Starting phenix.real_space_refine on Wed Mar 4 20:35:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ne3_9356/03_2026/6ne3_9356.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ne3_9356/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6ne3_9356/03_2026/6ne3_9356.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ne3_9356/03_2026/6ne3_9356.map" model { file = "/net/cci-nas-00/data/ceres_data/6ne3_9356/03_2026/6ne3_9356.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ne3_9356/03_2026/6ne3_9356.cif" } 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-dev-5986/lib/python3.9/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: 3.74, 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: 1.36 Conformation dependent library (CDL) restraints added in 490.5 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: 2.23 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: 3.57 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=" C GLN C 24 " pdb=" N PHE C 25 " ideal model delta sigma weight residual 1.331 1.284 0.048 1.59e-02 3.96e+03 8.99e+00 bond pdb=" C GLN G 24 " pdb=" N PHE G 25 " ideal model delta sigma weight residual 1.331 1.259 0.072 2.83e-02 1.25e+03 6.46e+00 bond pdb=" C3' DG J 2 " pdb=" O3' DG J 2 " ideal model delta sigma weight residual 1.422 1.495 -0.073 3.00e-02 1.11e+03 5.96e+00 bond pdb=" C3' DC J 118 " pdb=" O3' DC J 118 " ideal model delta sigma weight residual 1.422 1.481 -0.059 3.00e-02 1.11e+03 3.93e+00 bond pdb=" CG1 ILE H 91 " pdb=" CD1 ILE H 91 " ideal model delta sigma weight residual 1.513 1.437 0.076 3.90e-02 6.57e+02 3.78e+00 ... (remaining 17273 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 24171 2.64 - 5.28: 473 5.28 - 7.92: 36 7.92 - 10.56: 8 10.56 - 13.20: 4 Bond angle restraints: 24692 Sorted by residual: 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=" C GLN E 85 " pdb=" N SER E 86 " pdb=" CA SER E 86 " ideal model delta sigma weight residual 121.54 131.21 -9.67 1.91e+00 2.74e-01 2.56e+01 angle pdb=" C GLN A 85 " pdb=" N SER A 86 " pdb=" CA SER A 86 " ideal model delta sigma weight residual 121.54 130.16 -8.62 1.91e+00 2.74e-01 2.03e+01 angle pdb=" C3' DG J 2 " pdb=" O3' DG J 2 " pdb=" P DG J 3 " ideal model delta sigma weight residual 120.20 125.97 -5.77 1.50e+00 4.44e-01 1.48e+01 angle pdb=" CA LEU F 62 " pdb=" CB LEU F 62 " pdb=" CG LEU F 62 " ideal model delta sigma weight residual 116.30 129.50 -13.20 3.50e+00 8.16e-02 1.42e+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: 2483 0.080 - 0.159: 296 0.159 - 0.239: 17 0.239 - 0.319: 0 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=" 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 chirality pdb=" CB ILE W 504 " pdb=" CA ILE W 504 " pdb=" CG1 ILE W 504 " pdb=" CG2 ILE W 504 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.25e+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: 1.700 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: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.210 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 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 : 0.008 0.076 17280 Z= 0.368 Angle : 0.951 13.198 24692 Z= 0.543 Chirality : 0.052 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 covalent geometry : bond 0.00821 (17278) covalent geometry : angle 0.95096 (24692) hydrogen bonds : bond 0.11160 ( 928) hydrogen bonds : angle 5.15667 ( 2372) Misc. bond : bond 0.00110 ( 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 : 0.466 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: 0.6958 (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: 0.7337 (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: 0.6178 (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: 0.6210 (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: 0.8307 (ttp80) REVERT: W 623 MET cc_start: 0.5508 (mtm) cc_final: 0.5257 (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: 0.1639 time to fit residues: 54.6211 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 : 0.458 ------------------------------------------------------------------------------- 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: 5.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 68 GLN A 85 GLN C 68 ASN C 84 GLN C 104 GLN D 46 HIS ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN F 25 ASN H 79 HIS ** W 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 242 HIS W 243 ASN W 266 GLN W 331 ASN ** W 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.106668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.081181 restraints weight = 40518.