Starting phenix.real_space_refine on Sat Sep 12 13:50:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ne3_9356/09_2026/6ne3_9356.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ne3_9356/09_2026/6ne3_9356.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6ne3_9356/09_2026/6ne3_9356.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ne3_9356/09_2026/6ne3_9356.cif" model { file = "/net/cci-nas-00/data/ceres_data/6ne3_9356/09_2026/6ne3_9356.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ne3_9356/09_2026/6ne3_9356.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ne3_9356/09_2026/6ne3_9356.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ne3_9356/09_2026/6ne3_9356.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.072 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 313 5.49 5 S 36 5.16 5 C 9321 2.51 5 N 3024 2.21 5 O 3642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16336 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 806 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 704 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 867 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 108} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 780 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 96} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 813 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 652 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 81} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 831 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "J" Number of atoms: 3178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3178 Classifications: {'DNA': 156} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 155} Chain: "I" Number of atoms: 3215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3215 Classifications: {'DNA': 156} Link IDs: {'rna3p': 155} Chain: "W" Number of atoms: 3737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3737 Classifications: {'peptide': 461} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 441} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 3, 'GLU:plan': 2, 'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "W" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 10 residue: pdb=" N ALA B 15 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA B 15 " occ=0.00 residue: pdb=" N LEU B 22 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU B 22 " occ=0.00 residue: pdb=" N ARG B 23 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG B 23 " occ=0.00 residue: pdb=" N GLY C 8 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY C 8 " occ=0.00 residue: pdb=" N LYS C 9 " occ=0.00 ... (3 atoms not shown) pdb=" CB LYS C 9 " occ=0.00 residue: pdb=" N LYS C 13 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS C 13 " occ=0.00 residue: pdb=" N ALA C 14 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA C 14 " occ=0.00 residue: pdb=" N GLU C 121 " occ=0.00 ... (7 atoms not shown) pdb=" OE2 GLU C 121 " occ=0.00 residue: pdb=" N ARG G 11 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG G 11 " occ=0.00 residue: pdb=" N ALA G 12 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA G 12 " occ=0.00 Time building chain proxies: 3.68, per 1000 atoms: 0.23 Number of scatterers: 16336 At special positions: 0 Unit cell: (96.0324, 145.872, 154.381, 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 36 16.00 P 313 15.00 O 3642 8.00 N 3024 7.00 C 9321 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM16331 O3A ADP W 801 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 463.6 milliseconds 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2348 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 8 sheets defined 62.2% alpha, 4.0% beta 154 base pairs and 271 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.815A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.577A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.010A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.902A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 72 removed outlier: 3.680A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.754A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.559A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.759A pdb=" N GLY F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 76 removed outlier: 3.898A pdb=" N TYR F 72 " --> pdb=" O ASP F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.735A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.879A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.529A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.785A pdb=" N VAL H 38 " --> pdb=" O TYR H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 81 Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.682A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 121 Processing helix chain 'W' and resid 181 through 198 Processing helix chain 'W' and resid 210 through 226 removed outlier: 3.624A pdb=" N HIS W 224 " --> pdb=" O GLY W 220 " (cutoff:3.500A) Processing helix chain 'W' and resid 237 through 239 No H-bonds generated for 'chain 'W' and resid 237 through 239' Processing helix chain 'W' and resid 240 through 251 Processing helix chain 'W' and resid 263 through 275 Processing helix chain 'W' and resid 287 through 293 Processing helix chain 'W' and resid 293 through 298 Processing helix chain 'W' and resid 318 through 326 Processing helix chain 'W' and resid 344 through 355 Processing helix chain 'W' and resid 356 through 359 Processing helix chain 'W' and resid 361 through 369 removed outlier: 3.610A pdb=" N PHE W 365 " --> pdb=" O SER W 361 " (cutoff:3.500A) Processing helix chain 'W' and resid 379 through 392 Proline residue: W 390 - end of helix Processing helix chain 'W' and resid 396 through 401 removed outlier: 3.706A pdb=" N VAL W 400 " --> pdb=" O ILE W 396 " (cutoff:3.500A) Processing helix chain 'W' and resid 417 through 429 Processing helix chain 'W' and resid 448 through 459 Processing helix chain 'W' and resid 460 through 463 Processing helix chain 'W' and resid 482 through 499 Proline residue: W 493 - end of helix Processing helix chain 'W' and resid 508 through 522 Processing helix chain 'W' and resid 534 through 537 Processing helix chain 'W' and resid 538 