Starting phenix.real_space_refine on Thu Aug 6 16:49:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hak_34594/08_2026/8hak_34594.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hak_34594/08_2026/8hak_34594.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hak_34594/08_2026/8hak_34594.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hak_34594/08_2026/8hak_34594.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8hak_34594/08_2026/8hak_34594.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hak_34594/08_2026/8hak_34594.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hak_34594/08_2026/8hak_34594.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hak_34594/08_2026/8hak_34594.map" } resolution = 4.5 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= 0.000 sd= 0.003 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 292 5.49 5 S 47 5.16 5 C 9421 2.51 5 N 2979 2.21 5 O 3603 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 119 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16342 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 794 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 806 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 717 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 89} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ALY:plan-2': 2, 'ALY:plan-1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 815 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 100} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 741 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "J" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3016 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 2973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2973 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "N" Number of atoms: 4295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4295 Classifications: {'peptide': 520} Link IDs: {'PCIS': 3, 'PTRANS': 29, 'TRANS': 487} Chain breaks: 3 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ALA C 14 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA C 14 " occ=0.00 Time building chain proxies: 3.44, per 1000 atoms: 0.21 Number of scatterers: 16342 At special positions: 0 Unit cell: (123.48, 124.95, 152.88, 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 47 16.00 P 292 15.00 O 3603 8.00 N 2979 7.00 C 9421 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 Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 515.6 milliseconds 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2422 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 13 sheets defined 61.8% alpha, 7.0% beta 101 base pairs and 219 stacking pairs defined. Time for finding SS restraints: 2.16 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 63 through 77 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.702A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.522A pdb=" N GLY B 28 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.787A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 3.947A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.600A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.511A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.881A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 122 removed outlier: 4.119A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.538A 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 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.782A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.342A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.818A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 Processing helix chain 'N' and resid 1052 through 1068 Proline residue: N1060 - end of helix removed outlier: 3.523A pdb=" N GLN N1068 " --> pdb=" O ALA N1064 " (cutoff:3.500A) Processing helix chain 'N' and resid 1072 through 1076 Processing helix chain 'N' and resid 1080 through 1085 Processing helix chain 'N' and resid 1098 through 1109 removed outlier: 3.610A pdb=" N ILE N1102 " --> pdb=" O ASP N1098 " (cutoff:3.500A) Processing helix chain 'N' and resid 1113 through 1131 removed outlier: 3.958A pdb=" N TYR N1117 " --> pdb=" O GLU N1113 " (cutoff:3.500A) Processing helix chain 'N' and resid 1136 through 1160 removed outlier: 3.728A pdb=" N LYS N1140 " --> pdb=" O SER N1136 " (cutoff:3.500A) Proline residue: N1155 - end of helix Processing helix chain 'N' and resid 1256 through 1260 Processing helix chain 'N' and resid 1272 through 1280 Processing helix chain 'N' and resid 1289 through 1293 Processing helix chain 'N' and resid 1296 through 1314 Processing helix chain 'N' and resid 1336 through 1343 removed outlier: 3.818A pdb=" N ARG N1342 " --> pdb=" O GLY N1338 " (cutoff:3.500A) Processing helix chain 'N' and resid 1406 through 1429 removed outlier: 4.391A pdb=" N THR N1411 " --> pdb=" O LYS N1407 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ALA N1412 " --> pdb=" O CYS N1408 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU N1422 " --> pdb=" O LEU N1418 " (cutoff:3.500A) Processing helix chain 'N' and resid 1459 through 1477 Processing helix chain 'N' and resid 1486 through 1494 Processing helix chain 'N' and resid 1497 through 1501 Processing helix chain 'N' and resid 1507 through 1519 removed outlier: 3.893A pdb=" N ASN N1511 " --> pdb=" O ASP N1507 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU N1514 " --> pdb=" O PRO N1510 " (cutoff:3.500A) Processing helix chain 'N' and resid 1580 through 1591 Processing helix chain 'N' and resid 1626 through 1638 removed outlier: 4.070A pdb=" N PHE N1630 " --> pdb=" O GLY N1626 " (cutoff:3.500A) Processing helix chain 'N' and resid 1643 through 1662 removed outlier: 3.591A pdb=" N SER N1662 " --> pdb=" O LEU N1658 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.870A 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 'A' and resid 118 