Starting phenix.real_space_refine on Fri Feb 16 05:24:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5p_29752/02_2024/8g5p_29752_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5p_29752/02_2024/8g5p_29752.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5p_29752/02_2024/8g5p_29752.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5p_29752/02_2024/8g5p_29752.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5p_29752/02_2024/8g5p_29752_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5p_29752/02_2024/8g5p_29752_neut.pdb" } resolution = 2.78 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= 0.014 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: 5 Type Number sf(0) Gaussians P 38 5.49 5 S 79 5.16 5 C 9110 2.51 5 N 2542 2.21 5 O 2731 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 489": "OE1" <-> "OE2" Residue "A PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 873": "OE1" <-> "OE2" Residue "A GLU 895": "OE1" <-> "OE2" Residue "B GLU 236": "OE1" <-> "OE2" Residue "C GLU 419": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14500 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 919, 7214 Classifications: {'peptide': 919} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 61, 'TRANS': 857} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'HIS:plan': 1, 'ARG:plan': 7, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 68 Chain: "B" Number of atoms: 3259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3259 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 18, 'TRANS': 388} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 3230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3230 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 18, 'TRANS': 389} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "R" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 370 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 6} Link IDs: {'rna2p': 2, 'rna3p': 14} Chain: "T" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 427 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" P DT T 5 " occ=0.50 ... (18 atoms not shown) pdb=" C6 DT T 5 " occ=0.50 residue: pdb=" P DA T 6 " occ=0.50 ... (19 atoms not shown) pdb=" C4 DA T 6 " occ=0.50 residue: pdb=" P DG T 7 " occ=0.50 ... (20 atoms not shown) pdb=" C4 DG T 7 " occ=0.50 Time building chain proxies: 8.56, per 1000 atoms: 0.59 Number of scatterers: 14500 At special positions: 0 Unit cell: (106.502, 104.851, 142.829, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 79 16.00 P 38 15.00 O 2731 8.00 N 2542 7.00 C 9110 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: 6.16 Conformation dependent library (CDL) restraints added in 2.8 seconds 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3226 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 10 sheets defined 37.0% alpha, 11.5% beta 16 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 4.88 Creating SS restraints... Processing helix chain 'A' and resid 96 through 109 removed outlier: 3.999A pdb=" N LYS A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 160 removed outlier: 3.573A pdb=" N HIS A 138 " --> pdb=" O ASN A 134 " (cutoff:3.500A) Proline residue: A 149 - end of helix removed outlier: 3.932A pdb=" N ALA A 153 " --> pdb=" O PRO A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 277 removed outlier: 3.718A pdb=" N HIS A 277 " --> pdb=" O PHE A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 305 through 315 removed outlier: 3.912A pdb=" N SER A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 381 through 388 Processing helix chain 'A' and resid 388 through 418 Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 421 through 431 Processing helix chain 'A' and resid 440 through 470 Processing helix chain 'A' and resid 471 through 475 removed outlier: 3.548A pdb=" N LEU A 474 " --> pdb=" O CYS A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 541 removed outlier: 3.524A pdb=" N GLN A 541 " --> pdb=" O GLU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 577 Processing helix chain 'A' and resid 598 through 603 Processing helix chain 'A' and resid 788 through 809 removed outlier: 3.532A pdb=" N LEU A 792 " --> pdb=" O GLY A 788 " (cutoff:3.500A) WARNING: missing atoms! removed outlier: 5.145A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN A 803 " --> pdb=" O SER A 799 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N LYS A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ARG A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 908 Processing helix chain 'A' and resid 915 through 923 removed outlier: 4.040A pdb=" N MET A 919 " --> pdb=" O ALA A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 940 Processing helix chain 'A' and resid 945 through 955 removed outlier: 3.752A pdb=" N TYR A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A 953 " --> pdb=" O PHE A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 970 removed outlier: 3.670A pdb=" N ASN A 970 " --> pdb=" O LEU A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 977 Processing helix chain 'A' and resid 982 through 987 Processing helix chain 'A' and resid 1058 through 1066 removed outlier: 3.523A pdb=" N GLU A1062 " --> pdb=" O PHE A1058 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1084 removed outlier: 3.577A pdb=" N