Starting phenix.real_space_refine on Fri Feb 16 02:23:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5i_29745/02_2024/8g5i_29745.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5i_29745/02_2024/8g5i_29745.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5i_29745/02_2024/8g5i_29745.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5i_29745/02_2024/8g5i_29745.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5i_29745/02_2024/8g5i_29745.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5i_29745/02_2024/8g5i_29745.pdb" } resolution = 2.75 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 80 5.16 5 C 8859 2.51 5 N 2480 2.21 5 O 2627 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 181": "OE1" <-> "OE2" Residue "A GLU 200": "OE1" <-> "OE2" Residue "A GLU 416": "OE1" <-> "OE2" Residue "A GLU 447": "OE1" <-> "OE2" Residue "A GLU 453": "OE1" <-> "OE2" Residue "A GLU 489": "OE1" <-> "OE2" Residue "A GLU 536": "OE1" <-> "OE2" Residue "A GLU 537": "OE1" <-> "OE2" Residue "A GLU 557": "OE1" <-> "OE2" Residue "A GLU 793": "OE1" <-> "OE2" Residue "A GLU 1136": "OE1" <-> "OE2" Residue "B GLU 405": "OE1" <-> "OE2" Residue "B GLU 445": "OE1" <-> "OE2" Residue "B GLU 464": "OE1" <-> "OE2" Residue "C GLU 123": "OE1" <-> "OE2" Residue "C GLU 310": "OE1" <-> "OE2" Residue "C GLU 394": "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: 14084 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 941, 7430 Classifications: {'peptide': 941} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 63, 'TRANS': 877} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "B" Number of atoms: 2986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2986 Classifications: {'peptide': 372} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 16, 'TRANS': 355} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 2890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2890 Classifications: {'peptide': 358} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 340} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "P" Number of atoms: 392 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 18, 372 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 18, 372 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 395 Chain: "T" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 386 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" P A DA P 27 " occ=0.50 ... (38 atoms not shown) pdb=" C4 B DA P 27 " occ=0.50 Time building chain proxies: 8.39, per 1000 atoms: 0.60 Number of scatterers: 14084 At special positions: 0 Unit cell: (94.164, 106.554, 141.246, 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 80 16.00 P 38 15.00 O 2627 8.00 N 2480 7.00 C 8859 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: 6.24 Conformation dependent library (CDL) restraints added in 3.4 seconds 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3104 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 9 sheets defined 41.6% alpha, 11.3% beta 17 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 5.35 Creating SS restraints... Processing helix chain 'A' and resid 99 through 109 removed outlier: 4.277A pdb=" N SER A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 159 Proline residue: A 149 - end of helix removed outlier: 3.503A pdb=" N GLN A 159 " --> pdb=" O ASN A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 277 through 283 removed outlier: 6.875A pdb=" N GLU A 280 " --> pdb=" O HIS A 277 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR A 282 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 283 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 306 through 315 Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 375 through 380 Processing helix chain 'A' and resid 381 through 388 removed outlier: 3.501A pdb=" N ILE A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 418 Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 420 through 431 removed outlier: 4.000A pdb=" N LEU A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY A 431 " --> pdb=" O MET A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 471 removed outlier: 3.599A pdb=" N ARG A 443 " --> pdb=" O GLN A 439 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 488 removed outlier: 4.414A pdb=" N ASP A 487 " --> pdb=" O TRP A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 538 removed outlier: 3.767A pdb=" N GLU A 538 " --> pdb=" O GLU A 535 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 535 through 538' Processing helix chain 'A' and resid 539 through 556 removed outlier: 3.676A pdb=" N LEU A 549 " --> pdb=" O ALA A 545 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 577 removed outlier: 3.623A