Starting phenix.real_space_refine on Mon Nov 18 16:15:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hah_34589/11_2024/8hah_34589.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hah_34589/11_2024/8hah_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hah_34589/11_2024/8hah_34589.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hah_34589/11_2024/8hah_34589.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hah_34589/11_2024/8hah_34589.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hah_34589/11_2024/8hah_34589.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: 10.43, per 1000 atoms: 0.61 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: 4.32 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 7.13 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: 8.73 Time building geometry restraints manager: 5.03 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' DA I 156 " pdb=" O3' DA I 156 " ideal model delta sigma weight residual 1.422 1.467 -0.045 3.00e-02 1.11e+03 2.23e+00 bond pdb=" CA ILE H 54 " pdb=" CB ILE H 54 " ideal model delta sigma weight residual 1.533 1.551 -0.018 1.37e-02 5.33e+03 1.76e+00 bond pdb=" CG GLU C 61 " pdb=" CD GLU C 61 " ideal model delta sigma weight residual 1.516 1.490 0.026 2.50e-02 1.60e+03 1.10e+00 bond pdb=" C3' DT I 109 " pdb=" C2' DT I 109 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.00e-02 2.50e+03 8.22e-01 bond pdb=" C3' DG J 142 " pdb=" C2' DG J 142 " ideal model delta sigma weight residual 1.525 1.542 -0.017 2.00e-02 2.50e+03 7.56e-01 ... (remaining 18104 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 25361 1.90 - 3.80: 466 3.80 - 5.70: 32 5.70 - 7.60: 5 7.60 - 9.50: 2 Bond angle restraints: 25866 Sorted by residual: angle pdb=" CA ARG K1055 " pdb=" CB ARG K1055 " pdb=" CG ARG K1055 " ideal model delta sigma weight residual 114.10 121.67 -7.57 2.00e+00 2.50e-01 1.43e+01 angle pdb=" CB MET A 120 " pdb=" CG MET A 120 " pdb=" SD MET A 120 " ideal model delta sigma weight residual 112.70 122.20 -9.50 3.00e+00 1.11e-01 1.00e+01 angle pdb=" C TYR K1194 " pdb=" N GLN K1195 " pdb=" CA GLN K1195 " ideal model delta sigma weight residual 121.54 126.89 -5.35 1.91e+00 2.74e-01 7.83e+00 angle pdb=" N GLU D 76 " pdb=" CA GLU D 76 " pdb=" CB GLU D 76 " ideal model delta sigma weight residual 110.16 114.14 -3.98 1.48e+00 4.57e-01 7.23e+00 angle pdb=" N MET K1059 " pdb=" CA MET K1059 " pdb=" C MET K1059 " ideal model delta sigma weight residual 109.81 115.43 -5.62 2.21e+00 2.05e-01 6.47e+00 ... (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: 2253 0.035 - 0.070: 505 0.070 - 0.104: 95 0.104 - 0.139: 27 0.139 - 0.174: 2 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=" 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 chirality pdb=" CA MET K1059 " pdb=" N MET K1059 " pdb=" C MET K1059 " pdb=" CB MET K1059 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.84e-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: 2.160 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: 0.790 Check model and map are aligned: 0.120 Set scattering table: 0.190 Process input model: 46.460 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6151 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 : 0.003 0.045 18109 Z= 0.148 Angle : 0.550 9.504 25866 Z= 0.337 Chirality : 0.032 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.007 0.001 TRP K1649 HIS 0.007 0.001 HIS D 109 PHE 0.008 0.001 PHE K1125 TYR 0.015 0.001 TYR C 57 ARG 0.017 0.000 ARG H 79 *********************** 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 : 1.539 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: 0.2870 time to fit residues: 27.7768 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 : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9980 chunk 118 optimal weight: 50.0000 chunk 65 optimal weight: 0.0070 chunk 40 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 63 optimal weight: 30.0000 chunk 122 optimal weight: 30.0000 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 141 optimal weight: 1.9990 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS D 49 HIS F 25 ASN ** K1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1481 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6434 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18109 Z= 0.189 Angle : 0.553 7.685 25866 Z= 0.320 Chirality : 0.034 0.195 2882 Planarity : 0.004 0.036 2154 Dihedral : 26.984 143.931 5102 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.45 % Allowed : 4.86 % Favored : 94.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.24), residues: 1263 helix: 1.88 (0.20), residues: 720 sheet: 0.58 (0.68), residues: 66 loop : 0.44 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K1466 HIS 0.005 0.001 HIS B 75 PHE 0.019 0.001 PHE K1090 TYR 0.018 0.002 TYR F 88 ARG 0.005 0.000 ARG K1055 *********************** 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 60 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 1.522 Fit side-chains revert: symmetry clash REVERT: B 84 MET cc_start: 0.7970 (tmm) cc_final: 0.7458 (tmm) REVERT: F 84 MET cc_start: 0.8104 (mmp) cc_final: 0.7444 (mmp) REVERT: K 1470 MET cc_start: 0.0350 (tmm) cc_final: -0.0022 (ttp) outliers start: 5 outliers final: 3 residues processed: 58 average time/residue: 0.2638 time to fit residues: 25.7528 Evaluate side-chains 47 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 89 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 141 optimal weight: 30.0000 chunk 153 optimal weight: 6.9990 chunk 126 optimal weight: 8.9990 chunk 