GLU A1084 " --> pdb=" O ARG A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1123 removed outlier: 3.733A pdb=" N PHE A1123 " --> pdb=" O LEU A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1167 removed outlier: 3.571A pdb=" N LEU A1153 " --> pdb=" O ALA A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1175 through 1179 removed outlier: 3.759A pdb=" N PHE A1179 " --> pdb=" O SER A1176 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1206 Processing helix chain 'A' and resid 1217 through 1221 Processing helix chain 'A' and resid 1226 through 1230 removed outlier: 4.000A pdb=" N GLY A1229 " --> pdb=" O LEU A1226 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 100 through 119 Processing helix chain 'B' and resid 185 through 193 Processing helix chain 'B' and resid 194 through 201 removed outlier: 3.749A pdb=" N ASP B 198 " --> pdb=" O ASN B 195 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU B 199 " --> pdb=" O CYS B 196 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B 200 " --> pdb=" O LEU B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 265 Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 308 through 315 removed outlier: 3.520A pdb=" N TYR B 315 " --> pdb=" O LEU B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 354 Processing helix chain 'B' and resid 393 through 397 removed outlier: 3.703A pdb=" N GLN B 397 " --> pdb=" O GLU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 408 removed outlier: 3.927A pdb=" N LEU B 402 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ASN B 404 " --> pdb=" O GLN B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 435 Processing helix chain 'B' and resid 444 through 448 removed outlier: 3.811A pdb=" N LEU B 448 " --> pdb=" O GLU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 484 removed outlier: 3.624A pdb=" N ASN B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 75 removed outlier: 3.662A pdb=" N ILE C 72 " --> pdb=" O ALA C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 78 No H-bonds generated for 'chain 'C' and resid 76 through 78' Processing helix chain 'C' and resid 100 through 119 Processing helix chain 'C' and resid 185 through 201 removed outlier: 3.730A pdb=" N ALA C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N VAL C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ASN C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 266 removed outlier: 4.071A pdb=" N PHE C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 308 through 314 Processing helix chain 'C' and resid 342 through 354 Processing helix chain 'C' and resid 395 through 409 Processing helix chain 'C' and resid 424 through 435 Processing helix chain 'C' and resid 444 through 451 removed outlier: 3.841A pdb=" N LEU C 448 " --> pdb=" O THR C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 484 Processing sheet with id=AA1, first strand: chain 'A' and resid 183 through 187 removed outlier: 3.690A pdb=" N TRP A 175 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TRP A 220 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ALA A 200 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ALA A 212 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ALA A 198 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ALA A 214 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL A 196 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 195 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL A 266 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 435 through 436 Processing sheet with id=AA3, first strand: chain 'A' and resid 1127 through 1132 removed outlier: 6.826A pdb=" N GLY A1127 " --> pdb=" O ARG A1142 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ARG A1142 " --> pdb=" O GLY A1127 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N PHE A1129 " --> pdb=" O LEU A1140 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU A1140 " --> pdb=" O PHE A1129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.660A pdb=" N ILE B 300 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N LEU B 299 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N TYR B 291 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LYS B 285 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 324 through 326 Processing sheet with id=AA6, first strand: chain 'B' and resid 413 through 415 removed outlier: 7.051A pdb=" N TRP B 414 " --> pdb=" O ILE B 381 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N VAL B 383 " --> pdb=" O TRP B 414 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LYS B 382 " --> pdb=" O PHE B 439 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N VAL B 441 " --> pdb=" O LYS B 382 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ALA B 384 " --> pdb=" O VAL B 441 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N VAL B 443 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ASP B 386 " --> pdb=" O VAL B 443 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 125 through 127 removed outlier: 6.196A pdb=" N PHE C 126 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N ILE C 211 " --> pdb=" O PHE C 126 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 133 through 134 Processing sheet with id=AA9, first strand: chain 'C' and resid 324 through 326 Processing sheet with id=AB1, first strand: chain 'C' and resid 413 through 415 removed outlier: 7.106A pdb=" N TRP C 414 " --> pdb=" O ILE C 381 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL C 383 " --> pdb=" O TRP C 414 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LYS C 382 " --> pdb=" O PHE C 439 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL C 441 " --> pdb=" O LYS C 382 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ALA C 384 " --> pdb=" O VAL C 441 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL C 443 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASP C 386 " --> pdb=" O VAL C 443 " (cutoff:3.500A) 515 hydrogen bonds defined for protein. 