Starting phenix.real_space_refine on Fri Mar 15 12:09:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rua_24701/03_2024/7rua_24701_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rua_24701/03_2024/7rua_24701.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rua_24701/03_2024/7rua_24701.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rua_24701/03_2024/7rua_24701.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rua_24701/03_2024/7rua_24701_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rua_24701/03_2024/7rua_24701_updated.pdb" } resolution = 3.4 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= 0.000 sd= 0.002 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 6 5.49 5 Mg 2 5.21 5 S 64 5.16 5 C 7350 2.51 5 N 1992 2.21 5 O 2188 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 224": "NH1" <-> "NH2" Residue "A GLU 258": "OE1" <-> "OE2" Residue "A PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 224": "NH1" <-> "NH2" Residue "B GLU 258": "OE1" <-> "OE2" Residue "B PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11603 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2412 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 18, 'TRANS': 286} Chain breaks: 1 Chain: "B" Number of atoms: 2412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2412 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 18, 'TRANS': 286} Chain breaks: 1 Chain: "C" Number of atoms: 2175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2175 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 11, 'TRANS': 259} Chain: "D" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 790 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 12, 'TRANS': 87} Chain breaks: 1 Chain: "E" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 392 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 47} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 2175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2175 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 11, 'TRANS': 259} Chain: "G" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 790 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 12, 'TRANS': 87} Chain breaks: 1 Chain: "H" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 392 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 47} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1947 SG CYS A 283 54.502 65.935 97.337 1.00 99.40 S ATOM 1970 SG CYS A 286 55.392 68.382 94.693 1.00 92.44 S ATOM 4359 SG CYS B 283 52.748 69.358 97.346 1.00 99.64 S ATOM 4382 SG CYS B 286 51.857 66.912 94.703 1.00 92.38 S Time building chain proxies: 6.08, per 1000 atoms: 0.52 Number of scatterers: 11603 At special positions: 0 Unit cell: (108.075, 136.125, 112.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 64 16.00 P 6 15.00 Mg 2 11.99 O 2188 8.00 N 1992 7.00 C 7350 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=0, symmetry=0 Time building additional restraints: 5.19 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 403 " pdb="ZN ZN A 403 " - pdb=" SG CYS B 286 " pdb="ZN ZN A 403 " - pdb=" SG CYS A 286 " pdb="ZN ZN A 403 " - pdb=" SG CYS A 283 " pdb="ZN ZN A 403 " - pdb=" SG CYS B 283 " Number of angles added : 6 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2760 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 70 helices and 2 sheets defined 63.4% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.00 Creating SS restraints... Processing helix chain 'A' and resid 22 through 27 Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.534A pdb=" N ALA A 57 " --> pdb=" O VAL A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 77 Processing helix chain 'A' and resid 117 through 132 removed outlier: 4.177A pdb=" N MET A 130 " --> pdb=" O MET A 126 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N SER A 131 " --> pdb=" O GLN A 127 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA A 132 " --> pdb=" O GLU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 151 removed outlier: 4.335A pdb=" N ASP A 137 " --> pdb=" O PRO A 134 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU A 138 " --> pdb=" O GLY A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 186 Proline residue: A 174 - end of helix Processing helix chain 'A' and resid 212 through 230 Proline residue: A 221 - end of helix Processing helix chain 'A' and resid 246 through 262 Processing helix chain 'A' and resid 279 through 281 No H-bonds generated for 'chain 'A' and resid 279 through 281' Processing helix chain 'A' and resid 284 through 303 Processing helix chain 'A' and resid 322 through 333 removed outlier: 3.546A pdb=" N GLN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 27 Processing helix chain 'B' and resid 44 through 57 removed outlier: 3.534A pdb=" N ALA B 57 " --> pdb=" O VAL B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 77 Processing helix chain 'B' and resid 117 through 132 removed outlier: 4.178A pdb=" N MET B 130 " --> pdb=" O MET B 126 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N SER B 131 " --> pdb=" O GLN B 127 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA B 132 " --> pdb=" O GLU B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 151 removed outlier: 4.336A pdb=" N ASP B 137 " --> pdb=" O PRO B 134 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU B 138 " --> pdb=" O GLY B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 186 Proline residue: B 174 - end of helix Processing helix chain 'B' and resid 212 through 230 Proline residue: B 221 - end of helix Processing helix chain 'B' and resid 246 through 262 Processing helix chain 'B' and resid 279 through 281 No H-bonds generated for 'chain 'B' and resid 279 through 281' Processing helix chain 'B' and resid 284 through 303 Processing helix chain 'B' and resid 322 through 333 removed outlier: 3.546A pdb=" N GLN B 331 " --> pdb=" O THR B 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 36 Processing helix chain 'C' and resid 39 through 55 Processing helix chain 'C' and resid 59 through 75 Processing helix chain 'C' and resid 79 through 96 Processing helix chain 'C' and resid 102 