Starting phenix.real_space_refine on Sun Mar 17 01:21:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hak_34594/03_2024/8hak_34594_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hak_34594/03_2024/8hak_34594.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hak_34594/03_2024/8hak_34594.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hak_34594/03_2024/8hak_34594.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hak_34594/03_2024/8hak_34594_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hak_34594/03_2024/8hak_34594_updated.pdb" } resolution = 4.5 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 292 5.49 5 S 47 5.16 5 C 9421 2.51 5 N 2979 2.21 5 O 3603 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 40": "NH1" <-> "NH2" Residue "A ARG 42": "NH1" <-> "NH2" Residue "A ARG 49": "NH1" <-> "NH2" Residue "A ARG 52": "NH1" <-> "NH2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A ARG 69": "NH1" <-> "NH2" Residue "A ARG 72": "NH1" <-> "NH2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A ARG 83": "NH1" <-> "NH2" Residue "A PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "A ARG 116": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "A ARG 131": "NH1" <-> "NH2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "B ARG 23": "NH1" <-> "NH2" Residue "B ARG 35": "NH1" <-> "NH2" Residue "B ARG 36": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 40": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 55": "NH1" <-> "NH2" Residue "B ARG 67": "NH1" <-> "NH2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B ARG 92": "NH1" <-> "NH2" Residue "B ARG 95": "NH1" <-> "NH2" Residue "C ARG 17": "NH1" <-> "NH2" Residue "C ARG 20": "NH1" <-> "NH2" Residue "C ARG 29": "NH1" <-> "NH2" Residue "C ARG 32": "NH1" <-> "NH2" Residue "C ARG 35": "NH1" <-> "NH2" Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 42": "NH1" <-> "NH2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C ARG 71": "NH1" <-> "NH2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ARG 99": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 72": "NH1" <-> "NH2" Residue "D ARG 79": "NH1" <-> "NH2" Residue "D TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 86": "NH1" <-> "NH2" Residue "D ARG 92": "NH1" <-> "NH2" Residue "D ARG 99": "NH1" <-> "NH2" Residue "D GLU 113": "OE1" <-> "OE2" Residue "E ARG 40": "NH1" <-> "NH2" Residue "E ARG 42": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 52": "NH1" <-> "NH2" Residue "E ARG 53": "NH1" <-> "NH2" Residue "E ARG 63": "NH1" <-> "NH2" Residue "E PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 69": "NH1" <-> "NH2" Residue "E ARG 72": "NH1" <-> "NH2" Residue "E ARG 83": "NH1" <-> "NH2" Residue "E ASP 106": "OD1" <-> "OD2" Residue "E ARG 116": "NH1" <-> "NH2" Residue "E ARG 128": "NH1" <-> "NH2" Residue "E ARG 129": "NH1" <-> "NH2" Residue "E ARG 131": "NH1" <-> "NH2" Residue "E ARG 134": "NH1" <-> "NH2" Residue "F ARG 19": "NH1" <-> "NH2" Residue "F ARG 23": "NH1" <-> "NH2" Residue "F ARG 35": "NH1" <-> "NH2" Residue "F ARG 36": "NH1" <-> "NH2" Residue "F ARG 39": "NH1" <-> "NH2" Residue "F ARG 40": "NH1" <-> "NH2" Residue "F ARG 45": "NH1" <-> "NH2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F ARG 55": "NH1" <-> "NH2" Residue "F ARG 67": "NH1" <-> "NH2" Residue "F TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 78": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F ARG 95": "NH1" <-> "NH2" Residue "G ARG 17": "NH1" <-> "NH2" Residue "G ARG 20": "NH1" <-> "NH2" Residue "G ARG 29": "NH1" <-> "NH2" Residue "G ARG 32": "NH1" <-> "NH2" Residue "G ARG 35": "NH1" <-> "NH2" Residue "G ARG 42": "NH1" <-> "NH2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 71": "NH1" <-> "NH2" Residue "G ARG 77": "NH1" <-> "NH2" Residue "G ARG 81": "NH1" <-> "NH2" Residue "G ARG 88": "NH1" <-> "NH2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "G ARG 99": "NH1" <-> "NH2" Residue "H ARG 33": "NH1" <-> "NH2" Residue "H PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 72": "NH1" <-> "NH2" Residue "H ARG 79": "NH1" <-> "NH2" Residue "H ARG 86": "NH1" <-> "NH2" Residue "H ARG 92": "NH1" <-> "NH2" Residue "H ARG 99": "NH1" <-> "NH2" Residue "N ASP 1080": "OD1" <-> "OD2" Residue "N TYR 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 1139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 1200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 1202": "OE1" <-> "OE2" Residue "N GLU 1317": "OE1" <-> "OE2" Residue "N ARG 1342": "NH1" <-> "NH2" Residue "N TYR 1355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 1361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 1482": "OD1" <-> "OD2" Residue "N PHE 1487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 1503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 