_start: 0.3441 (ptm) cc_final: 0.3066 (mmm) REVERT: E 145 TYR cc_start: 0.2525 (OUTLIER) cc_final: 0.0575 (m-80) REVERT: E 162 VAL cc_start: 0.3143 (OUTLIER) cc_final: 0.2517 (t) REVERT: G 78 ARG cc_start: 0.2889 (mtt90) cc_final: 0.2579 (ttm-80) REVERT: G 160 LYS cc_start: 0.0052 (ttmt) cc_final: -0.0863 (ttpt) REVERT: G 162 VAL cc_start: 0.2999 (t) cc_final: 0.2649 (p) REVERT: H 183 MET cc_start: 0.0033 (mmm) cc_final: -0.0464 (pmm) REVERT: J 60 MET cc_start: 0.0340 (OUTLIER) cc_final: 0.0136 (ttm) REVERT: J 160 LYS cc_start: 0.1495 (ttpt) cc_final: 0.0061 (pttt) REVERT: K 153 MET cc_start: 0.1579 (tpp) cc_final: -0.0488 (mtt) REVERT: L 35 ILE cc_start: 0.3828 (mt) cc_final: 0.3550 (mt) outliers start: 35 outliers final: 18 residues processed: 216 average time/residue: 0.2848 time to fit residues: 98.1956 Evaluate side-chains 194 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 173 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 178 ASN Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain H residue 178 ASN Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain 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 115 optimal weight: 1.9990 chunk 64 optimal weight: 20.0000 chunk 173 optimal weight: 0.0010 chunk 141 optimal weight: 0.4980 chunk 57 optimal weight: 4.9990 chunk 208 optimal weight: 0.8980 chunk 225 optimal weight: 0.0770 chunk 185 optimal weight: 6.9990 chunk 206 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 167 optimal weight: 7.9990 overall best weight: 0.4946 ------------------------------------------------------------------------------- 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 ** K 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0760 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18134 Z= 0.178 Angle : 0.640 12.307 24544 Z= 0.336 Chirality : 0.044 0.275 2947 Planarity : 0.004 0.060 3103 Dihedral : 7.008 56.188 2541 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.23 % Allowed : 7.57 % Favored : 91.21 % 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: 0.32 (0.17), residues: 2310 helix: 1.12 (0.16), residues: 1092 sheet: 0.07 (0.31), residues: 247 loop : -0.74 (0.18), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 183 HIS 0.002 0.000 HIS D 48 PHE 0.029 0.002 PHE J 22 TYR 0.015 0.002 TYR L 218 ARG 0.004 0.000 ARG B 40 *********************** 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 201 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 177 time to evaluate : 2.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 PHE cc_start: 0.3167 (t80) cc_final: 0.2414 (t80) REVERT: B 255 PHE cc_start: 0.1737 (m-80) cc_final: -0.0976 (m-80) REVERT: E 26 MET cc_start: 0.3315 (ptm) cc_final: 0.2960 (mmm) REVERT: E 42 MET cc_start: 0.1263 (pmm) cc_final: 0.0950 (ptt) REVERT: E 145 TYR cc_start: 0.2496 (OUTLIER) cc_final: 0.0484 (m-80) REVERT: E 162 VAL cc_start: 0.2931 (OUTLIER) cc_final: 0.2259 (t) REVERT: G 42 MET cc_start: 0.0694 (mpp) cc_final: -0.0095 (mpp) REVERT: G 78 ARG cc_start: 0.2421 (mtt90) cc_final: 0.2078 (mtt90) REVERT: G 160 LYS cc_start: -0.0147 (ttmt) cc_final: -0.0920 (ttpp) REVERT: G 162 VAL cc_start: 0.3019 (t) cc_final: 0.2224 (p) REVERT: H 183 MET cc_start: 0.0159 (mmm) cc_final: -0.0460 (pmm) REVERT: J 160 LYS cc_start: 0.1067 (ttpt) cc_final: -0.0079 (pttt) REVERT: K 153 MET cc_start: 0.1564 (mpp) cc_final: 0.0290 (mtt) REVERT: L 35 ILE cc_start: 0.4018 (mt) cc_final: 0.3720 (mt) outliers start: 24 outliers final: 19 residues processed: 191 average time/residue: 0.2914 time to fit residues: 87.4126 Evaluate side-chains 190 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 169 time to evaluate : 1.836 ------------------------------------------------------------------------------- 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 70 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain I residue 22 PHE Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain K residue 209 VAL Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain F residue 150 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 205 optimal weight: 2.9990 chunk 156 optimal weight: 0.6980 chunk 108 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 chunk 139 optimal weight: 0.0870 chunk 209 optimal weight: 6.9990 chunk 221 optimal weight: 0.0370 chunk 109 optimal weight: 0.8980 chunk 198 optimal weight: 0.9980 chunk 59 optimal weight: 30.0000 overall best weight: 0.4436 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0817 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18134 Z= 0.155 Angle : 0.603 11.771 24544 Z= 0.310 Chirality : 0.042 0.216 2947 Planarity : 0.004 0.054 3103 Dihedral : 6.122 56.120 2537 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.48 % Allowed : 7.87 % Favored : 90.