through 546 Processing helix chain 'W' and resid 559 through 564 Processing helix chain 'W' and resid 582 through 592 removed outlier: 3.641A pdb=" N ASP W 586 " --> pdb=" O ASN W 582 " (cutoff:3.500A) Processing helix chain 'W' and resid 613 through 633 removed outlier: 4.223A pdb=" N VAL W 631 " --> pdb=" O LEU W 627 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.914A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.453A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.124A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.416A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.476A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'W' and resid 201 through 203 removed outlier: 3.581A pdb=" N LEU W 334 " --> pdb=" O GLY W 201 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N LEU W 305 " --> pdb=" O LEU W 333 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU W 335 " --> pdb=" O LEU W 305 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ILE W 307 " --> pdb=" O LEU W 335 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N MET W 233 " --> pdb=" O VAL W 306 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ASP W 308 " --> pdb=" O MET W 233 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N LEU W 235 " --> pdb=" O ASP W 308 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N HIS W 232 " --> pdb=" O CYS W 283 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N THR W 285 " --> pdb=" O HIS W 232 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N VAL W 234 " --> pdb=" O THR W 285 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL W 258 " --> pdb=" O VAL W 284 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N SER W 286 " --> pdb=" O VAL W 258 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N LEU W 260 " --> pdb=" O SER W 286 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'W' and resid 408 through 413 removed outlier: 3.887A pdb=" N ARG W 606 " --> pdb=" O VAL W 410 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL W 574 " --> pdb=" O PHE W 605 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N PHE W 607 " --> pdb=" O VAL W 574 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LEU W 576 " --> pdb=" O PHE W 607 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU W 503 " --> pdb=" O ILE W 575 " (cutoff:3.500A) 535 hydrogen bonds defined for protein. 1590 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 393 hydrogen bonds 782 hydrogen bond angles 0 basepair planarities 154 basepair parallelities 271 stacking parallelities Total time for adding SS restraints: 4.11 Time building geometry restraints manager: 1.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3095 1.33 - 1.45: 5471 1.45 - 1.57: 8024 1.57 - 1.69: 624 1.69 - 1.81: 64 Bond restraints: 17278 Sorted by residual: bond pdb=" C3' DG J 2 " pdb=" O3' DG J 2 " ideal model delta sigma weight residual 1.435 1.495 -0.060 1.30e-02 5.92e+03 2.15e+01 bond pdb=" C3' DA J 102 " pdb=" O3' DA J 102 " ideal model delta sigma weight residual 1.435 1.378 0.057 1.30e-02 5.92e+03 1.91e+01 bond pdb=" N7 DA I 160 " pdb=" C5 DA I 160 " ideal model delta sigma weight residual 1.388 1.364 0.024 6.00e-03 2.78e+04 1.65e+01 bond pdb=" N1 DC J 55 " pdb=" C6 DC J 55 " ideal model delta sigma weight residual 1.367 1.343 0.024 6.00e-03 2.78e+04 1.54e+01 bond pdb=" N7 DA I 181 " pdb=" C5 DA I 181 " ideal model delta sigma weight residual 1.388 1.365 0.023 6.00e-03 2.78e+04 1.52e+01 ... (remaining 17273 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 23960 2.64 - 5.28: 676 5.28 - 7.92: 44 7.92 - 10.56: 8 10.56 - 13.20: 4 Bond angle restraints: 24692 Sorted by residual: angle pdb=" O4' DG I 185 " pdb=" C4' DG I 185 " pdb=" C3' DG I 185 " ideal model delta sigma weight residual 106.00 101.43 4.57 6.00e-01 2.78e+00 5.79e+01 angle pdb=" O4' DG J 49 " pdb=" C4' DG J 49 " pdb=" C3' DG J 49 " ideal model delta sigma weight residual 106.00 101.99 4.01 6.00e-01 2.78e+00 4.47e+01 angle pdb=" N VAL W 602 " pdb=" CA VAL W 602 " pdb=" C VAL W 602 " ideal model delta sigma weight residual 106.21 112.15 -5.94 1.07e+00 8.73e-01 3.09e+01 angle pdb=" O4' DG J 39 " pdb=" C4' DG J 39 " pdb=" C3' DG J 39 " ideal model delta sigma weight residual 106.00 102.67 3.33 6.00e-01 2.78e+00 3.07e+01 angle pdb=" O4' DG I 101 " pdb=" C4' DG I 101 " pdb=" C3' DG I 101 " ideal model delta sigma weight residual 106.00 102.77 3.23 6.00e-01 2.78e+00 2.90e+01 ... (remaining 24687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.08: 7814 35.08 - 70.17: 1733 70.17 - 105.25: 58 105.25 - 140.34: 5 140.34 - 175.42: 2 Dihedral angle restraints: 9612 sinusoidal: 5983 harmonic: 3629 Sorted by residual: dihedral pdb=" CA PRO W 470 " pdb=" C PRO W 470 " pdb=" N PRO W 471 " pdb=" CA PRO W 471 " ideal model delta harmonic sigma weight residual 180.00 142.62 37.38 0 5.00e+00 4.00e-02 5.59e+01 dihedral pdb=" CA GLY W 469 " pdb=" C GLY W 469 " pdb=" N PRO W 470 " pdb=" CA PRO W 470 " ideal model delta harmonic sigma weight residual 180.00 -144.13 -35.87 0 5.00e+00 4.00e-02 5.15e+01 dihedral pdb=" C5' ADP W 801 " pdb=" O5' ADP W 801 " pdb=" PA ADP W 801 " pdb=" O2A ADP W 801 " ideal model delta sinusoidal sigma weight residual -60.00 69.52 -129.52 1 2.00e+01 2.50e-03 3.93e+01 ... (remaining 9609 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 2390 0.080 - 0.159: 385 0.159 - 0.239: 20 0.239 - 0.319: 1 0.319 - 0.399: 1 Chirality restraints: 2797 Sorted by residual: chirality pdb=" CB ILE W 202 " pdb=" CA ILE W 202 " pdb=" CG1 ILE W 202 " pdb=" CG2 ILE W 202 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.97e+00 chirality pdb=" C3' DC I 186 " pdb=" C4' DC I 186 " pdb=" O3' DC I 186 " pdb=" C2' DC I 186 " both_signs ideal model delta sigma weight residual False -2.73 -2.49 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CB ILE W 608 " pdb=" CA ILE W 608 " pdb=" CG1 ILE W 608 " pdb=" CG2 ILE W 608 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 2794 not shown) Planarity restraints: 2042 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG J 20 " 0.052 2.00e-02 2.50e+03 2.09e-02 1.31e+01 pdb=" N9 DG J 20 " -0.043 2.00e-02 2.50e+03 pdb=" C8 DG J 20 " -0.009 2.00e-02 2.50e+03 pdb=" N7 DG J 20 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DG J 20 