Starting phenix.real_space_refine on Fri Jul 3 21:11:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hak_34594/07_2026/8hak_34594.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hak_34594/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hak_34594/07_2026/8hak_34594.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hak_34594/07_2026/8hak_34594.map" model { file = "/net/cci-nas-00/data/ceres_data/8hak_34594/07_2026/8hak_34594.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hak_34594/07_2026/8hak_34594.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8hak_34594/07_2026/8hak_34594.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hak_34594/07_2026/8hak_34594.cif" } 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-dev-6108/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: 2.75, per 1000 atoms: 0.17 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: 1.10 Conformation dependent library (CDL) restraints added in 367.1 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: 1.58 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: 2.84 Time building geometry restraints manager: 1.42 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: 23404 1.81 - 3.63: 1097 3.63 - 5.44: 52 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: 0.920 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.840 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 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:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.300 ------------------------------------------------------------------------------- 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 : 0.774 9.072 24572 Z= 0.638 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 0.77429 / 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 : 0.420 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: 0.8665 (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: 0.8264 (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: 0.9099 (t) REVERT: N 1349 MET cc_start: -0.2944 (tpt) cc_final: -0.3440 (tpt) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.1018 time to fit residues: 28.8897 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 : 0.449 ------------------------------------------------------------------------------- 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... C 104 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** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.066885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.045089 restraints weight = 156453.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.046306 restraints weight = 80694.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.047109 restraints weight = 53688.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.047418 restraints weight = 42462.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.047710 restraints weight = 37838.580| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 17266 Z= 0.267 Angle : 0.781 10.467 24572 Z= 0.439 Chirality : 0.048 0.393 2738 Planarity : 0.006 0.064 2114 Dihedral : 29.089 172.899 4715 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.18 % Allowed : 5.41 % Favored : 94.41 % 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: 0.84 (0.22), residues: 1256 helix: 1.17 (0.18), residues: 755 sheet: 0.60 (0.69), residues: 60 loop : -0.40 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N1166 TYR 0.018 0.002 TYR C 50 PHE 0.059 0.003 PHE N1149 TRP 0.040 0.004 TRP N1122 HIS 0.011 0.002 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.27 (17266) covalent geometry : angle 0.78081 / 0.44 (24572) hydrogen bonds : bond 0.10378 / 6.92 ( 831) hydrogen bonds : angle 4.23524 / 3.10 ( 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 : 0.500 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: 0.8728 (m-10) cc_final: 0.8359 (m-10) REVERT: A 90 MET cc_start: 0.9145 (mmp) cc_final: 0.8931 (mmm) REVERT: C 38 ASN cc_start: 0.8254 (t0) cc_final: 0.7365 (t0) REVERT: D 121 TYR cc_start: 0.8096 (t80) cc_final: 0.7888 (t80) REVERT: E 90 MET cc_start: 0.9123 (mmp) cc_final: 0.8905 (mmm) REVERT: E 97 GLU cc_start: 0.9411 (mt-10) cc_final: 0.8606 (mm-30) REVERT: E 120 MET cc_start: 0.8637 (tpt) cc_final: 0.8379 (mmm) REVERT: F 62 LEU cc_start: 0.9730 (mt) cc_final: 0.9529 (mp) REVERT: F 93 GLN cc_start: 0.8826 (tt0) cc_final: 0.8350 (tm-30) REVERT: G 38 ASN cc_start: 0.8980 (m-40) cc_final: 0.8108 (t0) REVERT: G 64 GLU