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (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: 0.42 (0.17), residues: 2310 helix: 1.27 (0.16), residues: 1084 sheet: -0.01 (0.31), residues: 250 loop : -0.72 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 6 HIS 0.002 0.000 HIS L 207 PHE 0.024 0.002 PHE J 22 TYR 0.014 0.001 TYR L 218 ARG 0.010 0.000 ARG H 78 *********************** 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 201 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 172 time to evaluate : 1.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 129 MET cc_start: 0.0002 (mtt) cc_final: -0.0406 (mtm) REVERT: B 131 MET cc_start: 0.1121 (tpp) cc_final: 0.0666 (mmt) REVERT: E 26 MET cc_start: 0.3218 (OUTLIER) cc_final: 0.2976 (mmm) REVERT: E 60 MET cc_start: -0.2533 (ttt) cc_final: -0.4551 (mtt) REVERT: E 141 ASP cc_start: 0.0964 (OUTLIER) cc_final: -0.1245 (m-30) REVERT: E 162 VAL cc_start: 0.3137 (OUTLIER) cc_final: 0.2249 (t) REVERT: G 42 MET cc_start: 0.0569 (mpp) cc_final: 0.0039 (mpp) REVERT: G 78 ARG cc_start: 0.2253 (mtt90) cc_final: 0.0914 (mtt90) REVERT: G 160 LYS cc_start: -0.0260 (ttmt) cc_final: -0.1110 (ttpp) REVERT: G 162 VAL cc_start: 0.2985 (t) cc_final: 0.2245 (p) REVERT: H 183 MET cc_start: 0.0003 (mmm) cc_final: -0.0917 (pmm) REVERT: J 160 LYS cc_start: 0.1039 (ttpt) cc_final: -0.0060 (pttt) REVERT: K 91 MET cc_start: 0.2874 (ptt) cc_final: 0.1738 (mtt) REVERT: K 153 MET cc_start: 0.2235 (mpp) cc_final: 0.0579 (mtt) outliers start: 29 outliers final: 22 residues processed: 189 average time/residue: 0.2538 time to fit residues: 77.0591 Evaluate side-chains 186 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 161 time to evaluate : 1.825 ------------------------------------------------------------------------------- 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 78 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 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 I residue 42 MET Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain K residue 209 VAL Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain F residue 22 PHE Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain F residue 150 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 184 optimal weight: 9.9990 chunk 125 optimal weight: 0.0060 chunk 3 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 188 optimal weight: 4.9990 chunk 153 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 113 optimal weight: 7.9990 chunk 198 optimal weight: 0.2980 chunk 55 optimal weight: 40.0000 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 ASN D 63 GLN G 45 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1066 moved from start: 0.4994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 18134 Z= 0.183 Angle : 0.631 11.523 24544 Z= 0.322 Chirality : 0.043 0.215 2947 Planarity : 0.004 0.049 3103 Dihedral : 5.907 59.064 2537 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.04 % Allowed : 8.49 % Favored : 89.47 % 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: 0.32 (0.17), residues: 2310 helix: 1.29 (0.16), residues: 1083 sheet: -0.27 (0.31), residues: 249 loop : -0.85 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 146 HIS 0.002 0.000 HIS B 46 PHE 0.020 0.002 PHE H 84 TYR 0.018 0.002 TYR A 238 ARG 0.008 0.001 ARG H 78 *********************** 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 209 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 169 time to evaluate : 1.