Starting phenix.real_space_refine on Sat Sep 12 16:07:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hah_34589/09_2026/8hah_34589.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hah_34589/09_2026/8hah_34589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hah_34589/09_2026/8hah_34589.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hah_34589/09_2026/8hah_34589.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hah_34589/09_2026/8hah_34589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hah_34589/09_2026/8hah_34589.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 328 5.49 5 S 47 5.16 5 C 9780 2.51 5 N 3123 2.21 5 O 3818 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 113 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17096 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 838 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 761 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 756 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "I" Number of atoms: 3365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 3365 Classifications: {'DNA': 164} Link IDs: {'rna3p': 163} Chain: "J" Number of atoms: 3359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 3359 Classifications: {'DNA': 164} Link IDs: {'rna3p': 163} Chain: "K" Number of atoms: 4267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4267 Classifications: {'peptide': 517} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 483} Chain breaks: 3 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N ARG B 23 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG B 23 " occ=0.00 residue: pdb=" N LYS C 13 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS C 13 " occ=0.00 residue: pdb=" N ALA C 14 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA C 14 " occ=0.00 Time building chain proxies: 3.49, per 1000 atoms: 0.20 Number of scatterers: 17096 At special positions: 0 Unit cell: (105.283, 164.142, 129.324, 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 328 15.00 O 3818 8.00 N 3123 7.00 C 9780 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: 1.07 Conformation dependent library (CDL) restraints added in 575.5 milliseconds 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2424 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 8 sheets defined 60.0% alpha, 6.5% beta 157 base pairs and 272 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 removed outlier: 3.784A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.582A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.506A pdb=" N LEU A 100 " --> pdb=" O CYS A 96 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS A 110 " --> pdb=" O ASP A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.897A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 40 removed outlier: 3.616A pdb=" N ARG B 40 " --> pdb=" O ARG B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 76 removed outlier: 3.640A pdb=" N VAL B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 91 removed outlier: 3.543A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 94 No H-bonds generated for 'chain 'B' and resid 92 through 94' Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.680A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA C 53 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA C 69 " --> pdb=" O LEU C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.570A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.783A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.745A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 85 removed outlier: 3.961A pdb=" N MET D 59 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY D 60 " --> pdb=" O SER D 56 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 4.049A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 124 removed outlier: 4.050A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 55 removed outlier: 4.152A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU E 50 " --> pdb=" O VAL E 46 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN E 55 " --> pdb=" O ILE E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.623A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.977A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N TYR E 99 " --> pdb=" O ALA E 95 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU E 100 " --> pdb=" O CYS E 96 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL E 101 " --> pdb=" O GLU E 97 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.771A 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 50 through 76 removed outlier: 3.698A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N PHE F 61 " --> pdb=" O VAL F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.654A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 72 Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.906A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL H 48 " --> pdb=" O VAL H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 83 Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.741A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 124 removed outlier: 4.221A pdb=" N HIS H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 1055 through 1068 Proline residue: K1060 - end of helix removed outlier: 3.679A pdb=" N GLN K1068 " --> pdb=" O ALA K1064 " (cutoff:3.500A) Processing helix chain 'K' and resid 1072 through 1077 removed outlier: 4.305A pdb=" N GLN K1077 " --> pdb=" O LEU K1073 " (cutoff:3.500A) Processing helix chain 'K' and resid 1080 through 1084 Processing helix chain 'K' and resid 1088 through 1093 Processing helix chain 'K' and resid 1098 through 1108 Processing helix chain 'K' and resid 1113 through 1132 removed outlier: 3.944A pdb=" N TYR K1117 " --> pdb=" O GLU K1113 " (cutoff:3.500A) Processing helix chain 'K' and resid 1136 through 1161 removed outlier: 3.906A pdb=" N ASP K1154 " --> pdb=" O GLU K1150 " (cutoff:3.500A) Proline residue: K1155 - end of helix Processing helix chain 'K' and resid 1256 through 1260 Processing helix chain 'K' and resid 1272 through 1279 Processing helix chain 'K' and resid 1289 through 1293 Processing helix chain 'K' and resid 1296 through 1314 Processing helix chain 'K' and resid 1336 through 1343 removed outlier: 3.584A pdb=" N ARG K1342 " --> pdb=" O GLY K1338 " (cutoff:3.500A) Processing helix chain 'K' and resid 1409 through 1429 Processing helix chain 'K' and resid 1459 through 1477 Processing helix chain 'K' and resid 1486 through 1494 Processing helix chain 'K' and resid 1497 through 1501 Processing helix chain 'K' and resid 1507 through 1517 removed outlier: 3.965A pdb=" N ASN K1511 " --> pdb=" O ASP K1507 " (cutoff:3.500A) Processing helix chain 'K' and resid 1579 through 1591 Processing helix chain 'K' and resid 1626 through 1637 removed outlier: 3.871A pdb=" N PHE K1630 " --> pdb=" O GLY K1626 " (cutoff:3.500A) Processing helix chain 'K' and resid 1643 through 1663 Processing sheet with id=AA1, first strand: chain 'C' and resid 100 through 102 removed outlier: 4.006A pdb=" N TYR F 98 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.394A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.455A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'K' and resid 1175 through 1176 removed outlier: 3.632A pdb=" N LEU K1175 " --> pdb=" O ILE K1185 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 1198 through 1201 Processing sheet with id=AA7, first strand: chain 'K' and resid 1244 through 1246 Processing sheet with id=AA8, first strand: chain 'K' and resid 1320 through 1334 removed outlier: 4.135A pdb=" N GLU K1320 " --> pdb=" O GLU K1365 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA K1359 " --> pdb=" O VAL K1326 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA K1328 " --> pdb=" O THR K1357 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N THR K1357 " --> pdb=" O ALA K1328 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ASP K1330 " --> pdb=" O TYR K1355 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TYR K1355 " --> pdb=" O ASP K1330 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N THR K1332 " --> pdb=" O PHE K1353 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE K1353 " --> pdb=" O THR K1332 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU K1360 " --> pdb=" O MET K1376 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE K1374 " --> pdb=" O ALA K1362 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLU K1364 " --> pdb=" O CYS K1372 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N CYS K1372 " --> pdb=" O GLU K1364 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE K1366 " --> pdb=" O ASP K1370 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ASP K1370 " --> pdb=" O ILE K1366 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N PHE K1373 " --> pdb=" O SER K1400 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N SER K1400 " --> pdb=" O PHE K1373 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N GLY K1375 " --> pdb=" O LEU K1398 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N LEU K1398 " --> pdb=" O GLY K1375 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N HIS K1377 " --> pdb=" O SER K1396 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG K1392 " --> pdb=" O TYR K1381 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TRP K1436 " --> pdb=" O ILE K1395 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TYR K1397 " --> pdb=" O TRP K1436 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP K1482 " --> pdb=" O ARG K1599 " (cutoff:3.500A) 534 hydrogen bonds defined for protein. 