cc_start: 0.9185 (mm-30) cc_final: 0.8852 (mm-30) REVERT: G 68 ASN cc_start: 0.8999 (m-40) cc_final: 0.8631 (t0) REVERT: G 72 ASP cc_start: 0.9200 (m-30) cc_final: 0.8694 (m-30) REVERT: G 74 LYS cc_start: 0.9412 (mmmm) cc_final: 0.9195 (tptp) outliers start: 2 outliers final: 0 residues processed: 156 average time/residue: 0.1155 time to fit residues: 27.7173 Evaluate side-chains 113 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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: 3.9990 chunk 128 optimal weight: 0.6980 chunk 94 optimal weight: 20.0000 chunk 146 optimal weight: 10.0000 chunk 106 optimal weight: 0.7980 chunk 71 optimal weight: 30.0000 chunk 40 optimal weight: 0.9990 chunk 129 optimal weight: 20.0000 chunk 14 optimal weight: 1.9990 chunk 80 optimal weight: 20.0000 chunk 82 optimal weight: 20.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.067798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.045903 restraints weight = 154733.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.047173 restraints weight = 78416.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.047988 restraints weight = 51823.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.048344 restraints weight = 40897.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.048417 restraints weight = 36480.645| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17266 Z= 0.150 Angle : 0.605 8.200 24572 Z= 0.353 Chirality : 0.041 0.338 2738 Planarity : 0.005 0.067 2114 Dihedral : 29.139 175.733 4715 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.18 % Allowed : 1.98 % Favored : 97.84 % 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: 1.14 (0.23), residues: 1256 helix: 1.43 (0.18), residues: 759 sheet: 0.30 (0.73), residues: 55 loop : -0.27 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.000 ARG G 29 TYR 0.017 0.001 TYR F 98 PHE 0.016 0.001 PHE E 67 TRP 0.017 0.002 TRP N1509 HIS 0.006 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.15 (17266) covalent geometry : angle 0.60527 / 0.35 (24572) hydrogen bonds : bond 0.05480 / 3.65 ( 831) hydrogen bonds : angle 3.75711 / 2.76 ( 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 172 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 170 time to evaluate : 0.454 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: 0.8522 (m-10) cc_final: 0.8189 (m-80) REVERT: B 74 GLU cc_start: 0.9311 (pp20) cc_final: 0.9093 (pp20) REVERT: B 97 LEU cc_start: 0.9137 (tp) cc_final: 0.8889 (tp) REVERT: D 86 ARG cc_start: 0.8968 (mmp80) cc_final: 0.8656 (mmp80) REVERT: D 95 GLN cc_start: 0.9440 (mt0) cc_final: 0.9204 (mt0) REVERT: E 90 MET cc_start: 0.8979 (mmp) cc_final: 0.8333 (mmp) REVERT: E 97 GLU cc_start: 0.9422 (mt-10) cc_final: 0.8506 (mm-30) REVERT: E 120 MET cc_start: 0.8641 (tpt) cc_final: 0.8382 (mmm) REVERT: F 70 VAL cc_start: 0.9720 (m) cc_final: 0.9506 (m) REVERT: F 74 GLU cc_start: 0.9182 (pp20) cc_final: 0.8644 (pp20) REVERT: F 93 GLN cc_start: 0.8862 (tt0) cc_final: 0.8333 (tm-30) REVERT: G 38 ASN cc_start: 0.8908 (m-40) cc_final: 0.8647 (p0) REVERT: G 64 GLU cc_start: 0.9025 (mm-30) cc_final: 0.8731 (mm-30) REVERT: G 68 ASN cc_start: 0.8951 (m-40) cc_final: 0.8582 (t0) REVERT: G 72 ASP cc_start: 0.9141 (m-30) cc_final: 0.8576 (m-30) REVERT: G 74 LYS cc_start: 0.9412 (mmmm) cc_final: 0.9158 (tptp) REVERT: N 1349 MET cc_start: 0.2199 (tpt) cc_final: 0.1322 (tpt) REVERT: N 1624 MET cc_start: -0.1524 (mmm) cc_final: -0.1756 (mmm) outliers start: 2 outliers final: 1 residues processed: 171 average time/residue: 0.1174 time to fit residues: 30.1687 Evaluate side-chains 121 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 0.403 ------------------------------------------------------------------------------- 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: 9.9990 chunk 73 optimal weight: 50.0000 chunk 66 optimal weight: 10.0000 chunk 59 optimal weight: 0.8980 chunk 149 optimal weight: 30.0000 chunk 22 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 chunk 152 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 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** G 110 ASN ** N1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N1451 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.063093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.041439 restraints weight = 159158.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.042601 restraints weight = 81784.