through 119 removed outlier: 3.536A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.229A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.535A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.844A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.091A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'N' and resid 1198 through 1200 Processing sheet with id=AB3, first strand: chain 'N' and resid 1244 through 1246 Processing sheet with id=AB4, first strand: chain 'N' and resid 1321 through 1334 removed outlier: 6.510A pdb=" N ALA N1359 " --> pdb=" O VAL N1326 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA N1328 " --> pdb=" O THR N1357 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N THR N1357 " --> pdb=" O ALA N1328 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASP N1330 " --> pdb=" O TYR N1355 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N TYR N1355 " --> pdb=" O ASP N1330 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR N1332 " --> pdb=" O PHE N1353 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N PHE N1353 " --> pdb=" O THR N1332 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N TYR N1381 " --> pdb=" O PRO N1354 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ARG N1356 " --> pdb=" O GLN N1379 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLN N1379 " --> pdb=" O ARG N1356 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LYS N1358 " --> pdb=" O HIS N1377 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N HIS N1377 " --> pdb=" O LYS N1358 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU N1360 " --> pdb=" O GLY N1375 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLY N1375 " --> pdb=" O LEU N1360 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA N1362 " --> pdb=" O PHE N1373 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR N1397 " --> pdb=" O HIS N1377 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N GLN N1379 " --> pdb=" O ILE N1395 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ILE N1395 " --> pdb=" O GLN N1379 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N TYR N1381 " --> pdb=" O VAL N1393 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N VAL N1393 " --> pdb=" O TYR N1381 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N TRP N1436 " --> pdb=" O ILE N1395 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N TYR N1397 " --> pdb=" O TRP N1436 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP N1482 " --> pdb=" O ARG N1599 " (cutoff:3.500A) 588 hydrogen bonds defined for protein. 1728 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 243 hydrogen bonds 486 hydrogen bond angles 0 basepair planarities 101 basepair parallelities 219 stacking parallelities Total time for adding SS restraints: 3.59 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3703 1.34 - 1.46: 4900 1.46 - 1.57: 8011 1.57 - 1.69: 582 1.69 - 1.81: 70 Bond restraints: 17266 Sorted by residual: bond pdb=" C3' DG J 76 " pdb=" C2' DG J 76 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.36e+01 bond pdb=" C3' DG J 80 " pdb=" C2' DG J 80 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DG K 111 " pdb=" C2' DG K 111 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.73e+00 bond pdb=" C3' DT J 145 " pdb=" C2' DT J 145 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.04e+00 bond pdb=" C3' DT K 136 " pdb=" C2' DT K 136 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.82e+00 ... (remaining 17261 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 23403 1.81 - 3.63: 1097 3.63 - 5.44: 53 5.44 - 7.26: 16 7.26 - 9.07: 3 Bond angle restraints: 24572 Sorted by residual: angle pdb=" N GLU F 74 " pdb=" CA GLU F 74 " pdb=" CB GLU F 74 " ideal model delta sigma weight residual 110.30 117.95 -7.65 1.54e+00 4.22e-01 2.47e+01 angle pdb=" O4' DC K 66 " pdb=" C1' DC K 66 " pdb=" N1 DC K 66 " ideal model delta sigma weight residual 108.00 111.44 -3.44 7.00e-01 2.04e+00 2.42e+01 angle pdb=" N GLU B 63 " pdb=" CA GLU B 63 " pdb=" CB GLU B 63 " ideal model delta sigma weight residual 110.28 117.64 -7.36 1.55e+00 4.16e-01 2.26e+01 angle pdb=" O4' DG J 56 " pdb=" C4' DG J 56 " pdb=" C3' DG J 56 " ideal model delta sigma weight residual 106.00 103.24 2.76 6.00e-01 2.78e+00 2.11e+01 angle pdb=" N3 DT K 40 " pdb=" C4 DT K 40 " pdb=" O4 DT K 40 " ideal model delta sigma weight residual 119.90 122.62 -2.72 6.00e-01 2.78e+00 2.05e+01 ... (remaining 24567 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.08: 8349 34.08 - 68.16: 1354 68.16 - 102.24: 34 102.24 - 136.32: 0 136.32 - 170.40: 2 Dihedral angle restraints: 9739 sinusoidal: 5988 harmonic: 3751 Sorted by residual: dihedral pdb=" C4' DT K 136 " pdb=" C3' DT K 136 " pdb=" O3' DT K 136 " pdb=" P DT K 137 " ideal model delta sinusoidal sigma weight residual -140.00 30.40 -170.40 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DA J 59 " pdb=" C3' DA J 59 " pdb=" O3' DA J 59 " pdb=" P DA J 60 " ideal model delta sinusoidal sigma weight residual 220.00 51.81 168.19 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" CG ARG E 128 " pdb=" CD ARG E 128 " pdb=" NE ARG E 128 " pdb=" CZ ARG E 128 " ideal model delta sinusoidal sigma weight residual -90.00 -134.23 44.23 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 9736 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1718 0.037 - 0.074: 731 0.074 - 0.111: 255 0.111 - 0.148: 31 0.148 - 0.185: 3 Chirality restraints: 2738 Sorted by residual: chirality pdb=" CG LEU C 55 " pdb=" CB LEU C 55 " pdb=" CD1 LEU C 55 " pdb=" CD2 LEU C 55 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.57e-01 chirality pdb=" C3' DA J 59 " pdb=" C4' DA J 59 " pdb=" O3' DA J 59 " pdb=" C2' DA J 59 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.20e-01 chirality pdb=" CA ASP B 24 " pdb=" N ASP B 24 " pdb=" C ASP B 24 " pdb=" CB ASP B 24 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.88e-01 ... (remaining 2735 not shown) Planarity restraints: 2114 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 67 " -0.014 2.00e-02 2.50e+03 2.18e-02 8.35e+00 pdb=" CG PHE E 67 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE E 67 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE E 67 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 PHE E 67 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE E 67 " 0.011 2.00e-02 2.50e+03 pdb=" CZ PHE E 67 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP N1069 " -0.038 5.00e-02 4.00e+02 5.77e-02 5.32e+00 pdb=" N PRO N1070 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO N1070 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO N1070 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU H 113 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.17e+00 pdb=" CD GLU H 113 " -0.035 2.00e-02 2.50e+03 pdb=" OE1 GLU H 113 " 0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU H 113 " 0.013 2.00e-02 2.50e+03 ... (remaining 2111 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1764 2.75 - 3.29: 16104 3.29 - 3.83: 31878 3.83 - 4.36: 36857 4.36 - 4.90: 53627 Nonbonded interactions: 140230 Sorted by model distance: nonbonded pdb=" OG SER C 18 " pdb=" O LEU C 23 " model vdw 2.214 3.040 nonbonded pdb=" O GLU B 74 " pdb=" NH2 ARG D 92 " model vdw 2.216 3.120 nonbonded pdb=" N THR H 90 " pdb=" OE2 GLU H 93 " model vdw 2.264 3.120 nonbonded pdb=" O VAL N1156 " pdb=" OG SER N1159 " model vdw 2.275 3.040 nonbonded pdb=" NH1 ARG G 29 " pdb=" O SER H 36 " model vdw 2.287 3.120 ... (remaining 140225 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' selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 21 through 101) } ncs_group { reference = chain 'C' selection = (chain 'G' and (resid 14 through 117 or (resid 118 and (name N or name CA or nam \ e C or name O or name CB )))) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 31 through 124) } ncs_group { reference = (chain 'J' and resid 19 through 162) selection = (chain 'K' and resid 19 through 162) } 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.410 Find NCS groups from input model: 0.220 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 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 : 0.005 0.059 17266 Z= 0.448 Angle : 0.779 9.072 24572 Z= 0.642 Chirality : 0.044 0.185 2738 Planarity : 0.004 0.058 2114 Dihedral : 24.736 170.401 7317 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.55 (0.22), residues: 1256 helix: 0.91 (0.18), residues: 744 sheet: 0.55 (0.73), residues: 54 loop : -0.44 (0.26), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 99 TYR 0.022 0.001 TYR C 50 PHE 0.047 0.002 PHE E 67 TRP 0.033 0.002 TRP N1129 HIS 0.005 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.45 (17266) covalent geometry : angle 0.77870 / 0.64 (24572) hydrogen bonds : bond 0.12636 / 8.47 ( 831) hydrogen bonds : angle 5.52509 / 4.01 ( 2214) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8492 (mt-10) REVERT: A 106 ASP cc_start: 0.8794 (m-30) cc_final: 0.8572 (m-30) REVERT: B 63 GLU cc_start: 0.9155 (pm20) cc_final: 0.8664 (pm20) REVERT: D 68 ASP cc_start: 0.9087 (m-30) cc_final: 0.8875 (m-30) REVERT: D 95 GLN cc_start: 0.9339 (mt0) cc_final: 0.9049 (mp10) REVERT: D 108 LYS cc_start: 0.9620 (mtpp) cc_final: 0.9390 (mmmt) REVERT: E 77 ASP cc_start: 0.8590 (m-30) cc_final: 0.8219 (t0) REVERT: E 90 MET cc_start: 0.9021 (mmp) cc_final: 0.8524 (mmp) REVERT: E 120 MET cc_start: 0.8273 (tpt) cc_final: 0.8053 (mmm) REVERT: F 62 LEU cc_start: 0.9690 (mt) cc_final: 0.9388 (mt) REVERT: F 93 GLN cc_start: 0.8752 (tt0) cc_final: 0.8184 (tm-30) REVERT: G 24 GLN cc_start: 0.8919 (mp10) cc_final: 0.8692 (mp10) REVERT: G 38 ASN cc_start: 0.8572 (m-40) cc_final: 0.8267 (p0) REVERT: G 51 LEU cc_start: 0.9515 (tp) cc_final: 0.9256 (tp) REVERT: G 68 ASN cc_start: 0.8798 (m-40) cc_final: 0.8256 (t0) REVERT: G 72 ASP cc_start: 0.9130 (m-30) cc_final: 0.8781 (m-30) REVERT: H 41 VAL cc_start: 0.9328 (t) cc_final: 0.9100 (t) REVERT: N 1349 MET cc_start: -0.2944 (tpt) cc_final: -0.3439 (tpt) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.1176 time to fit residues: 33.3128 Evaluate side-chains 123 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 chunk 149 optimal weight: 30.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N1236 ASN N1255 HIS N1379 GLN N1415 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.067244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.045429 restraints weight = 156015.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.046698 restraints weight = 80411.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.047481 restraints weight = 53572.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.047770 restraints weight = 42118.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.047859 restraints weight = 37913.076| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 17266 Z= 0.262 Angle : 0.761 10.973 24572 Z= 0.427 Chirality : 0.046 0.408 2738 Planarity : 0.006 0.063 2114 Dihedral : 28.952 172.199 4715 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.18 % Allowed : 5.50 % Favored : 94.