1575 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 384 hydrogen bonds 768 hydrogen bond angles 0 basepair planarities 157 basepair parallelities 272 stacking parallelities Total time for adding SS restraints: 3.23 Time building geometry restraints manager: 1.49 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: 3819 1.34 - 1.46: 5326 1.46 - 1.58: 8240 1.58 - 1.70: 654 1.70 - 1.82: 70 Bond restraints: 18109 Sorted by residual: bond pdb=" C3' DT I 109 " pdb=" C2' DT I 109 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.15e+01 bond pdb=" C3' DG J 142 " pdb=" C2' DG J 142 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DT I 136 " pdb=" C2' DT I 136 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DG I 50 " pdb=" C2' DG I 50 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DT J 10 " pdb=" C2' DT J 10 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 ... (remaining 18104 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 24915 1.90 - 3.80: 911 3.80 - 5.70: 33 5.70 - 7.60: 5 7.60 - 9.50: 2 Bond angle restraints: 25866 Sorted by residual: angle pdb=" O4' DA J 112 " pdb=" C4' DA J 112 " pdb=" C3' DA J 112 " ideal model delta sigma weight residual 106.00 103.02 2.98 6.00e-01 2.78e+00 2.46e+01 angle pdb=" N3 DT J 109 " pdb=" C4 DT J 109 " pdb=" O4 DT J 109 " ideal model delta sigma weight residual 119.90 122.68 -2.78 6.00e-01 2.78e+00 2.14e+01 angle pdb=" N3 DT J 51 " pdb=" C4 DT J 51 " pdb=" O4 DT J 51 " ideal model delta sigma weight residual 119.90 122.65 -2.75 6.00e-01 2.78e+00 2.10e+01 angle pdb=" N3 DT J 69 " pdb=" C4 DT J 69 " pdb=" O4 DT J 69 " ideal model delta sigma weight residual 119.90 122.64 -2.74 6.00e-01 2.78e+00 2.09e+01 angle pdb=" N3 DT I 40 " pdb=" C4 DT I 40 " pdb=" O4 DT I 40 " ideal model delta sigma weight residual 119.90 122.61 -2.71 6.00e-01 2.78e+00 2.04e+01 ... (remaining 25861 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.93: 8413 28.93 - 57.86: 1621 57.86 - 86.80: 110 86.80 - 115.73: 0 115.73 - 144.66: 3 Dihedral angle restraints: 10147 sinusoidal: 6392 harmonic: 3755 Sorted by residual: dihedral pdb=" CA PRO H 103 " pdb=" C PRO H 103 " pdb=" N GLY H 104 " pdb=" CA GLY H 104 " ideal model delta harmonic sigma weight residual -180.00 -160.36 -19.64 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" C4' DT I 136 " pdb=" C3' DT I 136 " pdb=" O3' DT I 136 " pdb=" P DT I 137 " ideal model delta sinusoidal sigma weight residual 220.00 75.34 144.66 1 3.50e+01 8.16e-04 1.42e+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 77.47 142.53 1 3.50e+01 8.16e-04 1.41e+01 ... (remaining 10144 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1775 0.035 - 0.070: 764 0.070 - 0.104: 261 0.104 - 0.139: 79 0.139 - 0.174: 3 Chirality restraints: 2882 Sorted by residual: chirality pdb=" CA ILE C 79 " pdb=" N ILE C 79 " pdb=" C ILE C 79 " pdb=" CB ILE C 79 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.56e-01 chirality pdb=" C3' DA I 156 " pdb=" C4' DA I 156 " pdb=" O3' DA I 156 " pdb=" C2' DA I 156 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.21e-01 chirality pdb=" CA ILE K1598 " pdb=" N ILE K1598 " pdb=" C ILE K1598 " pdb=" CB ILE K1598 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.88e-01 ... (remaining 2879 not shown) Planarity restraints: 2154 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D 116 " 0.010 2.00e-02 2.50e+03 1.98e-02 3.93e+00 pdb=" C LYS D 116 " -0.034 2.00e-02 2.50e+03 pdb=" O LYS D 116 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA D 117 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 114 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.41e+00 pdb=" C GLY D 114 " -0.032 2.00e-02 2.50e+03 pdb=" O GLY D 114 " 0.012 2.00e-02 2.50e+03 pdb=" N THR D 115 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 117 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.05e+00 pdb=" C ALA D 117 " -0.030 2.00e-02 2.50e+03 pdb=" O ALA D 117 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL D 118 " 0.010 2.00e-02 2.50e+03 ... (remaining 2151 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3584 2.80 - 3.32: 15178 3.32 - 3.85: 30584 3.85 - 4.37: 34732 4.37 - 4.90: 51853 Nonbonded interactions: 135931 Sorted by model distance: nonbonded pdb=" O THR D 119 " pdb=" OG1 THR D 122 " model vdw 2.274 3.040 nonbonded pdb=" O HIS B 75 " pdb=" NH1 ARG D 92 " model vdw 2.298 3.120 nonbonded pdb=" NH1 ARG H 29 " pdb=" OP1 DG J 120 " model vdw 2.316 3.120 nonbonded pdb=" O LYS D 116 " pdb=" OG1 THR D 119 " model vdw 2.319 3.040 nonbonded pdb=" NH1 ARG C 42 " pdb=" O VAL C 43 " model vdw 2.327 3.120 ... (remaining 135926 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 37 through 135) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 23 through 102) } ncs_group { reference = (chain 'C' and resid 14 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 29 through 124) selection = chain 