Starting phenix.real_space_refine on Thu Feb 15 15:39:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ahx_15452/02_2024/8ahx_15452_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ahx_15452/02_2024/8ahx_15452.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ahx_15452/02_2024/8ahx_15452.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ahx_15452/02_2024/8ahx_15452.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ahx_15452/02_2024/8ahx_15452_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ahx_15452/02_2024/8ahx_15452_updated.pdb" } resolution = 3.11 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= 0.002 sd= 0.020 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 Fe 18 7.16 5 P 3 5.49 5 S 97 5.16 5 C 8158 2.51 5 N 2073 2.21 5 O 2338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12687 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1394 Classifications: {'peptide': 189} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 179} Chain: "B" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 811 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain breaks: 2 Chain: "C" Number of atoms: 3511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3511 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 37, 'TRANS': 438} Chain: "D" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2629 Classifications: {'peptide': 349} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 325} Chain: "E" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1601 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 203} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1514 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 7, 'TRANS': 189} Chain: "H" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 548 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 4, 'TRANS': 66} Chain: "A" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 74 Unusual residues: {'FES': 1, 'LMT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 47 Unusual residues: {'FMN': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 372 Unusual residues: {'FMN': 1, 'LMT': 9, 'RBF': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "E" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 140 Unusual residues: {'LMT': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 184 SG CYS A 25 36.955 84.906 50.802 1.00102.81 S ATOM 9154 SG CYS E 122 38.370 82.240 48.485 1.00113.43 S ATOM 844 SG CYS A 113 40.644 85.907 45.869 1.00 96.89 S ATOM 8545 SG CYS E 39 39.697 88.711 48.565 1.00101.07 S ATOM 1798 SG CYS B 119 27.814 44.779 90.307 1.00125.95 S ATOM 1971 SG CYS B 145 22.385 46.145 90.650 1.00126.07 S ATOM 1952 SG CYS B 142 26.271 48.407 85.782 1.00140.38 S ATOM 1935 SG CYS B 139 25.704 51.418 91.308 1.00104.29 S ATOM 1722 SG CYS B 109 20.061 40.010 99.643 1.00148.19 S ATOM 1740 SG CYS B 112 18.807 36.197 94.061 1.00146.84 S ATOM 1764 SG CYS B 115 23.153 40.817 94.676 1.00132.05 S ATOM 2001 SG CYS B 149 16.360 40.766 94.111 1.00160.09 S ATOM 4935 SG CYS C 376 43.011 92.402 90.586 1.00108.55 S ATOM 5250 SG CYS C 419 38.769 93.959 91.338 1.00 74.60 S ATOM 4893 SG CYS C 370 39.659 93.659 84.721 1.00 77.21 S ATOM 4918 SG CYS C 373 42.804 97.958 88.721 1.00 83.32 S ATOM 5181 SG CYS C 409 44.506 81.635 94.360 1.00 84.55 S ATOM 5203 SG CYS C 412 46.572 86.143 98.786 1.00 80.78 S ATOM 5219 SG CYS C 415 43.806 87.799 93.438 1.00 98.49 S ATOM 4961 SG CYS C 380 49.219 86.421 93.141 1.00 89.09 S Time building chain proxies: 7.28, per 1000 atoms: 0.57 Number of scatterers: 12687 At special positions: 0 Unit cell: (84.46, 151.7, 145.14, 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) Fe 18 26.01 S 97 16.00 P 3 15.00 O 2338 8.00 N 2073 7.00 C 8158 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 - 3.50 Amino acid : False - 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.52 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A 201 " pdb="FE1 FES A 201 " - pdb=" SG CYS E 122 " pdb="FE1 FES A 201 " - pdb=" SG CYS A 25 " pdb="FE2 FES A 201 " - pdb=" SG CYS A 113 " pdb="FE2 FES A 201 " - pdb=" SG CYS E 39 " pdb=" SF4 B 201 " pdb="FE3 SF4 B 201 " - pdb=" SG CYS B 142 " pdb="FE2 SF4 B 201 " - pdb=" SG CYS B 145 " pdb="FE4 SF4 B 201 " - pdb=" SG CYS B 139 " pdb="FE1 SF4 B 201 " - pdb=" SG CYS B 119 " pdb=" SF4 B 202 " pdb="FE2 SF4 B 202 " - pdb=" SG CYS B 112 " pdb="FE3 SF4 B 202 " - pdb=" SG CYS B 115 " pdb="FE1 SF4 B 202 " - pdb=" SG CYS B 109 " pdb="FE4 SF4 B 202 " - pdb=" SG CYS B 149 " pdb=" SF4 C 501 " pdb="FE1 SF4 C 501 " - pdb=" SG CYS C 376 " pdb="FE2 SF4 C 501 " - pdb=" SG CYS C 419 " pdb="FE4 SF4 C 501 " - pdb=" SG CYS C 373 " pdb="FE3 SF4 C 501 " - pdb=" SG CYS C 370 " pdb=" SF4 C 502 " pdb="FE3 SF4 C 502 " - pdb=" SG CYS C 415 " pdb="FE2 SF4 C 502 " - pdb=" SG CYS C 412 " pdb="FE1 SF4 C 502 " - pdb=" SG CYS C 409 " pdb="FE4 SF4 C 502 " - pdb=" SG CYS C 380 " Number of angles added : 54 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2904 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 8 sheets defined 49.3% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.41 Creating SS restraints... Processing helix chain 'A' and resid 4 through 11 Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 34 through 61 Processing helix chain 'A' and resid 63 through 66 No H-bonds generated for 'chain 'A' and resid 63 through 66' Processing helix chain 'A' and resid 70 through 92 removed outlier: 4.263A pdb=" N ILE A 73 " --> pdb=" O PHE A 70 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE A 90 " --> pdb=" O ILE A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 109 Proline residue: A 107 - end of helix No H-bonds generated for 'chain 'A' and resid 103 through 109' Processing helix chain 'A' and resid 114 through 125 Proline