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DG J 20 " 0.008 2.00e-02 2.50e+03 pdb=" O6 DG J 20 " 0.016 2.00e-02 2.50e+03 pdb=" N1 DG J 20 " 0.006 2.00e-02 2.50e+03 pdb=" C2 DG J 20 " -0.002 2.00e-02 2.50e+03 pdb=" N2 DG J 20 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DG J 20 " -0.011 2.00e-02 2.50e+03 pdb=" C4 DG J 20 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J 21 " 0.046 2.00e-02 2.50e+03 1.92e-02 1.11e+01 pdb=" N9 DG J 21 " -0.041 2.00e-02 2.50e+03 pdb=" C8 DG J 21 " -0.011 2.00e-02 2.50e+03 pdb=" N7 DG J 21 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DG J 21 " 0.011 2.00e-02 2.50e+03 pdb=" C6 DG J 21 " 0.006 2.00e-02 2.50e+03 pdb=" O6 DG J 21 " 0.014 2.00e-02 2.50e+03 pdb=" N1 DG J 21 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG J 21 " -0.006 2.00e-02 2.50e+03 pdb=" N2 DG J 21 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DG J 21 " -0.007 2.00e-02 2.50e+03 pdb=" C4 DG J 21 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA J 102 " 0.042 2.00e-02 2.50e+03 1.84e-02 9.33e+00 pdb=" N9 DA J 102 " -0.033 2.00e-02 2.50e+03 pdb=" C8 DA J 102 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DA J 102 " -0.016 2.00e-02 2.50e+03 pdb=" C5 DA J 102 " 0.006 2.00e-02 2.50e+03 pdb=" C6 DA J 102 " 0.008 2.00e-02 2.50e+03 pdb=" N6 DA J 102 " 0.015 2.00e-02 2.50e+03 pdb=" N1 DA J 102 " 0.006 2.00e-02 2.50e+03 pdb=" C2 DA J 102 " -0.010 2.00e-02 2.50e+03 pdb=" N3 DA J 102 " -0.011 2.00e-02 2.50e+03 pdb=" C4 DA J 102 " -0.005 2.00e-02 2.50e+03 ... (remaining 2039 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4255 2.81 - 3.33: 14870 3.33 - 3.85: 33394 3.85 - 4.38: 36586 4.38 - 4.90: 53158 Nonbonded interactions: 142263 Sorted by model distance: nonbonded pdb=" O ARG W 538 " pdb=" OG SER W 541 " model vdw 2.287 3.040 nonbonded pdb=" O THR G 16 " pdb=" OG SER G 19 " model vdw 2.296 3.040 nonbonded pdb=" O2 DC J 94 " pdb=" N2 DG I 113 " model vdw 2.302 2.496 nonbonded pdb=" OG SER W 500 " pdb=" OD1 ASP W 572 " model vdw 2.307 3.040 nonbonded pdb=" OG SER C 18 " pdb=" O PHE C 25 " model vdw 2.310 3.040 ... (remaining 142258 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 37 through 134) selection = (chain 'E' and (resid 37 through 133 or (resid 134 and (name N or name CA or nam \ e C or name O or name CB )))) } ncs_group { reference = (chain 'B' and (resid 20 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 102)) selection = chain 'F' } ncs_group { reference = (chain 'C' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 117 or (resid 118 through 119 and (name N or n \ ame CA or name C or name O or name CB )))) selection = (chain 'G' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 119)) } ncs_group { reference = (chain 'D' and resid 29 through 121) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 17.880 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 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 : 0.009 0.076 17280 Z= 0.708 Angle : 1.059 13.198 24692 Z= 0.818 Chirality : 0.057 0.399 2797 Planarity : 0.007 0.070 2042 Dihedral : 28.201 175.419 7264 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.48 % Allowed : 10.51 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 4.65 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.61 (0.19), residues: 1225 helix: -1.82 (0.15), residues: 726 sheet: -3.25 (0.57), residues: 71 loop : -3.04 (0.26), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG W 592 TYR 0.015 0.002 TYR B 72 PHE 0.034 0.003 PHE W 391 TRP 0.011 0.002 TRP W 348 HIS 0.011 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00876 / 0.71 (17278) covalent geometry : angle 1.05861 / 0.82 (24692) hydrogen bonds : bond 0.11160 / 7.58 ( 928) hydrogen bonds : angle 5.15667 / 3.74 ( 2372) Misc. bond : bond 0.00110 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 238 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: B 27 GLN cc_start: 0.8082 (tp-100) cc_final: 0.7480 (tp40) REVERT: B 84 MET cc_start: 0.7237 (mmm) cc_final: 0.6957 (mmm) REVERT: C 36 LYS cc_start: 0.7818 (mtpp) cc_final: 0.7348 (mmtt) REVERT: C 56 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7336 (tm-30) REVERT: C 92 GLU cc_start: 0.7172 (mp0) cc_final: 0.6787 (mp0) REVERT: C 99 ARG cc_start: 0.8023 (mmt180) cc_final: 0.7797 (mmm160) REVERT: C 104 GLN cc_start: 0.7812 (mm110) cc_final: 0.6941 (tt0) REVERT: D 31 LYS cc_start: 0.8163 (tptm) cc_final: 0.7858 (tppt) REVERT: D 48 ASP cc_start: 0.8699 (t70) cc_final: 0.8179 (p0) REVERT: D 65 ASP cc_start: 0.7498 (OUTLIER) cc_final: 0.7086 (t0) REVERT: D 68 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7464 (tm-30) REVERT: D 90 GLU cc_start: 0.7220 (mp0) cc_final: 0.6186 (mp0) REVERT: D 110 GLU cc_start: 0.7006 (tp30) cc_final: 0.6802 (tp30) REVERT: E 61 LEU cc_start: 0.7567 (mt) cc_final: 0.7267 (mt) REVERT: E 76 GLN cc_start: 0.7679 (tp40) cc_final: 0.7344 (mm-40) REVERT: E 107 THR cc_start: 0.7707 (m) cc_final: 0.7416 (t) REVERT: E 110 CYS cc_start: 0.8543 (t) cc_final: 0.7630 (t) REVERT: E 123 ASP cc_start: 0.7592 (m-30) cc_final: 0.7201 (m-30) REVERT: F 59 LYS cc_start: 0.7452 (ttpt) cc_final: 0.7111 (ttpp) REVERT: F 77 LYS cc_start: 0.8305 (mttt) cc_final: 0.8076 (mmtp) REVERT: G 36 LYS cc_start: 0.8178 (mmtp) cc_final: 0.7670 (mmmm) REVERT: G 64 GLU cc_start: 0.7540 (tt0) cc_final: 0.7201 (pt0) REVERT: G 90 ASP cc_start: 0.6967 (t70) cc_final: 0.6211 (t70) REVERT: G 95 LYS cc_start: 0.8488 (tttp) cc_final: 0.7825 (tptp) REVERT: G 104 GLN cc_start: 0.8217 (tp40) cc_final: 0.7972 (tp40) REVERT: G 110 ASN cc_start: 0.8306 (t0) cc_final: 0.7912 (p0) REVERT: H 33 SER cc_start: 0.7967 (t) cc_final: 0.7430 (p) REVERT: H 73 GLU cc_start: 0.7605 (tp30) cc_final: 0.7116 (tp30) REVERT: H 117 LYS cc_start: 0.7048 (tptm) cc_final: 0.6795 (tptt) REVERT: W 174 TYR cc_start: 0.5134 (p90) cc_final: 0.4638 (p90) REVERT: W 233 MET cc_start: 0.7294 (ptp) cc_final: 0.6931 (ptp) REVERT: W 289 MET cc_start: 0.8810 (mmt) cc_final: 0.8603 (mmm) REVERT: W 309 GLU cc_start: 0.7672 (tp30) cc_final: 0.7244 (tp30) REVERT: W 322 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7995 (mm-30) REVERT: W 389 ARG cc_start: 0.7604 (ttm-80) cc_final: 0.7179 (mmm-85) REVERT: W 419 MET cc_start: 0.8346 (ttm) cc_final: 0.8056 (ttm) REVERT: W 590 MET cc_start: 0.8209 (tpp) cc_final: 0.7843 (tpp) REVERT: W 616 ARG cc_start: 0.8709 (mmp-170) cc_final: 0.8326 (ttp80) REVERT: W 623 MET cc_start: 0.5508 (mtm) cc_final: 0.5256 (mtp) REVERT: W 626 ARG cc_start: 0.8031 (tpt170) cc_final: 0.7616 (ttp-110) outliers start: 5 outliers final: 1 residues processed: 242 average time/residue: 0.1751 time to fit residues: 58.5807 Evaluate side-chains 177 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 175 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain W residue 574 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 0.6980 overall best weight: 4.