pdb=" N LEU A 576 " --> pdb=" O TRP A 572 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N CYS A 577 " --> pdb=" O TYR A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 603 removed outlier: 3.656A pdb=" N MET A 603 " --> pdb=" O THR A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 655 Processing helix chain 'A' and resid 754 through 758 removed outlier: 3.875A pdb=" N ASN A 758 " --> pdb=" O LYS A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 810 removed outlier: 4.715A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LYS A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ARG A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 828 removed outlier: 3.548A pdb=" N ILE A 826 " --> pdb=" O PRO A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 878 removed outlier: 3.527A pdb=" N LEU A 874 " --> pdb=" O GLY A 871 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS A 875 " --> pdb=" O SER A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 908 Processing helix chain 'A' and resid 914 through 921 Processing helix chain 'A' and resid 944 through 954 Processing helix chain 'A' and resid 958 through 969 removed outlier: 3.896A pdb=" N LEU A 965 " --> pdb=" O PHE A 961 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU A 966 " --> pdb=" O ALA A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 984 Processing helix chain 'A' and resid 1057 through 1066 removed outlier: 4.133A pdb=" N LEU A1061 " --> pdb=" O MET A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1123 removed outlier: 3.667A pdb=" N VAL A1100 " --> pdb=" O ARG A1096 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL A1101 " --> pdb=" O VAL A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1167 removed outlier: 3.729A pdb=" N ARG A1161 " --> pdb=" O ASN A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1221 removed outlier: 4.113A pdb=" N ILE A1220 " --> pdb=" O ALA A1217 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 77 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 200 removed outlier: 3.552A pdb=" N ALA B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N VAL B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ASN B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP B 198 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU B 199 " --> pdb=" O ASN B 195 " (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: 3.547A pdb=" N LEU B 312 " --> pdb=" O ASP B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 323 removed outlier: 3.637A pdb=" N HIS B 323 " --> pdb=" O SER B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 354 Processing helix chain 'B' and resid 395 through 410 Processing helix chain 'B' and resid 421 through 425 removed outlier: 4.570A pdb=" N SER B 424 " --> pdb=" O MET B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 435 Processing helix chain 'B' and resid 445 through 450 removed outlier: 4.147A pdb=" N GLU B 449 " --> pdb=" O GLU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 484 removed outlier: 4.184A pdb=" N LYS B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASN B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 76 Processing helix chain 'C' and resid 82 through 87 removed outlier: 4.364A pdb=" N SER C 87 " --> pdb=" O LYS C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 93 Processing helix chain 'C' and resid 100 through 119 Processing helix chain 'C' and resid 184 through 191 removed outlier: 4.213A pdb=" N GLY C 188 " --> pdb=" O ASN C 184 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU C 191 " --> pdb=" O HIS C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 200 removed outlier: 3.717A pdb=" N ASP C 198 " --> pdb=" O VAL C 194 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU C 199 " --> pdb=" O ASN C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 266 removed outlier: 4.233A pdb=" N PHE C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 271 No H-bonds generated for 'chain 'C' and resid 269 through 271' Processing helix chain 'C' and resid 342 through 354 Processing helix chain 'C' and resid 393 through 409 removed outlier: 3.643A pdb=" N ASN C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 435 Processing helix chain 'C' and resid 444 through 449 Processing helix chain 'C' and resid 470 through 485 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 187 removed outlier: 3.868A pdb=" N TRP A 175 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU A 195 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN A 264 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N LEU A 292 " --> pdb=" O GLN A 264 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL A 266 