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.043306 restraints weight = 54964.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.043580 restraints weight = 43918.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.043793 restraints weight = 39686.798| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17266 Z= 0.237 Angle : 0.740 12.315 24572 Z= 0.414 Chirality : 0.045 0.293 2738 Planarity : 0.006 0.073 2114 Dihedral : 29.801 177.657 4715 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.18 % Allowed : 3.61 % Favored : 96.21 % 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: 0.71 (0.22), residues: 1256 helix: 1.07 (0.18), residues: 755 sheet: 0.18 (0.68), residues: 60 loop : -0.40 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 86 TYR 0.018 0.002 TYR H 42 PHE 0.018 0.002 PHE C 25 TRP 0.008 0.002 TRP N1466 HIS 0.015 0.002 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.24 (17266) covalent geometry : angle 0.74022 / 0.41 (24572) hydrogen bonds : bond 0.09823 / 6.55 ( 831) hydrogen bonds : angle 4.07666 / 2.96 ( 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 155 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 153 time to evaluate : 0.317 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 50 GLU cc_start: 0.9494 (mm-30) cc_final: 0.9181 (mm-30) REVERT: A 97 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8330 (pt0) REVERT: A 106 ASP cc_start: 0.9220 (m-30) cc_final: 0.8800 (m-30) REVERT: B 74 GLU cc_start: 0.9308 (pp20) cc_final: 0.9066 (pp20) REVERT: D 62 MET cc_start: 0.9684 (mmm) cc_final: 0.9461 (mmm) REVERT: D 65 PHE cc_start: 0.9744 (t80) cc_final: 0.9393 (t80) REVERT: D 68 ASP cc_start: 0.9034 (m-30) cc_final: 0.8742 (m-30) REVERT: D 86 ARG cc_start: 0.9031 (mmp80) cc_final: 0.8744 (mmp80) REVERT: E 90 MET cc_start: 0.9015 (mmp) cc_final: 0.8752 (mmm) REVERT: E 97 GLU cc_start: 0.9432 (mt-10) cc_final: 0.8747 (mm-30) REVERT: E 110 CYS cc_start: 0.9742 (m) cc_final: 0.9152 (t) REVERT: F 88 TYR cc_start: 0.8863 (m-10) cc_final: 0.6210 (m-10) REVERT: F 93 GLN cc_start: 0.8806 (tt0) cc_final: 0.8433 (tm-30) REVERT: G 68 ASN cc_start: 0.8872 (m-40) cc_final: 0.8646 (m-40) REVERT: G 74 LYS cc_start: 0.9450 (mmmm) cc_final: 0.9198 (tptp) REVERT: G 99 ARG cc_start: 0.7610 (tpt90) cc_final: 0.7363 (mmm160) REVERT: H 83 TYR cc_start: 0.9006 (m-10) cc_final: 0.8701 (m-80) REVERT: N 1624 MET cc_start: -0.1378 (mmm) cc_final: -0.1580 (mmm) outliers start: 2 outliers final: 2 residues processed: 154 average time/residue: 0.1181 time to fit residues: 27.1484 Evaluate side-chains 113 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 111 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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: 5.9990 chunk 112 optimal weight: 30.0000 chunk 133 optimal weight: 30.0000 chunk 15 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 132 optimal weight: 30.0000 chunk 10 optimal weight: 0.9980 chunk 62 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 68 ASN ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.063710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.041905 restraints weight = 157262.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.043072 restraints weight = 80811.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.043845 restraints weight = 54133.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.044126 restraints weight = 43007.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.044329 restraints weight = 38673.173| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3641 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= 0.172 Angle : 0.630 9.022 24572 Z= 0.365 Chirality : 0.041 0.341 2738 Planarity : 0.005 0.072 2114 Dihedral : 29.865 179.268 4715 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.09 % Allowed : 1.71 % Favored : 98.20 % 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: 0.99 (0.22), residues: 1256 helix: 1.34 (0.18), residues: 760 sheet: -0.09 (0.71), residues: 55 loop : -0.34 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 86 TYR 0.029 0.002 TYR G 39 PHE 0.017 0.002 PHE N1508 TRP 0.017 0.002 TRP N1436 HIS 0.008 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.17 (17266) covalent geometry : angle 0.63021 / 0.36 (24572) hydrogen bonds : bond 0.05919 / 3.91 ( 831) hydrogen bonds : angle 3.86328 / 2.81 ( 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 155 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 154 time to evaluate : 0.367 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: 0.9065 (tt0) cc_final: 0.8771 (tt0) REVERT: A 97 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8308 (mt-10) REVERT: A 106 ASP cc_start: 0.9058 (m-30) cc_final: 0.8710 (m-30) REVERT: A 110 CYS cc_start: 0.8590 (t) cc_final: 0.8267 (t) REVERT: B 74 GLU cc_start: 0.9365 (pp20) cc_final: 0.9031 (pp20) REVERT: B 84 MET cc_start: 0.8662 (tpt) cc_final: 0.8313 (tpp) REVERT: D 37 TYR cc_start: 0.9310 (m-80) cc_final: 0.8763 (m-80) REVERT: D 65 PHE cc_start: 0.9757 (t80) cc_final: 0.9482 (t80) REVERT: D 68 ASP cc_start: 0.9121 (m-30) cc_final: 0.8811 (m-30) REVERT: D 86 ARG cc_start: 0.8986 (mmp80) cc_final: 0.8688 (mmp80) REVERT: D 95 GLN cc_start: 0.9467 (mt0) cc_final: 0.9204 (mt0) REVERT: E 90 MET cc_start: 0.8993 (mmp) cc_final: 0.8707 (mmm) REVERT: E 97 GLU cc_start: 0.9418 (mt-10) cc_final: 0.8758 (mm-30) REVERT: E 110 CYS cc_start: 0.9665 (m) cc_final: 0.9083 (t) REVERT: E 120 MET cc_start: 0.8935 (tpt) cc_final: 0.8733 (mmm) REVERT: F 62 LEU cc_start: 0.9722 (mt) cc_final: 0.9503 (mp) REVERT: F 70 VAL cc_start: 0.9727 (m) cc_final: 0.9427 (m) REVERT: F 74 GLU cc_start: 0.9214 (pp20) cc_final: 0.8661 (pp20) REVERT: F 84 MET cc_start: 0.9005 (tpt) cc_final: 0.8463 (tpp) REVERT: F 93 GLN cc_start: 0.8838 (tt0) cc_final: 0.8446 (tm-30) REVERT: G 38 ASN cc_start: 0.9183 (m-40) cc_final: 0.8831 (p0) REVERT: G 39 TYR cc_start: 0.8945 (m-10) cc_final: 0.8668 (m-80) REVERT: G 64 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8865 (mm-30) REVERT: G 68 ASN cc_start: 0.8843 (m-40) cc_final: 0.8635 (m-40) REVERT: G 74 LYS cc_start: 0.9445 (mmmm) cc_final: 0.9199 (mmmm) REVERT: G 99 ARG cc_start: 0.7595 (tpt90) cc_final: 0.7307 (mmm160) REVERT: G 100 VAL cc_start: 0.8858 (t) cc_final: 0.8642 (t) REVERT: N 1349 MET cc_start: 0.3782 (tpt) cc_final: 0.3033 (tpt) outliers start: 1 outliers final: 0 residues processed: 155 average time/residue: 0.1146 time to fit residues: 26.2256 Evaluate side-chains 114 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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: 0.8980 chunk 112 optimal weight: 20.0000 chunk 2 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 136 optimal weight: 9.9990 chunk 73 optimal weight: 50.0000 chunk 17 optimal weight: 5.9990 chunk 145 optimal weight: 20.0000 chunk 36 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 123 optimal weight: 7.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 55 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** 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 = 0.3615 r_free = 0.3615 target = 0.063093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.041049 restraints weight = 155930.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.042139 restraints weight = 80257.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.042863 restraints weight = 54066.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.043247 restraints weight = 43527.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.043321 restraints weight = 38416.798| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 17266 Z= 0.165 Angle : 0.627 8.472 24572 Z= 0.359 Chirality : 0.041 0.332 2738 Planarity : 0.005 0.074 2114 Dihedral : 29.940 179.786 4715 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % 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: 1.10 (0.22), residues: 1256 helix: 1.47 (0.18), residues: 760 sheet: -0.16 (0.71), residues: 55 loop : -0.37 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N1391 TYR 0.019 0.001 TYR G 57 PHE 0.012 0.001 PHE A 67 TRP 0.008 0.001 TRP N1466 HIS 0.007 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.16 (17266) covalent geometry : angle 0.62691 / 0.36 (24572) hydrogen bonds : bond 0.05925 / 3.90 ( 831) hydrogen bonds : angle 3.76202 / 2.76 ( 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 149 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.355 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: 0.8995 (tt0) cc_final: 0.8514 (tt0) REVERT: A 97 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8068 (mp0) REVERT: A 110 CYS cc_start: 0.8725 (t) cc_final: 0.8378 (t) REVERT: B 74 GLU cc_start: 0.9309 (pp20) cc_final: 0.8877 (pp20) REVERT: B 84 MET cc_start: 0.8666 (tpt) cc_final: 0.8275 (tpp) REVERT: D 65 PHE cc_start: 0.9781 (t80) cc_final: 0.9556 (t80) REVERT: D 68 ASP cc_start: 0.9138 (m-30) cc_final: 0.8796 (m-30) REVERT: D 86 ARG cc_start: 