140 optimal weight: 40.0000 chunk 48 optimal weight: 10.0000 chunk 113 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS C 38 ASN C 112 GLN G 38 ASN K1195 GLN K1379 GLN K1591 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.6978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.117 18109 Z= 0.423 Angle : 0.824 9.279 25866 Z= 0.467 Chirality : 0.045 0.407 2882 Planarity : 0.007 0.086 2154 Dihedral : 28.957 149.077 5102 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.62 % Allowed : 7.91 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.23), residues: 1263 helix: 0.75 (0.19), residues: 738 sheet: 0.07 (0.70), residues: 67 loop : 0.07 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K1129 HIS 0.010 0.002 HIS A 113 PHE 0.021 0.002 PHE A 67 TYR 0.048 0.003 TYR F 88 ARG 0.011 0.001 ARG E 83 *********************** 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 71 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 53 time to evaluate : 1.467 Fit side-chains REVERT: A 64 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7341 (mtmm) REVERT: C 38 ASN cc_start: 0.8135 (OUTLIER) cc_final: 0.7793 (t0) REVERT: E 90 MET cc_start: 0.8704 (ppp) cc_final: 0.8447 (ppp) REVERT: H 71 GLU cc_start: 0.8948 (tt0) cc_final: 0.8469 (tp30) REVERT: K 1097 MET cc_start: 0.8297 (ppp) cc_final: 0.8096 (ppp) REVERT: K 1654 MET cc_start: 0.6414 (mmm) cc_final: 0.6174 (tpt) outliers start: 18 outliers final: 8 residues processed: 66 average time/residue: 0.2578 time to fit residues: 29.1998 Evaluate side-chains 47 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 49 VAL 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 H residue 59 MET Chi-restraints excluded: chain K residue 1135 THR Chi-restraints excluded: chain K residue 1624 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 10.0000 chunk 106 optimal weight: 5.9990 chunk 73 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 chunk 142 optimal weight: 0.2980 chunk 150 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 134 optimal weight: 50.0000 chunk 40 optimal weight: 0.6980 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.7308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 18109 Z= 0.216 Angle : 0.595 6.718 25866 Z= 0.345 Chirality : 0.035 0.169 2882 Planarity : 0.004 0.032 2154 Dihedral : 28.866 147.340 5102 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.17 % Allowed : 10.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.23), residues: 1263 helix: 1.35 (0.19), residues: 734 sheet: 0.32 (0.69), residues: 71 loop : 0.06 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K1122 HIS 0.003 0.001 HIS H 82 PHE 0.015 0.001 PHE A 84 TYR 0.033 0.002 TYR F 88 ARG 0.005 0.000 ARG C 42 *********************** 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 62 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 1.403 Fit side-chains revert: symmetry clash REVERT: H 71 GLU cc_start: 0.8903 (tt0) cc_final: 0.8434 (tp30) outliers start: 13 outliers final: 8 residues processed: 60 average time/residue: 0.2467 time to fit residues: 25.0783 Evaluate side-chains 45 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 1.540 ------------------------------------------------------------------------------- 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 113 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain K residue 1102 ILE Chi-restraints excluded: chain K residue 1135 THR 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 125 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 2 optimal weight: 0.0570 chunk 112 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 128 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 76 optimal weight: 10.0000 chunk 135 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 overall best weight: 3.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN ** K1255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.8867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 18109 Z= 0.275 Angle : 0.646 13.148 25866 Z= 0.368 Chirality : 0.036 0.168 2882 Planarity : 0.005 0.051 2154 Dihedral : 28.891 144.337 5102 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.98 % Allowed : 10.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.23), residues: 1263 helix: 1.28 (0.19), residues: 734 sheet: 0.28 (0.70), residues: 71 loop : 0.13 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K1129 HIS 0.008 0.001 HIS B 75 PHE 0.021 0.002 PHE G 25 TYR 0.018 0.002 TYR C 50 ARG 0.004 0.001 ARG B 45 *********************** 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 67 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 45 time to evaluate : 1.366 Fit side-chains REVERT: A 64 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7404 (mtmm) REVERT: E 94 GLU cc_start: 0.8022 (tp30) cc_final: 0.7810 (tp30) REVERT: H 71 GLU cc_start: 0.8929 (tt0) cc_final: 0.8418 (tp30) REVERT: K 1097 MET cc_start: 0.7668 (ppp) cc_final: 0.7440 (ppp) REVERT: K 1470 MET cc_start: 0.0227 (tmm) cc_final: -0.0080 (ttp) outliers start: 22 outliers final: 12 residues processed: 64 average time/residue: 0.2681 time to fit residues: 27.9705 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 : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain B residue 81 VAL 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 94 ILE 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 G residue 62 ILE Chi-restraints excluded: chain H residue 59 MET Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 1135 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 