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 436 through 438 removed outlier: 4.785A pdb=" N TYR A 837 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A 814 " --> pdb=" O ALA A 839 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 605 through 606 Processing sheet with id=AA4, first strand: chain 'A' and resid 1130 through 1133 removed outlier: 3.641A pdb=" N ARG A1138 " --> pdb=" O ILE A1131 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A1133 " --> pdb=" O GLU A1136 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU A1136 " --> pdb=" O ILE A1133 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A1137 " --> pdb=" O ALA A 889 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.127A pdb=" N PHE B 126 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ILE B 211 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE B 300 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LEU B 299 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N TYR B 291 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N LYS B 285 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 324 through 325 Processing sheet with id=AA7, first strand: chain 'B' and resid 413 through 414 removed outlier: 7.068A pdb=" N TRP B 414 " --> pdb=" O ILE B 381 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL B 383 " --> pdb=" O TRP B 414 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LYS B 382 " --> pdb=" O ILE B 437 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 126 through 127 removed outlier: 6.269A pdb=" N PHE C 126 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N ILE C 211 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE C 300 " --> pdb=" O ASP C 341 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N LEU C 299 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N TYR C 291 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 413 through 415 removed outlier: 7.111A pdb=" N VAL C 383 " --> pdb=" O TRP C 414 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ALA C 384 " --> pdb=" O VAL C 441 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N VAL C 443 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASP C 386 " --> pdb=" O VAL C 443 " (cutoff:3.500A) 536 hydrogen bonds defined for protein. 1524 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 5.17 Time building geometry restraints manager: 6.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4439 1.34 - 1.46: 2856 1.46 - 1.58: 7023 1.58 - 1.70: 73 1.70 - 1.82: 125 Bond restraints: 14516 Sorted by residual: bond pdb=" O3' DG P 26 " pdb=" P A DA P 27 " ideal model delta sigma weight residual 1.607 1.524 0.083 1.50e-02 4.44e+03 3.07e+01 bond pdb=" N ARG A 852 " pdb=" CA ARG A 852 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.15e-02 7.56e+03 7.68e+00 bond pdb=" N LEU A 605 " pdb=" CA LEU A 605 " ideal model delta sigma weight residual 1.455 1.488 -0.032 1.21e-02 6.83e+03 7.20e+00 bond pdb=" N ARG A 853 " pdb=" CA ARG A 853 " ideal model delta sigma weight residual 1.456 1.488 -0.033 1.22e-02 6.72e+03 7.14e+00 bond pdb=" N VAL A1101 " pdb=" CA VAL A1101 " ideal model delta sigma weight residual 1.459 1.494 -0.034 1.30e-02 5.92e+03 6.94e+00 ... (remaining 14511 not shown) Histogram of bond angle deviations from ideal: 100.06 - 106.89: 753 106.89 - 113.72: 7760 113.72 - 120.56: 6070 120.56 - 127.39: 4946 127.39 - 134.22: 303 Bond angle restraints: 19832 Sorted by residual: angle pdb=" N PRO A 560 " pdb=" CA PRO A 560 " pdb=" CB PRO A 560 " ideal model delta sigma weight residual 103.25 111.48 -8.23 1.05e+00 9.07e-01 6.15e+01 angle pdb=" N PRO A 625 " pdb=" CA PRO A 625 " pdb=" CB PRO A 625 " ideal model delta sigma weight residual 103.33 110.42 -7.09 9.30e-01 1.16e+00 5.81e+01 angle pdb=" N PRO A 250 " pdb=" CA PRO A 250 " pdb=" CB PRO A 250 " ideal model delta sigma weight residual 103.25 111.10 -7.85 1.05e+00 9.07e-01 5.59e+01 angle pdb=" C3' DG P 26 " pdb=" O3' DG P 26 " pdb=" P B DA P 27 " ideal model delta sigma weight residual 120.20 111.04 9.16 1.50e+00 4.44e-01 3.73e+01 angle pdb=" N ILE A 954 " pdb=" CA ILE A 954 " pdb=" C ILE A 954 " ideal model delta sigma weight residual 110.21 104.84 5.37 1.13e+00 7.83e-01 2.26e+01 ... (remaining 19827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.68: 8015 30.68 - 61.36: 487 61.36 - 92.04: 27 92.04 - 122.72: 0 122.72 - 153.41: 2 Dihedral angle restraints: 8531 sinusoidal: 3718 harmonic: 4813 Sorted by residual: dihedral pdb=" CA PRO A1070 " pdb=" C PRO A1070 " pdb=" N ARG A1071 " pdb=" CA ARG A1071 " ideal model delta harmonic sigma weight residual -180.00 -154.51 -25.49 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CD ARG B 75 " pdb=" NE ARG B 75 " pdb=" CZ ARG B 75 " pdb=" NH1 ARG B 75 " ideal model delta sinusoidal sigma weight residual 0.00 -37.38 37.38 1 1.00e+01 1.00e-02 1.97e+01 dihedral pdb=" CA LEU B 393 " pdb=" C LEU B 393 " pdb=" N GLU B 394 " pdb=" CA GLU B 394 " ideal model delta harmonic sigma weight residual -180.00 -160.68 -19.32 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 8528 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 2088 0.111 - 0.222: 49 0.222 - 0.333: 0 0.333 - 0.444: 0 0.444 - 0.555: 1 Chirality restraints: 2138 Sorted by residual: chirality pdb=" P DG P 26 " pdb=" OP1 DG P 26 " pdb=" OP2 DG P 26 " pdb=" O5' DG P 26 " both_signs ideal model delta sigma weight residual True 2.35 -2.90 -0.56 2.00e-01 2.50e+01 7.71e+00 chirality pdb=" CA PRO A 625 " pdb=" N PRO A 625 " pdb=" C PRO A 625 " pdb=" CB PRO A 625 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.75e-01 chirality pdb=" CA LEU A 605 " pdb=" N LEU A 605 " pdb=" C LEU A 605 " pdb=" CB LEU A 605 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.13e-01 ... (remaining 2135 not shown) Planarity restraints: 2416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 75 " 0.665 9.50e-02 1.11e+02 2.98e-01 5.43e+01 pdb=" NE ARG B 75 " -0.038 2.00e-02 2.50e+03 pdb=" CZ ARG B 75 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 75 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 75 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 363 " 0.546 9.50e-02 1.11e+02 2.45e-01 3.66e+01 pdb=" NE ARG B 363 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ARG B 363 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG B 363 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 363 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 852 " -0.406 9.50e-02 1.11e+02 1.82e-01 2.03e+01 pdb=" NE ARG A 852 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG A 852 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 852 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 852 " -0.013 2.00e-02 2.50e+03 ... (remaining 2413 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 261 2.65 - 3.21: 13315 3.21 - 3.77: 22571 3.77 - 4.34: 30448 4.34 - 4.90: 49068 Nonbonded interactions: 115663 Sorted by model distance: nonbonded pdb=" OG SER C 90 " pdb=" O CYS C 95 " model vdw 2.085 2.440 nonbonded pdb=" O PRO A 857 " pdb=" OG1 THR A 861 " model vdw 2.107 2.440 nonbonded pdb=" OG1 THR A 885 " pdb=" O ASP A1186 " model vdw 2.121 2.440 nonbonded pdb=" O LYS A 553 " pdb=" NZ LYS A 553 " model vdw 2.122 2.520 nonbonded pdb=" N GLU A 280 " pdb=" OE1 GLU A 280 " model vdw 2.153 2.520 ... (remaining 115658 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 68 through 104 or (resid 105 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD )) or resid 106 through 136 or re \ sid 180 through 219 or resid 227 through 355 or resid 368 through 420 or (resid \ 421 and (name N or name CA or name C or name O or name CB )) or resid 422 throug \ h 485)) selection = (chain 'C' and (resid 68 through 136 or resid 180 through 227 or (resid 228 and \ (name N or name CA or name C or name O or name CB )) or resid 229 through 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: 1.600 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: 7.820 Check model and map are aligned: 0.230 Set scattering table: 0.120 Process input model: 46.760 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.070 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:11.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 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 : 0.004 0.083 14516 Z= 0.256 Angle : 0.800 13.928 19832 Z= 0.433 Chirality : 0.044 0.555 2138 Planarity : 0.010 0.298 2416 Dihedral : 17.633 153.406 5427 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.76 % Favored : 93.12 % Rotamer: Outliers : 1.33 % Allowed : 26.97 % Favored : 71.70 % 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: -0.24 (0.21), residues: 1643 helix: 1.15 (0.22), residues: 595 sheet: 0.04 (0.37), residues: 194 loop : -1.18 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1118 HIS 0.010 0.001 HIS C 313 PHE 0.037 0.001 PHE A 539 TYR 0.014 0.001 TYR A1108 ARG 0.013 0.001 ARG B 325 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 217 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 539 PHE cc_start: 0.6585 (p90) cc_final: 0.5406 (p90) REVERT: A 579 ARG cc_start: 0.8022 (mmm160) cc_final: 0.7730 (mmm160) REVERT: A 1195 MET cc_start: 0.7873 (ttm) cc_final: 0.7600 (ptp) REVERT: C 422 GLN cc_start: 0.5878 (tp-100) cc_final: 0.5364 (tp40) outliers start: 19 outliers final: 9 residues processed: 234 average time/residue: 1.2239 time to fit residues: 315.7113 Evaluate side-chains 201 