1446 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 43 hydrogen bonds 86 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 4.76 Time building geometry restraints manager: 6.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 2285 1.28 - 1.42: 4054 1.42 - 1.55: 8385 1.55 - 1.69: 91 1.69 - 1.82: 125 Bond restraints: 14940 Sorted by residual: bond pdb=" C CYS B 399 " pdb=" O CYS B 399 " ideal model delta sigma weight residual 1.236 1.151 0.086 1.15e-02 7.56e+03 5.55e+01 bond pdb=" N ILE A 278 " pdb=" CA ILE A 278 " ideal model delta sigma weight residual 1.452 1.495 -0.042 1.18e-02 7.18e+03 1.29e+01 bond pdb=" CA PRO C 244 " pdb=" C PRO C 244 " ideal model delta sigma weight residual 1.514 1.533 -0.019 5.50e-03 3.31e+04 1.14e+01 bond pdb=" N GLY C 307 " pdb=" CA GLY C 307 " ideal model delta sigma weight residual 1.448 1.477 -0.029 9.00e-03 1.23e+04 1.06e+01 bond pdb=" C PRO C 244 " pdb=" O PRO C 244 " ideal model delta sigma weight residual 1.246 1.218 0.028 8.50e-03 1.38e+04 1.05e+01 ... (remaining 14935 not shown) Histogram of bond angle deviations from ideal: 99.35 - 106.37: 745 106.37 - 113.39: 7881 113.39 - 120.40: 5903 120.40 - 127.42: 5591 127.42 - 134.44: 316 Bond angle restraints: 20436 Sorted by residual: angle pdb=" CA PRO C 137 " pdb=" N PRO C 137 " pdb=" CD PRO C 137 " ideal model delta sigma weight residual 112.00 101.15 10.85 1.40e+00 5.10e-01 6.00e+01 angle pdb=" C3' U R 9 " pdb=" C2' U R 9 " pdb=" O2' U R 9 " ideal model delta sigma weight residual 110.70 99.86 10.84 1.50e+00 4.44e-01 5.23e+01 angle pdb=" N GLN A 281 " pdb=" CA GLN A 281 " pdb=" C GLN A 281 " ideal model delta sigma weight residual 113.50 104.99 8.51 1.23e+00 6.61e-01 4.79e+01 angle pdb=" N PRO A 625 " pdb=" CA PRO A 625 " pdb=" CB PRO A 625 " ideal model delta sigma weight residual 103.38 110.50 -7.12 1.05e+00 9.07e-01 4.59e+01 angle pdb=" N PRO A 340 " pdb=" CA PRO A 340 " pdb=" CB PRO A 340 " ideal model delta sigma weight residual 103.00 110.41 -7.41 1.10e+00 8.26e-01 4.54e+01 ... (remaining 20431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.96: 8479 34.96 - 69.92: 394 69.92 - 104.87: 16 104.87 - 139.83: 0 139.83 - 174.79: 2 Dihedral angle restraints: 8891 sinusoidal: 3891 harmonic: 5000 Sorted by residual: dihedral pdb=" CD ARG B 76 " pdb=" NE ARG B 76 " pdb=" CZ ARG B 76 " pdb=" NH1 ARG B 76 " ideal model delta sinusoidal sigma weight residual 0.00 -76.58 76.58 1 1.00e+01 1.00e-02 7.37e+01 dihedral pdb=" CD ARG A 227 " pdb=" NE ARG A 227 " pdb=" CZ ARG A 227 " pdb=" NH1 ARG A 227 " ideal model delta sinusoidal sigma weight residual 0.00 -63.97 63.97 1 1.00e+01 1.00e-02 5.39e+01 dihedral pdb=" CD ARG A 279 " pdb=" NE ARG A 279 " pdb=" CZ ARG A 279 " pdb=" NH1 ARG A 279 " ideal model delta sinusoidal sigma weight residual 0.00 -46.90 46.90 1 1.00e+01 1.00e-02 3.04e+01 ... (remaining 8888 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 2119 0.129 - 0.257: 77 0.257 - 0.386: 1 0.386 - 0.515: 22 0.515 - 0.643: 16 Chirality restraints: 2235 Sorted by residual: chirality pdb=" P DA T 8 " pdb=" OP1 DA T 8 " pdb=" OP2 DA T 8 " pdb=" O5' DA T 8 " both_signs ideal model delta sigma weight residual True 2.35 -2.99 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" P DT T 5 " pdb=" OP1 DT T 5 " pdb=" OP2 DT T 5 " pdb=" O5' DT T 5 " both_signs ideal model delta sigma weight residual True 2.35 2.97 -0.63 2.00e-01 2.50e+01 9.80e+00 chirality pdb=" P DC T 21 " pdb=" OP1 DC T 21 " pdb=" OP2 DC T 21 " pdb=" O5' DC T 21 " both_signs ideal model delta sigma weight residual True 2.35 -2.96 -0.62 2.00e-01 2.50e+01 9.51e+00 ... (remaining 2232 not shown) Planarity restraints: 2488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 76 " 1.060 9.50e-02 1.11e+02 4.75e-01 1.36e+02 pdb=" NE ARG B 76 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARG B 76 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG B 76 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG B 76 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 227 " -0.990 9.50e-02 1.11e+02 4.44e-01 1.19e+02 pdb=" NE ARG A 227 " 0.058 2.00e-02 2.50e+03 pdb=" CZ ARG A 227 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 227 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 227 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 279 " 0.791 9.50e-02 1.11e+02 3.54e-01 7.64e+01 pdb=" NE ARG A 279 " -0.048 2.00e-02 2.50e+03 pdb=" CZ ARG A 279 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 279 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 279 " 0.023 2.00e-02 2.50e+03 ... (remaining 2485 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 157 2.59 - 3.17: 12613 3.17 - 3.75: 22851 3.75 - 4.32: 30516 4.32 - 4.90: 49614 Nonbonded interactions: 115751 Sorted by model distance: nonbonded pdb=" O THR C 444 " pdb=" OG1 THR C 447 " model vdw 2.013 2.440 nonbonded pdb=" OH TYR C 193 " pdb=" O LEU C 322 " model vdw 2.041 2.440 nonbonded pdb=" OG1 THR A 885 " pdb=" O ASP A1186 " model vdw 2.053 2.440 nonbonded pdb=" OG SER B 87 " pdb=" OD1 ASP B 89 " model vdw 2.072 2.440 nonbonded pdb=" OG SER A 302 " pdb=" OH TYR A 363 " model vdw 2.091 2.440 ... (remaining 115746 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 'B' and (resid 66 through 146 or (resid 147 and (name N or name CA or nam \ e C or name O or name CB )) or resid 148 through 170 or (resid 171 through 176 a \ nd (name N or name CA or name C or name O or name CB )) or resid 177 through 222 \ or (resid 223 and (name N or name CA or name C or name O or name CB )) or resid \ 224 or (resid 225 and (name N or name CA or name C or name O or name CB )) or r \ esid 226 through 283 or (resid 284 and (name N or name CA or name C or name O or \ name CB )) or resid 285 through 355 or resid 368 through 485)) selection = (chain 'C' and (resid 66 or (resid 67 through 68 and (name N or name CA or name \ C or name O or name CB )) or resid 69 through 137 or (resid 138 and (name N or n \ ame CA or name C or name O or name CB )) or resid 139 through 160 or resid 170 t \ hrough 485)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.890 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: 7.490 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 44.680 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 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:13.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6425 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 : 0.006 0.118 14940 Z= 0.399 Angle : 1.046 11.759 20436 Z= 0.609 Chirality : 0.085 0.643 2235 Planarity : 0.019 0.475 2488 Dihedral : 17.668 174.789 5665 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.77 % Favored : 92.17 % Rotamer: Outliers : 2.33 % Allowed : 22.33 % Favored : 75.34 % 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: -0.71 (0.21), residues: 1712 helix: 1.23 (0.23), residues: 577 sheet: 0.23 (0.34), residues: 226 loop : -1.89 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A1099 HIS 0.023 0.001 HIS B 309 PHE 0.015 0.001 PHE A 139 TYR 0.036 0.002 TYR C 291 ARG 0.020 0.001 ARG C 325 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 213 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 544 MET cc_start: 0.7498 (tpt) cc_final: 0.7224 (tpp) REVERT: A 553 LYS cc_start: 0.8127 (tmmt) cc_final: 0.7531 (mppt) REVERT: C 325 ARG cc_start: 0.6931 (mtp-110) cc_final: 0.6337 (ptp-170) REVERT: C 349 TYR cc_start: 0.8233 (m-10) cc_final: 0.8012 (m-10) outliers start: 34 outliers final: 11 residues processed: 239 average time/residue: 1.0332 time to fit residues: 276.7917 Evaluate side-chains 184 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 173 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 1196 ASP Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain C residue 78 PHE Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 413 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 6.9990 chunk 131 optimal weight: 7.9990 chunk 73 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 88 optimal weight: 20.0000 chunk 70 optimal weight: 7.9990 chunk 136 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 82 optimal weight: 0.1980 chunk 101 optimal weight: 7.9990 chunk 158 optimal weight: 1.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 GLN A 398 GLN A 493 GLN A 971 HIS A1089 GLN A1098 ASN A1102 GLN A1214 GLN B 132 HIS B 158 GLN B 195 ASN B 258 HIS C 77 HIS C 84 GLN C 85 GLN C 292 ASN C 339 ASN C 355 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14940 Z= 0.281 Angle : 0.701 12.783 20436 Z= 0.356 Chirality : 0.046 0.327 2235 Planarity : 0.005 0.075 2488 Dihedral : 16.089 171.975 2396 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.18 % Favored : 91.76 % Rotamer: Outliers : 4.32 % Allowed : 21.16 % Favored : 74.52 % 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: -0.67 (0.21), residues: 1712 helix: 1.35 (0.22), residues: 586 sheet: 0.25 (0.34), residues: 237 loop : -2.00 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 918 HIS 0.012 0.001 HIS C 258 PHE 0.017 0.002 PHE B 266 TYR 0.017 0.002 TYR C 291 ARG 0.008 0.001 ARG C 154 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 201 time to evaluate : 1.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 553 LYS cc_start: 0.8273 (tmmt) cc_final: 0.8057 (mmmt) REVERT: A 580 LEU cc_start: 0.6813 (mp) cc_final: 0.6433 (tm) REVERT: A 612 LEU cc_start: 0.5829 (OUTLIER) cc_final: 0.5176 (tp) REVERT: A 793 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7464 (tm-30) REVERT: A 797 MET cc_start: 0.8013 (mtp) cc_final: 0.7783 (mtp) REVERT: A 968 GLN cc_start: 0.8468 (mt0) cc_final: 0.8188 (tm-30) REVERT: B 330 ASN cc_start: 0.7840 (OUTLIER) cc_final: 0.7383 (m-40) REVERT: C 92 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7405 (mm) REVERT: C 325 ARG cc_start: 0.6957 (mtp-110) cc_final: 0.6506 (ptm-80) outliers start: 63 outliers final: 23 residues processed: 239 average time/residue: 1.0148 time to fit residues: 273.4837 Evaluate side-chains 200 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 174 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 1196 ASP Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 452 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 131 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 158 optimal weight: 0.9980 chunk 171 optimal weight: 30.0000 chunk 140 optimal weight: 6.9990 chunk 156 optimal weight: 0.0970 chunk 53 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 overall best weight: 1.