'H' } ncs_group { reference = (chain 'I' and resid 12 through 169) selection = (chain 'J' and resid 12 through 169) } 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: 3.730 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.020 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6168 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 0.036 18109 Z= 0.462 Angle : 0.698 9.504 25866 Z= 0.615 Chirality : 0.044 0.174 2882 Planarity : 0.003 0.039 2154 Dihedral : 24.017 144.661 7723 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 1.59 (0.24), residues: 1263 helix: 1.62 (0.20), residues: 714 sheet: 0.60 (0.67), residues: 66 loop : 0.40 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG H 79 TYR 0.015 0.001 TYR C 57 PHE 0.008 0.001 PHE K1125 TRP 0.007 0.001 TRP K1649 HIS 0.007 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.46 (18109) covalent geometry : angle 0.69844 / 0.61 (25866) hydrogen bonds : bond 0.12255 / 8.37 ( 918) hydrogen bonds : angle 3.93359 / 2.80 ( 2343) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: B 84 MET cc_start: 0.7692 (tmm) cc_final: 0.7207 (tmm) REVERT: K 1470 MET cc_start: 0.0448 (tmm) cc_final: 0.0027 (ttp) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1156 time to fit residues: 11.2386 Evaluate side-chains 49 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 40.0000 chunk 124 optimal weight: 40.0000 chunk 103 optimal weight: 30.0000 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 30.0000 chunk 149 optimal weight: 30.0000 overall best weight: 6.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN B 75 HIS C 112 GLN ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** K1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1481 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.086626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.067752 restraints weight = 200523.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.068834 restraints weight = 124437.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.069871 restraints weight = 89783.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.070222 restraints weight = 72017.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.070516 restraints weight = 62921.667| |-----------------------------------------------------------------------------| r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 18109 Z= 0.266 Angle : 0.848 10.374 25866 Z= 0.473 Chirality : 0.047 0.268 2882 Planarity : 0.006 0.064 2154 Dihedral : 27.979 143.774 5102 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.08 % Allowed : 5.85 % Favored : 93.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.23), residues: 1263 helix: 1.14 (0.19), residues: 717 sheet: 0.16 (0.67), residues: 66 loop : 0.23 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 42 TYR 0.046 0.003 TYR F 88 PHE 0.040 0.002 PHE K1090 TRP 0.008 0.001 TRP K1129 HIS 0.010 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.27 (18109) covalent geometry : angle 0.84848 / 0.47 (25866) hydrogen bonds : bond 0.12801 / 8.34 ( 918) hydrogen bonds : angle 3.86431 / 2.76 ( 2343) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.502 Fit side-chains REVERT: H 71 GLU cc_start: 0.9096 (tt0) cc_final: 0.8485 (tp30) REVERT: K 1470 MET cc_start: 0.0465 (tmm) cc_final: 0.0247 (ttp) outliers start: 12 outliers final: 6 residues processed: 56 average time/residue: 0.1097 time to fit residues: 10.3277 Evaluate side-chains 46 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain G residue 49 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 42 optimal weight: 10.0000 chunk 140 optimal weight: 50.0000 chunk 126 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 95 optimal weight: 40.0000 chunk 31 optimal weight: 4.9990 chunk 145 optimal weight: 20.0000 chunk 111 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K1195 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.104599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.074651 restraints weight = 174666.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.075994 restraints weight = 124407.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.077017 restraints weight = 99185.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.077277 restraints weight = 85176.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.078093 restraints weight = 78778.505| |-----------------------------------------------------------------------------| r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18109 Z= 0.152 Angle : 0.579 8.682 25866 Z= 0.344 Chirality : 0.039 0.373 2882 Planarity : 0.004 0.056 2154 Dihedral : 28.054 144.462 5102 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.99 % Allowed : 7.46 % Favored : 91.