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 232 MET cc_start: 0.2697 (ttp) cc_final: 0.0995 (pmm) REVERT: E 141 ASP cc_start: 0.0807 (OUTLIER) cc_final: -0.1567 (m-30) REVERT: E 145 TYR cc_start: 0.2173 (OUTLIER) cc_final: -0.0271 (m-80) REVERT: E 162 VAL cc_start: 0.3551 (OUTLIER) cc_final: 0.2754 (t) REVERT: G 60 MET cc_start: -0.0277 (ttt) cc_final: -0.0956 (mtp) REVERT: G 78 ARG cc_start: 0.1952 (mtt90) cc_final: 0.0815 (mtt90) REVERT: G 160 LYS cc_start: -0.0586 (ttmt) cc_final: -0.2141 (pttt) REVERT: G 162 VAL cc_start: 0.3154 (t) cc_final: 0.2646 (p) REVERT: H 183 MET cc_start: 0.0615 (mmm) cc_final: -0.0584 (pmm) REVERT: J 160 LYS cc_start: 0.1130 (ttpt) cc_final: 0.0071 (pttt) REVERT: K 153 MET cc_start: 0.2330 (mpp) cc_final: 0.0602 (mtt) outliers start: 40 outliers final: 26 residues processed: 195 average time/residue: 0.2705 time to fit residues: 83.0488 Evaluate side-chains 183 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 154 time to evaluate : 1.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 42 VAL 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 76 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain H residue 60 MET Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain J residue 13 PHE Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain K residue 209 VAL Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain F residue 22 PHE Chi-restraints excluded: chain F residue 150 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 74 optimal weight: 0.9990 chunk 199 optimal weight: 0.9990 chunk 43 optimal weight: 0.3980 chunk 129 optimal weight: 0.0020 chunk 54 optimal weight: 50.0000 chunk 221 optimal weight: 5.9990 chunk 183 optimal weight: 0.6980 chunk 102 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 chunk 73 optimal weight: 0.1980 chunk 116 optimal weight: 0.2980 overall best weight: 0.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0994 moved from start: 0.5195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18134 Z= 0.136 Angle : 0.577 12.417 24544 Z= 0.293 Chirality : 0.041 0.161 2947 Planarity : 0.004 0.050 3103 Dihedral : 5.674 58.890 2537 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.84 % Allowed : 9.10 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.17), residues: 2310 helix: 1.43 (0.16), residues: 1087 sheet: 0.02 (0.31), residues: 253 loop : -0.80 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 6 HIS 0.001 0.000 HIS B 46 PHE 0.035 0.001 PHE E 13 TYR 0.009 0.001 TYR K 218 ARG 0.005 0.000 ARG H 78 *********************** 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 200 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 164 time to evaluate : 1.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 131 MET cc_start: 0.1296 (tpp) cc_final: 0.0766 (mmt) REVERT: B 232 MET cc_start: 0.2381 (ttp) cc_final: 0.0818 (pmm) REVERT: E 141 ASP cc_start: 0.0517 (OUTLIER) cc_final: -0.2208 (m-30) REVERT: E 145 TYR cc_start: 0.1987 (OUTLIER) cc_final: -0.0501 (m-80) REVERT: E 162 VAL cc_start: 0.3281 (OUTLIER) cc_final: 0.2427 (t) REVERT: G 60 MET cc_start: -0.0438 (ttt) cc_final: -0.0712 (mtp) REVERT: G 78 ARG cc_start: 0.2110 (mtt90) cc_final: 0.0945 (mtt90) REVERT: G 160 LYS cc_start: -0.0580 (ttmt) cc_final: -0.1929 (pttt) REVERT: H 42 MET cc_start: 0.0693 (mtm) cc_final: 0.0141 (mtm) REVERT: H 183 MET cc_start: 0.0562 (mmm) cc_final: -0.0680 (pmm) REVERT: J 160 LYS cc_start: 0.0933 (ttpt) cc_final: -0.0219 (pttt) REVERT: K 91 MET cc_start: 0.2928 (ptt) cc_final: 0.1451 (mtt) REVERT: K 94 LEU cc_start: 0.0870 (OUTLIER) cc_final: 0.0242 (mp) REVERT: K 153 MET cc_start: 0.2271 (mpp) cc_final: 0.0728 (mtt) outliers start: 36 outliers final: 25 residues processed: 184 average time/residue: 0.2561 time to fit residues: 75.5100 Evaluate side-chains 183 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 154 time to evaluate : 1.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 60 MET Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain J residue 13 PHE Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain K residue 209 VAL Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain F residue 150 THR 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 213 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 161 optimal weight: 0.8980 chunk 125 optimal weight: 6.9990 chunk 186 optimal weight: 0.8980 chunk 123 optimal weight: 0.8980 chunk 220 optimal weight: 20.0000 chunk 138 optimal weight: 1.9990 chunk 134 optimal weight: 6.9990 chunk 101 