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.080351 restraints weight = 37112.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.080229 restraints weight = 37622.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.080387 restraints weight = 33414.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.080430 restraints weight = 30922.779| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 17280 Z= 0.276 Angle : 0.732 12.315 24692 Z= 0.411 Chirality : 0.042 0.191 2797 Planarity : 0.005 0.061 2042 Dihedral : 31.430 179.793 4810 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 2.67 % Allowed : 18.05 % Favored : 79.27 % 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: -1.64 (0.23), residues: 1225 helix: -0.03 (0.18), residues: 741 sheet: -2.59 (0.66), residues: 62 loop : -2.74 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 29 TYR 0.016 0.002 TYR C 57 PHE 0.013 0.002 PHE A 67 TRP 0.019 0.002 TRP W 280 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00626 (17278) covalent geometry : angle 0.73154 (24692) hydrogen bonds : bond 0.05313 ( 928) hydrogen bonds : angle 4.00535 ( 2372) Misc. bond : bond 0.00103 ( 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 214 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 186 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 27 GLN cc_start: 0.8256 (tp-100) cc_final: 0.7151 (tm-30) REVERT: B 84 MET cc_start: 0.8496 (mmm) cc_final: 0.8257 (mmm) REVERT: C 92 GLU cc_start: 0.7288 (mp0) cc_final: 0.6865 (mp0) REVERT: D 33 SER cc_start: 0.9169 (p) cc_final: 0.8901 (p) REVERT: E 123 ASP cc_start: 0.8532 (m-30) cc_final: 0.7942 (m-30) REVERT: G 36 LYS cc_start: 0.8463 (mmtp) cc_final: 0.8226 (mmmm) REVERT: H 33 SER cc_start: 0.9089 (t) cc_final: 0.8722 (p) REVERT: W 174 TYR cc_start: 0.5400 (p90) cc_final: 0.4933 (p90) REVERT: W 429 MET cc_start: 0.8033 (mpp) cc_final: 0.7690 (mpp) REVERT: W 575 ILE cc_start: 0.8834 (mm) cc_final: 0.8563 (mm) outliers start: 28 outliers final: 18 residues processed: 202 average time/residue: 0.1484 time to fit residues: 43.0440 Evaluate side-chains 171 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 153 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL 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 E residue 80 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 101 THR 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 478 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 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: 0.7980 chunk 116 optimal weight: 9.9990 chunk 118 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 128 optimal weight: 0.6980 chunk 94 optimal weight: 7.9990 chunk 146 optimal weight: 3.9990 chunk 106 optimal weight: 20.0000 chunk 71 optimal weight: 0.0070 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 GLN ** 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 110 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.111049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.084988 restraints weight = 40607.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.084089 restraints weight = 35250.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.084460 restraints weight = 36224.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.084645 restraints weight = 30768.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.084758 restraints weight = 27273.857| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17280 Z= 0.148 Angle : 0.627 11.219 24692 Z= 0.357 Chirality : 0.037 0.176 2797 Planarity : 0.004 0.047 2042 Dihedral : 30.881 178.698 4808 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.96 % Allowed : 20.15 % Favored : 76.89 % 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: -0.61 (0.24), residues: 1225 helix: 0.88 (0.19), residues: 742 sheet: -2.95 (0.56), residues: 77 loop : -2.32 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 29 TYR 0.014 0.001 TYR W 413 PHE 0.009 0.001 PHE A 67 TRP 0.020 0.001 TRP W 280 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00320 (17278) covalent geometry : angle 0.62744 (24692) hydrogen bonds : bond 0.03974 ( 928) hydrogen bonds : angle 3.46787 ( 2372) Misc. bond : bond 0.00053 ( 