0.8936 (mmp80) cc_final: 0.8642 (mmp80) REVERT: D 95 GLN cc_start: 0.9416 (mt0) cc_final: 0.9147 (mt0) REVERT: E 90 MET cc_start: 0.8985 (mmp) cc_final: 0.8697 (mmm) REVERT: E 97 GLU cc_start: 0.9426 (mt-10) cc_final: 0.8837 (mm-30) REVERT: E 110 CYS cc_start: 0.9668 (m) cc_final: 0.9096 (t) REVERT: E 120 MET cc_start: 0.9068 (tpt) cc_final: 0.8821 (mmm) REVERT: F 62 LEU cc_start: 0.9736 (mt) cc_final: 0.9512 (mp) REVERT: F 70 VAL cc_start: 0.9731 (m) cc_final: 0.9424 (m) REVERT: F 74 GLU cc_start: 0.9206 (pp20) cc_final: 0.8660 (pp20) REVERT: F 84 MET cc_start: 0.8875 (tpt) cc_final: 0.8431 (tpp) REVERT: F 93 GLN cc_start: 0.8881 (tt0) cc_final: 0.8532 (tm-30) REVERT: G 38 ASN cc_start: 0.9132 (m-40) cc_final: 0.8817 (p0) REVERT: G 39 TYR cc_start: 0.8978 (m-10) cc_final: 0.8692 (m-80) REVERT: G 68 ASN cc_start: 0.8923 (m-40) cc_final: 0.8358 (t0) REVERT: G 74 LYS cc_start: 0.9393 (mmmm) cc_final: 0.9164 (mmmm) REVERT: G 99 ARG cc_start: 0.7579 (tpt90) cc_final: 0.7329 (mmm160) REVERT: G 100 VAL cc_start: 0.8863 (t) cc_final: 0.8633 (t) REVERT: H 47 GLN cc_start: 0.9273 (tm-30) cc_final: 0.9041 (tm-30) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1138 time to fit residues: 25.7191 Evaluate side-chains 114 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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: 0.0270 chunk 51 optimal weight: 10.0000 chunk 114 optimal weight: 20.0000 chunk 21 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 104 optimal weight: 8.9990 chunk 10 optimal weight: 0.6980 chunk 116 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 94 optimal weight: 20.0000 overall best weight: 1.9240 ------------------------------------------------------------------------------- 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 = 0.3616 r_free = 0.3616 target = 0.063231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.041151 restraints weight = 154617.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.042235 restraints weight = 78728.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.042921 restraints weight = 52691.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.043345 restraints weight = 42049.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.043416 restraints weight = 37125.117| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17266 Z= 0.155 Angle : 0.624 9.143 24572 Z= 0.359 Chirality : 0.040 0.335 2738 Planarity : 0.005 0.075 2114 Dihedral : 29.936 179.690 4715 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.09 % Allowed : 1.17 % Favored : 98.74 % 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: 1.06 (0.22), residues: 1256 helix: 1.40 (0.18), residues: 765 sheet: -0.00 (0.71), residues: 55 loop : -0.36 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N1392 TYR 0.022 0.002 TYR G 57 PHE 0.014 0.001 PHE A 67 TRP 0.010 0.002 TRP N1436 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.16 (17266) covalent geometry : angle 0.62416 / 0.36 (24572) hydrogen bonds : bond 0.05347 / 3.51 ( 831) hydrogen bonds : angle 3.76047 / 2.75 ( 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 151 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 0.396 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 94 GLU cc_start: 0.9027 (tt0) cc_final: 0.8559 (tt0) REVERT: A 97 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8147 (mp0) REVERT: A 110 CYS cc_start: 0.8725 (t) cc_final: 0.8386 (t) REVERT: B 74 GLU cc_start: 0.9308 (pp20) cc_final: 0.8853 (pp20) REVERT: B 84 MET cc_start: 0.8577 (tpt) cc_final: 0.8266 (tpp) REVERT: D 65 PHE cc_start: 0.9741 (t80) cc_final: 0.9538 (t80) REVERT: D 68 ASP cc_start: 0.9084 (m-30) cc_final: 0.8723 (m-30) REVERT: D 95 GLN cc_start: 0.9422 (mt0) cc_final: 0.9162 (mt0) REVERT: E 90 MET cc_start: 0.9001 (mmp) cc_final: 0.8715 (mmm) REVERT: E 97 GLU cc_start: 0.9438 (mt-10) cc_final: 0.8910 (mm-30) REVERT: E 110 CYS cc_start: 0.9678 (m) cc_final: 0.9143 (t) REVERT: E 120 MET cc_start: 0.9109 (tpt) cc_final: 0.8788 (mmm) REVERT: F 62 LEU cc_start: 0.9743 (mt) cc_final: 0.9521 (mt) REVERT: F 63 GLU cc_start: 0.9301 (mt-10) cc_final: 0.8511 (mp0) REVERT: F 70 VAL cc_start: 0.9726 (m) cc_final: 0.9417 (m) REVERT: F 74 GLU cc_start: 0.9215 (pp20) cc_final: 0.8647 (pp20) REVERT: F 84 MET cc_start: 0.8998 (tpt) cc_final: 0.8576 (tpp) REVERT: F 93 GLN cc_start: 0.8886 (tt0) cc_final: 0.8531 (tm-30) REVERT: G 38 ASN cc_start: 0.9079 (m-40) cc_final: 0.8726 (p0) REVERT: G 39 TYR cc_start: 