1585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 1595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 1596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 1628": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16342 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 794 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 806 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 717 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 89} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ALY:plan-2': 2, 'ALY:plan-1': 1} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 815 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 100} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 741 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "J" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3016 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 2973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2973 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "N" Number of atoms: 4295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4295 Classifications: {'peptide': 520} Link IDs: {'PCIS': 3, 'PTRANS': 29, 'TRANS': 487} Chain breaks: 3 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ALA C 14 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA C 14 " occ=0.00 Time building chain proxies: 8.93, per 1000 atoms: 0.55 Number of scatterers: 16342 At special positions: 0 Unit cell: (123.48, 124.95, 152.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 47 16.00 P 292 15.00 O 3603 8.00 N 2979 7.00 C 9421 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 8.16 Conformation dependent library (CDL) restraints added in 1.9 seconds 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2422 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 3 sheets defined 54.1% alpha, 5.5% beta 101 base pairs and 219 stacking pairs defined. Time for finding SS restraints: 7.14 Creating SS restraints... Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 86 through 114 Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'B' and resid 25 through 28 No H-bonds generated for 'chain 'B' and resid 25 through 28' Processing helix chain 'B' and resid 31 through 40 Processing helix chain 'B' and resid 50 through 76 Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'C' and resid 17 through 20 No H-bonds generated for 'chain 'C' and resid 17 through 20' Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 45 through 72 removed outlier: 3.947A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'C' and resid 113 through 115 No H-bonds generated for 'chain 'C' and resid 113 through 115' Processing helix chain 'D' and resid 38 through 48 Processing helix chain 'D' and resid 56 through 83 Processing helix chain 'D' and resid 91 through 101 Processing helix chain 'D' and resid 105 through 123 removed outlier: 4.119A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 64 through 78 Processing helix chain 'E' and resid 86 through 113 Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 40 Processing helix chain 'F' and resid 48 through 75 removed outlier: 3.860A pdb=" N TYR F 51 " --> pdb=" O GLY F 48 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU F 52 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE F 66 " --> pdb=" O GLU F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 92 Processing helix chain 'G' and resid 17 through 20 No H-bonds generated for 'chain 'G' and resid 17 through 20' Processing helix chain 'G' and resid 27 through 35 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.342A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 89 Processing helix chain 'G' and resid 91 through 96 Processing helix chain 'H' and resid 38 through 48 Processing helix chain 'H' and resid 56 through 83 Processing helix chain 'H' and resid 91 through 101 Processing helix chain 'H' and resid 104 through 122 Processing helix chain 'N' and resid 1052 through 1067 Proline residue: N1060 - end of helix Processing helix chain 'N' and resid 1073 through 1075 No H-bonds generated for 'chain 'N' and resid 1073 through 1075' Processing helix chain 'N' and resid 1081 through 1084 No H-bonds generated for 'chain 'N' and resid 1081 through 1084' Processing helix chain 'N' and resid 1099 through 1108 Processing helix chain 'N' and resid 1114 through 1130 Processing helix chain 'N' and resid 1137 through 1159 Proline residue: N1155 - end of helix Processing helix chain 'N' and resid 1256 through 1259 No H-bonds generated for 'chain 'N' and resid 1256 through 1259' Processing helix chain 'N' and resid 1273 through 1278 Processing helix chain 'N' and resid 1290 through 1292 No H-bonds generated for 'chain 'N' and resid 1290 through 1292' Processing