through 114 Processing helix chain 'C' and resid 120 through 132 Processing helix chain 'C' and resid 143 through 155 Processing helix chain 'C' and resid 159 through 168 Processing helix chain 'C' and resid 173 through 185 Processing helix chain 'C' and resid 192 through 205 removed outlier: 3.821A pdb=" N VAL C 196 " --> pdb=" O VAL C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 222 Processing helix chain 'C' and resid 235 through 249 Processing helix chain 'C' and resid 252 through 261 Processing helix chain 'C' and resid 263 through 268 removed outlier: 3.814A pdb=" N ARG C 268 " --> pdb=" O PRO C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 283 removed outlier: 3.800A pdb=" N GLY C 280 " --> pdb=" O ASP C 277 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N PHE C 283 " --> pdb=" O GLY C 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 1010 through 1013 No H-bonds generated for 'chain 'D' and resid 1010 through 1013' Processing helix chain 'D' and resid 1016 through 1031 Proline residue: D1020 - end of helix removed outlier: 3.535A pdb=" N GLN D1023 " --> pdb=" O VAL D1019 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS D1031 " --> pdb=" O GLN D1027 " (cutoff:3.500A) Processing helix chain 'D' and resid 1040 through 1045 removed outlier: 4.059A pdb=" N GLY D1045 " --> pdb=" O ALA D1041 " (cutoff:3.500A) Processing helix chain 'D' and resid 1063 through 1074 Processing helix chain 'D' and resid 1082 through 1087 Processing helix chain 'D' and resid 1093 through 1112 removed outlier: 4.199A pdb=" N TYR D1098 " --> pdb=" O VAL D1094 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 105 removed outlier: 4.427A pdb=" N ARG E 105 " --> pdb=" O LYS E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 128 Processing helix chain 'E' and resid 132 through 139 Processing helix chain 'F' and resid 21 through 36 Processing helix chain 'F' and resid 39 through 55 Processing helix chain 'F' and resid 59 through 75 Processing helix chain 'F' and resid 79 through 96 Processing helix chain 'F' and resid 102 through 114 Processing helix chain 'F' and resid 120 through 132 Processing helix chain 'F' and resid 143 through 155 Processing helix chain 'F' and resid 159 through 168 Processing helix chain 'F' and resid 173 through 185 Processing helix chain 'F' and resid 192 through 205 removed outlier: 3.821A pdb=" N VAL F 196 " --> pdb=" O VAL F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 222 Processing helix chain 'F' and resid 235 through 249 Processing helix chain 'F' and resid 252 through 261 Processing helix chain 'F' and resid 263 through 268 removed outlier: 3.814A pdb=" N ARG F 268 " --> pdb=" O PRO F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 283 removed outlier: 3.799A pdb=" N GLY F 280 " --> pdb=" O ASP F 277 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N PHE F 283 " --> pdb=" O GLY F 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 1010 through 1013 No H-bonds generated for 'chain 'G' and resid 1010 through 1013' Processing helix chain 'G' and resid 1016 through 1031 Proline residue: G1020 - end of helix removed outlier: 3.534A pdb=" N GLN G1023 " --> pdb=" O VAL G1019 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS G1031 " --> pdb=" O GLN G1027 " (cutoff:3.500A) Processing helix chain 'G' and resid 1040 through 1045 removed outlier: 4.059A pdb=" N GLY G1045 " --> pdb=" O ALA G1041 " (cutoff:3.500A) Processing helix chain 'G' and resid 1058 through 1069 Processing helix chain 'G' and resid 1077 through 1082 Processing helix chain 'G' and resid 1088 through 1107 removed outlier: 4.199A pdb=" N TYR G1093 " --> pdb=" O VAL G1089 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 105 removed outlier: 4.425A pdb=" N ARG H 105 " --> pdb=" O LYS H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 128 Processing helix chain 'H' and resid 132 through 139 Processing sheet with id= A, first strand: chain 'A' and resid 308 through 311 removed outlier: 9.946A pdb=" N ASN A 268 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N PHE A 238 " --> pdb=" O ASN A 268 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ILE A 270 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N CYS A 240 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ASN A 272 " --> pdb=" O CYS A 240 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N CYS A 242 " --> pdb=" O ASN A 272 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TRP A 33 " --> pdb=" O THR A 237 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE A 239 " --> pdb=" O TRP A 33 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N PHE A 35 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N VAL A 241 " --> pdb=" O PHE A 35 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N GLY A 37 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N ILE A 243 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL A 157 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N VAL A 36 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N PHE A 159 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N GLY A 38 " --> pdb=" O PHE A 159 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 308 through 311 removed outlier: 9.946A pdb=" N ASN B 268 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N PHE B 238 " --> pdb=" O ASN B 268 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ILE B 270 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N CYS B 240 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ASN B 272 " --> pdb=" O CYS B 240 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N CYS B 242 " --> pdb=" O ASN B 272 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP B 33 " --> pdb=" O THR B 237 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE B 239 " --> pdb=" O TRP B 33 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N PHE B 35 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL B 241 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N GLY B 37 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N ILE B 243 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL B 157 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N VAL B 36 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N PHE B 159 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N GLY B 38 " --> pdb=" O PHE B 159 " (cutoff:3.500A) 618 hydrogen bonds defined for protein. 