0.8995 (m-10) cc_final: 0.8691 (m-80) REVERT: G 74 LYS cc_start: 0.9439 (mmmm) cc_final: 0.9218 (mmmm) REVERT: G 99 ARG cc_start: 0.7503 (tpt90) cc_final: 0.7204 (mmm160) REVERT: G 100 VAL cc_start: 0.8882 (t) cc_final: 0.8618 (t) REVERT: H 47 GLN cc_start: 0.9250 (tm-30) cc_final: 0.9001 (tm-30) REVERT: H 62 MET cc_start: 0.9543 (tpp) cc_final: 0.9298 (tpt) REVERT: N 1349 MET cc_start: 0.4730 (tpt) cc_final: 0.4396 (tpt) outliers start: 1 outliers final: 1 residues processed: 151 average time/residue: 0.1070 time to fit residues: 24.3852 Evaluate side-chains 114 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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: 7.9990 chunk 45 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 94 optimal weight: 20.0000 chunk 75 optimal weight: 20.0000 chunk 88 optimal weight: 20.0000 chunk 67 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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** G 31 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.062159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.040258 restraints weight = 155463.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.041314 restraints weight = 79042.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.042039 restraints weight = 52291.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.042290 restraints weight = 41511.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.042374 restraints weight = 37588.547| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 17266 Z= 0.181 Angle : 0.646 9.964 24572 Z= 0.369 Chirality : 0.041 0.332 2738 Planarity : 0.005 0.077 2114 Dihedral : 30.032 179.076 4715 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % 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: 1.03 (0.23), residues: 1256 helix: 1.35 (0.18), residues: 763 sheet: -0.04 (0.72), residues: 55 loop : -0.29 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 42 TYR 0.022 0.001 TYR G 39 PHE 0.012 0.001 PHE A 67 TRP 0.013 0.002 TRP N1436 HIS 0.006 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.18 (17266) covalent geometry : angle 0.64648 / 0.37 (24572) hydrogen bonds : bond 0.06323 / 4.17 ( 831) hydrogen bonds : angle 3.86886 / 2.82 ( 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 142 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.428 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: A 94 GLU cc_start: 0.9043 (tt0) cc_final: 0.8573 (tt0) REVERT: A 97 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8068 (mp0) REVERT: A 110 CYS cc_start: 0.8859 (t) cc_final: 0.8532 (t) REVERT: B 74 GLU cc_start: 0.9313 (pp20) cc_final: 0.8893 (pp20) REVERT: B 84 MET cc_start: 0.8618 (tpt) cc_final: 0.8299 (tpp) REVERT: D 65 PHE cc_start: 0.9723 (t80) cc_final: 0.9355 (t80) REVERT: D 68 ASP cc_start: 0.9160 (m-30) cc_final: 0.8790 (m-30) REVERT: D 95 GLN cc_start: 0.9474 (mt0) cc_final: 0.9190 (mt0) REVERT: E 97 GLU cc_start: 0.9465 (mt-10) cc_final: 0.8833 (mm-30) REVERT: E 110 CYS cc_start: 0.9680 (m) cc_final: 0.9141 (t) REVERT: E 120 MET cc_start: 0.9062 (tpt) cc_final: 0.8730 (mmm) REVERT: F 62 LEU cc_start: 0.9742 (mt) cc_final: 0.9514 (mt) REVERT: F 63 GLU cc_start: 0.9294 (mt-10) cc_final: 0.8501 (mp0) REVERT: F 70 VAL cc_start: 0.9741 (m) cc_final: 0.9448 (m) REVERT: F 74 GLU cc_start: 0.9198 (pp20) cc_final: 0.8670 (pp20) REVERT: F 84 MET cc_start: 0.9013 (tpt) cc_final: 0.8570 (tpp) REVERT: F 93 GLN cc_start: 0.8908 (tt0) cc_final: 0.8595 (tm-30) REVERT: G 38 ASN cc_start: 0.9049 (m-40) cc_final: 0.8733 (p0) REVERT: G 39 TYR cc_start: 0.9061 (m-10) cc_final: 0.8689 (m-80) REVERT: G 68 ASN cc_start: 0.8702 (m-40) cc_final: 0.8311 (m-40) REVERT: G 74 LYS cc_start: 0.9414 (mmmm) cc_final: 0.9189 (mmmm) REVERT: G 99 ARG cc_start: 0.7495 (tpt90) cc_final: 0.7224 (mmm160) REVERT: G 100 VAL cc_start: 0.8941 (t) cc_final: 0.8635 (t) REVERT: H 62 MET cc_start: 0.9546 (tpp) cc_final: 0.9042 (ptt) REVERT: N 1349 MET cc_start: 0.5431 (tpt) cc_final: 0.5120 (tpt) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1070 time to fit residues: 23.6030 Evaluate side-chains 110 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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: 0.9990 chunk 77 optimal weight: 20.0000 chunk 69 optimal weight: 8.9990 chunk 121 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 55 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 85 optimal weight: 20.0000 chunk 33 optimal weight: 0.8980 chunk 99 optimal weight: 20.0000 chunk 17 optimal weight: 9.