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1126 moved from start: 0.5606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 18134 Z= 0.156 Angle : 0.576 11.451 24544 Z= 0.294 Chirality : 0.042 0.157 2947 Planarity : 0.004 0.049 3103 Dihedral : 5.611 60.967 2537 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.94 % Allowed : 9.36 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.17), residues: 2310 helix: 1.39 (0.16), residues: 1098 sheet: -0.12 (0.32), residues: 243 loop : -0.82 (0.19), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 212 HIS 0.002 0.000 HIS L 207 PHE 0.023 0.002 PHE J 13 TYR 0.017 0.001 TYR E 158 ARG 0.006 0.000 ARG I 78 *********************** 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 199 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 161 time to evaluate : 1.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 ARG cc_start: 0.4729 (OUTLIER) cc_final: 0.4303 (ptt90) REVERT: B 131 MET cc_start: 0.1945 (tpp) cc_final: 0.1276 (tpp) REVERT: B 186 MET cc_start: -0.1221 (ttt) cc_final: -0.3153 (ptm) REVERT: B 232 MET cc_start: 0.2464 (ttp) cc_final: 0.0833 (pmm) REVERT: E 141 ASP cc_start: 0.0539 (OUTLIER) cc_final: -0.2667 (m-30) REVERT: E 145 TYR cc_start: 0.2243 (OUTLIER) cc_final: -0.0611 (m-80) REVERT: E 162 VAL cc_start: 0.3738 (OUTLIER) cc_final: 0.3275 (p) REVERT: G 60 MET cc_start: -0.0429 (ttt) cc_final: -0.0635 (mtt) REVERT: G 78 ARG cc_start: 0.1935 (mtt90) cc_final: 0.0644 (mtt90) REVERT: G 160 LYS cc_start: -0.0628 (ttmt) cc_final: -0.2146 (pttt) REVERT: H 183 MET cc_start: 0.0735 (mmm) cc_final: -0.0559 (pmm) REVERT: I 26 MET cc_start: -0.0842 (tpt) cc_final: -0.1480 (mmm) REVERT: J 160 LYS cc_start: 0.1198 (ttpt) cc_final: -0.0145 (pttt) REVERT: K 91 MET cc_start: 0.2907 (ptt) cc_final: 0.1226 (mtt) REVERT: K 94 LEU cc_start: 0.0642 (OUTLIER) cc_final: 0.0411 (mp) REVERT: K 153 MET cc_start: 0.2835 (mpp) cc_final: 0.0784 (mtt) outliers start: 38 outliers final: 24 residues processed: 184 average time/residue: 0.2643 time to fit residues: 76.7769 Evaluate side-chains 185 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 156 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 LEU 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 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 H residue 72 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 150 THR 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 K residue 94 LEU Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain K residue 209 VAL Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain F residue 150 THR 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 136 optimal weight: 2.9990 chunk 88 optimal weight: 0.0570 chunk 131 optimal weight: 5.9990 chunk 66 optimal weight: 0.0570 chunk 43 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 140 optimal weight: 0.9980 chunk 150 optimal weight: 7.9990 chunk 109 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 173 optimal weight: 2.9990 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 GLN F 102 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1111 moved from start: 0.5820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18134 Z= 0.136 Angle : 0.569 11.942 24544 Z= 0.288 Chirality : 0.041 0.152 2947 Planarity : 0.004 0.050 3103 Dihedral : 5.483 60.740 2537 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.53 % Allowed : 10.07 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.17), residues: 2310 helix: 1.43 (0.16), residues: 1106 sheet: -0.10 (0.32), residues: 239 loop : -0.78 (0.19), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 6 HIS 0.001 0.000 HIS A 46 PHE 0.022 0.001 PHE J 22 TYR 0.010 0.001 TYR I 158 ARG 0.004 0.000 ARG J 78 *********************** 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 194 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 164 time to evaluate : 1.