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS A 68 GLN A 85 GLN C 68 ASN C 104 GLN D 46 HIS ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN F 25 ASN H 79 HIS W 189 ASN W 242 HIS W 243 ASN W 266 GLN W 331 ASN W 584 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.106251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.081222 restraints weight = 40525.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.079671 restraints weight = 38618.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.079832 restraints weight = 39265.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.080176 restraints weight = 35336.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.080132 restraints weight = 32076.918| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 17280 Z= 0.291 Angle : 0.861 12.324 24692 Z= 0.470 Chirality : 0.057 0.273 2797 Planarity : 0.006 0.066 2042 Dihedral : 31.910 173.627 4810 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.15 % Allowed : 15.85 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.23), residues: 1225 helix: -0.28 (0.18), residues: 735 sheet: -3.16 (0.58), residues: 73 loop : -2.79 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG W 256 TYR 0.014 0.002 TYR E 54 PHE 0.017 0.002 PHE W 605 TRP 0.018 0.002 TRP W 280 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00614 / 0.29 (17278) covalent geometry : angle 0.86078 / 0.47 (24692) hydrogen bonds : bond 0.06441 / 4.33 ( 928) hydrogen bonds : angle 4.28872 / 3.11 ( 2372) Misc. bond : bond 0.00137 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 179 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 GLN cc_start: 0.8198 (tp-100) cc_final: 0.7081 (tm-30) REVERT: D 33 SER cc_start: 0.9174 (p) cc_final: 0.8853 (p) REVERT: D 73 GLU cc_start: 0.8166 (tp30) cc_final: 0.7883 (tp30) REVERT: E 73 GLU cc_start: 0.8041 (tt0) cc_final: 0.7729 (tt0) REVERT: E 123 ASP cc_start: 0.8471 (m-30) cc_final: 0.7834 (m-30) REVERT: F 85 ASP cc_start: 0.7984 (m-30) cc_final: 0.7740 (m-30) REVERT: G 36 LYS cc_start: 0.8442 (mmtp) cc_final: 0.8184 (mmmm) REVERT: H 33 SER cc_start: 0.8999 (t) cc_final: 0.8623 (p) REVERT: W 174 TYR cc_start: 0.5570 (p90) cc_final: 0.5024 (p90) outliers start: 33 outliers final: 22 residues processed: 198 average time/residue: 0.1491 time to fit residues: 42.9790 Evaluate side-chains 171 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain W residue 334 LEU Chi-restraints excluded: chain W residue 345 HIS Chi-restraints excluded: chain W residue 391 PHE Chi-restraints excluded: chain W residue 478 LEU Chi-restraints excluded: chain W residue 488 LEU Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 564 LEU Chi-restraints excluded: chain W residue 574 VAL Chi-restraints excluded: chain W residue 613 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 50 optimal weight: 0.9980 chunk 116 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 128 optimal weight: 20.0000 chunk 94 optimal weight: 20.0000 chunk 146 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 71 optimal weight: 8.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN E 76 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.108318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.081781 restraints weight = 40405.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.081183 restraints weight = 38511.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.081399 restraints weight = 38922.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.081660 restraints weight = 35623.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.081631 restraints weight = 33188.813| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17280 Z= 0.175 Angle : 0.749 14.841 24692 Z= 0.418 Chirality : 0.050 0.314 2797 Planarity : 0.005 0.043 2042 Dihedral : 31.699 173.317 4808 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.67 % Allowed : 19.96 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.24), residues: 1225 helix: 0.43 (0.19), residues: 738 sheet: -3.05 (0.54), residues: 78 loop : -2.50 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 45 TYR 0.014 0.001 TYR W 413 PHE 0.015 0.001 PHE W 605 TRP 0.031 0.002 TRP W 190 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.17 (17278) covalent geometry : angle 0.74942 / 0.42 (24692) hydrogen bonds : bond 0.05255 / 3.54 ( 928) hydrogen bonds : angle 3.91958 / 2.85 ( 2372) Misc. bond : bond 0.00037 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 181 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASP cc_start: 0.7410 (t0) cc_final: 0.7138 (t0) REVERT: B 27 GLN cc_start: 0.8324 (tp-100) cc_final: 0.8059 (tp40) REVERT: D 33 SER cc_start: 0.9272 (p) cc_final: 0.8957 (p) REVERT: D 73 GLU cc_start: 0.8057 (tp30) cc_final: 0.7726 (tp30) REVERT: E 73 GLU cc_start: 0.8069 (tt0) cc_final: 0.7697 (tt0) REVERT: E 123 ASP cc_start: 0.8440 (m-30) cc_final: 0.8030 (m-30) REVERT: G 36 LYS cc_start: 0.8476 (mmtp) cc_final: 0.8214 (mmmm) REVERT: H 33 SER cc_start: 0.8978 (t) cc_final: 0.8602 (p) REVERT: W 174 TYR cc_start: 0.5458 (p90) cc_final: 0.5007 (p90) REVERT: W 222 MET cc_start: 0.7966 (mmp) cc_final: 0.7703 (mmm) outliers start: 28 outliers final: 18 residues processed: 193 average time/residue: 0.1440 time to fit residues: 40.9590 Evaluate side-chains 175 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain W residue 305 LEU Chi-restraints excluded: chain W residue 334 LEU Chi-restraints excluded: chain W residue 345 HIS Chi-restraints excluded: chain W residue 478 LEU Chi-restraints excluded: chain W residue 488 LEU Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 504 ILE Chi-restraints excluded: chain W residue 574 VAL Chi-restraints excluded: chain W residue 613 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 66 optimal weight: 3.9990 chunk 64 optimal weight: 0.3980 chunk 98 optimal weight: 20.0000 chunk 143 optimal weight: 9.9990 chunk 78 optimal weight: 20.0000 chunk 6 optimal weight: 0.9990 chunk 137 optimal weight: 8.9990 chunk 113 optimal weight: 5.9990 chunk 73 optimal weight: 40.0000 chunk 59 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 594 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.109261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.083085 restraints weight = 39963.