residue: A 119 - end of helix removed outlier: 3.533A pdb=" N ARG A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 159 removed outlier: 4.002A pdb=" N LEU A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 186 removed outlier: 4.289A pdb=" N GLY A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N PHE A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.855A pdb=" N ALA B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 84 removed outlier: 3.521A pdb=" N LYS B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 117 No H-bonds generated for 'chain 'B' and resid 114 through 117' Processing helix chain 'B' and resid 163 through 165 No H-bonds generated for 'chain 'B' and resid 163 through 165' Processing helix chain 'C' and resid 120 through 122 No H-bonds generated for 'chain 'C' and resid 120 through 122' Processing helix chain 'C' and resid 125 through 135 removed outlier: 3.681A pdb=" N ALA C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 156 removed outlier: 3.560A pdb=" N ARG C 156 " --> pdb=" O LYS C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 182 Processing helix chain 'C' and resid 184 through 197 Processing helix chain 'C' and resid 212 through 221 Processing helix chain 'C' and resid 237 through 239 No H-bonds generated for 'chain 'C' and resid 237 through 239' Processing helix chain 'C' and resid 242 through 249 removed outlier: 3.557A pdb=" N GLN C 247 " --> pdb=" O LYS C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 282 removed outlier: 3.656A pdb=" N TYR C 274 " --> pdb=" O ALA C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 318 Processing helix chain 'C' and resid 386 through 394 Processing helix chain 'C' and resid 398 through 404 removed outlier: 3.597A pdb=" N GLU C 403 " --> pdb=" O ASP C 399 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR C 404 " --> pdb=" O GLY C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 418 removed outlier: 3.876A pdb=" N VAL C 418 " --> pdb=" O CYS C 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 414 through 418' Processing helix chain 'C' and resid 425 through 477 Processing helix chain 'D' and resid 18 through 40 Proline residue: D 31 - end of helix Processing helix chain 'D' and resid 42 through 66 Processing helix chain 'D' and resid 70 through 75 removed outlier: 3.738A pdb=" N ASP D 75 " --> pdb=" O ARG D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 88 removed outlier: 3.735A pdb=" N THR D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 105 Processing helix chain 'D' and resid 111 through 113 No H-bonds generated for 'chain 'D' and resid 111 through 113' Processing helix chain 'D' and resid 123 through 134 Processing helix chain 'D' and resid 156 through 163 Processing helix chain 'D' and resid 179 through 187 Processing helix chain 'D' and resid 192 through 197 removed outlier: 3.789A pdb=" N LEU D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 207 Processing helix chain 'D' and resid 221 through 231 Processing helix chain 'D' and resid 237 through 257 Processing helix chain 'D' and resid 266 through 269 No H-bonds generated for 'chain 'D' and resid 266 through 269' Processing helix chain 'D' and resid 274 through 280 Processing helix chain 'D' and resid 285 through 287 No H-bonds generated for 'chain 'D' and resid 285 through 287' Processing helix chain 'D' and resid 292 through 311 Processing helix chain 'D' and resid 319 through 336 Proline residue: D 331 - end of helix Processing helix chain 'E' and resid 17 through 26 removed outlier: 3.859A pdb=" N ALA E 24 " --> pdb=" O PHE E 21 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TRP E 26 " --> pdb=" O SER E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 43 Processing helix chain 'E' and resid 48 through 71 Processing helix chain 'E' and resid 73 through 75 No H-bonds generated for 'chain 'E' and resid 73 through 75' Processing helix chain 'E' and resid 78 through 100 removed outlier: 3.764A pdb=" N ARG E 81 " --> pdb=" O PRO E 78 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ASN E 82 " --> pdb=" O GLU E 79 " (cutoff:3.500A) Proline residue: E 83 - end of helix removed outlier: 4.065A pdb=" N ILE E 86 " --> pdb=" O PRO E 83 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY E 91 " --> pdb=" O VAL E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 111 removed outlier: 3.590A pdb=" N VAL E 110 " --> pdb=" O GLU E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 116 No H-bonds generated for 'chain 'E' and resid 113 through 116' Processing helix chain 'E' and resid 122 through 130 Processing helix chain 'E' and resid 137 through 167 Processing helix chain 'E' and resid 174 through 178 Processing helix chain 'E' and resid 180 through 185 removed outlier: 4.468A pdb=" N TRP E 184 " --> pdb=" O HIS E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 199 No H-bonds generated for 'chain 'E' and resid 197 through 199' Processing helix chain 'E' and resid 202 through 227 removed outlier: 3.952A pdb=" N PHE E 206 " --> pdb=" O PRO E 203 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE E 207 " --> pdb=" O GLY E 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 79 removed outlier: 5.531A pdb=" N GLY G 63 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N THR G 64 " --> pdb=" O MET G 60 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU G 79 " --> pdb=" O ALA G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 85 No H-bonds generated for 'chain 'G' and resid 83 through 85' Processing helix chain 'G' and resid 90 through 92 No H-bonds generated for 'chain 'G' and resid 90 through 92' Processing helix chain 'G' and resid 160 through 162 No H-bonds generated for 'chain 'G' and resid 160 through 162' Processing