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 GLN ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6577 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14940 Z= 0.261 Angle : 0.688 13.784 20436 Z= 0.345 Chirality : 0.045 0.314 2235 Planarity : 0.005 0.065 2488 Dihedral : 15.952 177.888 2390 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.76 % Favored : 91.18 % Rotamer: Outliers : 5.14 % Allowed : 22.67 % Favored : 72.19 % 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: -0.77 (0.21), residues: 1712 helix: 1.26 (0.22), residues: 589 sheet: 0.16 (0.33), residues: 239 loop : -2.06 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 345 HIS 0.011 0.001 HIS A 298 PHE 0.016 0.001 PHE C 403 TYR 0.032 0.002 TYR C 291 ARG 0.009 0.000 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 183 time to evaluate : 1.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 557 GLU cc_start: 0.8499 (tp30) cc_final: 0.8223 (mm-30) REVERT: A 580 LEU cc_start: 0.6925 (mp) cc_final: 0.6568 (tm) REVERT: A 612 LEU cc_start: 0.5894 (OUTLIER) cc_final: 0.5369 (tp) REVERT: A 793 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7593 (tm-30) REVERT: A 797 MET cc_start: 0.8122 (mtp) cc_final: 0.7788 (mtp) REVERT: B 325 ARG cc_start: 0.6647 (mmt90) cc_final: 0.6265 (mmt90) REVERT: B 330 ASN cc_start: 0.7823 (OUTLIER) cc_final: 0.6941 (m-40) REVERT: B 405 GLU cc_start: 0.8131 (tt0) cc_final: 0.7849 (pt0) REVERT: C 92 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7398 (mm) REVERT: C 321 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8160 (pmtt) outliers start: 75 outliers final: 35 residues processed: 230 average time/residue: 0.9106 time to fit residues: 238.6257 Evaluate side-chains 205 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 166 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 932 HIS Chi-restraints excluded: chain A residue 1054 GLU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1196 ASP Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 321 LYS Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain C residue 452 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 9.9990 chunk 119 optimal weight: 0.5980 chunk 82 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 75 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 158 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 140 optimal weight: 0.9980 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 90 GLN ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 ASN ** A 906 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6532 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14940 Z= 0.181 Angle : 0.671 13.280 20436 Z= 0.329 Chirality : 0.044 0.313 2235 Planarity : 0.004 0.065 2488 Dihedral : 15.820 176.853 2390 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.64 % Favored : 91.30 % Rotamer: Outliers : 5.27 % Allowed : 22.88 % Favored : 71.85 % 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: -0.61 (0.21), residues: 1712 helix: 1.41 (0.22), residues: 582 sheet: 0.37 (0.34), residues: 240 loop : -1.99 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 345 HIS 0.009 0.001 HIS B 309 PHE 0.017 0.001 PHE C 403 TYR 0.021 0.001 TYR C 291 ARG 0.007 0.000 ARG C 325 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 181 time to evaluate : 1.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 472 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.6977 (mp10) REVERT: A 557 GLU cc_start: 0.8579 (tp30) cc_final: 0.8274 (mm-30) REVERT: A 580 LEU cc_start: 0.6826 (mp) cc_final: 0.6513 (tm) REVERT: A 793 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7317 (tm-30) REVERT: B 325 ARG cc_start: 0.6610 (mmt90) cc_final: 0.6258 (mmt90) REVERT: B 330 ASN cc_start: 0.7756 (OUTLIER) cc_final: 0.6867 (m-40) REVERT: B 405 GLU cc_start: 0.8069 (tt0) cc_final: 0.7861 (pt0) REVERT: C 92 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7390 (mm) REVERT: C 321 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8184 (pmtt) REVERT: C 325 ARG cc_start: 0.7006 (mtm110) cc_final: 0.6454 (mmm160) REVERT: C 349 TYR cc_start: 0.8233 (m-10) cc_final: 0.7971 (m-10) outliers start: 77 outliers final: 35 residues processed: 231 average time/residue: 0.9212 time to fit residues: 241.5430 Evaluate side-chains 213 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 174 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 740 ASN Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 1054 GLU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1196 ASP Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 321 LYS Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain C residue 452 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 143 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 85 optimal weight: 8.9990 chunk 150 optimal weight: 3.9990 