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 192 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 459 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 3.9990 chunk 127 optimal weight: 0.3980 chunk 70 optimal weight: 0.0050 chunk 43 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 131 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 80 optimal weight: 0.0980 chunk 98 optimal weight: 2.9990 chunk 152 optimal weight: 8.9990 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN A 134 ASN A 138 HIS A 144 GLN A 159 GLN A 226 GLN A 439 GLN A 472 GLN A 493 GLN ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 618 HIS A 843 GLN ** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 GLN ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1102 GLN A1110 HIS A1134 HIS A1157 ASN ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN B 355 GLN ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14516 Z= 0.204 Angle : 0.661 12.355 19832 Z= 0.328 Chirality : 0.043 0.171 2138 Planarity : 0.005 0.051 2416 Dihedral : 14.901 150.117 2221 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.00 % Favored : 92.94 % Rotamer: Outliers : 4.56 % Allowed : 23.38 % Favored : 72.05 % 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: -0.02 (0.21), residues: 1643 helix: 1.34 (0.22), residues: 611 sheet: 0.01 (0.35), residues: 206 loop : -1.07 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 607 HIS 0.010 0.001 HIS A1134 PHE 0.010 0.001 PHE A 539 TYR 0.014 0.001 TYR B 429 ARG 0.005 0.000 ARG B 325 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 213 time to evaluate : 1.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1195 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.7489 (ptp) REVERT: B 191 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7481 (mt-10) REVERT: B 201 ASN cc_start: 0.8169 (p0) cc_final: 0.7553 (t0) REVERT: C 396 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7712 (mpp-170) outliers start: 65 outliers final: 25 residues processed: 252 average time/residue: 1.1043 time to fit residues: 308.2239 Evaluate side-chains 210 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 183 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 450 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 126 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 152 optimal weight: 0.8980 chunk 165 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 52 optimal weight: 0.4980 chunk 122 optimal weight: 7.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 GLN ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1134 HIS ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 HIS B 258 HIS ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 ASN ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 GLN ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14516 Z= 0.313 Angle : 0.700 11.294 19832 Z= 0.349 Chirality : 0.044 0.161 2138 Planarity : 0.005 0.051 2416 Dihedral : 15.032 150.456 2211 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.36 % Favored : 92.57 % Rotamer: Outliers : 5.41 % Allowed : 23.88 % Favored : 70.72 % 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: -0.26 (0.21), residues: 1643 helix: 1.06 (0.21), residues: 625 sheet: 0.08 (0.36), residues: 194 loop : -1.23 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 607 HIS 0.008 0.001 HIS A1134 PHE 0.016 0.002 PHE A 610 TYR 0.012 0.001 TYR A1108 ARG 0.008 0.001 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 196 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 GLN cc_start: 0.7695 (tm-30) cc_final: 0.7477 (tm-30) REVERT: A 536 GLU cc_start: 0.6950 (tp30) cc_final: 0.6735 (tp30) REVERT: A 1112 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7599 (mtt) REVERT: C 396 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7766 (mpp80) outliers start: 77 outliers final: 35 residues processed: 241 average time/residue: 1.1286 time to fit residues: 301.5205 Evaluate side-chains 212 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 175 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1112 MET Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1202 ASN Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 459 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 7.9990 chunk 114 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 102 optimal weight: 0.6980 chunk 153 optimal weight: 3.9990 chunk 162 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 43 optimal weight: 0.4980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 ASN A1134 HIS ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14516 Z= 0.261 Angle : 0.681 13.963 19832 Z= 0.337 Chirality : 0.044 0.173 2138 Planarity : 0.004 0.052 