helix chain 'G' and resid 169 through 171 No H-bonds generated for 'chain 'G' and resid 169 through 171' Processing helix chain 'G' and resid 189 through 191 No H-bonds generated for 'chain 'G' and resid 189 through 191' Processing helix chain 'G' and resid 203 through 221 Processing helix chain 'G' and resid 224 through 227 No H-bonds generated for 'chain 'G' and resid 224 through 227' Processing helix chain 'H' and resid 26 through 33 Processing helix chain 'H' and resid 35 through 38 No H-bonds generated for 'chain 'H' and resid 35 through 38' Processing sheet with id= A, first strand: chain 'C' and resid 34 through 38 removed outlier: 3.702A pdb=" N ALA C 84 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLU C 104 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ILE C 82 " --> pdb=" O GLU C 104 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 87 through 89 Processing sheet with id= C, first strand: chain 'C' and resid 161 through 165 Processing sheet with id= D, first strand: chain 'C' and resid 204 through 208 removed outlier: 6.181A pdb=" N GLU C 229 " --> pdb=" O ILE C 205 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ILE C 207 " --> pdb=" O GLU C 229 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N MET C 231 " --> pdb=" O ILE C 207 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 288 through 293 Processing sheet with id= F, first strand: chain 'C' and resid 328 through 330 Processing sheet with id= G, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.566A pdb=" N ALA G 118 " --> pdb=" O ALA G 110 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N MET G 135 " --> pdb=" O VAL G 149 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N VAL G 149 " --> pdb=" O MET G 135 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N SER G 137 " --> pdb=" O VAL G 147 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL G 147 " --> pdb=" O SER G 137 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 14 through 18 539 hydrogen bonds defined for protein. 1413 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.40 Time building geometry restraints manager: 5.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.41: 5029 1.41 - 1.63: 7766 1.63 - 1.85: 121 1.85 - 2.07: 0 2.07 - 2.28: 52 Bond restraints: 12968 Sorted by residual: bond pdb=" O5' FMN C 500 " pdb=" P FMN C 500 " ideal model delta sigma weight residual 1.610 1.826 -0.216 2.00e-02 2.50e+03 1.16e+02 bond pdb=" CA VAL C 204 " pdb=" C VAL C 204 " ideal model delta sigma weight residual 1.523 1.460 0.063 1.27e-02 6.20e+03 2.48e+01 bond pdb=" C THR E 45 " pdb=" O THR E 45 " ideal model delta sigma weight residual 1.235 1.199 0.036 7.50e-03 1.78e+04 2.24e+01 bond pdb=" CA LEU A 74 " pdb=" C LEU A 74 " ideal model delta sigma weight residual 1.523 1.466 0.057 1.34e-02 5.57e+03 1.83e+01 bond pdb=" C4A FMN C 500 " pdb=" N5 FMN C 500 " ideal model delta sigma weight residual 1.380 1.295 0.085 2.00e-02 2.50e+03 1.79e+01 ... (remaining 12963 not shown) Histogram of bond angle deviations from ideal: 73.60 - 85.69: 50 85.69 - 97.77: 0 97.77 - 109.86: 1817 109.86 - 121.94: 13405 121.94 - 134.03: 2391 Bond angle restraints: 17663 Sorted by residual: angle pdb=" C VAL A 30 " pdb=" CA VAL A 30 " pdb=" CB VAL A 30 " ideal model delta sigma weight residual 110.84 104.94 5.90 1.25e+00 6.40e-01 2.22e+01 angle pdb=" C ASN A 112 " pdb=" N CYS A 113 " pdb=" CA CYS A 113 " ideal model delta sigma weight residual 121.54 129.34 -7.80 1.91e+00 2.74e-01 1.67e+01 angle pdb=" N THR G 202 " pdb=" CA THR G 202 " pdb=" C THR G 202 " ideal model delta sigma weight residual 114.04 109.19 4.85 1.24e+00 6.50e-01 1.53e+01 angle pdb=" C ALA D 170 " pdb=" CA ALA D 170 " pdb=" CB ALA D 170 " ideal model delta sigma weight residual 115.89 110.80 5.09 1.32e+00 5.74e-01 1.49e+01 angle pdb=" CA ARG A 92 " pdb=" C ARG A 92 " pdb=" O ARG A 92 " ideal model delta sigma weight residual 119.34 123.21 -3.87 1.09e+00 8.42e-01 1.26e+01 ... (remaining 17658 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.94: 7935 33.94 - 67.87: 234 67.87 - 101.81: 63 101.81 - 135.74: 43 135.74 - 169.68: 1 Dihedral angle restraints: 8276 sinusoidal: 3740 harmonic: 4536 Sorted by residual: dihedral pdb=" C10 FMN D 411 " pdb=" C1' FMN D 411 " pdb=" N10 FMN D 411 " pdb=" C2' FMN D 411 " ideal model delta sinusoidal sigma weight residual 257.59 87.91 169.68 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C5' FMN G 301 " pdb=" O5' FMN G 301 " pdb=" P FMN G 301 " pdb=" O1P FMN G 301 " ideal model delta sinusoidal sigma weight residual 75.26 -151.91 -132.83 1 2.00e+01 2.50e-03 4.03e+01 dihedral pdb=" C4' FMN D 411 " pdb=" C5' FMN D 411 " pdb=" O5' FMN D 411 " pdb=" P FMN D 411 " ideal model delta sinusoidal sigma weight residual -172.30 -80.18 -92.12 1 2.00e+01 2.50e-03 2.49e+01 ... (remaining 8273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.004: 2155 1.004 - 2.007: 0 2.007 - 3.011: 0 3.011 - 4.015: 0 4.015 - 5.019: 4 Chirality restraints: 2159 Sorted by residual: chirality pdb=" C2' FMN G 301 " pdb=" C1' FMN G 301 " pdb=" C3' FMN G 301 " pdb=" O2' FMN G 301 " both_signs ideal model delta sigma weight residual False -2.47 2.55 -5.02 2.00e-01 2.50e+01 6.30e+02 chirality pdb=" CB THR G 202 " pdb=" CA THR G 202 " pdb=" OG1 THR G 202 " pdb=" CG2 THR G 202 " both_signs ideal model delta sigma weight residual False 2.55 -2.46 5.01 2.00e-01 2.50e+01 6.28e+02 chirality pdb=" C4' FMN D 411 " pdb=" C3' FMN D 411 " pdb=" C5' FMN D 411 " pdb=" O4' FMN D 411 " both_signs ideal model delta sigma weight residual False -2.47 2.42 -4.89 2.00e-01 2.50e+01 5.98e+02 ... (remaining 2156 not shown) Planarity restraints: 2125 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMN G 301 " 0.144 2.00e-02 2.50e+03 4.51e-02 