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.86 (0.22), residues: 1256 helix: 1.17 (0.18), residues: 756 sheet: 0.61 (0.69), residues: 60 loop : -0.39 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 79 TYR 0.017 0.002 TYR C 50 PHE 0.052 0.002 PHE N1149 TRP 0.036 0.004 TRP N1122 HIS 0.010 0.002 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.26 (17266) covalent geometry : angle 0.76085 / 0.43 (24572) hydrogen bonds : bond 0.10178 / 6.80 ( 831) hydrogen bonds : angle 4.19914 / 3.08 ( 2214) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 155 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 PHE cc_start: 0.8704 (m-10) cc_final: 0.8382 (m-10) REVERT: A 90 MET cc_start: 0.9108 (mmp) cc_final: 0.8897 (mmm) REVERT: C 38 ASN cc_start: 0.8243 (t0) cc_final: 0.7326 (t0) REVERT: E 90 MET cc_start: 0.9120 (mmp) cc_final: 0.8899 (mmm) REVERT: E 97 GLU cc_start: 0.9411 (mt-10) cc_final: 0.8586 (mm-30) REVERT: E 120 MET cc_start: 0.8726 (tpt) cc_final: 0.8498 (mmm) REVERT: F 62 LEU cc_start: 0.9727 (mt) cc_final: 0.9516 (mp) REVERT: F 93 GLN cc_start: 0.8819 (tt0) cc_final: 0.8331 (tm-30) REVERT: G 38 ASN cc_start: 0.8965 (m-40) cc_final: 0.8026 (t0) REVERT: G 64 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8786 (mm-30) REVERT: G 68 ASN cc_start: 0.8994 (m-40) cc_final: 0.8622 (t0) REVERT: G 72 ASP cc_start: 0.9200 (m-30) cc_final: 0.8759 (m-30) REVERT: G 74 LYS cc_start: 0.9397 (mmmm) cc_final: 0.9178 (tptp) outliers start: 2 outliers final: 0 residues processed: 156 average time/residue: 0.1246 time to fit residues: 30.0520 Evaluate side-chains 116 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 35 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 chunk 94 optimal weight: 20.0000 chunk 146 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 71 optimal weight: 30.0000 chunk 40 optimal weight: 0.6980 chunk 129 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 80 optimal weight: 20.0000 chunk 82 optimal weight: 20.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN ** N1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N1236 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.065398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.043651 restraints weight = 156869.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.044922 restraints weight = 79520.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.045712 restraints weight = 52222.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.045984 restraints weight = 41137.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.046053 restraints weight = 37053.336| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 17266 Z= 0.210 Angle : 0.683 11.951 24572 Z= 0.390 Chirality : 0.043 0.382 2738 Planarity : 0.005 0.070 2114 Dihedral : 29.347 178.264 4715 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.09 % Allowed : 2.61 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.02 (0.22), residues: 1256 helix: 1.32 (0.18), residues: 757 sheet: 0.31 (0.68), residues: 60 loop : -0.30 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N1137 TYR 0.019 0.002 TYR F 98 PHE 0.016 0.002 PHE D 70 TRP 0.034 0.004 TRP N1509 HIS 0.013 0.002 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.21 (17266) covalent geometry : angle 0.68293 / 0.39 (24572) hydrogen bonds : bond 0.06567 / 4.41 ( 831) hydrogen bonds : angle 4.05537 / 2.97 ( 2214) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 165 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 PHE cc_start: 0.8673 (m-10) cc_final: 0.8321 (m-80) REVERT: B 74 GLU cc_start: 0.9314 (pp20) cc_final: 0.8996 (pp20) REVERT: D 65 PHE cc_start: 0.9659 (t80) cc_final: 0.9246 (t80) REVERT: D 95 GLN cc_start: 0.9436 (mt0) cc_final: 0.9207 (mt0) REVERT: E 90 MET cc_start: 0.9019 (mmp) cc_final: 0.8771 (mmm) REVERT: E 97 GLU cc_start: 0.9453 (mt-10) cc_final: 0.8691 (mm-30) REVERT: F 62 LEU cc_start: 0.9716 (mt) cc_final: 0.9496 (mp) REVERT: F 93 GLN cc_start: 0.8836 (tt0) cc_final: 0.8438 (tm-30) REVERT: G 39 TYR cc_start: 0.9279 (m-80) cc_final: 0.8672 (m-80) REVERT: G 68 ASN cc_start: 0.8912 (m-40) cc_final: 0.8303 (t0) REVERT: G 74 LYS cc_start: 0.9434 (mmmm) cc_final: 0.9170 (tptp) REVERT: G 99 ARG cc_start: 0.7633 (tpt90) cc_final: 0.7361 (mmm160) REVERT: G 100 VAL cc_start: 0.8919 (t) cc_final: 0.8695 (t) REVERT: H 35 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7849 (tm-30) REVERT: N 1349 MET cc_start: 0.3614 (tpt) cc_final: 0.2848 (tpt) outliers start: 1 outliers final: 1 residues processed: 165 average time/residue: 0.1352 time to fit residues: 33.4362 Evaluate side-chains 119 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 113 optimal weight: 5.9990 chunk 73 optimal weight: 50.0000 chunk 66 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 149 optimal weight: 40.0000 chunk 22 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 55 optimal weight: 8.9990 chunk 152 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N1236 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.065080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.042931 restraints weight = 154089.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.044096 restraints weight = 78212.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.044829 restraints weight = 51942.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.045115 restraints weight = 41227.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.045416 restraints weight = 37230.756| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17266 Z= 0.159 Angle : 0.625 7.341 24572 Z= 0.358 Chirality : 0.041 0.339 2738 Planarity : 0.005 0.070 2114 Dihedral : 29.452 177.129 4715 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.27 % Allowed : 2.52 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.19 (0.23), residues: 1256 helix: 1.51 (0.18), residues: 756 sheet: 0.22 (0.68), residues: 60 loop : -0.31 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG H 86 TYR 0.017 0.001 TYR G 57 PHE 0.020 0.002 PHE E 104 TRP 0.010 0.001 TRP N1466 HIS 0.010 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.16 (17266) covalent geometry : angle 0.62517 / 0.36 (24572) hydrogen bonds : bond 0.05916 / 3.90 ( 831) hydrogen bonds : angle 3.71342 / 2.73 ( 2214) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 163 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 PHE cc_start: 0.8682 (m-10) cc_final: 0.8312 (m-80) REVERT: A 94 GLU cc_start: 0.9052 (tt0) cc_final: 0.8818 (tt0) REVERT: A 97 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8445 (mt-10) REVERT: B 74 GLU cc_start: 0.9296 (pp20) cc_final: 0.8968 (pp20) REVERT: B 84 MET cc_start: 0.8644 (tpt) cc_final: 0.8406 (tpp) REVERT: D 65 PHE cc_start: 0.9735 (t80) cc_final: 0.9336 (t80) REVERT: D 68 ASP cc_start: 0.9004 (m-30) cc_final: 0.8678 (m-30) REVERT: D 86 ARG cc_start: 0.9008 (mmp80) cc_final: 0.8599 (mmp80) REVERT: E 90 MET cc_start: 0.8964 (mmp) cc_final: 0.8647 (mmm) REVERT: E 97 GLU cc_start: 0.9444 (mt-10) cc_final: 0.8764 (mm-30) REVERT: E 110 CYS cc_start: 0.9655 (m) cc_final: 0.9040 (t) REVERT: F 74 GLU cc_start: 0.9204 (pp20) cc_final: 0.8682 (pp20) REVERT: F 88 TYR cc_start: 0.8829 (m-10) cc_final: 0.7563 (m-10) REVERT: F 93 GLN cc_start: 0.8867 (tt0) cc_final: 0.8467 (tm-30) REVERT: G 38 ASN cc_start: 0.9098 (m-40) cc_final: 0.8865 (m-40) REVERT: G 39 TYR cc_start: 0.9222 (m-80) cc_final: 0.8462 (m-80) REVERT: G 74 LYS cc_start: 0.9447 (mmmm) cc_final: 0.9180 (tptp) REVERT: G 99 ARG cc_start: 0.7520 (tpt90) cc_final: 0.7276 (mmm160) REVERT: H 35 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7669 (tm-30) REVERT: H 47 GLN cc_start: 0.9223 (tm-30) cc_final: 0.9005 (tm-30) REVERT: H 62 MET cc_start: 0.9601 (tpp) cc_final: 0.9396 (tpt) REVERT: H 83 TYR cc_start: 0.8813 (m-10) cc_final: 0.8560 (m-80) outliers start: 3 outliers final: 1 residues processed: 165 average time/residue: 0.1314 time to fit residues: 32.9688 Evaluate side-chains 123 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 0 optimal weight: 20.0000 chunk 150 optimal weight: 7.9990 chunk 112 optimal weight: 0.4980 chunk 133 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 126 optimal weight: 40.0000 chunk 132 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 9 optimal weight: 0.7980 chunk 38 optimal weight: 8.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N1451 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.063650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.041747 restraints weight = 156181.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.042892 restraints weight = 79798.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.043623 restraints weight = 53118.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.043882 restraints weight = 42127.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.044226 restraints weight = 38413.436| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17266 Z= 0.180 Angle : 0.636 7.941 24572 Z= 0.364 Chirality : 0.041 0.361 2738 Planarity : 0.005 0.073 2114 Dihedral : 29.637 178.654 4715 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.09 % Allowed : 1.89 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.24 (0.23), residues: 1256 helix: 1.53 (0.18), residues: 755 sheet: 0.14 (0.72), residues: 55 loop : -0.21 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 128 TYR 0.015 0.001 TYR N1117 PHE 0.012 0.001 PHE A 67 TRP 0.008 0.001 TRP N1466 HIS 0.004 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.18 (17266) covalent geometry : angle 0.63598 / 0.36 (24572) hydrogen bonds : bond 0.06293 / 4.17 ( 831) hydrogen bonds : angle 3.80204 / 2.79 ( 2214) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9065 (tt0) cc_final: 0.8626 (tt0) REVERT: A 97 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8155 (mp0) REVERT: B 74 GLU cc_start: 0.9350 (pp20) cc_final: 0.9021 (pp20) REVERT: B 84 MET cc_start: 0.8711 (tpt) cc_final: 0.8385 (tpp) REVERT: D 65 PHE cc_start: 0.9693 (t80) cc_final: 0.9474 (t80) REVERT: D 68 ASP cc_start: 0.8987 (m-30) cc_final: 0.8699 (m-30) REVERT: D 95 GLN cc_start: 0.9458 (mt0) cc_final: 0.9243 (mt0) REVERT: E 90 MET cc_start: 0.9018 (mmp) cc_final: 0.8784 (mmm) REVERT: E 97 GLU cc_start: 0.9429 (mt-10) cc_final: 0.8851 (mm-30) REVERT: E 110 CYS cc_start: 0.9695 (m) cc_final: 0.9071 (t) REVERT: F 62 LEU cc_start: 0.9726 (mt) cc_final: 0.9521 (mp) REVERT: F 70 VAL cc_start: 0.9740 (m) cc_final: 0.9442 (m) REVERT: F 74 GLU cc_start: 0.9240 (pp20) cc_final: 0.8689 (pp20) REVERT: F 93 GLN cc_start: 0.8878 (tt0) cc_final: 0.8457 (tm-30) REVERT: G 39 TYR cc_start: 0.9180 (m-80) cc_final: 0.8271 (m-80) REVERT: G 68 ASN cc_start: 0.8917 (m-40) cc_final: 0.8673 (m-40) REVERT: G 74 LYS cc_start: 0.9438 (mmmm) cc_final: 0.9191 (mmmm) REVERT: G 99 ARG cc_start: 0.7628 (tpt90) cc_final: 0.7340 (mmm160) REVERT: G 100 VAL cc_start: 0.8834 (t) cc_final: 0.8625 (t) REVERT: H 62 MET cc_start: 0.9645 (tpp) cc_final: 0.9435 (tpt) REVERT: N 1349 MET cc_start: 0.3315 (tpt) cc_final: 0.2754 (tpt) outliers start: 1 outliers final: 0 residues processed: 158 average time/residue: 0.1368 time to fit residues: 32.4466 Evaluate side-chains 109 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 57 optimal weight: 0.5980 chunk 112 optimal weight: 20.0000 chunk 2 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 136 optimal weight: 20.0000 chunk 73 optimal weight: 50.0000 chunk 17 optimal weight: 5.9990 chunk 145 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 123 optimal weight: 9.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 GLN E 55 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** F 25 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 = 0.3636 r_free = 0.3636 target = 0.063963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.041953 restraints weight = 154666.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.043079 restraints weight = 77764.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.043809 restraints weight = 51392.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.044136 restraints weight = 40764.