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 215 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 ILE cc_start: 0.9004 (pt) cc_final: 0.8550 (mt) REVERT: B 84 MET cc_start: 0.8469 (mmm) cc_final: 0.8214 (mmm) REVERT: C 23 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8217 (tp) REVERT: D 33 SER cc_start: 0.9142 (p) cc_final: 0.8667 (m) REVERT: D 76 ARG cc_start: 0.7518 (mtm180) cc_final: 0.7188 (mtm-85) REVERT: E 123 ASP cc_start: 0.8443 (m-30) cc_final: 0.7939 (m-30) REVERT: E 133 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7238 (mt-10) REVERT: G 36 LYS cc_start: 0.8474 (mmtp) cc_final: 0.8111 (mmmm) REVERT: H 33 SER cc_start: 0.9045 (t) cc_final: 0.8684 (p) REVERT: H 73 GLU cc_start: 0.7366 (mm-30) cc_final: 0.6968 (tp30) REVERT: W 218 LEU cc_start: 0.6789 (tt) cc_final: 0.6432 (tt) REVERT: W 334 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7286 (mp) REVERT: W 590 MET cc_start: 0.7416 (tpp) cc_final: 0.7213 (tpp) outliers start: 31 outliers final: 17 residues processed: 201 average time/residue: 0.1450 time to fit residues: 42.5011 Evaluate side-chains 175 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 82 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 101 THR 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 495 LEU 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: 1.9990 chunk 64 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 143 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 59 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN G 104 GLN W 584 GLN W 594 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.108845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.082284 restraints weight = 40003.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.081509 restraints weight = 36363.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.081571 restraints weight = 33462.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.081660 restraints weight = 32963.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.081763 restraints weight = 29188.980| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 17280 Z= 0.214 Angle : 0.670 13.160 24692 Z= 0.376 Chirality : 0.039 0.166 2797 Planarity : 0.004 0.041 2042 Dihedral : 30.888 177.901 4808 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 4.30 % Allowed : 21.01 % Favored : 74.69 % 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 (0.25), residues: 1225 helix: 0.93 (0.19), residues: 751 sheet: -2.95 (0.55), residues: 78 loop : -2.17 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG W 592 TYR 0.015 0.001 TYR C 57 PHE 0.010 0.001 PHE G 25 TRP 0.021 0.002 TRP W 280 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00487 (17278) covalent geometry : angle 0.66964 (24692) hydrogen bonds : bond 0.04637 ( 928) hydrogen bonds : angle 3.63328 ( 2372) Misc. bond : bond 0.00065 ( 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 213 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 168 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8575 (mmm) cc_final: 0.8319 (mmm) REVERT: C 92 GLU cc_start: 0.7111 (mp0) cc_final: 0.6852 (mp0) REVERT: C 110 ASN cc_start: 0.7697 (t0) cc_final: 0.7179 (p0) REVERT: D 33 SER cc_start: 0.9119 (p) cc_final: 0.8639 (m) REVERT: D 76 ARG cc_start: 0.7615 (mtm180) cc_final: 0.7310 (mtm-85) REVERT: D 102 GLU cc_start: 0.7159 (pm20) cc_final: 0.6867 (pm20) REVERT: E 123 ASP cc_start: 0.8537 (m-30) cc_final: 0.8099 (m-30) REVERT: E 133 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7386 (mt-10) REVERT: G 36 LYS cc_start: 0.8454 (mmtp) cc_final: 0.8167 (mmmm) REVERT: H 33 SER cc_start: 0.9081 (t) cc_final: 0.8674 (p) REVERT: W 174 TYR cc_start: 0.5159 (p90) cc_final: 0.4779 (p90) REVERT: W 305 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7788 (tp) REVERT: W 334 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7517 (mp) REVERT: W 516 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7752 (tm-30) outliers start: 45 outliers final: 25 residues processed: 197 average time/residue: 0.1415 time to fit residues: 40.6887 Evaluate side-chains 180 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 E residue 96 SER Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 34 ILE 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 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 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 Chi-restraints excluded: chain W residue 613 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 80 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 17 optimal weight: 0.0000 chunk 122 optimal weight: 7.9990 chunk 104 optimal weight: 9.9990 chunk 142 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 133 optimal weight: 30.0000 overall best weight: 2.