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 1.61 (0.23), residues: 1263 helix: 1.72 (0.19), residues: 716 sheet: 0.37 (0.69), residues: 66 loop : 0.31 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 99 TYR 0.052 0.002 TYR F 88 PHE 0.019 0.001 PHE K1374 TRP 0.008 0.001 TRP K1649 HIS 0.005 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.15 (18109) covalent geometry : angle 0.57908 / 0.34 (25866) hydrogen bonds : bond 0.05345 / 3.43 ( 918) hydrogen bonds : angle 3.32432 / 2.34 ( 2343) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.636 Fit side-chains revert: symmetry clash REVERT: A 64 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8827 (mtmm) REVERT: F 84 MET cc_start: 0.9345 (tpp) cc_final: 0.9018 (tpp) REVERT: H 71 GLU cc_start: 0.9496 (tt0) cc_final: 0.8865 (tp30) REVERT: K 1376 MET cc_start: 0.0418 (mpp) cc_final: 0.0173 (mtt) REVERT: K 1470 MET cc_start: 0.0490 (tmm) cc_final: 0.0223 (ttp) outliers start: 11 outliers final: 6 residues processed: 54 average time/residue: 0.1272 time to fit residues: 11.3641 Evaluate side-chains 47 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain K residue 1059 MET Chi-restraints excluded: chain K residue 1102 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 51 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 87 optimal weight: 40.0000 chunk 68 optimal weight: 4.9990 chunk 132 optimal weight: 40.0000 chunk 93 optimal weight: 20.0000 chunk 50 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 103 optimal weight: 30.0000 chunk 123 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** K1255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1379 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.082440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.063334 restraints weight = 187489.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.064460 restraints weight = 117911.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.064928 restraints weight = 87244.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.066083 restraints weight = 72828.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 71)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.066500 restraints weight = 61462.925| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.6108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 18109 Z= 0.252 Angle : 0.780 12.145 25866 Z= 0.438 Chirality : 0.043 0.505 2882 Planarity : 0.006 0.071 2154 Dihedral : 28.510 144.577 5102 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.01 % Favored : 96.91 % Rotamer: Outliers : 2.07 % Allowed : 8.72 % Favored : 89.21 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.23), residues: 1263 helix: 1.23 (0.19), residues: 726 sheet: 0.41 (0.68), residues: 67 loop : -0.02 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 42 TYR 0.028 0.003 TYR F 88 PHE 0.019 0.002 PHE K1374 TRP 0.009 0.001 TRP K1129 HIS 0.006 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.25 (18109) covalent geometry : angle 0.78012 / 0.44 (25866) hydrogen bonds : bond 0.12310 / 8.09 ( 918) hydrogen bonds : angle 3.73562 / 2.65 ( 2343) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 45 time to evaluate : 0.489 Fit side-chains REVERT: G 25 PHE cc_start: 0.7198 (OUTLIER) cc_final: 0.6672 (m-10) REVERT: H 71 GLU cc_start: 0.9332 (tt0) cc_final: 0.9014 (tp30) REVERT: K 1654 MET cc_start: 0.6251 (mmm) cc_final: 0.6048 (tpt) outliers start: 23 outliers final: 14 residues processed: 65 average time/residue: 0.1188 time to fit residues: 12.6450 Evaluate side-chains 50 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 35 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 25 PHE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 1102 ILE Chi-restraints excluded: chain K residue 1613 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 14 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 108 optimal weight: 20.0000 chunk 35 optimal weight: 5.9990 chunk 130 optimal weight: 40.0000 chunk 12 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 129 optimal weight: 8.9990 chunk 60 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.077523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.055401 restraints weight = 184959.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.056596 restraints weight = 110187.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.057512 restraints weight = 79801.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.058266 restraints weight = 65458.