2416 Dihedral : 15.075 150.755 2211 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.30 % Favored : 92.64 % Rotamer: Outliers : 6.25 % Allowed : 23.81 % Favored : 69.94 % 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: -0.27 (0.21), residues: 1643 helix: 1.09 (0.21), residues: 620 sheet: 0.09 (0.36), residues: 194 loop : -1.26 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 607 HIS 0.005 0.001 HIS B 77 PHE 0.010 0.001 PHE B 266 TYR 0.013 0.001 TYR A1108 ARG 0.008 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 192 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 GLN cc_start: 0.7789 (tm-30) cc_final: 0.7496 (tm-30) REVERT: A 550 GLN cc_start: 0.7191 (OUTLIER) cc_final: 0.6926 (mp10) REVERT: A 774 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7668 (ptm) REVERT: A 1112 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7538 (mtt) REVERT: A 1143 GLU cc_start: 0.7433 (pm20) cc_final: 0.7224 (pt0) REVERT: C 396 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7766 (mpp80) outliers start: 89 outliers final: 45 residues processed: 245 average time/residue: 1.1365 time to fit residues: 309.3643 Evaluate side-chains 229 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 180 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1112 MET Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 459 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 2.9990 chunk 92 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 120 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 138 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 298 HIS ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1134 HIS ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14516 Z= 0.257 Angle : 0.686 11.323 19832 Z= 0.340 Chirality : 0.043 0.163 2138 Planarity : 0.004 0.051 2416 Dihedral : 15.097 150.807 2211 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.36 % Favored : 92.57 % Rotamer: Outliers : 6.11 % Allowed : 24.72 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.21), residues: 1643 helix: 1.02 (0.21), residues: 625 sheet: 0.02 (0.36), residues: 192 loop : -1.28 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 607 HIS 0.008 0.001 HIS C 258 PHE 0.010 0.001 PHE B 266 TYR 0.017 0.001 TYR B 432 ARG 0.006 0.000 ARG B 325 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 190 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 GLN cc_start: 0.7872 (tm-30) cc_final: 0.7551 (tm-30) REVERT: A 594 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7324 (mm) REVERT: A 774 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7703 (ptm) REVERT: A 1112 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7562 (mtt) REVERT: A 1143 GLU cc_start: 0.7215 (pm20) cc_final: 0.6756 (pm20) REVERT: C 396 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7844 (ttp-110) outliers start: 87 outliers final: 43 residues processed: 242 average time/residue: 1.1711 time to fit residues: 312.8141 Evaluate side-chains 223 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 176 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1112 MET Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 459 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 162 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 264 GLN ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 ASN ** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1222 GLN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN B 318 ASN ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14516 Z= 0.258 Angle : 0.692 14.422 19832 Z= 0.342 Chirality : 0.043 0.163 2138 Planarity : 0.005 0.065 2416 Dihedral : 15.130 150.988 2211 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.97 % Favored : 91.97 % Rotamer: Outliers : 5.69 % Allowed : 25.77 % Favored : 68.54 % 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: -0.31 (0.21), residues: 1643 helix: 1.02 (0.21), residues: 620 sheet: 0.07 (0.36), residues: 194 loop : -1.25 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 607 HIS 0.004 0.001 HIS B 77 PHE 0.013 0.001 PHE A 610 TYR 0.016 0.001 TYR B 193 ARG 0.012 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 181 time to evaluate : 1.