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 131 MET cc_start: 0.1725 (tpp) cc_final: 0.1086 (tpp) REVERT: B 186 MET cc_start: -0.1368 (ttt) cc_final: -0.3231 (ptm) REVERT: B 232 MET cc_start: 0.2325 (ttp) cc_final: 0.0906 (pmm) REVERT: E 141 ASP cc_start: 0.1319 (OUTLIER) cc_final: -0.1709 (m-30) REVERT: E 145 TYR cc_start: 0.2162 (OUTLIER) cc_final: -0.0589 (m-80) REVERT: E 162 VAL cc_start: 0.3623 (OUTLIER) cc_final: 0.3105 (p) REVERT: G 78 ARG cc_start: 0.1917 (mtt90) cc_final: 0.0878 (mtt90) REVERT: G 160 LYS cc_start: -0.0483 (ttmt) cc_final: -0.2082 (pttt) REVERT: H 183 MET cc_start: 0.0478 (mmm) cc_final: -0.0654 (pmm) REVERT: I 26 MET cc_start: -0.1024 (tpt) cc_final: -0.1464 (mmt) REVERT: J 160 LYS cc_start: 0.1112 (ttpt) cc_final: -0.0367 (pttt) REVERT: K 91 MET cc_start: 0.2888 (ptt) cc_final: 0.1076 (mtt) REVERT: K 94 LEU cc_start: 0.0726 (OUTLIER) cc_final: 0.0480 (mp) REVERT: K 153 MET cc_start: 0.2749 (mpp) cc_final: 0.0855 (mtt) REVERT: F 26 MET cc_start: -0.1166 (tpt) cc_final: -0.1608 (mmt) outliers start: 30 outliers final: 25 residues processed: 184 average time/residue: 0.2683 time to fit residues: 77.5507 Evaluate side-chains 191 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 162 time to evaluate : 1.760 ------------------------------------------------------------------------------- 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 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 148 VAL Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain I residue 42 MET 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 179 THR Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain 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 200 optimal weight: 0.6980 chunk 211 optimal weight: 2.9990 chunk 192 optimal weight: 4.9990 chunk 205 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 161 optimal weight: 0.4980 chunk 63 optimal weight: 8.9990 chunk 185 optimal weight: 0.8980 chunk 194 optimal weight: 3.9990 chunk 204 optimal weight: 7.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 ASN D 59 GLN I 102 GLN K 117 HIS K 123 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1304 moved from start: 0.6328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18134 Z= 0.172 Angle : 0.613 10.895 24544 Z= 0.310 Chirality : 0.043 0.185 2947 Planarity : 0.004 0.050 3103 Dihedral : 5.636 63.393 2537 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.58 % Allowed : 10.28 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.17), residues: 2310 helix: 1.42 (0.16), residues: 1094 sheet: -0.34 (0.31), residues: 243 loop : -0.90 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 212 HIS 0.002 0.000 HIS A 194 PHE 0.018 0.002 PHE I 13 TYR 0.019 0.001 TYR J 158 ARG 0.004 0.000 ARG L 195 *********************** 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 195 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 164 time to evaluate : 1.859 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 129 MET cc_start: -0.0512 (mpp) cc_final: -0.0797 (mpp) REVERT: B 186 MET cc_start: -0.1417 (ttt) cc_final: -0.3086 (ptm) REVERT: B 232 MET cc_start: 0.2595 (ttp) cc_final: 0.1022 (pmm) REVERT: E 126 MET cc_start: -0.0810 (mtt) cc_final: -0.1214 (mtt) REVERT: E 141 ASP cc_start: 0.1287 (OUTLIER) cc_final: -0.2393 (m-30) REVERT: G 78 ARG cc_start: 0.1727 (OUTLIER) cc_final: 0.0609 (mtt90) REVERT: G 162 VAL cc_start: 0.1882 (t) cc_final: 0.1099 (p) REVERT: H 183 MET cc_start: 0.0480 (mmm) cc_final: -0.0040 (pmm) REVERT: I 26 MET cc_start: -0.1118 (tpt) cc_final: -0.1468 (mmt) REVERT: K 43 ILE cc_start: 0.0783 (mt) cc_final: 0.0341 (mt) REVERT: K 91 MET cc_start: 0.3154 (ptt) cc_final: 0.2941 (ptt) REVERT: K 153 MET cc_start: 0.2653 (mpp) cc_final: 0.0759 (mtt) REVERT: F 26 MET cc_start: -0.1019 (tpt) cc_final: -0.1377 (mmt) outliers start: 31 outliers final: 25 residues processed: 183 average time/residue: 0.2727 time to fit residues: 78.5630 Evaluate side-chains 182 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 155 time to evaluate : 1.976 ------------------------------------------------------------------------------- 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 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 194 THR Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 150 THR 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 179 THR Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain 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 135 optimal weight: 9.9990 chunk 217 optimal weight: 0.9980 chunk 132 optimal weight: 7.9990 chunk 103 optimal weight: 0.6980 chunk 151 optimal weight: 40.0000 chunk 228 optimal