9.66e+01 pdb=" C10 FMN G 301 " 0.005 2.00e-02 2.50e+03 pdb=" C2 FMN G 301 " -0.039 2.00e-02 2.50e+03 pdb=" C4 FMN G 301 " 0.007 2.00e-02 2.50e+03 pdb=" C4A FMN G 301 " 0.016 2.00e-02 2.50e+03 pdb=" C5A FMN G 301 " 0.017 2.00e-02 2.50e+03 pdb=" C6 FMN G 301 " 0.008 2.00e-02 2.50e+03 pdb=" C7 FMN G 301 " -0.012 2.00e-02 2.50e+03 pdb=" C7M FMN G 301 " -0.006 2.00e-02 2.50e+03 pdb=" C8 FMN G 301 " -0.023 2.00e-02 2.50e+03 pdb=" C8M FMN G 301 " -0.070 2.00e-02 2.50e+03 pdb=" C9 FMN G 301 " -0.012 2.00e-02 2.50e+03 pdb=" C9A FMN G 301 " 0.009 2.00e-02 2.50e+03 pdb=" N1 FMN G 301 " -0.022 2.00e-02 2.50e+03 pdb=" N10 FMN G 301 " 0.017 2.00e-02 2.50e+03 pdb=" N3 FMN G 301 " -0.024 2.00e-02 2.50e+03 pdb=" N5 FMN G 301 " 0.019 2.00e-02 2.50e+03 pdb=" O2 FMN G 301 " -0.079 2.00e-02 2.50e+03 pdb=" O4 FMN G 301 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS E 74 " 0.024 2.00e-02 2.50e+03 4.73e-02 2.24e+01 pdb=" C HIS E 74 " -0.082 2.00e-02 2.50e+03 pdb=" O HIS E 74 " 0.031 2.00e-02 2.50e+03 pdb=" N THR E 75 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA G 223 " -0.017 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C ALA G 223 " 0.060 2.00e-02 2.50e+03 pdb=" O ALA G 223 " -0.023 2.00e-02 2.50e+03 pdb=" N GLU G 224 " -0.020 2.00e-02 2.50e+03 ... (remaining 2122 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1286 2.74 - 3.28: 12649 3.28 - 3.82: 20794 3.82 - 4.36: 23712 4.36 - 4.90: 42280 Nonbonded interactions: 100721 Sorted by model distance: nonbonded pdb=" OG SER C 202 " pdb=" O ALA C 227 " model vdw 2.203 2.440 nonbonded pdb=" OG SER H 25 " pdb=" OE1 GLN H 28 " model vdw 2.208 2.440 nonbonded pdb=" OG SER D 201 " pdb=" OG SER D 204 " model vdw 2.212 2.440 nonbonded pdb=" O THR D 184 " pdb=" OG1 THR D 187 " model vdw 2.223 2.440 nonbonded pdb=" O SER D 314 " pdb=" OH TYR G 128 " model vdw 2.226 2.440 ... (remaining 100716 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.000 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 39.040 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 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 : 0.007 0.216 12968 Z= 0.459 Angle : 0.919 10.177 17663 Z= 0.390 Chirality : 0.219 5.019 2159 Planarity : 0.005 0.048 2125 Dihedral : 19.651 169.681 5372 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.09 % Favored : 94.65 % Rotamer: Outliers : 0.71 % Allowed : 6.74 % Favored : 92.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % 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: 0.91 (0.23), residues: 1590 helix: 1.79 (0.19), residues: 808 sheet: -0.60 (0.58), residues: 107 loop : -0.63 (0.26), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 83 HIS 0.002 0.001 HIS G 152 PHE 0.017 0.001 PHE G 173 TYR 0.012 0.001 TYR C 237 ARG 0.002 0.000 ARG E 221 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 182 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8863 (tm-30) cc_final: 0.8602 (tm-30) REVERT: A 93 LYS cc_start: 0.8566 (tttt) cc_final: 0.8262 (mptt) REVERT: A 125 GLU cc_start: 0.9101 (mp0) cc_final: 0.8774 (mp0) REVERT: A 161 ASN cc_start: 0.9082 (t0) cc_final: 0.8582 (t0) REVERT: B 3 GLU cc_start: 0.7802 (mt-10) cc_final: 0.6649 (tp30) REVERT: B 105 GLU cc_start: 0.7423 (mp0) cc_final: 0.6596 (mp0) REVERT: B 122 ASP cc_start: 0.8077 (t0) cc_final: 0.7418 (t0) REVERT: B 155 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8893 (mp) REVERT: B 158 PRO cc_start: 0.9004 (Cg_exo) cc_final: 0.8654 (Cg_endo) REVERT: C 3 PHE cc_start: 0.6129 (m-80) cc_final: 0.5725 (m-80) REVERT: C 225 PHE cc_start: 0.8869 (m-80) cc_final: 0.8501 (m-80) REVERT: D 197 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8388 (mm-30) REVERT: E 19 GLN cc_start: 0.8176 (tm-30) cc_final: 0.7727 (tm-30) REVERT: E 163 GLU cc_start: 0.8632 (tt0) cc_final: 0.8301 (tt0) REVERT: E 192 ASP cc_start: 0.7415 (t0) cc_final: 0.7178 (t0) REVERT: E 222 LYS cc_start: 0.7340 (mttt) cc_final: 0.7097 (mptt) REVERT: G 67 GLU cc_start: 0.8926 (tp30) cc_final: 0.8605 (tp30) REVERT: G 89 ASN cc_start: 0.8876 (t0) cc_final: 0.8507 (t0) REVERT: H 18 CYS cc_start: 0.8648 (p) cc_final: 0.8401 (m) REVERT: H 32 GLN cc_start: 0.9121 (tt0) cc_final: 0.8849 (tm-30) REVERT: H 37 ARG cc_start: 0.8622 (ptp-110) cc_final: 0.8247 (ptm-80) REVERT: H 57 LYS cc_start: 0.8525 (ttpp) cc_final: 0.8003 (ttpp) outliers start: 9 outliers final: 3 residues processed: 191 average time/residue: 0.3098 time to fit residues: 81.0113 Evaluate side-chains 149 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 145 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain G residue 202 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 40 optimal weight: 0.1980 chunk 80 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 123 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 chunk 91 optimal weight: 0.9990 chunk 142 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 430 GLN D 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.0832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 12968 Z= 0.187 Angle : 0.631 8.645 17663 Z= 0.281 Chirality : 0.044 0.293 2159 Planarity : 0.005 0.049 2125 Dihedral : 16.609 171.529 2677 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.09 % Favored : 94.78 % Rotamer: Outliers : 2.22 % Allowed : 9.12 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % 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: 0.81 (0.23), residues: 1590 helix: 1.69 (0.19), residues: 811 sheet: -0.65 (0.57), residues: 113 loop : -0.66 (0.26), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 83 HIS 0.002 0.000 HIS C 360 PHE 0.013 0.001 PHE A 143 TYR 0.019 0.001 TYR H 7 ARG 0.006 0.000 ARG B 146 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 162 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 