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 GLN cc_start: 0.7914 (tm-30) cc_final: 0.7604 (tm-30) REVERT: A 550 GLN cc_start: 0.7284 (OUTLIER) cc_final: 0.7003 (mp10) REVERT: A 594 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7121 (mm) REVERT: A 774 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7710 (ptm) REVERT: A 1112 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7573 (mtt) REVERT: A 1143 GLU cc_start: 0.7195 (pm20) cc_final: 0.6583 (pt0) REVERT: A 1208 ARG cc_start: 0.5136 (OUTLIER) cc_final: 0.4891 (ptt180) REVERT: C 396 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7845 (ttp-110) outliers start: 81 outliers final: 49 residues processed: 230 average time/residue: 1.1051 time to fit residues: 281.7935 Evaluate side-chains 226 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 171 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1112 MET Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain A residue 1208 ARG Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 459 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 92 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 136 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 chunk 161 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14516 Z= 0.216 Angle : 0.680 14.351 19832 Z= 0.336 Chirality : 0.042 0.164 2138 Planarity : 0.004 0.053 2416 Dihedral : 15.111 150.795 2211 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.79 % Favored : 92.15 % Rotamer: Outliers : 4.85 % Allowed : 26.19 % Favored : 68.96 % 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: -0.28 (0.21), residues: 1643 helix: 1.03 (0.21), residues: 624 sheet: 0.05 (0.36), residues: 192 loop : -1.22 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 607 HIS 0.011 0.001 HIS C 258 PHE 0.009 0.001 PHE C 403 TYR 0.017 0.001 TYR B 193 ARG 0.014 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 180 time to evaluate : 1.728 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 GLN cc_start: 0.7942 (tm-30) cc_final: 0.7622 (tm-30) REVERT: A 550 GLN cc_start: 0.7318 (OUTLIER) cc_final: 0.6497 (mp10) REVERT: A 594 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7288 (mm) REVERT: A 774 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7651 (ptm) REVERT: A 1112 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7543 (mtt) REVERT: A 1143 GLU cc_start: 0.7239 (pm20) cc_final: 0.6510 (pt0) REVERT: A 1208 ARG cc_start: 0.4968 (OUTLIER) cc_final: 0.4682 (ptt180) REVERT: C 396 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7792 (ttp-110) outliers start: 69 outliers final: 45 residues processed: 221 average time/residue: 1.1609 time to fit residues: 284.8103 Evaluate side-chains 217 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 166 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1079 ILE Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1112 MET Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain A residue 1208 ARG Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 468 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.9990 chunk 64 optimal weight: 0.0070 chunk 96 optimal weight: 3.9990 chunk 48 optimal weight: 0.2980 chunk 31 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 127 optimal weight: 6.9990 chunk 147 optimal weight: 0.3980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 ASN ** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14516 Z= 0.186 Angle : 0.679 13.790 19832 Z= 0.334 Chirality : 0.042 0.159 2138 Planarity : 0.004 0.051 2416 Dihedral : 15.071 150.047 2211 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.24 % Favored : 92.70 % Rotamer: Outliers : 4.28 % Allowed : 26.90 % Favored : 68.82 % 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: -0.15 (0.21), residues: 1643 helix: 1.15 (0.21), residues: 620 sheet: 0.19 (0.36), residues: 197 loop : -1.17 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP A 607 HIS 0.005 0.001 HIS B 77 PHE 0.009 0.001 PHE C 403 TYR 0.015 0.001 TYR B 193 ARG 0.013 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 189 time to evaluate : 1.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 GLN cc_start: 0.7946 (tm-30) cc_final: 0.7621 (tm-30) REVERT: A 228 LEU cc_start: 0.5208 (OUTLIER) cc_final: 0.4796 (tp) REVERT: A 550 GLN cc_start: 0.7273 (OUTLIER) cc_final: 0.6127 (mp10) REVERT: A 594 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7100 (mm) REVERT: B 75 ARG cc_start: 0.6924 (tpp-160) cc_final: 0.6619 (mmm-85) REVERT: C 191 GLU cc_start: 0.7994 (mp0) cc_final: 0.7780 (mp0) outliers start: 61 outliers final: 37 residues processed: 226 average time/residue: 1.1274 time to fit residues: 282.5414 Evaluate side-chains 215 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 175 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 468 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 118 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 136 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 ASN ** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14516 Z= 0.239 Angle : 0.711 13.311 19832 Z= 0.349 Chirality : 0.043 0.170 2138 Planarity : 0.004 0.050 2416 Dihedral : 15.098 150.961 2211 