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.044211 restraints weight = 36610.667| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17266 Z= 0.147 Angle : 0.614 7.883 24572 Z= 0.351 Chirality : 0.040 0.358 2738 Planarity : 0.005 0.074 2114 Dihedral : 29.681 177.982 4715 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.18 % Allowed : 1.53 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.24 (0.23), residues: 1256 helix: 1.54 (0.18), residues: 756 sheet: 0.15 (0.73), residues: 55 loop : -0.26 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 32 TYR 0.019 0.001 TYR G 57 PHE 0.011 0.001 PHE A 67 TRP 0.010 0.001 TRP N1509 HIS 0.008 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.15 (17266) covalent geometry : angle 0.61392 / 0.35 (24572) hydrogen bonds : bond 0.05208 / 3.43 ( 831) hydrogen bonds : angle 3.66031 / 2.69 ( 2214) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 158 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 PHE cc_start: 0.8728 (m-10) cc_final: 0.8341 (m-80) REVERT: A 94 GLU cc_start: 0.9057 (tt0) cc_final: 0.8570 (tt0) REVERT: A 97 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8127 (mp0) REVERT: B 63 GLU cc_start: 0.9264 (OUTLIER) cc_final: 0.9056 (pp20) REVERT: B 74 GLU cc_start: 0.9322 (pp20) cc_final: 0.8952 (pp20) REVERT: B 84 MET cc_start: 0.8542 (tpt) cc_final: 0.8306 (tpp) REVERT: D 62 MET cc_start: 0.9353 (mmp) cc_final: 0.9040 (mmp) REVERT: D 68 ASP cc_start: 0.9066 (m-30) cc_final: 0.8764 (m-30) REVERT: D 95 GLN cc_start: 0.9432 (mt0) cc_final: 0.9198 (mt0) REVERT: E 97 GLU cc_start: 0.9424 (mt-10) cc_final: 0.8818 (mm-30) REVERT: E 110 CYS cc_start: 0.9688 (m) cc_final: 0.9060 (t) REVERT: E 120 MET cc_start: 0.8942 (tpt) cc_final: 0.8688 (mmm) REVERT: F 59 LYS cc_start: 0.9102 (pttm) cc_final: 0.8894 (ptpp) REVERT: F 62 LEU cc_start: 0.9729 (mt) cc_final: 0.9475 (mp) REVERT: F 63 GLU cc_start: 0.9224 (mt-10) cc_final: 0.8581 (mp0) REVERT: F 70 VAL cc_start: 0.9725 (m) cc_final: 0.9409 (m) REVERT: F 74 GLU cc_start: 0.9227 (pp20) cc_final: 0.8691 (pp20) REVERT: F 93 GLN cc_start: 0.8910 (tt0) cc_final: 0.8529 (tm-30) REVERT: G 38 ASN cc_start: 0.8914 (m-40) cc_final: 0.8288 (p0) REVERT: G 39 TYR cc_start: 0.9170 (m-80) cc_final: 0.8241 (m-80) REVERT: G 68 ASN cc_start: 0.8899 (m-40) cc_final: 0.8657 (m-40) REVERT: G 74 LYS cc_start: 0.9455 (mmmm) cc_final: 0.9215 (mmmm) REVERT: G 99 ARG cc_start: 0.7605 (tpt90) cc_final: 0.7309 (mmm160) REVERT: G 100 VAL cc_start: 0.8868 (t) cc_final: 0.8637 (t) REVERT: H 47 GLN cc_start: 0.9334 (tm-30) cc_final: 0.9129 (tm-30) REVERT: N 1349 MET cc_start: 0.4317 (tpt) cc_final: 0.3850 (tpt) outliers start: 2 outliers final: 0 residues processed: 159 average time/residue: 0.1327 time to fit residues: 32.1101 Evaluate side-chains 120 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 38 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 114 optimal weight: 30.0000 chunk 21 optimal weight: 0.8980 chunk 1 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 104 optimal weight: 0.0000 chunk 10 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 77 optimal weight: 20.0000 chunk 94 optimal weight: 20.0000 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 68 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.064496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.042345 restraints weight = 153515.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.043487 restraints weight = 77842.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.044217 restraints weight = 52036.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.044501 restraints weight = 41439.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.044580 restraints weight = 37164.504| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17266 Z= 0.141 Angle : 0.622 12.273 24572 Z= 0.352 Chirality : 0.040 0.355 2738 Planarity : 0.005 0.074 2114 Dihedral : 29.619 178.299 4715 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.09 % Allowed : 1.26 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.22 (0.23), residues: 1256 helix: 1.50 (0.18), residues: 764 sheet: 0.03 (0.73), residues: 55 loop : -0.23 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 79 TYR 0.022 0.001 TYR N1394 PHE 0.018 0.001 PHE E 67 TRP 0.018 0.002 TRP N1436 HIS 0.007 0.001 HIS N1377 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.14 (17266) covalent geometry : angle 0.62231 / 0.35 (24572) hydrogen bonds : bond 0.04713 / 3.08 ( 831) hydrogen bonds : angle 3.62917 / 2.67 ( 2214) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 PHE cc_start: 0.8631 (m-10) cc_final: 0.8246 (m-80) REVERT: A 94 GLU cc_start: 0.9156 (tt0) cc_final: 0.8808 (tt0) REVERT: A 97 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8312 (mt-10) REVERT: B 74 GLU cc_start: 0.9340 (pp20) cc_final: 0.8947 (pp20) REVERT: B 84 MET cc_start: 0.8444 (tpt) cc_final: 0.8217 (tpp) REVERT: D 62 MET cc_start: 0.9387 (mmp) cc_final: 0.9185 (mmp) REVERT: D 68 ASP cc_start: 0.9043 (m-30) cc_final: 0.8724 (m-30) REVERT: D 95 GLN cc_start: 0.9428 (mt0) cc_final: 0.9216 (mt0) REVERT: E 90 MET cc_start: 0.9130 (mmp) cc_final: 0.8795 (mmm) REVERT: E 97 GLU cc_start: 0.9414 (mt-10) cc_final: 0.8841 (mm-30) REVERT: E 110 CYS cc_start: 0.9707 (m) cc_final: 0.9091 (t) REVERT: E 120 MET cc_start: 0.8942 (tpt) cc_final: 0.8623 (mmm) REVERT: F 59 LYS cc_start: 0.9106 (pttm) cc_final: 0.8883 (ptpp) REVERT: F 62 LEU cc_start: 0.9735 (mt) cc_final: 0.9520 (mt) REVERT: F 63 GLU cc_start: 0.9313 (mt-10) cc_final: 0.8586 (mp0) REVERT: F 70 VAL cc_start: 0.9728 (m) cc_final: 0.9401 (m) REVERT: F 74 GLU cc_start: 0.9230 (pp20) cc_final: 0.8690 (pp20) REVERT: F 93 GLN cc_start: 0.8921 (tt0) cc_final: 0.8532 (tm-30) REVERT: G 38 ASN cc_start: 0.8954 (m-40) cc_final: 0.8275 (p0) REVERT: G 39 TYR cc_start: 0.8838 (m-80) cc_final: 0.8162 (m-80) REVERT: G 64 GLU cc_start: 0.9388 (mm-30) cc_final: 0.9129 (mm-30) REVERT: G 68 ASN cc_start: 0.8864 (m-40) cc_final: 0.8622 (m-40) REVERT: G 74 LYS cc_start: 0.9407 (mmmm) cc_final: 0.9187 (mmmm) REVERT: G 99 ARG cc_start: 0.7605 (tpt90) cc_final: 0.7261 (mmm160) REVERT: G 100 VAL cc_start: 0.8875 (t) cc_final: 0.8627 (t) REVERT: H 47 GLN cc_start: 0.9385 (tm-30) cc_final: 0.9174 (tm-30) REVERT: N 1349 MET cc_start: 0.5536 (tpt) cc_final: 0.5251 (tpt) outliers start: 1 outliers final: 0 residues processed: 162 average time/residue: 0.1289 time to fit residues: 31.9450 Evaluate side-chains 119 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 38 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 94 optimal weight: 20.0000 chunk 75 optimal weight: 20.0000 chunk 88 optimal weight: 30.0000 chunk 67 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** F 25 ASN ** 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 = 0.3638 r_free = 0.3638 target = 0.064296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.042157 restraints weight = 153711.