3.9990 chunk 135 optimal weight: 0.1980 chunk 29 optimal weight: 6.9990 chunk 88 optimal weight: 20.0000 chunk 37 optimal weight: 6.9990 chunk 150 optimal weight: 30.0000 chunk 125 optimal weight: 0.9980 chunk 69 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K1255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.9406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18109 Z= 0.206 Angle : 0.589 10.771 25866 Z= 0.338 Chirality : 0.035 0.178 2882 Planarity : 0.003 0.035 2154 Dihedral : 29.055 147.869 5102 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.80 % Allowed : 10.97 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.24), residues: 1263 helix: 1.53 (0.19), residues: 734 sheet: 0.01 (0.67), residues: 76 loop : 0.22 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K1649 HIS 0.003 0.001 HIS F 75 PHE 0.009 0.001 PHE A 67 TYR 0.042 0.002 TYR F 88 ARG 0.012 0.000 ARG H 99 *********************** 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 65 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 45 time to evaluate : 1.490 Fit side-chains revert: symmetry clash REVERT: D 57 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8537 (pptt) REVERT: H 71 GLU cc_start: 0.8897 (tt0) cc_final: 0.8414 (tp30) outliers start: 20 outliers final: 16 residues processed: 64 average time/residue: 0.2704 time to fit residues: 28.7806 Evaluate side-chains 54 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 37 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 81 VAL 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 57 LYS Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 1102 ILE Chi-restraints excluded: chain K residue 1121 ILE Chi-restraints excluded: chain K residue 1135 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 9.9990 chunk 17 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 110 optimal weight: 30.0000 chunk 127 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 chunk 150 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1082 GLN ** K1199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1327 HIS ** K1451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1489 GLN ** K1661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1663 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 1.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.103 18109 Z= 0.470 Angle : 0.861 11.169 25866 Z= 0.486 Chirality : 0.049 0.379 2882 Planarity : 0.007 0.064 2154 Dihedral : 30.433 146.294 5102 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 26.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.06 % Allowed : 11.60 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.23), residues: 1263 helix: 0.55 (0.18), residues: 744 sheet: -0.49 (0.70), residues: 68 loop : -0.40 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP K1436 HIS 0.011 0.002 HIS K1659 PHE 0.027 0.003 PHE K1125 TYR 0.065 0.003 TYR B 88 ARG 0.010 0.001 ARG G 77 *********************** 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 80 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 46 time to evaluate : 1.492 Fit side-chains revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.6628 (mtmm) REVERT: D 57 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8802 (pptt) REVERT: H 71 GLU cc_start: 0.8902 (tt0) cc_final: 0.8443 (tp30) REVERT: K 1663 GLN cc_start: 0.7369 (OUTLIER) cc_final: 0.7077 (mp10) outliers start: 34 outliers final: 23 residues processed: 73 average time/residue: 0.2735 time to fit residues: 31.6729 Evaluate side-chains 66 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 40 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 94 ILE 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 F residue 85 ASP Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 59 MET Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 1102 ILE Chi-restraints excluded: chain K residue 1121 ILE Chi-restraints excluded: chain K residue 1135 THR Chi-restraints excluded: chain K residue 1446 TYR Chi-restraints excluded: chain K residue 1663 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 5.9990 chunk 89 optimal weight: 50.0000 chunk 45 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 136 optimal weight: 20.0000 chunk 144 optimal weight: 20.0000 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1082 GLN ** K1199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 1.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18109 Z= 0.229 Angle : 0.673 11.342 25866 Z= 0.382 Chirality : 0.038 0.258 2882 Planarity : 0.004 0.041 2154 Dihedral : 30.221 150.616 5102 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.07 % Allowed : 13.13 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.23), residues: 1263 helix: 1.11 (0.19), residues: 737 sheet: -0.27 (0.73), residues: 61 loop : -0.19 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K1649 HIS 0.010 0.001 HIS K1659 PHE 0.019 0.001 PHE K1090 TYR 0.069 0.002 TYR F 88 ARG 0.009 0.000 ARG H 99 *********************** 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 68 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 45 time to evaluate : 1.370 Fit side-chains REVERT: D 57 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8596 (pptt) REVERT: H 71 GLU cc_start: 0.8815 (tt0) cc_final: 0.8366 (tp30) REVERT: K 1097 MET cc_start: 0.8001 (ppp) cc_final: 0.7787 (ppp) outliers start: 23 outliers final: 16 residues processed: 67 average time/residue: 0.2613 time to fit residues: 28.8335 Evaluate side-chains 58 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 41 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 94 ILE 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 G residue 114 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 1121 ILE Chi-restraints excluded: chain K residue 1135 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 5.9990 chunk 140 optimal weight: 20.0000 chunk 144 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 110 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 chunk 132 optimal weight: 0.9980 chunk 139 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN ** K1199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 1.