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 93 GLN ** 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 = 0.3603 r_free = 0.3603 target = 0.062839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.040749 restraints weight = 153882.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.041808 restraints weight = 79066.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.042463 restraints weight = 52752.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.042734 restraints weight = 42216.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.042957 restraints weight = 38118.188| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 17266 Z= 0.147 Angle : 0.619 8.509 24572 Z= 0.357 Chirality : 0.040 0.333 2738 Planarity : 0.005 0.077 2114 Dihedral : 29.993 179.551 4715 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % 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: 1.44 (0.18), residues: 767 sheet: -0.04 (0.72), residues: 55 loop : -0.30 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 35 TYR 0.021 0.001 TYR G 39 PHE 0.018 0.001 PHE A 67 TRP 0.011 0.001 TRP N1436 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.15 (17266) covalent geometry : angle 0.61915 / 0.36 (24572) hydrogen bonds : bond 0.04967 / 3.25 ( 831) hydrogen bonds : angle 3.75284 / 2.73 ( 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 149 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9188 (tt0) cc_final: 0.8853 (tt0) REVERT: A 97 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8311 (mt-10) REVERT: A 110 CYS cc_start: 0.8847 (t) cc_final: 0.8498 (t) REVERT: B 63 GLU cc_start: 0.9222 (pm20) cc_final: 0.8841 (pm20) REVERT: B 74 GLU cc_start: 0.9306 (pp20) cc_final: 0.8843 (pp20) REVERT: B 84 MET cc_start: 0.8604 (tpt) cc_final: 0.8253 (tpp) REVERT: D 68 ASP cc_start: 0.9166 (m-30) cc_final: 0.8794 (m-30) REVERT: D 95 GLN cc_start: 0.9421 (mt0) cc_final: 0.9164 (mt0) REVERT: E 90 MET cc_start: 0.9084 (mmp) cc_final: 0.8727 (mmm) REVERT: E 97 GLU cc_start: 0.9455 (mt-10) cc_final: 0.8759 (mm-30) REVERT: E 110 CYS cc_start: 0.9665 (m) cc_final: 0.9145 (t) REVERT: E 120 MET cc_start: 0.8989 (tpt) cc_final: 0.8655 (mmm) REVERT: F 63 GLU cc_start: 0.9315 (mt-10) cc_final: 0.8705 (mt-10) REVERT: F 70 VAL cc_start: 0.9722 (m) cc_final: 0.9413 (m) REVERT: F 74 GLU cc_start: 0.9208 (pp20) cc_final: 0.8642 (pp20) REVERT: F 84 MET cc_start: 0.8982 (tpt) cc_final: 0.8511 (tpp) REVERT: F 93 GLN cc_start: 0.8904 (tt0) cc_final: 0.8583 (tm-30) REVERT: G 38 ASN cc_start: 0.9046 (m-40) cc_final: 0.8687 (p0) REVERT: G 68 ASN cc_start: 0.8950 (m-40) cc_final: 0.8470 (m-40) REVERT: G 74 LYS cc_start: 0.9439 (mmmm) cc_final: 0.9212 (mmmm) REVERT: G 99 ARG cc_start: 0.7603 (tpt90) cc_final: 0.7285 (mmm160) REVERT: G 100 VAL cc_start: 0.8904 (t) cc_final: 0.8653 (t) REVERT: H 47 GLN cc_start: 0.9326 (tm-30) cc_final: 0.9060 (tm-30) REVERT: H 68 ASP cc_start: 0.9373 (t0) cc_final: 0.9099 (t0) REVERT: N 1349 MET cc_start: 0.5200 (tpt) cc_final: 0.4940 (tpt) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1253 time to fit residues: 28.5042 Evaluate side-chains 110 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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: 50.0000 chunk 131 optimal weight: 7.9990 chunk 92 optimal weight: 30.0000 chunk 57 optimal weight: 5.9990 chunk 127 optimal weight: 8.9990 chunk 148 optimal weight: 0.0470 chunk 88 optimal weight: 30.0000 chunk 18 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 overall best weight: 2.3684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3586 r_free = 0.3586 target = 0.062042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.040113 restraints weight = 155913.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 73)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.041184 restraints weight = 80041.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 73)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.041914 restraints weight = 53385.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.042262 restraints weight = 42550.