1704 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: 3.18 Time building geometry restraints manager: 5.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3821 1.34 - 1.46: 2330 1.46 - 1.58: 5577 1.58 - 1.70: 10 1.70 - 1.82: 106 Bond restraints: 11844 Sorted by residual: bond pdb=" CA VAL D1019 " pdb=" CB VAL D1019 " ideal model delta sigma weight residual 1.539 1.544 -0.005 5.40e-03 3.43e+04 7.45e-01 bond pdb=" C1' ATP B 401 " pdb=" C2' ATP B 401 " ideal model delta sigma weight residual 1.531 1.521 0.010 1.20e-02 6.94e+03 6.72e-01 bond pdb=" CD ARG D1030 " pdb=" NE ARG D1030 " ideal model delta sigma weight residual 1.458 1.447 0.011 1.40e-02 5.10e+03 6.67e-01 bond pdb=" CD ARG G1030 " pdb=" NE ARG G1030 " ideal model delta sigma weight residual 1.458 1.447 0.011 1.40e-02 5.10e+03 6.67e-01 bond pdb=" CA VAL G1019 " pdb=" CB VAL G1019 " ideal model delta sigma weight residual 1.539 1.543 -0.004 5.40e-03 3.43e+04 6.44e-01 ... (remaining 11839 not shown) Histogram of bond angle deviations from ideal: 99.72 - 107.73: 549 107.73 - 115.75: 7155 115.75 - 123.76: 8040 123.76 - 131.78: 256 131.78 - 139.80: 20 Bond angle restraints: 16020 Sorted by residual: angle pdb=" NE ARG A 224 " pdb=" CZ ARG A 224 " pdb=" NH2 ARG A 224 " ideal model delta sigma weight residual 119.20 121.62 -2.42 9.00e-01 1.23e+00 7.22e+00 angle pdb=" NE ARG B 224 " pdb=" CZ ARG B 224 " pdb=" NH2 ARG B 224 " ideal model delta sigma weight residual 119.20 121.59 -2.39 9.00e-01 1.23e+00 7.07e+00 angle pdb=" C ARG G1094 " pdb=" N GLN G1095 " pdb=" CA GLN G1095 " ideal model delta sigma weight residual 120.72 116.53 4.19 1.67e+00 3.59e-01 6.30e+00 angle pdb=" C ARG D1099 " pdb=" N GLN D1100 " pdb=" CA GLN D1100 " ideal model delta sigma weight residual 120.72 116.54 4.18 1.67e+00 3.59e-01 6.27e+00 angle pdb=" C1' ATP B 401 " pdb=" C2' ATP B 401 " pdb=" O2' ATP B 401 " ideal model delta sigma weight residual 110.58 103.88 6.70 2.79e+00 1.28e-01 5.76e+00 ... (remaining 16015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 6480 17.58 - 35.15: 648 35.15 - 52.73: 136 52.73 - 70.31: 34 70.31 - 87.89: 12 Dihedral angle restraints: 7310 sinusoidal: 3072 harmonic: 4238 Sorted by residual: dihedral pdb=" CA SER F 137 " pdb=" C SER F 137 " pdb=" N GLY F 138 " pdb=" CA GLY F 138 " ideal model delta harmonic sigma weight residual 180.00 161.03 18.97 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA SER C 137 " pdb=" C SER C 137 " pdb=" N GLY C 138 " pdb=" CA GLY C 138 " ideal model delta harmonic sigma weight residual 180.00 161.05 18.95 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CD ARG A 224 " pdb=" NE ARG A 224 " pdb=" CZ ARG A 224 " pdb=" NH1 ARG A 224 " ideal model delta sinusoidal sigma weight residual 0.00 -26.87 26.87 1 1.00e+01 1.00e-02 1.04e+01 ... (remaining 7307 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1568 0.059 - 0.118: 184 0.118 - 0.177: 8 0.177 - 0.236: 2 0.236 - 0.295: 4 Chirality restraints: 1766 Sorted by residual: chirality pdb=" C2' ATP A 401 " pdb=" C1' ATP A 401 " pdb=" C3' ATP A 401 " pdb=" O2' ATP A 401 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C2' ATP B 401 " pdb=" C1' ATP B 401 " pdb=" C3' ATP B 401 " pdb=" O2' ATP B 401 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C3' ATP A 401 " pdb=" C2' ATP A 401 " pdb=" C4' ATP A 401 " pdb=" O3' ATP A 401 " both_signs ideal model delta sigma weight residual False -2.63 -2.91 0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 1763 not shown) Planarity restraints: 2072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 224 " -0.444 9.50e-02 1.11e+02 1.99e-01 2.51e+01 pdb=" NE ARG A 224 " 0.031 2.00e-02 2.50e+03 pdb=" CZ ARG A 224 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 224 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A 224 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 224 " 0.443 9.50e-02 1.11e+02 1.99e-01 2.50e+01 pdb=" NE ARG B 224 " -0.031 2.00e-02 2.50e+03 pdb=" CZ ARG B 224 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 224 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG B 224 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G1051 " -0.186 9.50e-02 1.11e+02 8.36e-02 4.41e+00 pdb=" NE ARG G1051 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG G1051 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG G1051 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG G1051 " -0.005 2.00e-02 2.50e+03 ... (remaining 2069 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 109 2.52 - 3.11: 9879 3.11 - 3.71: 19579 3.71 - 4.30: 26646 4.30 - 4.90: 43381 Nonbonded interactions: 99594 Sorted by model distance: nonbonded pdb=" O2G ATP A 401 " pdb="MG MG A 402 " model vdw 1.920 2.170 nonbonded pdb=" O2G ATP B 401 " pdb="MG MG B 402 " model vdw 1.921 2.170 nonbonded pdb=" OE1 GLU A 245 " pdb=" O3' ATP B 401 " model vdw 1.944 2.440 nonbonded pdb=" OE1 GLU B 245 " pdb=" O3' ATP A 401 " model vdw 1.946 2.440 nonbonded pdb=" OG1 THR B 45 " pdb="MG MG B 402 " model vdw 1.962 2.170 ... (remaining 99589 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 16 through 339 or resid 401 through 402)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'E' selection = chain 'H' } 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: 4.310 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: 10.150 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 35.660 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 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 : 0.003 0.030 11844 Z= 0.217 Angle : 0.566 6.704 16020 Z= 0.293 Chirality : 0.040 0.295 1766 Planarity : 0.008 0.199 2072 Dihedral : 14.914 87.887 4550 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.77 (0.23), residues: 1424 helix: 1.68 (0.17), residues: 944 sheet: 0.12 (0.61), residues: 82 loop : 0.34 (0.33), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 96 HIS 