LYS cc_start: 0.8500 (tttt) cc_final: 0.8290 (mptt) REVERT: A 125 GLU cc_start: 0.9112 (OUTLIER) cc_final: 0.7968 (mp0) REVERT: A 161 ASN cc_start: 0.9059 (t0) cc_final: 0.8525 (t0) REVERT: B 3 GLU cc_start: 0.7763 (mt-10) cc_final: 0.6577 (tp30) REVERT: B 105 GLU cc_start: 0.7414 (mp0) cc_final: 0.7207 (mp0) REVERT: B 122 ASP cc_start: 0.8049 (t0) cc_final: 0.7344 (t0) REVERT: C 225 PHE cc_start: 0.8834 (m-80) cc_final: 0.8484 (m-80) REVERT: C 266 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.9044 (tp) REVERT: D 197 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8342 (mm-30) REVERT: E 27 GLN cc_start: 0.8669 (tt0) cc_final: 0.8005 (tt0) REVERT: E 28 TYR cc_start: 0.8486 (m-80) cc_final: 0.7778 (m-10) REVERT: E 32 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8954 (mp) REVERT: E 79 GLU cc_start: 0.8610 (pm20) cc_final: 0.8404 (pm20) REVERT: E 163 GLU cc_start: 0.8603 (tt0) cc_final: 0.8286 (tt0) REVERT: E 192 ASP cc_start: 0.7670 (t0) cc_final: 0.7451 (t0) REVERT: G 67 GLU cc_start: 0.8938 (tp30) cc_final: 0.8654 (tp30) REVERT: H 18 CYS cc_start: 0.8737 (p) cc_final: 0.8306 (p) REVERT: H 32 GLN cc_start: 0.9195 (tt0) cc_final: 0.8759 (tm-30) REVERT: H 37 ARG cc_start: 0.8661 (ptp-110) cc_final: 0.8284 (mtm180) outliers start: 28 outliers final: 12 residues processed: 184 average time/residue: 0.2790 time to fit residues: 71.7545 Evaluate side-chains 163 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 148 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain C residue 4 ASN Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 63 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 0.0980 chunk 118 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 142 optimal weight: 2.9990 chunk 154 optimal weight: 0.0070 chunk 127 optimal weight: 10.0000 chunk 141 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 overall best weight: 1.6204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 12968 Z= 0.211 Angle : 0.613 8.876 17663 Z= 0.278 Chirality : 0.043 0.351 2159 Planarity : 0.004 0.049 2125 Dihedral : 12.864 172.044 2675 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.47 % Favored : 94.40 % Rotamer: Outliers : 2.54 % Allowed : 10.55 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % 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: 0.85 (0.23), residues: 1590 helix: 1.68 (0.19), residues: 811 sheet: -0.60 (0.57), residues: 113 loop : -0.59 (0.26), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 83 HIS 0.002 0.001 HIS C 196 PHE 0.011 0.001 PHE A 143 TYR 0.011 0.001 TYR H 7 ARG 0.004 0.000 ARG B 146 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 155 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 LYS cc_start: 0.8565 (tttt) cc_final: 0.8326 (mptt) REVERT: A 125 GLU cc_start: 0.9120 (OUTLIER) cc_final: 0.7970 (mp0) REVERT: A 161 ASN cc_start: 0.9081 (t0) cc_final: 0.8491 (t0) REVERT: B 3 GLU cc_start: 0.7765 (mt-10) cc_final: 0.6564 (tp30) REVERT: B 103 ARG cc_start: 0.8293 (tpp80) cc_final: 0.7912 (ttm110) REVERT: B 122 ASP cc_start: 0.7905 (t0) cc_final: 0.7222 (t0) REVERT: C 225 PHE cc_start: 0.8829 (m-80) cc_final: 0.8487 (m-80) REVERT: D 197 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8321 (mm-30) REVERT: D 214 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9133 (tt) REVERT: E 79 GLU cc_start: 0.8571 (pm20) cc_final: 0.8339 (pm20) REVERT: E 163 GLU cc_start: 0.8600 (tt0) cc_final: 0.8199 (tt0) REVERT: E 192 ASP cc_start: 0.7813 (t0) cc_final: 0.7604 (t0) REVERT: G 35 MET cc_start: 0.3977 (ttm) cc_final: 0.3777 (ttt) REVERT: G 67 GLU cc_start: 0.8946 (tp30) cc_final: 0.8660 (tp30) REVERT: G 133 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8358 (tp30) REVERT: H 18 CYS cc_start: 0.8663 (p) cc_final: 0.8154 (p) REVERT: H 32 GLN cc_start: 0.9257 (tt0) cc_final: 0.8692 (tm-30) REVERT: H 37 ARG cc_start: 0.8658 (ptp-110) cc_final: 0.8227 (mtm180) REVERT: H 60 SER cc_start: 0.8213 (m) cc_final: 0.7697 (t) outliers start: 32 outliers final: 19 residues processed: 177 average time/residue: 0.2802 time to fit residues: 69.7970 Evaluate side-chains 173 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 151 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain C residue 4 ASN Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain G residue 133 GLU Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 63 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 141 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 95 optimal weight: 8.9990 chunk 143 optimal weight: 5.9990 chunk 151 optimal weight: 9.9990 chunk 135 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 12968 Z= 0.540 Angle : 0.737 7.228 17663 Z= 0.344 Chirality : 0.048 0.365 2159 Planarity : 0.005 0.048 2125 Dihedral : 11.956 173.141 2675 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.48 % Favored : 93.40 % Rotamer: Outliers : 2.93 % Allowed : 12.13 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % 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: 0.27 (0.22), residues: 1590 helix: 1.21 (0.19), residues: 822 sheet: -0.79 (0.56), residues: 113 loop : -0.94 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 142 HIS 0.004 0.001 HIS C 17 PHE 0.018 0.002 PHE E 206 TYR 0.015 0.002 TYR E 28 ARG 0.005 0.001 ARG D 128 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 149 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 LYS cc_start: 0.8672 (tttt) cc_final: 0.8321 (mptt) REVERT: B 3 GLU cc_start: 0.7834 (mt-10) cc_final: 0.6757 (tp30) REVERT: B 122 ASP cc_start: 0.7978 (t0) cc_final: 0.7409 (t0) REVERT: C 225 PHE cc_start: 0.8964 (m-80) cc_final: 0.8585 (m-80) REVERT: D 173 MET cc_start: 0.8976 (mtp) cc_final: 0.8512 (mtt) REVERT: D 194 GLU cc_start: 0.8158 (mp0) cc_final: 0.7838 (mp0) REVERT: D 197 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8328 (mm-30) REVERT: D 214 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9175 (tt) REVERT: E 27 GLN cc_start: 0.8773 (tt0) cc_final: 0.8116 (tt0) REVERT: E 28 TYR cc_start: 0.8501 (m-10) cc_final: 0.7899 (m-10) REVERT: E 163 GLU cc_start: 0.8663 (tt0) cc_final: 0.8244 (tt0) REVERT: G 67 GLU cc_start: 0.9031 (tp30) cc_final: 0.8787 (tp30) REVERT: G 133 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8359 (tp30) REVERT: H 9 ASP cc_start: 0.8734 (t0) cc_final: 0.8090 (t0) REVERT: H 18 CYS cc_start: 0.8748 (p) cc_final: 0.8292 (p) REVERT: H 32 GLN cc_start: 0.9154 (tt0) cc_final: 0.8629 (tm-30) REVERT: H 37 ARG cc_start: 0.8718 (ptp-110) cc_final: 0.8407 (mtm180) outliers start: 37 outliers final: 27 residues processed: 174 average time/residue: 0.2859 time to fit residues: 69.7467 Evaluate side-chains 175 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 146 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 4 ASN Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain G residue 133 GLU Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 63 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 86 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 129 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 12968 Z= 0.176 Angle : 0.570 7.116 17663 Z= 0.269 Chirality : 0.041 0.354 2159 Planarity : 0.004 0.045 2125 Dihedral : 11.066 170.445 2674 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.16 % Favored : 94.72 % Rotamer: Outliers : 2.30 % Allowed : 13.88 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % 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: 0.60 (0.23), residues: 1590 helix: 1.48 (0.19), residues: 821 sheet: -0.82 (0.56), residues: 115 loop : -0.73 (0.26), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 83 HIS 0.002 0.001 HIS C 196 PHE 0.012 0.001 PHE A 143 TYR 0.017 0.001 TYR C 237 ARG 0.005 0.000 ARG B 103 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 158 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8899 (tm-30) cc_final: 0.8525 (tm-30) REVERT: A 93 LYS cc_start: 0.8692 (tttt) cc_final: 0.8295 (mptt) REVERT: A 125 GLU cc_start: 0.9183 (OUTLIER) cc_final: 0.8019 (mp0) REVERT: B 3 GLU cc_start: 0.7773 (mt-10) cc_final: 0.6574 (tp30) REVERT: B 122 ASP cc_start: 0.7952 (t0) cc_final: 0.7306 (t0) REVERT: B 164 ASP cc_start: 0.8546 (t0) cc_final: 0.8341 (t0) REVERT: C 225 PHE cc_start: 0.8857 (m-80) cc_final: 0.8506 (m-80) REVERT: D 113 TYR cc_start: 0.9532 (m-80) cc_final: 0.9332 (m-80) REVERT: D 173 MET cc_start: 0.8999 (mtp) cc_final: 0.8513 (mtt) REVERT: D 197 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8273 (mm-30) REVERT: D 214 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9164 (tt) REVERT: E 27 GLN cc_start: 0.8664 (tt0) cc_final: 0.7968 (tt0) REVERT: E 28 TYR cc_start: 0.8453 (m-10) cc_final: 0.7819 (m-10) REVERT: E 163 GLU cc_start: 0.8638 (tt0) cc_final: 0.8199 (tt0) REVERT: G 67 GLU cc_start: 0.8968 (tp30) cc_final: 0.8672 (tp30) REVERT: H 9 ASP cc_start: 0.8700 (t0) cc_final: 0.8120 (t0) REVERT: H 18 CYS cc_start: 0.8677 (p) cc_final: 0.8221 (p) REVERT: H 32 GLN cc_start: 0.9131 (tt0) cc_final: 0.8608 (tm-30) REVERT: H 37 ARG cc_start: 0.8675 (ptp-110) cc_final: 0.8177 (mtm180) outliers start: 29 outliers final: 24 residues processed: 176 average time/residue: 0.2858 time to fit residues: 70.0428 Evaluate side-chains 178 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 152 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain C residue 4 ASN Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 63 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 136 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 151 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 chunk 70 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 146 optimal weight: 0.4980 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 12968 Z= 0.168 Angle : 0.539 7.030 17663 Z= 0.256 Chirality : 0.041 0.302 2159 Planarity : 0.004 0.044 2125 Dihedral : 10.453 170.484 2674 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.22 % Favored : 94.65 % Rotamer: Outliers : 2.30 % Allowed : 14.20 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % 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: 0.71 (0.23), residues: 1590 helix: 1.59 (0.19), residues: 819 sheet: -0.78 (0.56), residues: 115 loop : -0.70 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 83 HIS 0.002 0.000 HIS C 360 PHE 0.011 0.001 PHE A 143 TYR 0.012 0.001 TYR C 237 ARG 0.007 0.000 ARG G 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 162 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8528 (tm-30) REVERT: A 93 LYS cc_start: 0.8645 (tttt) cc_final: 0.8236 (mptt) REVERT: A 125 GLU cc_start: 0.9177 (OUTLIER) cc_final: 0.8018 (mp0) REVERT: B 3 GLU cc_start: 0.7762 (mt-10) cc_final: 0.6724 (tp30) REVERT: B 100 MET cc_start: 0.8449 (tpp) cc_final: 0.7929 (mmm) REVERT: B 122 ASP cc_start: 0.7904 (t0) cc_final: 0.7225 (t0) REVERT: C 225 PHE cc_start: 0.8823 (m-80) cc_final: 0.8526 (m-80) REVERT: D 173 MET cc_start: 0.9020 (mtp) cc_final: 0.8550 (mtt) REVERT: D 197 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8274 (mm-30) REVERT: D 214 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9161 (tt) REVERT: E 163 GLU cc_start: 0.8643 (tt0) cc_final: 0.8215 (tt0) REVERT: G 67 GLU cc_start: 0.8934 (tp30) cc_final: 0.8628 (tp30) REVERT: H 9 ASP cc_start: 0.8681 (t0) cc_final: 0.8117 (t0) REVERT: H 18 CYS cc_start: 0.8766 (p) cc_final: 0.8279 (p) REVERT: H 32 GLN cc_start: 0.9132 (tt0) cc_final: 0.8615 (tm-30) REVERT: H 37 ARG cc_start: 0.8665 (ptp-110) cc_final: 0.8153 (mtm180) outliers start: 29 