chunk 42 optimal weight: 0.0980 chunk 56 optimal weight: 0.1980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 740 ASN ** A 906 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 14940 Z= 0.226 Angle : 0.669 11.517 20436 Z= 0.330 Chirality : 0.044 0.238 2235 Planarity : 0.004 0.065 2488 Dihedral : 15.773 177.054 2390 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.11 % Favored : 90.83 % Rotamer: Outliers : 4.79 % Allowed : 24.59 % Favored : 70.62 % 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: -0.67 (0.21), residues: 1712 helix: 1.37 (0.22), residues: 583 sheet: 0.35 (0.34), residues: 236 loop : -2.03 (0.20), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 918 HIS 0.009 0.001 HIS B 309 PHE 0.016 0.001 PHE C 403 TYR 0.023 0.002 TYR C 291 ARG 0.003 0.000 ARG C 325 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 175 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 472 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.6943 (mp10) REVERT: A 557 GLU cc_start: 0.8612 (tp30) cc_final: 0.8310 (mm-30) REVERT: A 580 LEU cc_start: 0.6893 (mp) cc_final: 0.6555 (tm) REVERT: A 793 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7850 (tm-30) REVERT: A 812 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7335 (ttp) REVERT: A 873 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7330 (pp20) REVERT: A 968 GLN cc_start: 0.8431 (tt0) cc_final: 0.8001 (tm-30) REVERT: A 1163 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.6438 (tpt) REVERT: B 325 ARG cc_start: 0.6660 (mmt90) cc_final: 0.6313 (mmt90) REVERT: B 330 ASN cc_start: 0.7803 (OUTLIER) cc_final: 0.6918 (m-40) REVERT: C 92 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7415 (mm) REVERT: C 155 GLU cc_start: 0.5739 (OUTLIER) cc_final: 0.5460 (mt-10) REVERT: C 349 TYR cc_start: 0.8312 (m-10) cc_final: 0.8033 (m-10) outliers start: 70 outliers final: 41 residues processed: 223 average time/residue: 0.9378 time to fit residues: 238.9029 Evaluate side-chains 215 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 167 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1196 ASP Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 459 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 chunk 168 optimal weight: 8.9990 chunk 139 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 162 optimal weight: 3.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 HIS A 277 HIS A 540 GLN ** A 906 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 14940 Z= 0.431 Angle : 0.790 11.895 20436 Z= 0.397 Chirality : 0.048 0.219 2235 Planarity : 0.005 0.064 2488 Dihedral : 15.934 178.375 2390 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.92 % Favored : 89.02 % Rotamer: Outliers : 6.03 % Allowed : 24.04 % Favored : 69.93 % 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: -1.22 (0.20), residues: 1712 helix: 0.78 (0.21), residues: 585 sheet: -0.14 (0.33), residues: 230 loop : -2.19 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 607 HIS 0.009 0.001 HIS B 309 PHE 0.025 0.002 PHE B 266 TYR 0.048 0.003 TYR C 291 ARG 0.010 0.001 ARG C 325 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 172 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLU cc_start: 0.6287 (OUTLIER) cc_final: 0.5864 (tp30) REVERT: A 284 ILE cc_start: 0.8247 (pp) cc_final: 0.8000 (pt) REVERT: A 557 GLU cc_start: 0.8637 (tp30) cc_final: 0.8359 (mm-30) REVERT: A 580 LEU cc_start: 0.7220 (OUTLIER) cc_final: 0.6774 (tm) REVERT: A 793 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7575 (tm-30) REVERT: B 325 ARG cc_start: 0.6760 (mmt90) cc_final: 0.6420 (mmt90) REVERT: B 330 ASN cc_start: 0.8034 (OUTLIER) cc_final: 0.7081 (m-40) REVERT: C 92 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7594 (mm) REVERT: C 155 GLU cc_start: 0.5926 (OUTLIER) cc_final: 0.5577 (mt-10) REVERT: C 321 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8193 (pmtt) outliers start: 88 outliers final: 40 residues processed: 236 average time/residue: 0.9369 time to fit residues: 250.9928 Evaluate side-chains 208 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 162 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 1054 GLU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1196 ASP Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 321 LYS Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 460 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 141 optimal weight: 20.0000 chunk 94 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 103 optimal weight: 0.0970 chunk 66 optimal weight: 0.0040 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 879 GLN A 894 GLN ** A 906 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6584 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14940 Z= 0.195 Angle : 0.713 12.391 20436 Z= 0.351 Chirality : 0.045 0.234 2235 Planarity : 0.004 0.064 2488 Dihedral : 15.756 178.509 2390 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.94 % Favored : 91.00 % Rotamer: Outliers : 4.18 % Allowed : 25.96 % Favored : 69.86 % 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: -0.86 (0.21), residues: 1712 helix: 1.15 (0.22), residues: 582 sheet: 0.16 (0.33), residues: 239 loop : -2.07 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 347 HIS 0.009 0.001 HIS B 309 PHE 0.015 0.001 PHE C 403 TYR 0.024 0.001 TYR C 291 ARG 0.009 0.000 ARG C 325 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 172 time to evaluate : 1.