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.082329 restraints weight = 37834.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.082444 restraints weight = 38096.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.082549 restraints weight = 32430.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.082722 restraints weight = 30649.598| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17280 Z= 0.153 Angle : 0.710 12.211 24692 Z= 0.396 Chirality : 0.048 0.317 2797 Planarity : 0.004 0.041 2042 Dihedral : 31.436 175.103 4808 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.63 % Allowed : 20.25 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.24), residues: 1225 helix: 0.83 (0.19), residues: 738 sheet: -2.85 (0.55), residues: 78 loop : -2.27 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 29 TYR 0.020 0.001 TYR W 518 PHE 0.012 0.001 PHE W 605 TRP 0.012 0.002 TRP W 302 HIS 0.007 0.001 HIS W 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.15 (17278) covalent geometry : angle 0.70974 / 0.40 (24692) hydrogen bonds : bond 0.04834 / 3.27 ( 928) hydrogen bonds : angle 3.73060 / 2.74 ( 2372) Misc. bond : bond 0.00062 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 177 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 33 SER cc_start: 0.9211 (p) cc_final: 0.8655 (m) REVERT: D 68 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7446 (tm-30) REVERT: E 73 GLU cc_start: 0.7913 (tt0) cc_final: 0.7636 (tt0) REVERT: E 123 ASP cc_start: 0.8461 (m-30) cc_final: 0.8054 (m-30) REVERT: E 133 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7451 (mt-10) REVERT: G 36 LYS cc_start: 0.8451 (mmtp) cc_final: 0.8169 (mmmm) REVERT: H 33 SER cc_start: 0.8975 (t) cc_final: 0.8610 (p) REVERT: H 73 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7116 (tp30) REVERT: W 174 TYR cc_start: 0.5391 (p90) cc_final: 0.4974 (p90) REVERT: W 334 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7478 (mp) outliers start: 38 outliers final: 19 residues processed: 198 average time/residue: 0.1471 time to fit residues: 42.7368 Evaluate side-chains 176 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain W residue 199 ILE Chi-restraints excluded: chain W residue 305 LEU Chi-restraints excluded: chain W residue 334 LEU Chi-restraints excluded: chain W residue 345 HIS Chi-restraints excluded: chain W residue 391 PHE Chi-restraints excluded: chain W residue 488 LEU Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 574 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 80 optimal weight: 20.0000 chunk 72 optimal weight: 4.9990 chunk 146 optimal weight: 9.9990 chunk 116 optimal weight: 9.9990 chunk 17 optimal weight: 0.0060 chunk 122 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 112 optimal weight: 7.9990 chunk 133 optimal weight: 20.0000 overall best weight: 5.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 31 HIS ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN G 24 GLN W 452 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.106758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.079778 restraints weight = 39903.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.078700 restraints weight = 42304.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.079234 restraints weight = 39936.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.079318 restraints weight = 34881.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.079291 restraints weight = 34651.031| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 17280 Z= 0.300 Angle : 0.828 14.456 24692 Z= 0.447 Chirality : 0.054 0.314 2797 Planarity : 0.005 0.052 2042 Dihedral : 31.487 174.351 4808 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 5.16 % Allowed : 21.59 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.24), residues: 1225 helix: 0.59 (0.19), residues: 739 sheet: -2.92 (0.55), residues: 78 loop : -2.31 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG W 616 TYR 0.017 0.002 TYR E 54 PHE 0.018 0.002 PHE G 25 TRP 0.009 0.001 TRP W 521 HIS 0.007 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00646 / 0.30 (17278) covalent geometry : angle 0.82845 / 0.45 (24692) hydrogen bonds : bond 0.06183 / 4.18 ( 928) hydrogen bonds : angle 4.05203 / 2.95 ( 2372) Misc. bond : bond 0.00084 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 161 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 33 SER cc_start: 0.9123 (p) cc_final: 0.8866 (p) REVERT: D 73 GLU cc_start: 0.7980 (tp30) cc_final: 0.7725 (tp30) REVERT: E 73 GLU cc_start: 0.7992 (tt0) cc_final: 0.7701 (tt0) REVERT: E 123 ASP cc_start: 0.8682 (m-30) cc_final: 0.8285 (m-30) REVERT: E 133 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7296 (mt-10) REVERT: G 36 LYS cc_start: 0.8471 (mmtp) cc_final: 0.8171 (mmmm) REVERT: G 95 LYS cc_start: 0.8324 (tttp) cc_final: 0.8040 (tttp) REVERT: H 33 SER cc_start: 0.9042 (t) cc_final: 0.8776 (p) REVERT: W 174 TYR cc_start: 0.5599 (p90) cc_final: 0.5063 (p90) REVERT: W 222 MET cc_start: 0.7940 (mmp) cc_final: 0.7540 (mmm) REVERT: W 516 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7828 (tm-30) outliers start: 54 outliers final: 37 residues processed: 199 average time/residue: 0.1376 time to fit residues: 41.1590 Evaluate side-chains 188 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 150 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain W residue 199 ILE Chi-restraints excluded: chain W residue 305 LEU Chi-restraints excluded: chain W residue 323 ILE Chi-restraints excluded: chain W residue 334 LEU Chi-restraints excluded: chain W residue 345 HIS Chi-restraints excluded: chain W residue 391 PHE Chi-restraints excluded: chain W residue 450 LEU Chi-restraints excluded: chain W residue 451 MET Chi-restraints excluded: chain W residue 478 LEU Chi-restraints excluded: chain W residue 488 LEU Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 516 GLU Chi-restraints excluded: chain W residue 533 THR Chi-restraints excluded: chain W residue 564 LEU Chi-restraints excluded: chain W residue 574 VAL Chi-restraints excluded: chain W residue 586 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 98 optimal weight: 20.0000 chunk 11 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 120 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 141 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 131 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** 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 = 0.3713 r_free = 0.3713 target = 0.109455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.082669 restraints weight = 39623.