0.007 0.001 HIS C 43 PHE 0.009 0.001 PHE B 328 TYR 0.011 0.001 TYR A 250 ARG 0.016 0.001 ARG A 224 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 1.393 Fit side-chains revert: symmetry clash REVERT: A 118 MET cc_start: 0.2998 (mmt) cc_final: 0.2411 (mmm) REVERT: A 121 MET cc_start: 0.1612 (mtt) cc_final: 0.1220 (ptt) REVERT: A 126 MET cc_start: 0.4497 (ttt) cc_final: 0.4143 (tmm) REVERT: A 281 ARG cc_start: 0.6460 (ptm160) cc_final: 0.6199 (ptp-170) REVERT: A 287 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7441 (mt-10) REVERT: B 89 LYS cc_start: 0.8138 (ttmm) cc_final: 0.7539 (mtmt) REVERT: B 118 MET cc_start: 0.3322 (mmt) cc_final: 0.2716 (mmm) REVERT: B 121 MET cc_start: 0.1677 (mtt) cc_final: 0.1408 (ptt) REVERT: B 126 MET cc_start: 0.4622 (ttt) cc_final: 0.4197 (tmm) REVERT: B 281 ARG cc_start: 0.6445 (ptm160) cc_final: 0.6182 (ptp-170) REVERT: B 287 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7434 (mt-10) REVERT: C 27 GLU cc_start: 0.7266 (tt0) cc_final: 0.6905 (mt-10) REVERT: C 36 LYS cc_start: 0.8199 (mtpp) cc_final: 0.7983 (ttpt) REVERT: C 66 MET cc_start: 0.8502 (mmm) cc_final: 0.8278 (mmm) REVERT: C 128 ARG cc_start: 0.7385 (mmm-85) cc_final: 0.7123 (mtp180) REVERT: C 238 ASN cc_start: 0.7991 (m-40) cc_final: 0.7717 (m110) REVERT: C 258 LEU cc_start: 0.7103 (mm) cc_final: 0.6882 (mt) REVERT: D 1042 TYR cc_start: 0.7344 (t80) cc_final: 0.7133 (t80) REVERT: F 27 GLU cc_start: 0.7259 (tt0) cc_final: 0.6905 (mt-10) REVERT: F 36 LYS cc_start: 0.8206 (mtpp) cc_final: 0.7993 (ttpt) REVERT: F 66 MET cc_start: 0.8500 (mmm) cc_final: 0.8259 (mmp) REVERT: F 128 ARG cc_start: 0.7408 (mmm-85) cc_final: 0.7116 (mtp180) REVERT: F 238 ASN cc_start: 0.8020 (m-40) cc_final: 0.7734 (m110) REVERT: F 255 PHE cc_start: 0.8342 (t80) cc_final: 0.8094 (t80) REVERT: F 260 GLU cc_start: 0.8140 (tp30) cc_final: 0.7830 (tm-30) REVERT: G 1042 TYR cc_start: 0.7279 (t80) cc_final: 0.6991 (t80) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.2449 time to fit residues: 90.5281 Evaluate side-chains 182 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 72 optimal weight: 0.4980 chunk 57 optimal weight: 0.7980 chunk 111 optimal weight: 0.0470 chunk 43 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1027 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11844 Z= 0.222 Angle : 0.581 10.017 16020 Z= 0.293 Chirality : 0.040 0.133 1766 Planarity : 0.005 0.045 2072 Dihedral : 7.683 64.444 1630 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.72 % Allowed : 8.54 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.12 (0.22), residues: 1424 helix: 2.03 (0.17), residues: 941 sheet: 0.03 (0.59), residues: 82 loop : 0.30 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 96 HIS 0.004 0.001 HIS E 106 PHE 0.021 0.002 PHE C 232 TYR 0.020 0.002 TYR F 272 ARG 0.004 0.000 ARG A 224 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 195 time to evaluate : 1.332 Fit side-chains REVERT: A 89 LYS cc_start: 0.8423 (tptt) cc_final: 0.7737 (mtmt) REVERT: A 118 MET cc_start: 0.3177 (mmt) cc_final: 0.2584 (mpp) REVERT: A 121 MET cc_start: 0.1702 (mtt) cc_final: 0.1187 (ptt) REVERT: A 125 MET cc_start: 0.6162 (tmm) cc_final: 0.5788 (tmm) REVERT: A 126 MET cc_start: 0.5274 (ttt) cc_final: 0.4148 (tmm) REVERT: A 225 SER cc_start: 0.8646 (OUTLIER) cc_final: 0.8402 (p) REVERT: A 281 ARG cc_start: 0.6701 (ptm160) cc_final: 0.6407 (ptp-170) REVERT: B 89 LYS cc_start: 0.8157 (ttmm) cc_final: 0.7623 (mtmt) REVERT: B 118 MET cc_start: 0.3211 (mmt) cc_final: 0.2761 (mpp) REVERT: B 121 MET cc_start: 0.2043 (mtt) cc_final: 0.1622 (ptt) REVERT: B 125 MET cc_start: 0.6078 (tmm) cc_final: 0.5760 (tmm) REVERT: B 126 MET cc_start: 0.5303 (ttt) cc_final: 0.4145 (tmm) REVERT: B 179 ARG cc_start: 0.6680 (mtm110) cc_final: 0.6292 (ttt-90) REVERT: B 281 ARG cc_start: 0.6655 (ptm160) cc_final: 0.6376 (ptp-170) REVERT: C 27 GLU cc_start: 0.7160 (tt0) cc_final: 0.6928 (mt-10) REVERT: C 66 MET cc_start: 0.8476 (mmm) cc_final: 0.8132 (mmm) REVERT: C 87 MET cc_start: 0.8321 (mmm) cc_final: 0.8030 (mmm) REVERT: C 103 GLU cc_start: 0.7288 (pm20) cc_final: 0.6947 (pm20) REVERT: C 128 ARG cc_start: 0.7599 (mmm-85) cc_final: 0.7261 (mtp180) REVERT: C 238 ASN cc_start: 0.8079 (m-40) cc_final: 0.7584 (m110) REVERT: F 27 GLU cc_start: 0.7138 (tt0) cc_final: 0.6920 (mt-10) REVERT: F 66 MET cc_start: 0.8496 (mmm) cc_final: 0.8155 (mmm) REVERT: F 87 MET cc_start: 0.8319 (mmm) cc_final: 0.8033 (mmm) REVERT: F 103 GLU cc_start: 0.7310 (pm20) cc_final: 0.6961 (pm20) REVERT: F 128 ARG cc_start: 0.7644 (mmm-85) cc_final: 0.7309 (mtp180) REVERT: F 238 ASN cc_start: 0.8066 (m-40) cc_final: 0.7549 (m110) REVERT: F 255 PHE cc_start: 0.8344 (t80) cc_final: 0.8077 (t80) outliers start: 22 outliers final: 13 residues processed: 208 average time/residue: 0.2298 time to fit residues: 68.7826 Evaluate side-chains 180 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 166 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain G residue 1028 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 87 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 139 optimal weight: 40.0000 chunk 115 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 GLN ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1024 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 11844 Z= 0.417 Angle : 0.607 5.344 16020 Z= 0.312 Chirality : 0.043 0.168 1766 Planarity : 0.005 0.052 2072 Dihedral : 7.952 64.264 1630 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.90 % Allowed : 10.19 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.62 (0.22), residues: 1424 helix: 1.73 (0.16), residues: 939 sheet: -0.73 (0.58), residues: 76 loop : 0.02 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 241 HIS 0.006 0.002 HIS C 165 PHE 0.020 0.002 PHE C 239 TYR 0.021 0.002 TYR B 336 ARG 0.006 0.001 ARG A 263 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 174 time to evaluate : 1.376 Fit side-chains REVERT: A 89 LYS cc_start: 0.8472 (tptt) cc_final: 0.7822 (mtmt) REVERT: A 118 MET cc_start: 0.2949 (mmt) cc_final: 0.2327 (mpp) REVERT: A 121 MET cc_start: 0.1791 (mtt) cc_final: 0.1323 (ptt) REVERT: A 126 MET cc_start: 0.5408 (ttt) cc_final: 0.4597 (tmm) REVERT: A 179 ARG cc_start: 0.6846 (mtm110) cc_final: 0.6560 (mtm110) REVERT: A 224 ARG cc_start: 0.7203 (mtm-85) cc_final: 0.6860 (mtm110) REVERT: B 89 LYS cc_start: 0.8291 (ttmm) cc_final: 0.7708 (mtmt) REVERT: B 118 MET cc_start: 0.3001 (mmt) cc_final: 0.2476 (mpp) REVERT: B 121 MET cc_start: 0.1913 (mtt) cc_final: 0.1568 (ptt) REVERT: B 126 MET cc_start: 0.5270 (ttt) cc_final: 0.4478 (tmm) REVERT: B 128 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7041 (pt0) REVERT: B 179 ARG cc_start: 0.6795 (mtm110) cc_final: 0.6251 (ttp80) REVERT: B 224 ARG cc_start: 0.7204 (mtm-85) cc_final: 0.6874 (mtm110) REVERT: C 27 GLU cc_start: 0.7288 (tt0) cc_final: 0.6875 (mt-10) REVERT: C 66 MET cc_start: 0.8623 (mmm) cc_final: 0.8408 (mmm) REVERT: C 103 GLU cc_start: 0.7304 (pm20) cc_final: 0.6916 (pm20) REVERT: C 112 PHE cc_start: 0.8891 (t80) cc_final: 0.8689 (t80) REVERT: C 128 ARG cc_start: 0.7686 (mmm-85) cc_final: 0.7401 (mtp180) REVERT: C 181 GLU cc_start: 0.7595 (tp30) cc_final: 0.7027 (tt0) REVERT: C 238 ASN cc_start: 0.8144 (m-40) cc_final: 0.7500 (m110) REVERT: C 244 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8066 (mp) REVERT: D 1024 GLN cc_start: 0.7404 (OUTLIER) cc_final: 0.6716 (tp-100) REVERT: F 27 GLU cc_start: 0.7286 (tt0) cc_final: 0.6883 (mt-10) REVERT: F 66 MET cc_start: 0.8648 (mmm) cc_final: 0.8425 (mmm) REVERT: F 103 GLU cc_start: 0.7353 (pm20) cc_final: 0.6963 (pm20) REVERT: F 128 ARG cc_start: 0.7646 (mmm-85) cc_final: 0.7358 (mtp180) REVERT: F 181 GLU cc_start: 0.7572 (tp30) cc_final: 0.7062 (tt0) REVERT: F 238 ASN cc_start: 0.8123 (m-40) cc_final: 0.7398 (m110) REVERT: F 244 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8037 (mp) outliers start: 37 outliers final: 27 residues processed: 196 average time/residue: 0.2487 time to fit residues: 68.9637 Evaluate side-chains 193 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 163 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain D residue 1024 GLN Chi-restraints excluded: chain D residue 1028 SER Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 277 ASP Chi-restraints excluded: chain G residue 1028 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 1.9990 chunk 97 optimal weight: 50.0000 chunk 67 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 129 optimal weight: 0.7980 chunk 137 optimal weight: 4.9990 chunk 122 optimal weight: 0.4980 chunk 36 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1023 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11844 Z= 0.254 Angle : 0.556 13.617 16020 Z= 0.280 Chirality : 0.040 0.177 1766 Planarity : 0.005 0.054 2072 Dihedral : 7.678 74.310 1630 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.53 % Allowed : 10.97 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.66 (0.22), residues: 1424 helix: 1.82 (0.17), residues: 938 sheet: -0.91 (0.55), residues: 76 loop : -0.07 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 241 HIS 0.004 0.001 HIS F 165 PHE 0.021 0.001 PHE F 112 TYR 0.017 0.002 TYR F 272 ARG 0.006 0.000 ARG A 263 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 178 time to evaluate : 1.334 Fit side-chains revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8413 (tptt) cc_final: 0.7778 (mtmt) REVERT: A 118 MET cc_start: 0.2923 (mmt) cc_final: 0.2278 (mpp) REVERT: A 121 MET cc_start: 0.1722 (mtt) cc_final: 0.1267 (ptt) REVERT: A 126 MET cc_start: 0.5437 (ttt) cc_final: 0.4567 (tmm) REVERT: A 157 VAL cc_start: 0.7991 (OUTLIER) cc_final: 0.7771 (t) REVERT: A 179 ARG cc_start: 0.6803 (mtm110) cc_final: 0.6520 (mtm110) REVERT: B 89 LYS cc_start: 0.8279 (ttmm) cc_final: 0.7675 (mtmt) REVERT: B 118 MET cc_start: 0.3050 (mmt) cc_final: 0.2487 (mpp) REVERT: B 121 MET cc_start: 0.1827 (mtt) cc_final: 0.1495 (ptt) REVERT: B 126 MET cc_start: 0.5375 (ttt) cc_final: 0.4520 (tmm) REVERT: B 128 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7042 (pt0) REVERT: B 157 VAL cc_start: 0.7988 (OUTLIER) cc_final: 0.7759 (t) REVERT: B 179 ARG cc_start: 0.6812 (mtm110) cc_final: 0.6264 (ttp80) REVERT: B 224 ARG cc_start: 0.7199 (mtm-85) cc_final: 0.6895 (mtm110) REVERT: C 27 GLU cc_start: 0.7367 (tt0) cc_final: 0.6884 (mt-10) REVERT: C 112 PHE cc_start: 0.8817 (t80) cc_final: 0.8587 (t80) REVERT: C 128 ARG cc_start: 0.7693 (mmm-85) cc_final: 0.7372 (mtp180) REVERT: C 181 GLU cc_start: 0.7594 (tp30) cc_final: 0.7065 (tt0) REVERT: C 238 ASN cc_start: 0.8159 (m-40) cc_final: 0.7443 (m110) REVERT: C 271 MET cc_start: 0.6555 (mtt) cc_final: 0.6159 (mmp) REVERT: D 1024 GLN cc_start: 0.7354 (OUTLIER) cc_final: 0.6814 (tp-100) REVERT: F 27 GLU cc_start: 0.7367 (tt0) cc_final: 0.6887 (mt-10) REVERT: F 103 GLU cc_start: 0.7324 (pm20) cc_final: 0.6922 (pm20) REVERT: F 128 ARG cc_start: 0.7720 (mmm-85) cc_final: 0.7373 (mtp180) REVERT: F 181 GLU cc_start: 0.7582 (tp30) cc_final: 0.7064 (tt0) REVERT: F 238 ASN cc_start: 0.8181 (m-40) cc_final: 0.7373 (m110) REVERT: F 260 GLU cc_start: 0.8057 (tp30) cc_final: 0.7644 (tm-30) outliers start: 45 outliers final: 31 residues processed: 207 average time/residue: 0.2242 time to fit residues: 66.9514 Evaluate side-chains 197 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 163 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain D residue 1023 GLN Chi-restraints excluded: chain D residue 1024 GLN Chi-restraints excluded: chain D residue 1028 SER Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 194 MET Chi-restraints excluded: chain F residue 233 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 0 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN D1023 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11844 Z= 0.252 Angle : 0.529 6.513 16020 Z= 0.269 Chirality : 0.039 0.153 1766 Planarity : 0.005 0.054 2072 Dihedral : 7.546 81.014 1630 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.21 % Allowed : 11.36 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.64 (0.22), residues: 1424 helix: 1.82 (0.17), residues: 935 sheet: -1.12 (0.51), residues: 86 loop : -0.03 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 241 HIS 0.003 