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** W 189 ASN ** 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 = 0.3695 r_free = 0.3695 target = 0.108528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.082292 restraints weight = 39944.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.081171 restraints weight = 36146.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.081377 restraints weight = 36815.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.081507 restraints weight = 33310.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.081598 restraints weight = 28977.040| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 17280 Z= 0.231 Angle : 0.682 13.690 24692 Z= 0.382 Chirality : 0.040 0.190 2797 Planarity : 0.004 0.040 2042 Dihedral : 30.859 176.460 4808 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 4.78 % Allowed : 23.02 % Favored : 72.21 % 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: -0.41 (0.25), residues: 1225 helix: 0.96 (0.19), residues: 743 sheet: -2.86 (0.57), residues: 76 loop : -2.07 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG W 592 TYR 0.013 0.002 TYR C 57 PHE 0.012 0.002 PHE G 25 TRP 0.022 0.002 TRP W 280 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00528 (17278) covalent geometry : angle 0.68192 (24692) hydrogen bonds : bond 0.04703 ( 928) hydrogen bonds : angle 3.63630 ( 2372) Misc. bond : bond 0.00057 ( 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 207 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 157 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8607 (mmm) cc_final: 0.8366 (mmm) REVERT: C 92 GLU cc_start: 0.7083 (mp0) cc_final: 0.6714 (mp0) REVERT: C 104 GLN cc_start: 0.7539 (OUTLIER) cc_final: 0.7333 (tm-30) REVERT: C 110 ASN cc_start: 0.7754 (t0) cc_final: 0.7221 (p0) REVERT: D 33 SER cc_start: 0.9144 (p) cc_final: 0.8851 (p) REVERT: D 59 MET cc_start: 0.8855 (mmm) cc_final: 0.8614 (tpp) REVERT: E 123 ASP cc_start: 0.8656 (m-30) cc_final: 0.8232 (m-30) REVERT: E 133 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7666 (mt-10) REVERT: G 18 SER cc_start: 0.8542 (t) cc_final: 0.8340 (t) REVERT: G 36 LYS cc_start: 0.8577 (mmtp) cc_final: 0.8191 (mmmm) REVERT: H 33 SER cc_start: 0.9029 (t) cc_final: 0.8619 (p) REVERT: W 218 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.6751 (tp) REVERT: W 429 MET cc_start: 0.8402 (mpp) cc_final: 0.8141 (mpp) REVERT: W 516 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7754 (tm-30) REVERT: W 530 ASP cc_start: 0.5683 (p0) cc_final: 0.4810 (t0) outliers start: 50 outliers final: 36 residues processed: 191 average time/residue: 0.1283 time to fit residues: 36.1859 Evaluate side-chains 189 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 150 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 82 LEU 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 82 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 104 GLN 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 E residue 118 THR Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 80 THR 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 218 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 450 LEU Chi-restraints excluded: chain W residue 451 MET Chi-restraints excluded: chain W residue 453 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 574 VAL Chi-restraints excluded: chain W residue 613 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 98 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 120 optimal weight: 0.0270 chunk 51 optimal weight: 0.8980 chunk 141 optimal weight: 9.9990 chunk 35 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 131 optimal weight: 7.9990 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN G 104 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.110997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.084494 restraints weight = 39699.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.083690 restraints weight = 39002.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.084062 restraints weight = 36039.