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.058686 restraints weight = 56875.781| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.6345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 18109 Z= 0.142 Angle : 0.585 9.539 25866 Z= 0.341 Chirality : 0.039 0.293 2882 Planarity : 0.004 0.048 2154 Dihedral : 28.645 145.350 5102 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.53 % Allowed : 10.07 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 1.51 (0.24), residues: 1263 helix: 1.69 (0.19), residues: 725 sheet: 0.11 (0.66), residues: 77 loop : 0.17 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 99 TYR 0.025 0.001 TYR F 88 PHE 0.012 0.001 PHE E 67 TRP 0.005 0.001 TRP K1649 HIS 0.006 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.14 (18109) covalent geometry : angle 0.58486 / 0.34 (25866) hydrogen bonds : bond 0.04883 / 3.14 ( 918) hydrogen bonds : angle 3.33161 / 2.34 ( 2343) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: G 25 PHE cc_start: 0.7048 (OUTLIER) cc_final: 0.6560 (m-10) REVERT: H 71 GLU cc_start: 0.9307 (tt0) cc_final: 0.9011 (tp30) outliers start: 17 outliers final: 10 residues processed: 58 average time/residue: 0.1001 time to fit residues: 10.1668 Evaluate side-chains 49 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain G residue 25 PHE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 1102 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 120 optimal weight: 0.0570 chunk 96 optimal weight: 20.0000 chunk 88 optimal weight: 50.0000 chunk 46 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 90 optimal weight: 50.0000 chunk 34 optimal weight: 4.9990 chunk 144 optimal weight: 7.9990 chunk 70 optimal weight: 9.9990 chunk 38 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 overall best weight: 1.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K1195 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.076966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.053708 restraints weight = 169929.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.054671 restraints weight = 112575.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.055361 restraints weight = 85969.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.055640 restraints weight = 72200.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.056112 restraints weight = 65144.409| |-----------------------------------------------------------------------------| r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.6692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 18109 Z= 0.137 Angle : 0.577 8.902 25866 Z= 0.336 Chirality : 0.038 0.291 2882 Planarity : 0.004 0.037 2154 Dihedral : 28.490 144.532 5102 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.62 % Allowed : 9.62 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 1.69 (0.24), residues: 1263 helix: 1.84 (0.19), residues: 725 sheet: 0.20 (0.67), residues: 77 loop : 0.24 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 99 TYR 0.030 0.001 TYR F 88 PHE 0.021 0.001 PHE A 84 TRP 0.005 0.001 TRP K1649 HIS 0.003 0.001 HIS K1638 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.14 (18109) covalent geometry : angle 0.57692 / 0.34 (25866) hydrogen bonds : bond 0.05698 / 3.71 ( 918) hydrogen bonds : angle 3.14712 / 2.21 ( 2343) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 44 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 25 PHE cc_start: 0.7092 (OUTLIER) cc_final: 0.6642 (m-10) REVERT: H 71 GLU cc_start: 0.9302 (tt0) cc_final: 0.9021 (tp30) outliers start: 18 outliers final: 11 residues processed: 62 average time/residue: 0.1064 time to fit residues: 11.3998 Evaluate side-chains 49 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain G residue 25 PHE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 1102 ILE Chi-restraints excluded: chain K residue 1445 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 7 optimal weight: 9.9990 chunk 146 optimal weight: 30.0000 chunk 45 optimal weight: 3.9990 chunk 87 optimal weight: 50.0000 chunk 12 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 73 optimal weight: 50.0000 chunk 35 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1255 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 = 0.3982 r_free = 0.3982 target = 0.074924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.052545 restraints weight = 182216.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.053667 restraints weight = 113469.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.054605 restraints weight = 83662.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.054992 restraints weight = 68466.