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 ILE cc_start: 0.8128 (pp) cc_final: 0.7878 (pt) REVERT: A 472 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.6991 (mp10) REVERT: A 873 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7354 (pp20) REVERT: B 219 PHE cc_start: 0.7976 (OUTLIER) cc_final: 0.7018 (p90) REVERT: B 325 ARG cc_start: 0.6689 (mmt90) cc_final: 0.6455 (mmt90) REVERT: B 330 ASN cc_start: 0.7932 (OUTLIER) cc_final: 0.6984 (m-40) REVERT: C 92 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7525 (mm) REVERT: C 325 ARG cc_start: 0.7223 (mtm110) cc_final: 0.6503 (mmm160) REVERT: C 349 TYR cc_start: 0.8254 (m-10) cc_final: 0.7959 (m-10) outliers start: 61 outliers final: 34 residues processed: 212 average time/residue: 0.9099 time to fit residues: 219.9479 Evaluate side-chains 207 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 168 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 1054 GLU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1196 ASP Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 460 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 0.0030 chunk 50 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 chunk 114 optimal weight: 0.0270 chunk 82 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 chunk 152 optimal weight: 9.9990 chunk 160 optimal weight: 0.3980 chunk 146 optimal weight: 6.9990 overall best weight: 1.0050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 906 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6582 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14940 Z= 0.201 Angle : 0.698 12.226 20436 Z= 0.342 Chirality : 0.044 0.209 2235 Planarity : 0.004 0.064 2488 Dihedral : 15.693 177.909 2389 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.35 % Favored : 90.60 % Rotamer: Outliers : 3.90 % Allowed : 26.85 % Favored : 69.25 % 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: -0.79 (0.21), residues: 1712 helix: 1.22 (0.22), residues: 589 sheet: 0.27 (0.33), residues: 237 loop : -2.09 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP A 347 HIS 0.009 0.001 HIS B 309 PHE 0.015 0.001 PHE C 403 TYR 0.026 0.002 TYR B 193 ARG 0.006 0.000 ARG C 325 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 178 time to evaluate : 1.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLU cc_start: 0.6256 (OUTLIER) cc_final: 0.5826 (tp30) REVERT: A 284 ILE cc_start: 0.8149 (pp) cc_final: 0.7927 (pt) REVERT: A 472 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.6942 (mp10) REVERT: A 580 LEU cc_start: 0.6933 (OUTLIER) cc_final: 0.6595 (tm) REVERT: A 793 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7518 (tm-30) REVERT: A 873 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7341 (pp20) REVERT: A 891 VAL cc_start: 0.8400 (m) cc_final: 0.8158 (m) REVERT: A 968 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.7968 (tm-30) REVERT: B 219 PHE cc_start: 0.7925 (OUTLIER) cc_final: 0.6998 (p90) REVERT: B 325 ARG cc_start: 0.6708 (mmt90) cc_final: 0.6460 (mmt90) REVERT: B 330 ASN cc_start: 0.7872 (OUTLIER) cc_final: 0.6989 (m-40) REVERT: C 92 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7495 (mm) REVERT: C 325 ARG cc_start: 0.7254 (mtm110) cc_final: 0.6523 (mmm160) REVERT: C 349 TYR cc_start: 0.8280 (m-10) cc_final: 0.7973 (m-10) outliers start: 57 outliers final: 36 residues processed: 219 average time/residue: 0.9667 time to fit residues: 242.4860 Evaluate side-chains 208 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 164 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 968 GLN Chi-restraints excluded: chain A residue 1054 GLU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1196 ASP Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 460 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 0.0470 chunk 160 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 141 optimal weight: 30.0000 chunk 147 optimal weight: 7.9990 chunk 155 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 165 optimal weight: 5.9990 overall best weight: 1.3482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 906 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6591 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14940 Z= 0.220 Angle : 0.705 11.938 20436 Z= 0.345 Chirality : 0.044 0.209 2235 Planarity : 0.004 0.064 2488 Dihedral : 15.683 177.905 2389 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.29 % Favored : 90.65 % Rotamer: Outliers : 3.63 % Allowed : 27.26 % Favored : 69.11 % 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: -0.84 (0.21), residues: 1712 helix: 1.22 (0.22), residues: 589 sheet: 0.18 (0.34), residues: 237 loop : -2.13 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP A 347 HIS 0.010 0.001 HIS B 309 PHE 0.020 0.001 PHE B 145 TYR 0.027 0.002 TYR B 193 ARG 0.006 0.000 ARG C 325 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 171 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 472 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.6970 (mp10) REVERT: A 553 LYS cc_start: 0.8023 (tmtt) cc_final: 0.7797 (tmmt) REVERT: A 580 LEU cc_start: 0.6888 (OUTLIER) cc_final: 0.6530 (tm) REVERT: A 793 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7379 (tm-30) REVERT: A 873 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7353 (pp20) REVERT: A 968 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.7986 (tm-30) REVERT: B 219 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.6991 (p90) REVERT: B 325 ARG cc_start: 0.6700 (mmt90) cc_final: 0.6467 (mmt90) REVERT: B 330 ASN cc_start: 0.7887 (OUTLIER) cc_final: 0.7011 (m-40) REVERT: C 92 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7511 (mm) REVERT: C 325 ARG cc_start: 0.7254 (mtm110) cc_final: 0.6522 (mmm160) REVERT: C 349 TYR cc_start: 0.8306 (m-10) cc_final: 0.8002 (m-10) outliers start: 53 outliers final: 35 residues processed: 212 average time/residue: 0.9386 time to fit residues: 226.7785 Evaluate side-chains 210 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 168 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 968 GLN Chi-restraints excluded: chain A residue 1054 GLU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1196 ASP Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 460 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 0.0470 chunk 78 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 173 optimal weight: 10.0000 chunk 159 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 106 optimal weight: 6.9990 chunk 84 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 chunk 147 optimal weight: 7.9990 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN A 613 HIS ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 906 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6564 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14940 Z= 0.197 Angle : 0.718 12.783 20436 Z= 0.347 Chirality : 0.044 0.209 2235 Planarity : 0.004 0.063 2488 Dihedral : 15.655 177.766 2389 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.23 % Favored : 90.71 % Rotamer: Outliers : 3.42 % Allowed : 27.60 % Favored : 68.97 % 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: -0.82 (0.21), residues: 1712 helix: 1.26 (0.23), residues: 587 sheet: 0.25 (0.34), residues: 237 loop : -2.15 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP A1099 HIS 0.009 0.001 HIS B 309 PHE 0.016 0.001 PHE C 403 TYR 0.027 0.002 TYR B 193 ARG 0.006 0.000 ARG C 325 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 171 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 472 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.6973 (mp10) REVERT: A 553 LYS cc_start: 0.8020 (tmtt) cc_final: 0.7796 (tmmt) REVERT: A 580 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.6533 (tm) REVERT: A 793 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7357 (tm-30) REVERT: A 873 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7232 (pp20) REVERT: A 968 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.7984 (tm-30) REVERT: B 219 PHE cc_start: 0.7906 (OUTLIER) cc_final: 0.6964 (p90) REVERT: B 325 ARG cc_start: 0.6718 (mmt90) cc_final: 0.6421 (mmt90) REVERT: B 330 ASN cc_start: 0.7866 (OUTLIER) cc_final: 0.6971 (m-40) REVERT: C 92 LEU cc_start: 0.7796 (mm) cc_final: 0.7540 (mm) REVERT: C 325 ARG cc_start: 0.7243 (mtm110) cc_final: 0.6522 (mmm160) REVERT: C 349 TYR cc_start: 0.8264 (m-10) cc_final: 0.7969 (m-10) outliers start: 50 outliers final: 34 residues processed: 207 average time/residue: 0.9226 time to fit residues: 217.4282 Evaluate side-chains 208 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 168 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 968 GLN Chi-restraints excluded: chain A residue 1054 GLU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1099 TRP Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1196 ASP Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 460 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 42 optimal weight: 0.4980 chunk 127 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 141 optimal weight: 40.0000 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 121 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 906 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 HIS C 272 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.161333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.115674 restraints weight = 27730.678| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 4.05 r_work: 0.3557 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3567 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3567 r_free = 0.3567 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3567 r_free = 0.3567 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3567 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14940 Z= 0.200 Angle : 0.711 13.544 20436 Z= 0.345 Chirality : 0.044 0.236 2235 Planarity : 0.004 0.064 2488 Dihedral : 15.622 177.545 2389 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.00 % Favored : 90.95 % Rotamer: Outliers : 3.08 % Allowed : 27.95 % Favored : 68.97 % 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: -0.80 (0.21), residues: 1712 helix: 1.28 (0.23), residues: 587 sheet: 0.27 (0.34), residues: 237 loop : -2.15 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP A 347 HIS 0.010 0.001 HIS B 309 PHE 0.033 0.001 PHE B 145 TYR 0.025 0.001 TYR B 193 ARG 0.006 0.000 ARG C 325 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5387.29 seconds wall clock time: 96 minutes 31.66 seconds (5791.66 seconds total)