0.001 HIS C 165 PHE 0.019 0.001 PHE F 255 TYR 0.017 0.002 TYR A 250 ARG 0.006 0.000 ARG B 263 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 164 time to evaluate : 1.340 Fit side-chains revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8426 (tptt) cc_final: 0.7808 (mtmt) REVERT: A 118 MET cc_start: 0.2938 (mmt) cc_final: 0.2250 (mpp) REVERT: A 121 MET cc_start: 0.1797 (mtt) cc_final: 0.1319 (ptt) REVERT: A 126 MET cc_start: 0.5488 (ttt) cc_final: 0.4596 (tmm) REVERT: A 157 VAL cc_start: 0.7987 (OUTLIER) cc_final: 0.7773 (t) REVERT: A 179 ARG cc_start: 0.6827 (mtm110) cc_final: 0.6248 (ttp80) REVERT: A 306 ASP cc_start: 0.7182 (t70) cc_final: 0.6709 (m-30) REVERT: B 89 LYS cc_start: 0.8281 (ttmm) cc_final: 0.7679 (mtmt) REVERT: B 118 MET cc_start: 0.2889 (mmt) cc_final: 0.2250 (mpp) REVERT: B 121 MET cc_start: 0.1851 (mtt) cc_final: 0.1524 (ptt) REVERT: B 126 MET cc_start: 0.5438 (ttt) cc_final: 0.4574 (tmm) REVERT: B 157 VAL cc_start: 0.7914 (OUTLIER) cc_final: 0.7699 (t) REVERT: B 179 ARG cc_start: 0.6773 (mtm110) cc_final: 0.6228 (ttp80) REVERT: B 224 ARG cc_start: 0.7167 (mtm-85) cc_final: 0.6851 (mtm110) REVERT: B 306 ASP cc_start: 0.7203 (t70) cc_final: 0.6781 (m-30) REVERT: C 27 GLU cc_start: 0.7342 (tt0) cc_final: 0.6875 (mt-10) REVERT: C 103 GLU cc_start: 0.7196 (pm20) cc_final: 0.6865 (pm20) REVERT: C 112 PHE cc_start: 0.8830 (t80) cc_final: 0.8593 (t80) REVERT: C 128 ARG cc_start: 0.7652 (mmm-85) cc_final: 0.7438 (mtp180) REVERT: C 181 GLU cc_start: 0.7595 (tp30) cc_final: 0.7068 (tt0) REVERT: C 238 ASN cc_start: 0.8128 (m-40) cc_final: 0.7403 (m110) REVERT: F 27 GLU cc_start: 0.7339 (tt0) cc_final: 0.6875 (mt-10) REVERT: F 103 GLU cc_start: 0.7298 (pm20) cc_final: 0.6889 (pm20) REVERT: F 128 ARG cc_start: 0.7670 (mmm-85) cc_final: 0.7459 (mtp180) REVERT: F 181 GLU cc_start: 0.7559 (tp30) cc_final: 0.7070 (tt0) REVERT: F 238 ASN cc_start: 0.8154 (m-40) cc_final: 0.7317 (m110) REVERT: F 260 GLU cc_start: 0.8038 (tp30) cc_final: 0.7663 (tm-30) REVERT: G 1024 GLN cc_start: 0.7184 (mt0) cc_final: 0.6968 (tp-100) outliers start: 41 outliers final: 36 residues processed: 190 average time/residue: 0.2418 time to fit residues: 65.2726 Evaluate side-chains 197 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 159 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain D residue 1023 GLN Chi-restraints excluded: chain D residue 1028 SER Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 194 MET Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 277 ASP Chi-restraints excluded: chain G residue 1028 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 132 optimal weight: 7.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11844 Z= 0.331 Angle : 0.591 16.311 16020 Z= 0.292 Chirality : 0.041 0.154 1766 Planarity : 0.005 0.055 2072 Dihedral : 7.533 85.923 1630 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.84 % Allowed : 11.52 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.50 (0.22), residues: 1424 helix: 1.74 (0.17), residues: 935 sheet: -1.28 (0.51), residues: 86 loop : -0.13 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 241 HIS 0.005 0.001 HIS C 165 PHE 0.018 0.002 PHE F 255 TYR 0.017 0.002 TYR B 250 ARG 0.007 0.000 ARG A 263 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 162 time to evaluate : 1.362 Fit side-chains REVERT: A 89 LYS cc_start: 0.8452 (tptt) cc_final: 0.7820 (mtmt) REVERT: A 118 MET cc_start: 0.2726 (mmt) cc_final: 0.1915 (mpp) REVERT: A 121 MET cc_start: 0.1848 (mtt) cc_final: 0.1335 (ptt) REVERT: A 126 MET cc_start: 0.5694 (ttt) cc_final: 0.4777 (tmm) REVERT: A 157 VAL cc_start: 0.8042 (OUTLIER) cc_final: 0.7825 (t) REVERT: A 179 ARG cc_start: 0.6864 (mtm110) cc_final: 0.6276 (ttp80) REVERT: A 224 ARG cc_start: 0.7215 (mtm-85) cc_final: 0.6911 (mtm110) REVERT: A 306 ASP cc_start: 0.7240 (t70) cc_final: 0.6860 (m-30) REVERT: B 89 LYS cc_start: 0.8282 (ttmm) cc_final: 0.7661 (mtmt) REVERT: B 118 MET cc_start: 0.2921 (mmt) cc_final: 0.2227 (mpp) REVERT: B 121 MET cc_start: 0.1928 (mtt) cc_final: 0.1515 (ptt) REVERT: B 126 MET cc_start: 0.5667 (ttt) cc_final: 0.4742 (tmm) REVERT: B 157 VAL cc_start: 0.7953 (OUTLIER) cc_final: 0.7740 (t) REVERT: B 179 ARG cc_start: 0.6857 (mtm110) cc_final: 0.6307 (ttp80) REVERT: B 224 ARG cc_start: 0.7198 (mtm-85) cc_final: 0.6927 (mtm110) REVERT: B 306 ASP cc_start: 0.7283 (t70) cc_final: 0.6945 (m-30) REVERT: C 27 GLU cc_start: 0.7322 (tt0) cc_final: 0.6845 (mt-10) REVERT: C 103 GLU cc_start: 0.7211 (pm20) cc_final: 0.6896 (pm20) REVERT: C 128 ARG cc_start: 0.7645 (mmm-85) cc_final: 0.7398 (mtp180) REVERT: C 181 GLU cc_start: 0.7591 (tp30) cc_final: 0.7061 (tt0) REVERT: C 238 ASN cc_start: 0.8168 (m-40) cc_final: 0.7405 (m110) REVERT: C 271 MET cc_start: 0.6669 (mtt) cc_final: 0.6143 (mmp) REVERT: F 27 GLU cc_start: 0.7342 (tt0) cc_final: 0.6844 (mt-10) REVERT: F 103 GLU cc_start: 0.7329 (pm20) cc_final: 0.6918 (pm20) REVERT: F 128 ARG cc_start: 0.7712 (mmm-85) cc_final: 0.7469 (mtp180) REVERT: F 181 GLU cc_start: 0.7568 (tp30) cc_final: 0.7069 (tt0) REVERT: F 238 ASN cc_start: 0.8139 (m-40) cc_final: 0.7300 (m110) REVERT: F 260 GLU cc_start: 0.8028 (tp30) cc_final: 0.7647 (tm-30) REVERT: G 1024 GLN cc_start: 0.7146 (mt0) cc_final: 0.6919 (tp-100) outliers start: 49 outliers final: 41 residues processed: 195 average time/residue: 0.2346 time to fit residues: 65.3579 Evaluate side-chains 196 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 153 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain D residue 1028 SER Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 194 MET Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 277 ASP Chi-restraints excluded: chain G residue 1028 SER Chi-restraints excluded: chain H residue 130 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 chunk 100 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 136 optimal weight: 7.9990 chunk 85 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11844 Z= 0.214 Angle : 0.530 8.462 16020 Z= 0.268 Chirality : 0.039 0.141 1766 Planarity : 0.005 0.054 2072 Dihedral : 7.283 84.507 1630 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.53 % Allowed : 12.15 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.63 (0.22), residues: 1424 helix: 1.87 (0.17), residues: 933 sheet: -1.37 (0.50), residues: 86 loop : -0.12 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 241 HIS 0.004 0.001 HIS C 43 PHE 0.034 0.002 PHE C 112 TYR 0.016 0.002 TYR A 250 ARG 0.007 0.000 ARG A 263 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 159 time to evaluate : 1.374 Fit side-chains REVERT: A 89 LYS cc_start: 0.8449 (tptt) cc_final: 0.7811 (mtmt) REVERT: A 118 MET cc_start: 0.2810 (mmt) cc_final: 0.1987 (mpp) REVERT: A 121 MET cc_start: 0.1886 (mtt) cc_final: 0.1401 (ptt) REVERT: A 126 MET cc_start: 0.5660 (ttt) cc_final: 0.4756 (tmm) REVERT: A 179 ARG cc_start: 0.6787 (mtm110) cc_final: 0.6317 (ttp80) REVERT: B 89 LYS cc_start: 0.8269 (ttmm) cc_final: 0.7661 (mtmt) REVERT: B 118 MET cc_start: 0.3094 (mmt) cc_final: 0.2364 (mpp) REVERT: B 121 MET cc_start: 0.1992 (mtt) cc_final: 0.1551 (ptt) REVERT: B 126 MET cc_start: 0.5675 (ttt) cc_final: 0.4751 (tmm) REVERT: B 179 ARG cc_start: 0.6795 (mtm110) cc_final: 0.6237 (ttp80) REVERT: B 224 ARG cc_start: 0.7175 (mtm-85) cc_final: 0.6929 (mtm110) REVERT: C 27 GLU cc_start: 0.7366 (tt0) cc_final: 0.6905 (mt-10) REVERT: C 103 GLU cc_start: 0.7213 (pm20) cc_final: 0.6889 (pm20) REVERT: C 181 GLU cc_start: 0.7589 (tp30) cc_final: 0.7053 (tt0) REVERT: C 238 ASN cc_start: 0.8153 (m-40) cc_final: 0.7395 (m110) REVERT: C 271 MET cc_start: 0.6652 (mtt) cc_final: 0.6157 (mmp) REVERT: F 27 GLU cc_start: 0.7341 (tt0) cc_final: 0.6847 (mt-10) REVERT: F 87 MET cc_start: 0.8377 (mmm) cc_final: 0.7468 (mmm) REVERT: F 103 GLU cc_start: 0.7318 (pm20) cc_final: 0.6904 (pm20) REVERT: F 128 ARG cc_start: 0.7640 (mmm-85) cc_final: 0.7377 (mtp180) REVERT: F 181 GLU cc_start: 0.7538 (tp30) cc_final: 0.7041 (tt0) REVERT: F 238 ASN cc_start: 0.8156 (m-40) cc_final: 0.7286 (m110) REVERT: F 260 GLU cc_start: 0.7963 (tp30) cc_final: 0.7578 (tm-30) REVERT: G 1024 GLN cc_start: 0.7147 (mt0) cc_final: 0.6925 (tp-100) outliers start: 45 outliers final: 39 residues processed: 189 average time/residue: 0.2328 time to fit residues: 63.4984 Evaluate side-chains 191 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 152 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain D residue 1028 SER Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 194 MET Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 277 ASP Chi-restraints excluded: chain G residue 1028 SER Chi-restraints excluded: chain H residue 130 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 41 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 chunk 87 optimal weight: 9.9990 chunk 93 optimal weight: 40.0000 chunk 67 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11844 Z= 0.225 Angle : 0.569 17.414 16020 Z= 0.280 Chirality : 0.039 0.180 1766 Planarity : 0.005 0.055 2072 Dihedral : 7.117 78.855 1630 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.13 % Allowed : 12.54 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.64 (0.22), residues: 1424 helix: 1.88 (0.17), residues: 933 sheet: -1.27 (0.49), residues: 86 loop : -0.15 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 241 HIS 0.004 0.001 HIS F 76 PHE 0.031 0.002 PHE C 239 TYR 0.016 0.002 TYR A 250 ARG 0.008 0.000 ARG A 263 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 156 time to evaluate : 1.382 Fit side-chains REVERT: A 89 LYS cc_start: 0.8448 (tptt) cc_final: 0.7820 (mtmt) REVERT: A 118 MET cc_start: 0.2817 (mmt) cc_final: 0.1974 (mpp) REVERT: A 121 MET cc_start: 0.1856 (mtt) cc_final: 0.1388 (ptt) REVERT: A 126 MET cc_start: 0.5704 (ttt) cc_final: 0.4741 (tmm) REVERT: A 179 ARG cc_start: 0.6783 (mtm110) cc_final: 0.6295 (ttp80) REVERT: B 89 LYS cc_start: 0.8282 (ttmm) cc_final: 0.7667 (mtmt) REVERT: B 118 MET cc_start: 0.2922 (mmt) cc_final: 0.2118 (mpp) REVERT: B 121 MET cc_start: 0.1929 (mtt) cc_final: 0.1481 (ptt) REVERT: B 126 MET cc_start: 0.5704 (ttt) cc_final: 0.4776 (tmm) REVERT: B 179 ARG cc_start: 0.6790 (mtm110) cc_final: 0.6310 (ttp80) REVERT: B 224 ARG cc_start: 0.7175 (mtm-85) cc_final: 0.6946 (mtm110) REVERT: C 87 MET cc_start: 0.8316 (mmm) cc_final: 0.7787 (mmm) REVERT: C 103 GLU cc_start: 0.7216 (pm20) cc_final: 0.6869 (pm20) REVERT: C 181 GLU cc_start: 0.7563 (tp30) cc_final: 0.7031 (tt0) REVERT: C 238 ASN cc_start: 0.8125 (m-40) cc_final: 0.7391 (m110) REVERT: C 241 TRP cc_start: 0.8430 (t60) cc_final: 0.8161 (t60) REVERT: C 271 MET cc_start: 0.6650 (mtt) cc_final: 0.6160 (mmp) REVERT: F 27 GLU cc_start: 0.7325 (tt0) cc_final: 0.6779 (mt-10) REVERT: F 103 GLU cc_start: 0.7302 (pm20) cc_final: 0.6897 (pm20) REVERT: F 128 ARG cc_start: 0.7634 (mmm-85) cc_final: 0.7430 (mtp180) REVERT: F 181 GLU cc_start: 0.7530 (tp30) cc_final: 0.7044 (tt0) REVERT: F 238 ASN cc_start: 0.8169 (m-40) cc_final: 0.7299 (m110) REVERT: F 260 GLU cc_start: 0.7943 (tp30) cc_final: 0.7735 (mm-30) REVERT: G 1024 GLN cc_start: 0.7168 (mt0) cc_final: 0.6893 (tp-100) outliers start: 40 outliers final: 38 residues processed: 183 average time/residue: 0.2306 time to fit residues: 60.8697 Evaluate side-chains 190 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 152 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 194 MET Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 277 ASP Chi-restraints excluded: chain G residue 1028 SER Chi-restraints excluded: chain H residue 130 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 131 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 39 optimal weight: 0.0770 chunk 115 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 134 optimal weight: 30.0000 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11844 Z= 0.291 Angle : 0.550 8.558 16020 Z= 0.280 Chirality : 0.040 0.152 1766 Planarity : 0.005 0.056 2072 Dihedral : 7.143 79.390 1630 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.37 % Allowed : 12.46 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.48 (0.22), residues: 1424 helix: 1.75 (0.17), residues: 931 sheet: -1.20 (0.50), residues: 86 loop : -0.21 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 241 HIS 