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.084034 restraints weight = 34485.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.084175 restraints weight = 30292.033| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17280 Z= 0.155 Angle : 0.634 12.480 24692 Z= 0.355 Chirality : 0.037 0.207 2797 Planarity : 0.004 0.041 2042 Dihedral : 30.598 176.839 4808 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.53 % Allowed : 23.97 % Favored : 72.49 % 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: 0.03 (0.25), residues: 1225 helix: 1.35 (0.19), residues: 740 sheet: -2.70 (0.57), residues: 75 loop : -1.96 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG W 592 TYR 0.012 0.001 TYR G 57 PHE 0.009 0.001 PHE F 100 TRP 0.011 0.001 TRP W 280 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00344 (17278) covalent geometry : angle 0.63369 (24692) hydrogen bonds : bond 0.03984 ( 928) hydrogen bonds : angle 3.36818 ( 2372) Misc. bond : bond 0.00044 ( 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 211 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 174 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.7728 (p0) cc_final: 0.7216 (m-30) REVERT: B 25 ASN cc_start: 0.8424 (OUTLIER) cc_final: 0.8118 (m-40) REVERT: C 110 ASN cc_start: 0.7690 (t0) cc_final: 0.7209 (p0) REVERT: D 33 SER cc_start: 0.9191 (p) cc_final: 0.8683 (m) REVERT: D 76 ARG cc_start: 0.7602 (mtm180) cc_final: 0.7250 (mtm-85) REVERT: D 86 ILE cc_start: 0.9176 (mt) cc_final: 0.8923 (mt) REVERT: D 102 GLU cc_start: 0.7296 (pm20) cc_final: 0.6992 (pm20) REVERT: E 123 ASP cc_start: 0.8620 (m-30) cc_final: 0.8217 (m-30) REVERT: E 133 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7462 (mt-10) REVERT: G 36 LYS cc_start: 0.8402 (mmtp) cc_final: 0.8136 (mmmm) REVERT: H 33 SER cc_start: 0.9080 (t) cc_final: 0.8837 (p) REVERT: H 73 GLU cc_start: 0.7303 (mm-30) cc_final: 0.7055 (mm-30) REVERT: W 289 MET cc_start: 0.8789 (mmp) cc_final: 0.8515 (mmm) REVERT: W 429 MET cc_start: 0.8347 (mpp) cc_final: 0.8100 (mpp) REVERT: W 476 MET cc_start: 0.6443 (tpp) cc_final: 0.6092 (tpp) outliers start: 37 outliers final: 25 residues processed: 195 average time/residue: 0.1323 time to fit residues: 38.2387 Evaluate side-chains 182 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU 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 82 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 118 THR 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 115 LEU Chi-restraints excluded: chain W residue 199 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 533 THR 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: 1.9990 chunk 45 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 148 optimal weight: 30.0000 chunk 67 optimal weight: 0.6980 chunk 102 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 46 optimal weight: 0.0030 chunk 133 optimal weight: 40.0000 overall best weight: 1.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** W 232 HIS ** 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 = 0.3728 r_free = 0.3728 target = 0.110610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.083285 restraints weight = 39762.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.082886 restraints weight = 38240.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.083178 restraints weight = 33444.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.083334 restraints weight = 29858.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.083405 restraints weight = 27877.609| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17280 Z= 0.173 Angle : 0.652 16.163 24692 Z= 0.361 Chirality : 0.038 0.207 2797 Planarity : 0.004 0.040 2042 Dihedral : 30.527 176.410 4808 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 4.11 % Allowed : 23.69 % Favored : 72.21 % 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: 0.10 (0.25), residues: 1225 helix: 1.42 (0.19), residues: 737 sheet: -2.56 (0.60), residues: 70 loop : -1.97 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 29 TYR 0.013 0.001 TYR G 57 PHE 0.009 0.001 PHE A 67 TRP 0.020 0.001 TRP W 280 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00391 (17278) covalent geometry : angle 0.65175 (24692) hydrogen bonds : bond 0.04154 ( 928) hydrogen bonds : angle 3.39531 ( 2372) Misc. bond : bond 0.00040 ( 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 204 