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.082174 restraints weight = 36450.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.082206 restraints weight = 36575.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.082621 restraints weight = 32715.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.082549 restraints weight = 29895.404| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17280 Z= 0.143 Angle : 0.708 13.062 24692 Z= 0.393 Chirality : 0.048 0.332 2797 Planarity : 0.004 0.064 2042 Dihedral : 31.269 175.332 4808 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 3.06 % Allowed : 24.07 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.24), residues: 1225 helix: 0.96 (0.19), residues: 741 sheet: -2.88 (0.54), residues: 78 loop : -2.17 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 29 TYR 0.016 0.001 TYR F 88 PHE 0.011 0.001 PHE W 365 TRP 0.009 0.001 TRP W 251 HIS 0.005 0.001 HIS W 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.14 (17278) covalent geometry : angle 0.70795 / 0.39 (24692) hydrogen bonds : bond 0.04775 / 3.23 ( 928) hydrogen bonds : angle 3.68254 / 2.70 ( 2372) Misc. bond : bond 0.00018 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 33 SER cc_start: 0.9219 (p) cc_final: 0.8713 (m) REVERT: D 59 MET cc_start: 0.8714 (mmm) cc_final: 0.8502 (tpp) REVERT: D 73 GLU cc_start: 0.7894 (tp30) cc_final: 0.7610 (tp30) REVERT: E 73 GLU cc_start: 0.7925 (tt0) cc_final: 0.7692 (tt0) REVERT: E 123 ASP cc_start: 0.8629 (m-30) cc_final: 0.8268 (m-30) REVERT: E 133 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7281 (mt-10) REVERT: G 36 LYS cc_start: 0.8494 (mmtp) cc_final: 0.8227 (mmmm) REVERT: H 33 SER cc_start: 0.9037 (t) cc_final: 0.8654 (p) REVERT: H 73 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7044 (mm-30) REVERT: W 174 TYR cc_start: 0.5240 (p90) cc_final: 0.4886 (p90) REVERT: W 222 MET cc_start: 0.7978 (mmp) cc_final: 0.7616 (mmm) REVERT: W 334 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7417 (mp) REVERT: W 429 MET cc_start: 0.8292 (mpp) cc_final: 0.7929 (mpp) outliers start: 32 outliers final: 20 residues processed: 186 average time/residue: 0.1404 time to fit residues: 39.0500 Evaluate side-chains 181 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain W residue 323 ILE Chi-restraints excluded: chain W residue 334 LEU Chi-restraints excluded: chain W residue 345 HIS Chi-restraints excluded: chain W residue 391 PHE Chi-restraints excluded: chain W residue 450 LEU Chi-restraints excluded: chain W residue 488 LEU Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 574 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 114 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 148 optimal weight: 30.0000 chunk 67 optimal weight: 2.9990 chunk 102 optimal weight: 30.0000 chunk 109 optimal weight: 10.0000 chunk 126 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 133 optimal weight: 20.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 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 = 0.3684 r_free = 0.3684 target = 0.107876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.080006 restraints weight = 39679.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.079460 restraints weight = 43979.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.079740 restraints weight = 43139.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.079800 restraints weight = 37219.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.079925 restraints weight = 34710.940| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 17280 Z= 0.233 Angle : 0.774 17.341 24692 Z= 0.420 Chirality : 0.051 0.325 2797 Planarity : 0.005 0.056 2042 Dihedral : 31.290 174.515 4808 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 4.58 % Allowed : 24.16 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.24), residues: 1225 helix: 0.91 (0.19), residues: 737 sheet: -2.83 (0.55), residues: 78 loop : -2.15 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG W 595 TYR 0.015 0.002 TYR C 57 PHE 0.015 0.002 PHE G 25 TRP 0.007 0.001 TRP W 348 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.23 (17278) covalent geometry : angle 0.77387 / 0.42 (24692) hydrogen bonds : bond 0.05520 / 3.75 ( 928) hydrogen bonds : angle 3.83826 / 2.80 ( 2372) Misc. bond : bond 0.00019 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 160 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: D 33 SER cc_start: 0.9132 (p) cc_final: 0.8834 (p) REVERT: D 76 ARG cc_start: 0.7632 (mtm180) cc_final: 0.7169 (mtm-85) REVERT: E 73 GLU cc_start: 0.8068 (tt0) cc_final: 0.7790 (tt0) REVERT: E 123 ASP cc_start: 0.8748 (m-30) cc_final: 0.8367 (m-30) REVERT: E 133 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7391 (mt-10) REVERT: G 36 LYS cc_start: 0.8560 (mmtp) cc_final: 0.8169 (mmmm) REVERT: H 33 SER cc_start: 0.9153 (t) cc_final: 0.8769 (p) REVERT: W 174 TYR cc_start: 0.5478 (p90) cc_final: 0.5002 (p90) REVERT: W 218 LEU cc_start: 0.7744 (tp) cc_final: 0.7536 (tt) REVERT: W 348 TRP cc_start: 0.7766 (t-100) cc_final: 0.7271 (t-100) REVERT: W 429 MET cc_start: 0.8435 (mpp) cc_final: 0.7983 (mpp) REVERT: W 516 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7840 (tm-30) outliers start: 48 outliers final: 32 residues processed: 194 average time/residue: 0.1381 time to fit residues: 40.2517 Evaluate