helix chain 'N' and resid 1297 through 1313 Processing helix chain 'N' and resid 1337 through 1342 removed outlier: 3.818A pdb=" N ARG N1342 " --> pdb=" O GLY N1338 " (cutoff:3.500A) Processing helix chain 'N' and resid 1407 through 1428 removed outlier: 4.391A pdb=" N THR N1411 " --> pdb=" O LYS N1407 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ALA N1412 " --> pdb=" O CYS N1408 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU N1422 " --> pdb=" O LEU N1418 " (cutoff:3.500A) Processing helix chain 'N' and resid 1460 through 1476 Processing helix chain 'N' and resid 1486 through 1493 Processing helix chain 'N' and resid 1498 through 1500 No H-bonds generated for 'chain 'N' and resid 1498 through 1500' Processing helix chain 'N' and resid 1508 through 1518 removed outlier: 3.811A pdb=" N GLU N1514 " --> pdb=" O PRO N1510 " (cutoff:3.500A) Processing helix chain 'N' and resid 1581 through 1590 Processing helix chain 'N' and resid 1627 through 1636 Processing helix chain 'N' and resid 1644 through 1661 Processing sheet with id= A, first strand: chain 'N' and resid 1232 through 1235 Processing sheet with id= B, first strand: chain 'N' and resid 1244 through 1246 Processing sheet with id= C, first strand: chain 'N' and resid 1482 through 1485 removed outlier: 3.536A pdb=" N ASP N1482 " --> pdb=" O ARG N1599 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N TRP N1436 " --> pdb=" O ILE N1395 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N TYR N1397 " --> pdb=" O TRP N1436 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N HIS N1377 " --> pdb=" O SER N1396 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU N1398 " --> pdb=" O GLY N1375 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLY N1375 " --> pdb=" O LEU N1398 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N SER N1400 " --> pdb=" O PHE N1373 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N PHE N1373 " --> pdb=" O SER N1400 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA N1362 " --> pdb=" O PHE N1373 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLY N1375 " --> pdb=" O LEU N1360 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU N1360 " --> pdb=" O GLY N1375 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N HIS N1377 " --> pdb=" O LYS N1358 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LYS N1358 " --> pdb=" O HIS N1377 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLN N1379 " --> pdb=" O ARG N1356 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ARG N1356 " --> pdb=" O GLN N1379 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N TYR N1381 " --> pdb=" O PRO N1354 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS N1327 " --> pdb=" O ALA N1359 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N PHE N1361 " --> pdb=" O VAL N1325 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N VAL N1325 " --> pdb=" O PHE N1361 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N PHE N1363 " --> pdb=" O VAL N1323 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N VAL N1323 " --> pdb=" O PHE N1363 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N GLU N1365 " --> pdb=" O VAL N1321 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N VAL N1321 " --> pdb=" O GLU N1365 " (cutoff:3.500A) 505 hydrogen bonds defined for protein. 1437 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 243 hydrogen bonds 486 hydrogen bond angles 0 basepair planarities 101 basepair parallelities 219 stacking parallelities Total time for adding SS restraints: 6.69 Time building geometry restraints manager: 8.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3703 1.34 - 1.46: 4900 1.46 - 1.57: 8011 1.57 - 1.69: 582 1.69 - 1.81: 70 Bond restraints: 17266 Sorted by residual: bond pdb=" CG GLU F 74 " pdb=" CD GLU F 74 " ideal model delta sigma weight residual 1.516 1.457 0.059 2.50e-02 1.60e+03 5.55e+00 bond pdb=" CG GLU H 113 " pdb=" CD GLU H 113 " ideal model delta sigma weight residual 1.516 1.462 0.054 2.50e-02 1.60e+03 4.74e+00 bond pdb=" NZ ALY F 12 " pdb=" CH ALY F 12 " ideal model delta sigma weight residual 1.343 1.384 -0.041 2.00e-02 2.50e+03 4.22e+00 bond pdb=" CG GLU B 74 " pdb=" CD GLU B 74 " ideal model delta sigma weight residual 1.516 1.477 0.039 2.50e-02 1.60e+03 2.49e+00 bond pdb=" CG GLU B 63 " pdb=" CD GLU B 63 " ideal model delta sigma weight residual 1.516 1.479 0.037 2.50e-02 1.60e+03 2.17e+00 ... (remaining 17261 not shown) Histogram of bond angle deviations from ideal: 97.94 - 105.15: 1307 105.15 - 112.35: 9372 112.35 - 119.56: 5219 119.56 - 126.76: 7688 126.76 - 133.97: 986 Bond angle restraints: 24572 Sorted by residual: angle pdb=" N GLU F 74 " pdb=" CA GLU F 74 " pdb=" CB GLU F 74 " ideal model delta sigma weight residual 110.30 