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.055691 restraints weight = 60914.412| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.7274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18109 Z= 0.153 Angle : 0.608 21.409 25866 Z= 0.347 Chirality : 0.039 0.302 2882 Planarity : 0.004 0.032 2154 Dihedral : 28.539 144.926 5102 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.71 % Allowed : 10.43 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 1.61 (0.24), residues: 1263 helix: 1.77 (0.19), residues: 728 sheet: 0.24 (0.67), residues: 77 loop : 0.20 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 99 TYR 0.020 0.001 TYR F 88 PHE 0.017 0.001 PHE A 84 TRP 0.031 0.002 TRP K1649 HIS 0.009 0.001 HIS K1434 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.15 (18109) covalent geometry : angle 0.60773 / 0.35 (25866) hydrogen bonds : bond 0.04839 / 3.13 ( 918) hydrogen bonds : angle 3.23422 / 2.27 ( 2343) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 42 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 25 PHE cc_start: 0.7103 (OUTLIER) cc_final: 0.6611 (m-10) REVERT: H 71 GLU cc_start: 0.9279 (tt0) cc_final: 0.9004 (tp30) outliers start: 19 outliers final: 12 residues processed: 60 average time/residue: 0.1202 time to fit residues: 12.0223 Evaluate side-chains 51 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain G residue 25 PHE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 1102 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 114 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 122 optimal weight: 0.8980 chunk 57 optimal weight: 7.9990 chunk 150 optimal weight: 6.9990 chunk 101 optimal weight: 30.0000 chunk 147 optimal weight: 5.9990 chunk 111 optimal weight: 20.0000 chunk 88 optimal weight: 50.0000 chunk 148 optimal weight: 10.0000 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS ** K1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1591 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.085442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.058037 restraints weight = 165780.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.058619 restraints weight = 132894.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.058924 restraints weight = 114950.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.059344 restraints weight = 105280.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.059490 restraints weight = 99017.850| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.9013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.197 18109 Z= 0.230 Angle : 0.724 13.996 25866 Z= 0.408 Chirality : 0.045 0.359 2882 Planarity : 0.006 0.104 2154 Dihedral : 29.024 145.189 5102 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.35 % Allowed : 11.06 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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 (0.24), residues: 1263 helix: 1.21 (0.19), residues: 737 sheet: 0.57 (0.78), residues: 61 loop : 0.12 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 72 TYR 0.019 0.002 TYR E 41 PHE 0.023 0.002 PHE E 84 TRP 0.011 0.002 TRP K1649 HIS 0.007 0.001 HIS K1434 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.23 (18109) covalent geometry : angle 0.72411 / 0.41 (25866) hydrogen bonds : bond 0.09836 / 6.39 ( 918) hydrogen bonds : angle 3.75427 / 2.65 ( 2343) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.513 Fit side-chains REVERT: E 50 GLU cc_start: 0.9531 (pm20) cc_final: 0.9330 (pm20) REVERT: H 71 GLU cc_start: 0.9434 (tt0) cc_final: 0.8804 (tp30) outliers start: 15 outliers final: 13 residues processed: 53 average time/residue: 0.1133 time to fit residues: 10.1819 Evaluate side-chains 50 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 1102 ILE Chi-restraints excluded: chain K residue 1445 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 49 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 147 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 150 optimal weight: 50.0000 chunk 34 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 132 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1082 GLN ** K1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1255 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 = 0.3895 r_free = 0.3895 target = 0.071167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.047926 restraints weight = 170302.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.048976 restraints weight = 105849.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.049653 restraints weight = 77946.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.049904 restraints weight = 64926.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.050320 restraints weight = 58983.505| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.9229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18109 Z= 0.145 Angle : 0.623 13.523 25866 Z= 0.355 Chirality : 0.041 0.296 2882 Planarity : 0.004 0.039 2154 Dihedral : 29.065 145.703 5102 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.26 % Allowed : 11.42 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 1.42 (0.24), residues: 1263 helix: 1.54 (0.19), residues: 734 sheet: 0.52 (0.78), residues: 61 loop : 0.16 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 71 TYR 0.018 0.001 TYR F 88 PHE 0.026 0.001 PHE K1090 TRP 0.010 0.001 TRP K1649 HIS 0.004 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.15 (18109) covalent geometry : angle 0.62290 / 0.36 (25866) hydrogen