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 161 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.7706 (p0) cc_final: 0.7147 (m-30) REVERT: C 110 ASN cc_start: 0.7630 (t0) cc_final: 0.7192 (p0) REVERT: D 33 SER cc_start: 0.9194 (p) cc_final: 0.8715 (m) REVERT: D 76 ARG cc_start: 0.7534 (mtm180) cc_final: 0.7257 (mtm-85) REVERT: E 123 ASP cc_start: 0.8597 (m-30) cc_final: 0.8182 (m-30) REVERT: E 133 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7461 (mt-10) REVERT: G 36 LYS cc_start: 0.8406 (mmtp) cc_final: 0.8205 (mmmm) REVERT: H 33 SER cc_start: 0.8989 (t) cc_final: 0.8652 (p) REVERT: H 73 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7181 (mm-30) REVERT: W 222 MET cc_start: 0.7659 (mmp) cc_final: 0.7200 (mmm) REVERT: W 289 MET cc_start: 0.8710 (mmp) cc_final: 0.8447 (mmm) REVERT: W 386 MET cc_start: 0.6608 (tpp) cc_final: 0.6401 (tmm) REVERT: W 424 TYR cc_start: 0.7650 (OUTLIER) cc_final: 0.7089 (t80) REVERT: W 476 MET cc_start: 0.6454 (tpp) cc_final: 0.6239 (tpp) REVERT: W 516 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7676 (tm-30) outliers start: 43 outliers final: 30 residues processed: 193 average time/residue: 0.1255 time to fit residues: 36.5234 Evaluate side-chains 186 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 82 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 80 THR 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 115 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain W residue 199 ILE Chi-restraints excluded: chain W residue 213 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 424 TYR 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 495 LEU Chi-restraints excluded: chain W residue 516 GLU Chi-restraints excluded: chain W residue 533 THR 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: 1.9990 chunk 68 optimal weight: 0.8980 chunk 139 optimal weight: 0.0370 chunk 24 optimal weight: 0.6980 chunk 105 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** 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 = 0.3755 r_free = 0.3755 target = 0.112311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.085597 restraints weight = 39906.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.085157 restraints weight = 38089.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.085302 restraints weight = 33223.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.085432 restraints weight = 30722.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.085494 restraints weight = 28503.035| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17280 Z= 0.150 Angle : 0.641 14.809 24692 Z= 0.355 Chirality : 0.037 0.199 2797 Planarity : 0.004 0.042 2042 Dihedral : 30.310 176.298 4808 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 3.25 % Allowed : 25.12 % Favored : 71.63 % 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: 0.35 (0.25), residues: 1225 helix: 1.58 (0.19), residues: 738 sheet: -1.95 (0.68), residues: 56 loop : -1.93 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG W 592 TYR 0.012 0.001 TYR G 57 PHE 0.010 0.001 PHE B 100 TRP 0.011 0.001 TRP W 280 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00330 (17278) covalent geometry : angle 0.64067 (24692) hydrogen bonds : bond 0.03880 ( 928) hydrogen bonds : angle 3.36462 ( 2372) Misc. bond : bond 0.00048 ( 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 195 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 161 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.7793 (p0) cc_final: 0.7367 (m-30) REVERT: C 104 GLN cc_start: 0.7154 (OUTLIER) cc_final: 0.6823 (tt0) REVERT: C 110 ASN cc_start: 0.7714 (t0) cc_final: 0.7216 (p0) REVERT: D 33 SER cc_start: 0.9140 (p) cc_final: 0.8653 (m) REVERT: D 39 TYR cc_start: 0.7738 (t80) cc_final: 0.7493 (m-80) REVERT: D 76 ARG cc_start: 0.7543 (mtm180) cc_final: 0.6985 (mtm-85) REVERT: E 123 ASP cc_start: 0.8633 (m-30) cc_final: 0.8169 (m-30) REVERT: E 133 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7435 (mt-10) REVERT: H 33 SER cc_start: 0.9053 (t) cc_final: 0.8745 (p) REVERT: H 73 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7131 (mm-30) REVERT: W 386 MET cc_start: 0.6709 (tpp) cc_final: 0.6364 (tmm) outliers start: 34 outliers final: 27 residues processed: 184 average time/residue: 0.1309 time to fit residues: 35.7874 Evaluate side-chains 179 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 58 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain W residue 199 ILE Chi-restraints excluded: chain W residue 213 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 399 ASP 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 495 LEU Chi-restraints excluded: chain W residue 533 THR 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: 7.9990 chunk 70 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 145 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 chunk 91 optimal weight: 7.