outliers final: 22 residues processed: 182 average time/residue: 0.2965 time to fit residues: 75.9584 Evaluate side-chains 179 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 155 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain C residue 4 ASN Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 63 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 17 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 110 optimal weight: 6.9990 chunk 85 optimal weight: 0.1980 chunk 127 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 chunk 151 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 92 optimal weight: 0.0010 chunk 69 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 12968 Z= 0.188 Angle : 0.551 7.517 17663 Z= 0.263 Chirality : 0.040 0.282 2159 Planarity : 0.004 0.042 2125 Dihedral : 10.111 170.690 2674 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.16 % Favored : 94.72 % Rotamer: Outliers : 2.22 % Allowed : 14.75 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % 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: 0.77 (0.23), residues: 1590 helix: 1.63 (0.19), residues: 819 sheet: -0.77 (0.56), residues: 115 loop : -0.67 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 166 HIS 0.002 0.000 HIS C 360 PHE 0.012 0.001 PHE A 143 TYR 0.012 0.001 TYR C 237 ARG 0.006 0.000 ARG G 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 162 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8898 (tm-30) cc_final: 0.8515 (tm-30) REVERT: A 93 LYS cc_start: 0.8595 (tttt) cc_final: 0.8224 (mptt) REVERT: A 125 GLU cc_start: 0.9180 (OUTLIER) cc_final: 0.8033 (mp0) REVERT: B 3 GLU cc_start: 0.7745 (mt-10) cc_final: 0.6694 (tp30) REVERT: B 122 ASP cc_start: 0.7976 (t0) cc_final: 0.7316 (t0) REVERT: C 225 PHE cc_start: 0.8812 (m-80) cc_final: 0.8525 (m-80) REVERT: D 173 MET cc_start: 0.9005 (mtp) cc_final: 0.8538 (mtt) REVERT: D 197 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8279 (mm-30) REVERT: D 214 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9162 (tt) REVERT: E 163 GLU cc_start: 0.8633 (tt0) cc_final: 0.8191 (tt0) REVERT: G 67 GLU cc_start: 0.8943 (tp30) cc_final: 0.8641 (tp30) REVERT: H 9 ASP cc_start: 0.8684 (t0) cc_final: 0.8151 (t0) REVERT: H 18 CYS cc_start: 0.8787 (p) cc_final: 0.8315 (p) REVERT: H 32 GLN cc_start: 0.9137 (tt0) cc_final: 0.8622 (tm-30) REVERT: H 37 ARG cc_start: 0.8671 (ptp-110) cc_final: 0.8311 (mtm180) outliers start: 28 outliers final: 26 residues processed: 181 average time/residue: 0.2898 time to fit residues: 73.1661 Evaluate side-chains 180 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 152 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain C residue 4 ASN Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 63 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 60 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 29 optimal weight: 10.0000 chunk 96 optimal weight: 8.9990 chunk 103 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 chunk 137 optimal weight: 8.9990 chunk 144 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 12968 Z= 0.265 Angle : 0.579 7.687 17663 Z= 0.277 Chirality : 0.041 0.278 2159 Planarity : 0.004 0.040 2125 Dihedral : 10.026 171.731 2674 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.91 % Favored : 93.96 % Rotamer: Outliers : 2.14 % Allowed : 15.38 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % 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: 0.82 (0.23), residues: 1590 helix: 1.66 (0.19), residues: 812 sheet: -0.72 (0.56), residues: 113 loop : -0.60 (0.26), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 166 HIS 0.002 0.001 HIS E 74 PHE 0.013 0.001 PHE E 206 TYR 0.012 0.001 TYR C 237 ARG 0.007 0.000 ARG G 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 157 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8516 (tm-30) REVERT: A 93 LYS cc_start: 0.8589 (tttt) cc_final: 0.8213 (mptt) REVERT: A 125 GLU cc_start: 0.9182 (OUTLIER) cc_final: 0.8057 (mp0) REVERT: B 3 GLU cc_start: 0.7767 (mt-10) cc_final: 0.6766 (tp30) REVERT: B 108 GLN cc_start: 0.8674 (mp10) cc_final: 0.8351 (mp10) REVERT: B 122 ASP cc_start: 0.7982 (t0) cc_final: 0.7293 (t0) REVERT: C 225 PHE cc_start: 0.8862 (m-80) cc_final: 0.8563 (m-80) REVERT: D 173 MET cc_start: 0.8997 (mtp) cc_final: 0.8533 (mtt) REVERT: D 197 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8275 (mm-30) REVERT: D 214 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9161 (tt) REVERT: E 163 GLU cc_start: 0.8647 (tt0) cc_final: 0.8200 (tt0) REVERT: G 67 GLU cc_start: 0.8984 (tp30) cc_final: 0.8692 (tp30) REVERT: H 9 ASP cc_start: 0.8684 (t0) cc_final: 0.8155 (t0) REVERT: H 18 CYS cc_start: 0.8805 (p) cc_final: 0.8316 (p) REVERT: H 32 GLN cc_start: 0.9179 (tt0) cc_final: 0.8610 (tm-30) REVERT: H 37 ARG cc_start: 0.8699 (ptp-110) cc_final: 0.8338 (mtm180) outliers start: 27 outliers final: 25 residues processed: 175 average time/residue: 0.3058 time to fit residues: 73.8032 Evaluate side-chains 182 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 155 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain C residue 4 ASN Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 63 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 chunk 144 optimal weight: 0.0870 chunk 84 optimal weight: 0.0670 chunk 61 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.9900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 12968 Z= 0.170 Angle : 0.557 8.694 17663 Z= 0.269 Chirality : 0.040 0.279 2159 Planarity : 0.004 0.039 2125 Dihedral : 9.772 170.446 2674 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.84 % Favored : 95.03 % Rotamer: Outliers : 2.30 % Allowed : 15.62 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % 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: 0.89 (0.23), residues: 1590 helix: 1.73 (0.19), residues: 808 sheet: -0.77 (0.55), residues: 115 loop : -0.54 (0.26), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 83 HIS 0.001 0.000 HIS C 196 PHE 0.010 0.001 PHE A 143 TYR 0.012 0.001 TYR C 237 ARG 0.007 0.000 ARG G 78 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 156 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8909 (tm-30) cc_final: 0.8532 (tm-30) REVERT: A 93 LYS cc_start: 0.8587 (tttt) cc_final: 0.8220 (mptt) REVERT: A 125 GLU cc_start: 0.9189 (OUTLIER) cc_final: 0.8071 (mp0) REVERT: B 3 GLU cc_start: 0.7740 (mt-10) cc_final: 0.6714 (tp30) REVERT: B 108 GLN cc_start: 0.8642 (mp10) cc_final: 0.8325 (mp10) REVERT: B 122 ASP cc_start: 0.7964 (t0) cc_final: 0.7265 (t0) REVERT: C 225 PHE cc_start: 0.8796 (m-80) cc_final: 0.8528 (m-80) REVERT: D 173 MET cc_start: 0.9006 (mtp) cc_final: 0.8519 (mtt) REVERT: D 197 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8282 (mm-30) REVERT: E 163 GLU cc_start: 0.8633 (tt0) cc_final: 0.8206 (tt0) REVERT: G 67 GLU cc_start: 0.8943 (tp30) cc_final: 0.8679 (tp30) REVERT: G 89 ASN cc_start: 0.8700 (t0) cc_final: 0.8426 (t0) REVERT: H 9 ASP cc_start: 0.8658 (t0) cc_final: 0.8153 (t0) REVERT: H 16 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8847 (mt) REVERT: H 18 CYS cc_start: 0.8806 (p) cc_final: 0.8359 (p) REVERT: H 32 GLN cc_start: 0.9149 (tt0) cc_final: 0.8602 (tm-30) REVERT: H 37 ARG cc_start: 0.8676 (ptp-110) cc_final: 0.8322 (mtm180) REVERT: H 47 GLN cc_start: 0.8761 (mp10) cc_final: 0.8509 (mp10) outliers start: 29 outliers final: 23 residues processed: 176 average time/residue: 0.2982 time to fit residues: 73.3277 Evaluate side-chains 180 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 155 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain C residue 4 ASN Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 63 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 149 optimal weight: 5.9990 chunk 91 optimal weight: 0.5980 chunk 70 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 156 optimal weight: 8.9990 chunk 143 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 96 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 98 optimal weight: 0.0770 overall best weight: 1.6542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 12968 Z= 0.206 Angle : 0.554 6.630 17663 Z= 0.267 Chirality : 0.040 0.276 2159 Planarity : 0.004 0.038 2125 Dihedral : 9.663 171.182 2674 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.47 % Favored : 94.40 % Rotamer: Outliers : 2.14 % Allowed : 15.54 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % 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: 0.92 (0.23), residues: 1590 helix: 1.76 (0.19), residues: 805 sheet: -0.63 (0.56), residues: 113 loop : -0.54 (0.26), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 166 HIS 0.002 0.000 HIS C 360 PHE 0.012 0.001 PHE A 143 TYR 0.012 0.001 TYR C 237 ARG 0.008 0.000 ARG G 78 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 157 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8504 (tm-30) REVERT: A 93 LYS cc_start: 0.8605 (tttt) cc_final: 0.8219 (mptt) REVERT: A 125 GLU cc_start: 0.9187 (OUTLIER) cc_final: 0.8074 (mp0) REVERT: B 3 GLU cc_start: 0.7745 (mt-10) cc_final: 0.6723 (tp30) REVERT: B 108 GLN cc_start: 0.8647 (mp10) cc_final: 0.8360 (mp10) REVERT: B 122 ASP cc_start: 0.8040 (t0) cc_final: 0.7351 (t0) REVERT: C 225 PHE cc_start: 0.8826 (m-80) cc_final: 0.8542 (m-80) REVERT: D 173 MET cc_start: 0.9003 (mtp) cc_final: 0.8533 (mtt) REVERT: D 197 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8285 (mm-30) REVERT: E 163 GLU cc_start: 0.8638 (tt0) cc_final: 0.8199 (tt0) REVERT: G 67 GLU cc_start: 0.8969 (tp30) cc_final: 0.8712 (tp30) REVERT: G 89 ASN cc_start: 0.8695 (t0) cc_final: 0.8423 (t0) REVERT: H 9 ASP cc_start: 0.8663 (t0) cc_final: 0.8162 (t0) REVERT: H 16 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8859 (mt) REVERT: H 18 CYS cc_start: 0.8861 (p) cc_final: 0.8377 (p) REVERT: H 32 GLN cc_start: 0.9169 (tt0) cc_final: 0.8638 (tm-30) REVERT: H 37 ARG cc_start: 0.8677 (ptp-110) cc_final: 0.8309 (mtm180) outliers start: 27 outliers final: 23 residues processed: 175 average time/residue: 0.2862 time to fit residues: 69.5553 Evaluate side-chains 180 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 155 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain C residue 4 ASN Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 63 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 114 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 109 optimal weight: 7.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 = 0.3328 r_free = 0.3328 target = 0.079222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.056285 restraints weight = 30114.636| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 2.43 r_work: 0.2694 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 12968 Z= 0.214 Angle : 0.566 9.019 17663 Z= 0.274 Chirality : 0.040 0.275 2159 Planarity : 0.004 0.037 2125 Dihedral : 9.598 171.182 2674 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.28 % Favored : 94.59 % Rotamer: Outliers : 2.06 % Allowed : 15.94 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % 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: 0.91 (0.23), residues: 1590 helix: 1.75 (0.19), residues: 805 sheet: -0.71 (0.55), residues: 115 loop : -0.53 (0.26), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 166 HIS 0.002 0.000 HIS C 360 PHE 0.011 0.001 PHE A 143 TYR 0.012 0.001 TYR C 237 ARG 0.009 0.000 ARG B 167 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2753.43 seconds wall clock time: 50 minutes 51.19 seconds (3051.19 seconds total)