side-chains 187 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain W residue 199 ILE Chi-restraints excluded: chain W residue 305 LEU Chi-restraints excluded: chain W residue 323 ILE Chi-restraints excluded: chain W residue 334 LEU Chi-restraints excluded: chain W residue 345 HIS Chi-restraints excluded: chain W residue 391 PHE Chi-restraints excluded: chain W residue 450 LEU Chi-restraints excluded: chain W residue 451 MET Chi-restraints excluded: chain W residue 488 LEU Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 516 GLU Chi-restraints excluded: chain W residue 564 LEU Chi-restraints excluded: chain W residue 574 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 135 optimal weight: 8.9990 chunk 68 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 105 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 102 optimal weight: 30.0000 chunk 121 optimal weight: 10.0000 chunk 141 optimal weight: 9.9990 chunk 128 optimal weight: 0.0270 overall best weight: 0.9242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.110436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.084001 restraints weight = 39850.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.083116 restraints weight = 36621.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.083310 restraints weight = 36030.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.083446 restraints weight = 32596.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.083628 restraints weight = 28504.593| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17280 Z= 0.140 Angle : 0.700 15.012 24692 Z= 0.387 Chirality : 0.046 0.343 2797 Planarity : 0.004 0.042 2042 Dihedral : 31.064 174.995 4808 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.15 % Allowed : 25.79 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.25), residues: 1225 helix: 1.17 (0.19), residues: 742 sheet: -2.80 (0.57), residues: 73 loop : -1.95 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 40 TYR 0.014 0.001 TYR D 37 PHE 0.011 0.001 PHE W 365 TRP 0.014 0.002 TRP W 302 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.14 (17278) covalent geometry : angle 0.70001 / 0.39 (24692) hydrogen bonds : bond 0.04550 / 3.09 ( 928) hydrogen bonds : angle 3.58865 / 2.63 ( 2372) Misc. bond : bond 0.00096 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 175 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ASP cc_start: 0.7305 (t0) cc_final: 0.7023 (t0) REVERT: D 33 SER cc_start: 0.9085 (p) cc_final: 0.8607 (m) REVERT: E 73 GLU cc_start: 0.7929 (tt0) cc_final: 0.7661 (tt0) REVERT: E 123 ASP cc_start: 0.8581 (m-30) cc_final: 0.8265 (m-30) REVERT: E 133 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7267 (mt-10) REVERT: G 36 LYS cc_start: 0.8459 (mmtp) cc_final: 0.8175 (mmmm) REVERT: H 73 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7122 (tp30) REVERT: W 174 TYR cc_start: 0.5112 (p90) cc_final: 0.4804 (p90) REVERT: W 218 LEU cc_start: 0.7561 (tp) cc_final: 0.7361 (tt) REVERT: W 305 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7890 (tp) REVERT: W 334 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7340 (mp) REVERT: W 429 MET cc_start: 0.8349 (mpp) cc_final: 0.8118 (mpp) REVERT: W 516 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7746 (tm-30) outliers start: 33 outliers final: 24 residues processed: 194 average time/residue: 0.1290 time to fit residues: 37.1763 Evaluate side-chains 183 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain W residue 305 LEU Chi-restraints excluded: chain W residue 323 ILE Chi-restraints excluded: chain W residue 334 LEU Chi-restraints excluded: chain W residue 345 HIS Chi-restraints excluded: chain W residue 391 PHE Chi-restraints excluded: chain W residue 450 LEU Chi-restraints excluded: chain W residue 451 MET Chi-restraints excluded: chain W residue 488 LEU Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 516 GLU Chi-restraints excluded: chain W residue 574 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 129 optimal weight: 30.0000 chunk 93 optimal weight: 20.0000 chunk 70 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 chunk 125 optimal weight: 6.9990 chunk 145 optimal weight: 9.9990 chunk 104 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 122 optimal weight: 30.0000 chunk 101 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 overall best weight: 4.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.107958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.079552 restraints weight = 39787.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.079622 restraints weight = 40431.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.080273 restraints weight = 34411.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.080221 restraints weight = 29887.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.080270 restraints weight = 28757.642| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 17280 Z= 0.256 Angle : 0.800 16.884 24692 Z= 0.430 Chirality : 0.051 0.330 2797 Planarity : 0.005 0.061 2042 Dihedral : 31.171 174.935 4808 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 3.72 % Allowed : 25.88 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.24), residues: 1225 helix: 0.87 (0.19), residues: 745 sheet: -2.65 (0.58), residues: 73 loop : -2.11 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 76 TYR 0.014 0.002 TYR E 54 PHE 0.024 0.002 PHE W 365 TRP 0.023 0.002 TRP W 348 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.26 (17278) covalent geometry : angle 0.80005 / 0.43 (24692) hydrogen bonds : bond 0.05594 / 3.80 ( 928) hydrogen bonds : angle 3.85754 / 2.80 ( 2372) Misc. bond : bond 0.00122 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 157 time to evaluate : 0.525 Fit side-chains revert: symmetry clash REVERT: D 33 SER cc_start: 0.9207 (p) cc_final: 0.8935 (p) REVERT: D 76 ARG cc_start: 0.7083 (mtm-85) cc_final: 0.6522 (mtm-85) REVERT: E 73 GLU cc_start: 0.8061 (tt0) cc_final: 0.7843 (tt0) REVERT: E 123 ASP cc_start: 0.8708 (m-30) cc_final: 0.8327 (m-30) REVERT: E 133 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7345 (mt-10) REVERT: F 88 TYR cc_start: 0.8139 (m-80) cc_final: 0.7860 (m-80) REVERT: G 36 LYS cc_start: 0.8441 (mmtp) cc_final: 0.8133 (mmmm) REVERT: W 174 TYR cc_start: 