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.043270 restraints weight = 78037.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.044000 restraints weight = 51580.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.044312 restraints weight = 40963.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.044519 restraints weight = 36728.292| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17266 Z= 0.143 Angle : 0.627 9.446 24572 Z= 0.353 Chirality : 0.040 0.347 2738 Planarity : 0.005 0.074 2114 Dihedral : 29.603 177.907 4715 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.09 % Allowed : 1.26 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.18 (0.23), residues: 1256 helix: 1.46 (0.18), residues: 765 sheet: -0.01 (0.72), residues: 55 loop : -0.21 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 72 TYR 0.021 0.001 TYR G 57 PHE 0.017 0.001 PHE E 67 TRP 0.009 0.001 TRP N1436 HIS 0.004 0.001 HIS N1377 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.14 (17266) covalent geometry : angle 0.62732 / 0.35 (24572) hydrogen bonds : bond 0.04892 / 3.19 ( 831) hydrogen bonds : angle 3.66209 / 2.68 ( 2214) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 PHE cc_start: 0.8733 (m-10) cc_final: 0.8353 (m-80) REVERT: A 94 GLU cc_start: 0.9152 (tt0) cc_final: 0.8799 (tt0) REVERT: A 97 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8296 (mt-10) REVERT: B 74 GLU cc_start: 0.9289 (pp20) cc_final: 0.8793 (pp20) REVERT: B 84 MET cc_start: 0.8503 (tpt) cc_final: 0.8192 (tpp) REVERT: D 65 PHE cc_start: 0.9788 (t80) cc_final: 0.9468 (t80) REVERT: D 68 ASP cc_start: 0.9059 (m-30) cc_final: 0.8753 (m-30) REVERT: D 95 GLN cc_start: 0.9437 (mt0) cc_final: 0.9236 (mt0) REVERT: D 121 TYR cc_start: 0.8834 (t80) cc_final: 0.8628 (t80) REVERT: E 90 MET cc_start: 0.9139 (mmp) cc_final: 0.8798 (mmm) REVERT: E 97 GLU cc_start: 0.9452 (mt-10) cc_final: 0.8866 (mm-30) REVERT: E 110 CYS cc_start: 0.9707 (m) cc_final: 0.9121 (t) REVERT: E 120 MET cc_start: 0.8961 (tpt) cc_final: 0.8579 (mmm) REVERT: F 59 LYS cc_start: 0.9094 (pttm) cc_final: 0.8867 (ptpp) REVERT: F 62 LEU cc_start: 0.9731 (mt) cc_final: 0.9522 (mt) REVERT: F 63 GLU cc_start: 0.9319 (mt-10) cc_final: 0.8662 (mp0) REVERT: F 70 VAL cc_start: 0.9726 (m) cc_final: 0.9406 (m) REVERT: F 74 GLU cc_start: 0.9236 (pp20) cc_final: 0.8713 (pp20) REVERT: F 93 GLN cc_start: 0.8910 (tt0) cc_final: 0.8536 (tm-30) REVERT: G 38 ASN cc_start: 0.8977 (m-40) cc_final: 0.8332 (p0) REVERT: G 39 TYR cc_start: 0.8782 (m-80) cc_final: 0.8176 (m-80) REVERT: G 64 GLU cc_start: 0.9395 (mm-30) cc_final: 0.9067 (mm-30) REVERT: G 68 ASN cc_start: 0.8902 (m-40) cc_final: 0.8653 (m-40) REVERT: G 74 LYS cc_start: 0.9389 (mmmm) cc_final: 0.9160 (mmmm) REVERT: G 99 ARG cc_start: 0.7638 (tpt90) cc_final: 0.7336 (mmm160) REVERT: G 100 VAL cc_start: 0.8823 (t) cc_final: 0.8578 (t) REVERT: H 41 VAL cc_start: 0.9497 (t) cc_final: 0.9138 (t) REVERT: H 62 MET cc_start: 0.9403 (tpp) cc_final: 0.8894 (ptt) outliers start: 1 outliers final: 1 residues processed: 158 average time/residue: 0.1251 time to fit residues: 30.2668 Evaluate side-chains 116 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 15 optimal weight: 5.9990 chunk 77 optimal weight: 20.0000 chunk 69 optimal weight: 8.9990 chunk 121 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 55 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 85 optimal weight: 20.0000 chunk 33 optimal weight: 0.7980 chunk 99 optimal weight: 20.0000 chunk 17 optimal weight: 7.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N1261 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.061217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.039441 restraints weight = 156915.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.040473 restraints weight = 81543.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 71)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.041180 restraints weight = 54660.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 70)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.041536 restraints weight = 43818.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.041655 restraints weight = 39200.738| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 17266 Z= 0.233 Angle : 0.719 11.367 24572 Z= 0.401 Chirality : 0.043 0.350 2738 Planarity : 0.006 0.076 2114 Dihedral : 29.982 177.621 4715 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.88 (0.23), residues: 1256 helix: 1.17 (0.18), residues: 766 sheet: 0.10 (0.74), residues: 55 loop : -0.26 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N1392 TYR 0.031 0.002 TYR N1394 PHE 0.015 0.002 PHE A 67 TRP 0.024 0.003 TRP N1436 HIS 0.007 0.002 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.23 (17266) covalent geometry : angle 0.71922 / 0.40 (24572) hydrogen bonds : bond 0.08361 / 5.55 ( 831) hydrogen bonds : angle 4.11242 / 3.00 ( 2214) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9035 (tt0) cc_final: 0.8529 (tt0) REVERT: A 97 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8196 (mp0) REVERT: B 74 GLU cc_start: 0.9337 (pp20) cc_final: 0.8962 (pp20) REVERT: B 84 MET cc_start: 0.8556 (tpt) cc_final: 0.8225 (tpp) REVERT: D 68 ASP cc_start: 0.9036 (m-30) cc_final: 0.8634 (m-30) REVERT: D 95 GLN cc_start: 0.9425 (mt0) cc_final: 0.9168 (mt0) REVERT: E 90 MET cc_start: 0.9139 (mmp) cc_final: 0.8818 (mmm) REVERT: E 97 GLU cc_start: 0.9459 (mt-10) cc_final: 0.8975 (mm-30) REVERT: E 110 CYS cc_start: 0.9711 (m) cc_final: 0.9163 (t) REVERT: E 120 MET cc_start: 0.9079 (tpt) cc_final: 0.8764 (mmm) REVERT: F 93 GLN cc_start: 0.8895 (tt0) cc_final: 0.8612 (tm-30) REVERT: G 39 TYR cc_start: 0.8842 (m-80) cc_final: 0.8304 (m-80) REVERT: G 68 ASN cc_start: 0.8806 (m-40) cc_final: 0.8567 (m-40) REVERT: G 74 LYS cc_start: 0.9424 (mmmm) cc_final: 0.9212 (mmmm) REVERT: G 99 ARG cc_start: 0.7524 (tpt90) cc_final: 0.7266 (mmm160) REVERT: N 1349 MET cc_start: 0.4629 (tpt) cc_final: 0.4204 (tpt) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1303 time to fit residues: 27.4665 Evaluate side-chains 99 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 130 optimal weight: 7.9990 chunk 131 optimal weight: 8.9990 chunk 92 optimal weight: 20.0000 chunk 57 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 88 optimal weight: 30.0000 chunk 18 optimal weight: 5.9990 chunk 102 optimal weight: 0.3980 chunk 27 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.061606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.039653 restraints weight = 156173.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.040687 restraints weight = 79981.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 72)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.041377 restraints weight = 53327.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.041667 restraints weight = 42512.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.041849 restraints weight = 38388.983| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17266 Z= 0.189 Angle : 0.681 14.069 24572 Z= 0.380 Chirality : 0.042 0.360 2738 Planarity : 0.005 0.077 2114 Dihedral : 30.104 176.545 4715 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.97 (0.23), residues: 1256 helix: 1.25 (0.18), residues: 763 sheet: 0.14 (0.74), residues: 55 loop : -0.26 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 42 TYR 0.016 0.002 TYR D 83 PHE 0.015 0.001 PHE A 67 TRP 0.016 0.002 TRP N1509 HIS 0.004 0.001 HIS N1377 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.19 (17266) covalent geometry : angle 0.68061 / 0.38 (24572) hydrogen bonds : bond 0.05984 / 3.94 ( 831) hydrogen bonds : angle 3.97052 / 2.90 ( 2214) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9140 (tt0) cc_final: 0.8577 (tt0) REVERT: A 97 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8192 (mp0) REVERT: B 63 GLU cc_start: 0.9240 (pm20) cc_final: 0.8874 (pm20) REVERT: B 74 GLU cc_start: 0.9390 (pp20) cc_final: 0.8975 (pp20) REVERT: B 84 MET cc_start: 0.8519 (tpt) cc_final: 0.8175 (tpp) REVERT: D 68 ASP cc_start: 0.9091 (m-30) cc_final: 0.8587 (m-30) REVERT: D 95 GLN cc_start: 0.9441 (mt0) cc_final: 0.9167 (mt0) REVERT: D 121 TYR cc_start: 0.9111 (t80) cc_final: 0.8814 (t80) REVERT: E 90 MET cc_start: 0.9136 (mmp) cc_final: 0.8816 (mmm) REVERT: E 93 GLN cc_start: 0.9172 (tt0) cc_final: 0.8948 (tt0) REVERT: E 97 GLU cc_start: 0.9464 (mt-10) cc_final: 0.8938 (mm-30) REVERT: E 110 CYS cc_start: 0.9702 (m) cc_final: 0.9171 (t) REVERT: E 120 MET cc_start: 0.9122 (tpt) cc_final: 0.8807 (mmm) REVERT: F 63 GLU cc_start: 0.9319 (mt-10) cc_final: 0.8704 (mt-10) REVERT: F 70 VAL cc_start: 0.9739 (m) cc_final: 0.9446 (m) REVERT: F 74 GLU cc_start: 0.9217 (pp20) cc_final: 0.8676 (pp20) REVERT: F 93 GLN cc_start: 0.9014 (tt0) cc_final: 0.8614 (tm-30) REVERT: G 38 ASN cc_start: 0.9214 (m-40) cc_final: 0.8778 (p0) REVERT: G 39 TYR cc_start: 0.8791 (m-80) cc_final: 0.8203 (m-80) REVERT: G 64 GLU cc_start: 0.9387 (mm-30) cc_final: 0.8874 (mm-30) REVERT: G 74 LYS cc_start: 0.9418 (mmmm) cc_final: 0.9187 (mmmm) REVERT: G 99 ARG cc_start: 0.7508 (tpt90) cc_final: 0.7278 (mmm160) REVERT: G 100 VAL cc_start: 0.8841 (t) cc_final: 0.8614 (t) REVERT: H 41 VAL cc_start: 0.9495 (t) cc_final: 0.9271 (t) REVERT: N 1349 MET cc_start: 0.5223 (tpt) cc_final: 0.4726 (tpt) REVERT: N 1624 MET cc_start: -0.1488 (mmm) cc_final: -0.1694 (mmm) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.1240 time to fit residues: 26.2761 Evaluate side-chains 99 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 107 optimal weight: 0.0170 chunk 69 optimal weight: 10.0000 chunk 84 optimal weight: 20.0000 chunk 61 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 98 optimal weight: 20.0000 chunk 30 optimal weight: 0.6980 chunk 73 optimal weight: 50.0000 chunk 138 optimal weight: 3.9990 chunk 77 optimal weight: 20.0000 chunk 44 optimal weight: 0.4980 overall best weight: 1.6422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.062359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.040101 restraints weight = 154117.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.041175 restraints weight = 78339.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 73)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.041904 restraints weight = 52042.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.042185 restraints weight = 41503.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.042262 restraints weight = 37312.222| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17266 Z= 0.149 Angle : 0.647 7.733 24572 Z= 0.364 Chirality : 0.041 0.352 2738 Planarity : 0.005 0.076 2114 Dihedral : 30.044 176.716 4715 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.13 (0.23), residues: 1256 helix: 1.39 (0.18), residues: 762 sheet: 0.16 (0.76), residues: 55 loop : -0.19 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 42 TYR 0.016 0.001 TYR D 83 PHE 0.015 0.001 PHE A 67 TRP 0.012 0.002 TRP N1509 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.15 (17266) covalent geometry : angle 0.64688 / 0.36 (24572) hydrogen bonds : bond 0.05174 / 3.39 ( 831) hydrogen bonds : angle 3.83381 / 2.81 ( 2214) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3398.96 seconds wall clock time: 59 minutes 23.26 seconds (3563.26 seconds total)