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.97 % Favored : 91.97 % Rotamer: Outliers : 4.92 % Allowed : 26.83 % Favored : 68.26 % 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: -0.24 (0.21), residues: 1643 helix: 1.09 (0.21), residues: 624 sheet: 0.12 (0.36), residues: 192 loop : -1.22 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.001 TRP A 607 HIS 0.005 0.001 HIS B 77 PHE 0.011 0.001 PHE A 610 TYR 0.017 0.001 TYR B 193 ARG 0.012 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 175 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 GLN cc_start: 0.8004 (tm-30) cc_final: 0.7682 (tm-30) REVERT: A 465 ASP cc_start: 0.7884 (t70) cc_final: 0.7661 (t70) REVERT: A 550 GLN cc_start: 0.7033 (OUTLIER) cc_final: 0.6044 (mp10) REVERT: A 594 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7324 (mm) REVERT: A 1208 ARG cc_start: 0.4951 (OUTLIER) cc_final: 0.4480 (ptt180) REVERT: B 75 ARG cc_start: 0.7002 (tpp-160) cc_final: 0.6665 (mmm-85) REVERT: C 396 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7780 (ttp-110) outliers start: 70 outliers final: 43 residues processed: 220 average time/residue: 1.2045 time to fit residues: 292.2644 Evaluate side-chains 218 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 171 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1079 ILE Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain A residue 1208 ARG Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 459 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 4.9990 chunk 75 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 chunk 167 optimal weight: 10.0000 chunk 154 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 105 optimal weight: 0.0370 chunk 141 optimal weight: 5.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 780 GLN ** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 14516 Z= 0.355 Angle : 0.779 14.242 19832 Z= 0.387 Chirality : 0.046 0.176 2138 Planarity : 0.005 0.054 2416 Dihedral : 15.246 151.948 2211 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.58 % Favored : 91.36 % Rotamer: Outliers : 3.79 % Allowed : 27.88 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.21), residues: 1643 helix: 0.80 (0.21), residues: 629 sheet: -0.01 (0.35), residues: 200 loop : -1.33 (0.23), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP A 607 HIS 0.005 0.001 HIS B 133 PHE 0.028 0.002 PHE A 539 TYR 0.020 0.002 TYR A 573 ARG 0.011 0.001 ARG B 75 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 179 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 GLN cc_start: 0.8052 (tm-30) cc_final: 0.7803 (tm-30) REVERT: A 550 GLN cc_start: 0.7054 (OUTLIER) cc_final: 0.6061 (mp10) REVERT: A 1208 ARG cc_start: 0.5146 (OUTLIER) cc_final: 0.4702 (ptt180) REVERT: B 75 ARG cc_start: 0.7078 (tpp-160) cc_final: 0.6534 (mmm160) REVERT: C 396 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7817 (ttp-110) outliers start: 54 outliers final: 40 residues processed: 216 average time/residue: 1.1387 time to fit residues: 272.3984 Evaluate side-chains 216 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 173 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain A residue 1208 ARG Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 459 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 19 optimal weight: 0.0770 chunk 37 optimal weight: 0.9990 chunk 133 optimal weight: 0.6980 chunk 55 optimal weight: 7.9990 chunk 137 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.154040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.123628 restraints weight = 27420.303| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 3.37 r_work: 0.3624 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3613 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3613 r_free = 0.3613 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3613 r_free = 0.3613 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3613 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14516 Z= 0.202 Angle : 0.717 13.610 19832 Z= 0.352 Chirality : 0.043 0.171 2138 Planarity : 0.004 0.047 2416 Dihedral : 15.126 151.137 2209 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.55 % Favored : 92.39 % Rotamer: Outliers : 3.23 % Allowed : 28.51 % Favored : 68.26 % 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: -0.36 (0.21), residues: 1643 helix: 0.92 (0.21), residues: 624 sheet: 0.09 (0.35), residues: 206 loop : -1.26 (0.23), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP A 607 HIS 0.006 0.001 HIS B 77 PHE 0.028 0.001 PHE A 539 TYR 0.012 0.001 TYR A 573 ARG 0.010 0.000 ARG B 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5544.71 seconds wall clock time: 98 minutes 56.82 seconds (5936.82 seconds total)