bonds : bond 0.05009 / 3.25 ( 918) hydrogen bonds : angle 3.44020 / 2.41 ( 2343) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: E 90 MET cc_start: 0.9420 (pmm) cc_final: 0.9175 (pmm) REVERT: H 71 GLU cc_start: 0.9486 (tt0) cc_final: 0.8960 (tp30) outliers start: 14 outliers final: 12 residues processed: 52 average time/residue: 0.1146 time to fit residues: 10.1514 Evaluate side-chains 47 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 1102 ILE Chi-restraints excluded: chain K residue 1445 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 108 optimal weight: 0.6980 chunk 90 optimal weight: 50.0000 chunk 105 optimal weight: 30.0000 chunk 33 optimal weight: 9.9990 chunk 102 optimal weight: 40.0000 chunk 8 optimal weight: 0.9990 chunk 107 optimal weight: 0.5980 chunk 21 optimal weight: 20.0000 chunk 93 optimal weight: 30.0000 chunk 137 optimal weight: 20.0000 chunk 47 optimal weight: 1.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1255 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 = 0.3853 r_free = 0.3853 target = 0.068490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.046914 restraints weight = 176949.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.046699 restraints weight = 128228.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.047109 restraints weight = 101113.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.047479 restraints weight = 87169.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.047636 restraints weight = 79458.230| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.9452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 18109 Z= 0.152 Angle : 0.622 11.947 25866 Z= 0.356 Chirality : 0.041 0.349 2882 Planarity : 0.004 0.038 2154 Dihedral : 28.991 145.796 5102 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.99 % Allowed : 11.96 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 1.50 (0.24), residues: 1263 helix: 1.63 (0.19), residues: 734 sheet: 0.52 (0.78), residues: 61 loop : 0.16 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 77 TYR 0.016 0.001 TYR F 88 PHE 0.014 0.001 PHE G 25 TRP 0.006 0.001 TRP K1649 HIS 0.004 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.15 (18109) covalent geometry : angle 0.62228 / 0.36 (25866) hydrogen bonds : bond 0.05543 / 3.60 ( 918) hydrogen bonds : angle 3.39353 / 2.38 ( 2343) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.391 Fit side-chains REVERT: D 71 GLU cc_start: 0.8915 (pp20) cc_final: 0.8609 (pp20) REVERT: H 71 GLU cc_start: 0.9134 (tt0) cc_final: 0.8612 (tp30) outliers start: 11 outliers final: 11 residues processed: 48 average time/residue: 0.1009 time to fit residues: 8.6637 Evaluate side-chains 48 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 1102 ILE Chi-restraints excluded: chain K residue 1239 LEU Chi-restraints excluded: chain K residue 1445 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 110 optimal weight: 20.0000 chunk 74 optimal weight: 50.0000 chunk 73 optimal weight: 40.0000 chunk 97 optimal weight: 30.0000 chunk 23 optimal weight: 6.9990 chunk 154 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 chunk 147 optimal weight: 5.9990 chunk 121 optimal weight: 0.9990 chunk 146 optimal weight: 7.9990 chunk 66 optimal weight: 0.0770 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1255 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 = 0.3813 r_free = 0.3813 target = 0.066064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.044257 restraints weight = 182176.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.043773 restraints weight = 114424.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.044293 restraints weight = 84556.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.044517 restraints weight = 72079.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.044766 restraints weight = 65597.834| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 1.0548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 18109 Z= 0.170 Angle : 0.669 23.605 25866 Z= 0.374 Chirality : 0.042 0.301 2882 Planarity : 0.004 0.035 2154 Dihedral : 29.123 146.204 5102 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.44 % Allowed : 11.87 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 1.34 (0.24), residues: 1263 helix: 1.53 (0.19), residues: 734 sheet: 0.22 (0.76), residues: 63 loop : 0.07 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 81 TYR 0.014 0.001 TYR D 40 PHE 0.021 0.001 PHE G 25 TRP 0.005 0.001 TRP K1649 HIS 0.009 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.17 (18109) covalent geometry : angle 0.66887 / 0.37 (25866) hydrogen bonds : bond 0.05202 / 3.43 ( 918) hydrogen bonds : angle 3.50540 / 2.46 ( 2343) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4683.36 seconds wall clock time: 80 minutes 49.43 seconds (4849.43 seconds total)