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN G 110 ASN ** W 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 452 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.109593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.082328 restraints weight = 39688.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.081531 restraints weight = 35795.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.081719 restraints weight = 32003.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.081857 restraints weight = 29670.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.081920 restraints weight = 28503.423| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 17280 Z= 0.224 Angle : 0.703 16.780 24692 Z= 0.385 Chirality : 0.040 0.206 2797 Planarity : 0.004 0.041 2042 Dihedral : 30.485 174.699 4808 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 3.92 % Allowed : 24.93 % Favored : 71.16 % 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: 0.14 (0.25), residues: 1225 helix: 1.35 (0.19), residues: 744 sheet: -1.89 (0.70), residues: 56 loop : -1.95 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 76 TYR 0.014 0.002 TYR G 57 PHE 0.010 0.001 PHE G 25 TRP 0.021 0.002 TRP W 280 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00513 (17278) covalent geometry : angle 0.70297 (24692) hydrogen bonds : bond 0.04601 ( 928) hydrogen bonds : angle 3.53939 ( 2372) Misc. bond : bond 0.00062 ( 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: 41 poor density : 155 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.6976 (mm-30) cc_final: 0.6755 (mm-30) REVERT: C 104 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.7205 (tt0) REVERT: C 110 ASN cc_start: 0.7710 (t0) cc_final: 0.7222 (p0) REVERT: D 33 SER cc_start: 0.9164 (p) cc_final: 0.8867 (p) REVERT: D 76 ARG cc_start: 0.7624 (mtm180) cc_final: 0.7298 (mtm-85) REVERT: E 123 ASP cc_start: 0.8673 (m-30) cc_final: 0.8250 (m-30) REVERT: E 133 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7614 (mt-10) REVERT: F 27 GLN cc_start: 0.8051 (mm110) cc_final: 0.7831 (mm110) REVERT: H 33 SER cc_start: 0.9062 (t) cc_final: 0.8849 (p) REVERT: W 222 MET cc_start: 0.7633 (mmp) cc_final: 0.7320 (mmm) REVERT: W 289 MET cc_start: 0.8751 (mmp) cc_final: 0.8508 (mmm) REVERT: W 516 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7663 (tm-30) outliers start: 41 outliers final: 32 residues processed: 185 average time/residue: 0.1349 time to fit residues: 37.2054 Evaluate side-chains 183 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 149 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL 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 51 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 96 SER 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 G residue 27 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain W residue 199 ILE 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 399 ASP 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 495 LEU Chi-restraints excluded: chain W residue 516 GLU Chi-restraints excluded: chain W residue 533 THR Chi-restraints excluded: chain W residue 574 VAL Chi-restraints excluded: chain W residue 613 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 64 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 137 optimal weight: 5.9990 chunk 132 optimal weight: 0.0970 chunk 136 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 148 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 119 optimal weight: 10.0000 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** 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 = 0.3764 r_free = 0.3764 target = 0.112669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.085260 restraints weight = 39846.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.085106 restraints weight = 40971.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.085856 restraints weight = 35738.