weight: 0.0970 chunk 209 optimal weight: 4.9990 chunk 181 optimal weight: 0.8980 chunk 18 optimal weight: 0.0870 chunk 140 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1256 moved from start: 0.6470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18134 Z= 0.142 Angle : 0.589 12.054 24544 Z= 0.295 Chirality : 0.041 0.169 2947 Planarity : 0.004 0.050 3103 Dihedral : 5.392 60.076 2536 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.46 % Favored : 96.49 % Rotamer: Outliers : 1.48 % Allowed : 10.58 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.17), residues: 2310 helix: 1.52 (0.16), residues: 1095 sheet: -0.33 (0.31), residues: 243 loop : -0.87 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 212 HIS 0.001 0.000 HIS L 117 PHE 0.022 0.001 PHE J 22 TYR 0.032 0.001 TYR K 218 ARG 0.008 0.000 ARG B 40 ********************** 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 191 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 162 time to evaluate : 1.930 Fit side-chains REVERT: B 131 MET cc_start: 0.2282 (tpp) cc_final: 0.1556 (tpp) REVERT: B 186 MET cc_start: -0.1633 (ttt) cc_final: -0.3281 (ptm) REVERT: B 232 MET cc_start: 0.1984 (ttp) cc_final: 0.0922 (pmm) REVERT: E 126 MET cc_start: -0.0857 (mtt) cc_final: -0.1258 (mtt) REVERT: E 134 MET cc_start: 0.1949 (mmt) cc_final: 0.1606 (mpp) REVERT: E 141 ASP cc_start: 0.1118 (OUTLIER) cc_final: -0.2792 (m-30) REVERT: G 78 ARG cc_start: 0.1769 (OUTLIER) cc_final: 0.0750 (mtt90) REVERT: H 183 MET cc_start: 0.0359 (mmm) cc_final: -0.0096 (pmm) REVERT: I 26 MET cc_start: -0.1270 (tpt) cc_final: -0.1576 (mmt) REVERT: K 43 ILE cc_start: 0.0674 (mt) cc_final: 0.0204 (mt) REVERT: K 91 MET cc_start: 0.2871 (ptt) cc_final: 0.0952 (mtt) REVERT: K 153 MET cc_start: 0.2702 (mpp) cc_final: 0.1038 (mtt) REVERT: L 44 MET cc_start: 0.2830 (ptt) cc_final: 0.2613 (ptt) REVERT: L 171 MET cc_start: 0.0397 (mtp) cc_final: 0.0118 (mtp) REVERT: F 26 MET cc_start: -0.0819 (tpt) cc_final: -0.1172 (mmt) outliers start: 29 outliers final: 23 residues processed: 181 average time/residue: 0.2740 time to fit residues: 77.7500 Evaluate side-chains 184 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 159 time to evaluate : 1.911 ------------------------------------------------------------------------------- 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 194 THR Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 150 THR 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 179 THR Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain 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 144 optimal weight: 0.9990 chunk 193 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 167 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 50 optimal weight: 0.1980 chunk 181 optimal weight: 0.8980 chunk 76 optimal weight: 20.0000 chunk 186 optimal weight: 0.2980 chunk 23 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5609 r_free = 0.5609 target = 0.349385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5449 r_free = 0.5449 target = 0.325874 restraints weight = 33172.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.5495 r_free = 0.5495 target = 0.332325 restraints weight = 18970.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.5522 r_free = 0.5522 target = 0.336395 restraints weight = 11835.368| |-----------------------------------------------------------------------------| r_work (final): 0.5511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1338 moved from start: 0.6644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 18134 Z= 0.143 Angle : 0.598 11.404 24544 Z= 0.299 Chirality : 0.042 0.174 2947 Planarity : 0.004 0.049 3103 Dihedral : 5.333 59.700 2536 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.77 % Favored : 96.19 % Rotamer: Outliers : 1.38 % Allowed : 10.69 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.17), residues: 2310 helix: 1.54 (0.16), residues: 1101 sheet: -0.33 (0.31), residues: 243 loop : -0.87 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 212 HIS 0.001 0.000 HIS A 46 PHE 0.026 0.001 PHE J 22 TYR 0.016 0.001 TYR K 218 ARG 0.011 0.000 ARG B 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3161.48 seconds wall clock time: 57 minutes 48.42 seconds (3468.42 seconds total)