0.004 0.001 HIS C 165 PHE 0.029 0.002 PHE C 255 TYR 0.018 0.002 TYR B 250 ARG 0.008 0.000 ARG B 263 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 153 time to evaluate : 1.403 Fit side-chains REVERT: A 89 LYS cc_start: 0.8450 (tptt) cc_final: 0.7836 (mtmt) REVERT: A 118 MET cc_start: 0.2740 (mmt) cc_final: 0.1892 (mpp) REVERT: A 121 MET cc_start: 0.1866 (mtt) cc_final: 0.1389 (ptt) REVERT: A 126 MET cc_start: 0.5771 (ttt) cc_final: 0.4883 (tmm) REVERT: A 179 ARG cc_start: 0.6837 (mtm110) cc_final: 0.6317 (ttp80) REVERT: A 224 ARG cc_start: 0.7188 (mtm-85) cc_final: 0.6927 (mtm110) REVERT: B 89 LYS cc_start: 0.8264 (ttmm) cc_final: 0.7619 (mtmt) REVERT: B 118 MET cc_start: 0.2865 (mmt) cc_final: 0.2018 (mpp) REVERT: B 121 MET cc_start: 0.1967 (mtt) cc_final: 0.1469 (ptt) REVERT: B 126 MET cc_start: 0.5712 (ttt) cc_final: 0.4848 (tmm) REVERT: B 179 ARG cc_start: 0.6820 (mtm110) cc_final: 0.6266 (ttp80) REVERT: B 224 ARG cc_start: 0.7187 (mtm-85) cc_final: 0.6950 (mtm110) REVERT: C 103 GLU cc_start: 0.7224 (pm20) cc_final: 0.6877 (pm20) REVERT: C 181 GLU cc_start: 0.7549 (tp30) cc_final: 0.7055 (tt0) REVERT: C 238 ASN cc_start: 0.8269 (m-40) cc_final: 0.7546 (m110) REVERT: C 241 TRP cc_start: 0.8422 (t60) cc_final: 0.8128 (t60) REVERT: C 271 MET cc_start: 0.6656 (mtt) cc_final: 0.6213 (mmp) REVERT: F 27 GLU cc_start: 0.7332 (tt0) cc_final: 0.6800 (mt-10) REVERT: F 87 MET cc_start: 0.8419 (mmm) cc_final: 0.7527 (mmm) REVERT: F 103 GLU cc_start: 0.7333 (pm20) cc_final: 0.6921 (pm20) REVERT: F 128 ARG cc_start: 0.7652 (mmm-85) cc_final: 0.7286 (mtp180) REVERT: F 181 GLU cc_start: 0.7566 (tp30) cc_final: 0.7086 (tt0) REVERT: F 238 ASN cc_start: 0.8210 (m-40) cc_final: 0.7331 (m110) outliers start: 43 outliers final: 42 residues processed: 183 average time/residue: 0.2360 time to fit residues: 62.1364 Evaluate side-chains 192 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 150 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain D residue 1028 SER Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 194 MET Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 277 ASP Chi-restraints excluded: chain G residue 1028 SER Chi-restraints excluded: chain H residue 130 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 93 optimal weight: 50.0000 chunk 141 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 11 optimal weight: 0.1980 chunk 87 optimal weight: 0.0070 chunk 69 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 overall best weight: 0.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1024 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11844 Z= 0.201 Angle : 0.566 17.864 16020 Z= 0.278 Chirality : 0.039 0.152 1766 Planarity : 0.005 0.054 2072 Dihedral : 6.855 73.176 1630 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.13 % Allowed : 13.09 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.61 (0.22), residues: 1424 helix: 1.87 (0.17), residues: 933 sheet: -1.14 (0.50), residues: 84 loop : -0.24 (0.28), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 241 HIS 0.004 0.001 HIS C 43 PHE 0.030 0.002 PHE C 255 TYR 0.015 0.001 TYR A 250 ARG 0.009 0.000 ARG A 263 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 150 time to evaluate : 1.286 Fit side-chains REVERT: A 89 LYS cc_start: 0.8462 (tptt) cc_final: 0.7834 (mtmt) REVERT: A 118 MET cc_start: 0.2862 (mmt) cc_final: 0.2010 (mpp) REVERT: A 121 MET cc_start: 0.1898 (mtt) cc_final: 0.1433 (ptt) REVERT: A 126 MET cc_start: 0.5754 (ttt) cc_final: 0.4873 (tmm) REVERT: A 179 ARG cc_start: 0.6767 (mtm110) cc_final: 0.6292 (ttp80) REVERT: B 89 LYS cc_start: 0.8248 (ttmm) cc_final: 0.7617 (mtmt) REVERT: B 118 MET cc_start: 0.3026 (mmt) cc_final: 0.2173 (mpp) REVERT: B 121 MET cc_start: 0.1914 (mtt) cc_final: 0.1449 (ptt) REVERT: B 126 MET cc_start: 0.5737 (ttt) cc_final: 0.4854 (tmm) REVERT: B 179 ARG cc_start: 0.6735 (mtm110) cc_final: 0.6264 (ttp80) REVERT: C 36 LYS cc_start: 0.8361 (mtpp) cc_final: 0.8127 (ttmt) REVERT: C 103 GLU cc_start: 0.7199 (pm20) cc_final: 0.6865 (pm20) REVERT: C 181 GLU cc_start: 0.7525 (tp30) cc_final: 0.7021 (tt0) REVERT: C 238 ASN cc_start: 0.8202 (m-40) cc_final: 0.7450 (m110) REVERT: C 241 TRP cc_start: 0.8419 (t60) cc_final: 0.8117 (t60) REVERT: C 271 MET cc_start: 0.6549 (mtt) cc_final: 0.6031 (mmp) REVERT: F 36 LYS cc_start: 0.8300 (mtpp) cc_final: 0.8064 (ttmt) REVERT: F 87 MET cc_start: 0.8421 (mmm) cc_final: 0.7492 (mmm) REVERT: F 103 GLU cc_start: 0.7317 (pm20) cc_final: 0.6913 (pm20) REVERT: F 128 ARG cc_start: 0.7630 (mmm-85) cc_final: 0.7331 (mtp180) REVERT: F 181 GLU cc_start: 0.7507 (tp30) cc_final: 0.7006 (tt0) REVERT: F 238 ASN cc_start: 0.8225 (m-40) cc_final: 0.7364 (m110) outliers start: 40 outliers final: 37 residues processed: 176 average time/residue: 0.2224 time to fit residues: 56.6137 Evaluate side-chains 184 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 147 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 194 MET Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 277 ASP Chi-restraints excluded: chain G residue 1028 SER Chi-restraints excluded: chain H residue 130 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 99 optimal weight: 8.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.177124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.132126 restraints weight = 16765.518| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.14 r_work: 0.3322 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11844 Z= 0.233 Angle : 0.525 8.501 16020 Z= 0.266 Chirality : 0.039 0.148 1766 Planarity : 0.005 0.056 2072 Dihedral : 6.917 75.830 1630 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.13 % Allowed : 13.09 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.57 (0.22), residues: 1424 helix: 1.83 (0.17), residues: 935 sheet: -1.13 (0.49), residues: 84 loop : -0.25 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 241 HIS 0.004 0.001 HIS F 168 PHE 0.029 0.002 PHE C 255 TYR 0.017 0.002 TYR B 250 ARG 0.009 0.000 ARG B 263 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2696.81 seconds wall clock time: 49 minutes 17.07 seconds (2957.07 seconds total)