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.042360 restraints weight = 38203.668| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17266 Z= 0.169 Angle : 0.645 8.808 24572 Z= 0.367 Chirality : 0.041 0.326 2738 Planarity : 0.005 0.076 2114 Dihedral : 30.033 177.911 4715 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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: 1.01 (0.23), residues: 1256 helix: 1.30 (0.18), residues: 767 sheet: -0.02 (0.74), residues: 55 loop : -0.25 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 42 TYR 0.016 0.001 TYR G 39 PHE 0.021 0.002 PHE E 67 TRP 0.024 0.002 TRP N1115 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.17 (17266) covalent geometry : angle 0.64487 / 0.37 (24572) hydrogen bonds : bond 0.05913 / 3.89 ( 831) hydrogen bonds : angle 3.90864 / 2.84 ( 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 142 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 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: A 94 GLU cc_start: 0.9171 (tt0) cc_final: 0.8650 (tt0) REVERT: A 97 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8181 (mp0) REVERT: A 110 CYS cc_start: 0.8922 (t) cc_final: 0.8593 (t) REVERT: B 63 GLU cc_start: 0.9226 (pm20) cc_final: 0.8897 (pm20) REVERT: B 74 GLU cc_start: 0.9311 (pp20) cc_final: 0.8898 (pp20) REVERT: B 84 MET cc_start: 0.8617 (tpt) cc_final: 0.8260 (tpp) REVERT: C 38 ASN cc_start: 0.8093 (t0) cc_final: 0.6865 (t0) REVERT: D 37 TYR cc_start: 0.9068 (m-80) cc_final: 0.8746 (m-80) REVERT: D 68 ASP cc_start: 0.9131 (m-30) cc_final: 0.8693 (m-30) REVERT: D 95 GLN cc_start: 0.9459 (mt0) cc_final: 0.9196 (mt0) REVERT: E 90 MET cc_start: 0.8943 (mmp) cc_final: 0.8427 (mmp) REVERT: E 97 GLU cc_start: 0.9434 (mt-10) cc_final: 0.8623 (mm-30) REVERT: E 110 CYS cc_start: 0.9667 (m) cc_final: 0.9164 (t) REVERT: E 120 MET cc_start: 0.8948 (tpt) cc_final: 0.8600 (mmm) REVERT: F 70 VAL cc_start: 0.9737 (m) cc_final: 0.9430 (m) REVERT: F 74 GLU cc_start: 0.9218 (pp20) cc_final: 0.8680 (pp20) REVERT: F 84 MET cc_start: 0.8904 (tpt) cc_final: 0.8592 (tpp) REVERT: F 93 GLN cc_start: 0.8897 (tt0) cc_final: 0.8596 (tm-30) REVERT: G 38 ASN cc_start: 0.8800 (m-40) cc_final: 0.7653 (t0) REVERT: G 39 TYR cc_start: 0.8702 (m-10) cc_final: 0.8410 (m-80) REVERT: G 68 ASN cc_start: 0.8787 (m-40) cc_final: 0.8458 (t0) REVERT: G 74 LYS cc_start: 0.9423 (mmmm) cc_final: 0.9197 (mmmm) REVERT: G 99 ARG cc_start: 0.7612 (tpt90) cc_final: 0.7332 (mmm160) REVERT: H 41 VAL cc_start: 0.9531 (t) cc_final: 0.8970 (t) REVERT: H 62 MET cc_start: 0.9497 (tpp) cc_final: 0.8969 (ptt) REVERT: N 1349 MET cc_start: 0.5032 (tpt) cc_final: 0.4689 (tpt) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1174 time to fit residues: 25.8636 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 : 0.496 ------------------------------------------------------------------------------- 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: 6.9990 chunk 69 optimal weight: 10.0000 chunk 84 optimal weight: 20.0000 chunk 61 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 98 optimal weight: 20.0000 chunk 30 optimal weight: 0.9980 chunk 73 optimal weight: 50.0000 chunk 138 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 44 optimal weight: 8.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N1591 HIS ** N1638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.056200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.034698 restraints weight = 142700.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.035654 restraints weight = 76400.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.036139 restraints weight = 52419.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.036545 restraints weight = 42513.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.036699 restraints weight = 37853.850| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.5324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 17266 Z= 0.243 Angle : 0.727 10.745 24572 Z= 0.410 Chirality : 0.043 0.333 2738 Planarity : 0.006 0.077 2114 Dihedral : 30.373 177.348 4715 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % 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: 0.78 (0.23), residues: 1256 helix: 1.10 (0.18), residues: 767 sheet: -0.20 (0.73), residues: 55 loop : -0.29 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 49 TYR 0.025 0.002 TYR H 42 PHE 0.015 0.002 PHE A 67 TRP 0.016 0.002 TRP N1436 HIS 0.007 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.24 (17266) covalent geometry : angle 0.72720 / 0.41 (24572) hydrogen bonds : bond 0.08458 / 5.62 ( 831) hydrogen bonds : angle 4.29437 / 3.11 ( 2214) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2911.76 seconds wall clock time: 50 minutes 52.27 seconds (3052.27 seconds total)