0.5399 (p90) cc_final: 0.4819 (p90) REVERT: W 305 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7852 (tp) REVERT: W 429 MET cc_start: 0.8399 (mpp) cc_final: 0.8170 (mpp) REVERT: W 476 MET cc_start: 0.6674 (tpp) cc_final: 0.6414 (tpp) REVERT: W 516 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7770 (tm-30) outliers start: 39 outliers final: 28 residues processed: 182 average time/residue: 0.1387 time to fit residues: 37.3018 Evaluate side-chains 181 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain W residue 199 ILE Chi-restraints excluded: chain W residue 305 LEU Chi-restraints excluded: chain W residue 323 ILE Chi-restraints excluded: chain W residue 345 HIS Chi-restraints excluded: chain W residue 391 PHE Chi-restraints excluded: chain W residue 450 LEU Chi-restraints excluded: chain W residue 451 MET Chi-restraints excluded: chain W residue 453 LEU Chi-restraints excluded: chain W residue 478 LEU Chi-restraints excluded: chain W residue 488 LEU Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 516 GLU Chi-restraints excluded: chain W residue 574 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 64 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 137 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 chunk 136 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 43 optimal weight: 0.6980 chunk 119 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS G 104 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.110551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.083198 restraints weight = 39562.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.082732 restraints weight = 39184.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.083057 restraints weight = 38953.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.083133 restraints weight = 33963.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.083320 restraints weight = 30940.470| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 17280 Z= 0.142 Angle : 0.722 15.121 24692 Z= 0.395 Chirality : 0.047 0.350 2797 Planarity : 0.004 0.049 2042 Dihedral : 30.980 174.399 4808 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.77 % Allowed : 27.13 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.25), residues: 1225 helix: 1.13 (0.19), residues: 741 sheet: -2.49 (0.59), residues: 73 loop : -1.96 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 76 TYR 0.016 0.001 TYR W 304 PHE 0.027 0.001 PHE W 365 TRP 0.022 0.002 TRP W 348 HIS 0.005 0.001 HIS W 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.14 (17278) covalent geometry : angle 0.72191 / 0.39 (24692) hydrogen bonds : bond 0.04573 / 3.11 ( 928) hydrogen bonds : angle 3.61882 / 2.64 ( 2372) Misc. bond : bond 0.00055 / 0.03 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 110 ASN cc_start: 0.7579 (t0) cc_final: 0.7082 (p0) REVERT: D 33 SER cc_start: 0.9064 (p) cc_final: 0.8590 (m) REVERT: D 76 ARG cc_start: 0.6906 (mtm-85) cc_final: 0.6383 (mtm-85) REVERT: E 73 GLU cc_start: 0.7963 (tt0) cc_final: 0.7719 (tt0) REVERT: E 123 ASP cc_start: 0.8600 (m-30) cc_final: 0.8291 (m-30) REVERT: E 133 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7305 (mt-10) REVERT: G 36 LYS cc_start: 0.8447 (mmtp) cc_final: 0.8132 (mmmm) REVERT: H 73 GLU cc_start: 0.7547 (mm-30) cc_final: 0.6796 (mm-30) REVERT: W 174 TYR cc_start: 0.5033 (p90) cc_final: 0.4661 (p90) REVERT: W 289 MET cc_start: 0.8671 (mmp) cc_final: 0.8342 (mmm) REVERT: W 305 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7751 (tp) REVERT: W 334 LEU cc_start: 0.7580 (mt) cc_final: 0.7359 (mp) REVERT: W 441 MET cc_start: 0.5072 (tmm) cc_final: 0.4725 (mmt) REVERT: W 476 MET cc_start: 0.6401 (tpp) cc_final: 0.6164 (tpp) REVERT: W 516 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7661 (tm-30) outliers start: 29 outliers final: 27 residues processed: 178 average time/residue: 0.1349 time to fit residues: 35.6753 Evaluate side-chains 181 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain W residue 199 ILE Chi-restraints excluded: chain W residue 305 LEU Chi-restraints excluded: chain W residue 323 ILE Chi-restraints excluded: chain W residue 345 HIS Chi-restraints excluded: chain W residue 391 PHE Chi-restraints excluded: chain W residue 450 LEU Chi-restraints excluded: chain W residue 451 MET Chi-restraints excluded: chain W residue 453 LEU Chi-restraints excluded: chain W residue 488 LEU Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 516 GLU Chi-restraints excluded: chain W residue 574 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 70 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 89 optimal weight: 40.0000 chunk 19 optimal weight: 0.9990 chunk 79 optimal weight: 20.0000 chunk 83 optimal weight: 20.0000 chunk 140 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 97 optimal weight: 20.0000 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.110370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.083288 restraints weight = 39602.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.082723 restraints weight = 41378.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.082932 restraints weight = 41997.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.083012 restraints weight = 36558.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.083413 restraints weight = 32570.133| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17280 Z= 0.149 Angle : 0.718 15.294 24692 Z= 0.390 Chirality : 0.047 0.343 2797 Planarity : 0.004 0.045 2042 Dihedral : 30.915 175.032 4808 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 3.15 % Allowed : 26.46 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.25), residues: 1225 helix: 1.22 (0.19), residues: 744 sheet: -2.40 (0.60), residues: 72 loop : -1.93 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 76 TYR 0.019 0.001 TYR W 304 PHE 0.025 0.001 PHE W 365 TRP 0.019 0.002 TRP W 348 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.15 (17278) covalent geometry : angle 0.71829 / 0.39 (24692) hydrogen bonds : bond 0.04622 / 3.15 ( 928) hydrogen bonds : angle 3.64302 / 2.66 ( 2372) Misc. bond : bond 0.00044 / 0.02 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2330.12 seconds wall clock time: 41 minutes 23.66 seconds (2483.66 seconds total)