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 18109 Z= 0.325 Angle : 0.726 16.810 25866 Z= 0.404 Chirality : 0.039 0.251 2882 Planarity : 0.005 0.048 2154 Dihedral : 30.098 152.906 5102 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.25 % Allowed : 13.40 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.23), residues: 1263 helix: 1.10 (0.19), residues: 735 sheet: -0.53 (0.72), residues: 62 loop : -0.23 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K1509 HIS 0.005 0.001 HIS K1659 PHE 0.019 0.002 PHE K1504 TYR 0.049 0.002 TYR B 88 ARG 0.009 0.001 ARG E 49 *********************** 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 71 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 46 time to evaluate : 1.533 Fit side-chains revert: symmetry clash REVERT: A 37 LYS cc_start: 0.6821 (tptp) cc_final: 0.6517 (tmtt) REVERT: A 64 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.6676 (mtmm) REVERT: A 120 MET cc_start: 0.9071 (mmm) cc_final: 0.8593 (mtm) REVERT: H 71 GLU cc_start: 0.8870 (tt0) cc_final: 0.8411 (tp30) REVERT: K 1654 MET cc_start: 0.6376 (mmm) cc_final: 0.6147 (mmm) outliers start: 25 outliers final: 21 residues processed: 69 average time/residue: 0.2913 time to fit residues: 32.5158 Evaluate side-chains 65 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 43 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain E residue 61 LEU 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 G residue 114 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 59 MET Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 1121 ILE Chi-restraints excluded: chain K residue 1135 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 155 optimal weight: 6.9990 chunk 143 optimal weight: 0.0770 chunk 123 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 overall best weight: 4.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN ** K1199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 1.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18109 Z= 0.253 Angle : 0.690 17.223 25866 Z= 0.383 Chirality : 0.038 0.261 2882 Planarity : 0.004 0.042 2154 Dihedral : 30.273 160.368 5102 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.07 % Allowed : 13.76 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.24), residues: 1263 helix: 1.24 (0.19), residues: 735 sheet: -0.59 (0.71), residues: 62 loop : -0.18 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K1649 HIS 0.004 0.001 HIS K1199 PHE 0.020 0.001 PHE K1090 TYR 0.067 0.002 TYR F 88 ARG 0.007 0.000 ARG H 99 ********************** 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 71 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 48 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 LYS cc_start: 0.6859 (tptp) cc_final: 0.6654 (tmtt) REVERT: A 64 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.6820 (mtmm) REVERT: A 120 MET cc_start: 0.9084 (mmm) cc_final: 0.8685 (mmm) REVERT: H 71 GLU cc_start: 0.8873 (tt0) cc_final: 0.8403 (tp30) outliers start: 23 outliers final: 20 residues processed: 71 average time/residue: 0.2830 time to fit residues: 32.3847 Evaluate side-chains 65 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 44 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 61 LEU 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 G residue 114 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 1121 ILE Chi-restraints excluded: chain K residue 1135 THR Chi-restraints excluded: chain K residue 1613 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 20.0000 chunk 37 optimal weight: 0.0170 chunk 114 optimal weight: 30.0000 chunk 18 optimal weight: 0.4980 chunk 34 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 127 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 overall best weight: 3.1024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN B 27 GLN ** K1199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.059018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.038121 restraints weight = 194094.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.038585 restraints weight = 116714.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.038949 restraints weight = 86947.314| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 1.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 18109 Z= 0.233 Angle : 0.673 17.465 25866 Z= 0.371 Chirality : 0.037 0.255 2882 Planarity : 0.004 0.040 2154 Dihedral : 30.089 164.488 5102 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.43 % Allowed : 13.31 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.24), residues: 1263 helix: 1.26 (0.19), residues: 738 sheet: -0.54 (0.67), residues: 69 loop : -0.06 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K1266 HIS 0.004 0.001 HIS K1199 PHE 0.014 0.001 PHE K1504 TYR 0.058 0.002 TYR F 88 ARG 0.007 0.000 ARG D 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2608.50 seconds wall clock time: 49 minutes 5.67 seconds (2945.67 seconds total)