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.085937 restraints weight = 29158.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.085938 restraints weight = 27754.679| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17280 Z= 0.147 Angle : 0.653 14.029 24692 Z= 0.359 Chirality : 0.037 0.197 2797 Planarity : 0.004 0.059 2042 Dihedral : 30.222 175.484 4808 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.67 % Allowed : 25.88 % Favored : 71.44 % 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: 0.36 (0.25), residues: 1225 helix: 1.59 (0.19), residues: 737 sheet: -2.01 (0.67), residues: 56 loop : -1.90 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 40 TYR 0.014 0.001 TYR F 88 PHE 0.012 0.001 PHE B 100 TRP 0.013 0.001 TRP W 280 HIS 0.004 0.001 HIS W 232 Details of bonding type rmsd covalent geometry : bond 0.00324 (17278) covalent geometry : angle 0.65324 (24692) hydrogen bonds : bond 0.03909 ( 928) hydrogen bonds : angle 3.34230 ( 2372) Misc. bond : bond 0.00053 ( 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 186 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 158 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.7355 (tp40) cc_final: 0.7100 (tp40) REVERT: A 106 ASP cc_start: 0.7753 (p0) cc_final: 0.7164 (m-30) REVERT: B 59 LYS cc_start: 0.8017 (ttmm) cc_final: 0.7748 (ttpt) REVERT: C 104 GLN cc_start: 0.7223 (OUTLIER) cc_final: 0.6955 (tt0) REVERT: C 110 ASN cc_start: 0.7551 (t0) cc_final: 0.7115 (p0) REVERT: D 33 SER cc_start: 0.9144 (p) cc_final: 0.8636 (m) REVERT: D 76 ARG cc_start: 0.7457 (mtm180) cc_final: 0.7250 (mtm-85) REVERT: E 123 ASP cc_start: 0.8518 (m-30) cc_final: 0.8179 (m-30) REVERT: E 133 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7440 (mt-10) REVERT: H 33 SER cc_start: 0.8757 (t) cc_final: 0.8477 (p) REVERT: H 73 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7086 (mm-30) REVERT: W 222 MET cc_start: 0.7576 (mmp) cc_final: 0.7281 (mmm) REVERT: W 289 MET cc_start: 0.8620 (mmp) cc_final: 0.8328 (mmm) REVERT: W 386 MET cc_start: 0.7182 (tmm) cc_final: 0.6887 (tmm) REVERT: W 516 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7542 (tm-30) outliers start: 28 outliers final: 22 residues processed: 177 average time/residue: 0.1264 time to fit residues: 33.1232 Evaluate side-chains 172 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 51 LEU 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 D residue 115 VAL Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain W residue 199 ILE 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 451 MET Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 516 GLU Chi-restraints excluded: chain W residue 533 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 70 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 83 optimal weight: 7.9990 chunk 140 optimal weight: 0.0270 chunk 34 optimal weight: 0.7980 chunk 97 optimal weight: 6.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.113092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.085847 restraints weight = 40022.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.085838 restraints weight = 40692.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.086522 restraints weight = 36870.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.086476 restraints weight = 32056.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.086541 restraints weight = 29144.920| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3529 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= 0.148 Angle : 0.656 14.365 24692 Z= 0.357 Chirality : 0.037 0.193 2797 Planarity : 0.004 0.044 2042 Dihedral : 30.180 175.776 4807 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.58 % Allowed : 26.36 % 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: 0.46 (0.25), residues: 1225 helix: 1.70 (0.19), residues: 739 sheet: -1.98 (0.66), residues: 56 loop : -1.92 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 40 TYR 0.012 0.001 TYR G 57 PHE 0.010 0.001 PHE C 25 TRP 0.014 0.001 TRP W 280 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00326 (17278) covalent geometry : angle 0.65612 (24692) hydrogen bonds : bond 0.03856 ( 928) hydrogen bonds : angle 3.31314 ( 2372) Misc. bond : bond 0.00047 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2225.70 seconds wall clock time: 39 minutes 17.53 seconds (2357.53 seconds total)