117.95 -7.65 1.54e+00 4.22e-01 2.47e+01 angle pdb=" N GLU B 63 " pdb=" CA GLU B 63 " pdb=" CB GLU B 63 " ideal model delta sigma weight residual 110.28 117.64 -7.36 1.55e+00 4.16e-01 2.26e+01 angle pdb=" N GLU H 113 " pdb=" CA GLU H 113 " pdb=" CB GLU H 113 " ideal model delta sigma weight residual 110.28 116.50 -6.22 1.55e+00 4.16e-01 1.61e+01 angle pdb=" N GLU C 56 " pdb=" CA GLU C 56 " pdb=" CB GLU C 56 " ideal model delta sigma weight residual 110.22 116.15 -5.93 1.54e+00 4.22e-01 1.49e+01 angle pdb=" N GLU B 74 " pdb=" CA GLU B 74 " pdb=" CB GLU B 74 " ideal model delta sigma weight residual 110.39 116.42 -6.03 1.66e+00 3.63e-01 1.32e+01 ... (remaining 24567 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.08: 8349 34.08 - 68.16: 1354 68.16 - 102.24: 34 102.24 - 136.32: 0 136.32 - 170.40: 2 Dihedral angle restraints: 9739 sinusoidal: 5988 harmonic: 3751 Sorted by residual: dihedral pdb=" C4' DT K 136 " pdb=" C3' DT K 136 " pdb=" O3' DT K 136 " pdb=" P DT K 137 " ideal model delta sinusoidal sigma weight residual -140.00 30.40 -170.40 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DA J 59 " pdb=" C3' DA J 59 " pdb=" O3' DA J 59 " pdb=" P DA J 60 " ideal model delta sinusoidal sigma weight residual 220.00 51.81 168.19 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" CG ARG E 128 " pdb=" CD ARG E 128 " pdb=" NE ARG E 128 " pdb=" CZ ARG E 128 " ideal model delta sinusoidal sigma weight residual -90.00 -134.23 44.23 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 9736 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2099 0.037 - 0.074: 486 0.074 - 0.111: 125 0.111 - 0.148: 26 0.148 - 0.185: 2 Chirality restraints: 2738 Sorted by residual: chirality pdb=" CG LEU C 55 " pdb=" CB LEU C 55 " pdb=" CD1 LEU C 55 " pdb=" CD2 LEU C 55 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.57e-01 chirality pdb=" CA ASP B 24 " pdb=" N ASP B 24 " pdb=" C ASP B 24 " pdb=" CB ASP B 24 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.88e-01 chirality pdb=" CA GLU G 61 " pdb=" N GLU G 61 " pdb=" C GLU G 61 " pdb=" CB GLU G 61 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.43e-01 ... (remaining 2735 not shown) Planarity restraints: 2114 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 67 " -0.014 2.00e-02 2.50e+03 2.18e-02 8.35e+00 pdb=" CG PHE E 67 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE E 67 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE E 67 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 PHE E 67 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE E 67 " 0.011 2.00e-02 2.50e+03 pdb=" CZ PHE E 67 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP N1069 " -0.038 5.00e-02 4.00e+02 5.77e-02 5.32e+00 pdb=" N PRO N1070 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO N1070 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO N1070 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU H 113 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.17e+00 pdb=" CD GLU H 113 " -0.035 2.00e-02 2.50e+03 pdb=" OE1 GLU H 113 " 0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU H 113 " 0.013 2.00e-02 2.50e+03 ... (remaining 2111 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1780 2.75 - 3.29: 16184 3.29 - 3.83: 31970 3.83 - 4.36: 36992 4.36 - 4.90: 53637 Nonbonded interactions: 140563 Sorted by model distance: nonbonded pdb=" OG SER C 18 " pdb=" O LEU C 23 " model vdw 2.214 2.440 nonbonded pdb=" O GLU B 74 " pdb=" NH2 ARG D 92 " model vdw 2.216 2.520 nonbonded pdb=" N THR H 90 " pdb=" OE2 GLU H 93 " model vdw 2.264 2.520 nonbonded pdb=" O VAL N1156 " pdb=" OG SER N1159 " model vdw 2.275 2.440 nonbonded pdb=" NH1 ARG G 29 " pdb=" O SER H 36 " model vdw 2.287 2.520 ... (remaining 140558 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 21 through 101) } ncs_group { reference = chain 'C' selection = (chain 'G' and (resid 14 through 117 or (resid 118 and (name N or name CA or nam \ e C or name O or name CB )))) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 31 through 124) } ncs_group { reference = (chain 'J' and resid 19 through 162) selection = (chain 'K' and resid 19 through 162) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 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: 0.030 Extract box with map and model: 4.370 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 50.560 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.070 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 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 0.059 17266 Z= 0.188 Angle : 0.652 9.072 24572 Z= 0.397 Chirality : 0.036 0.185 2738 Planarity : 0.004 0.058 2114 Dihedral : 24.736 170.401 7317 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.55 (0.22), residues: 1256 helix: 0.91 (0.18), residues: 744 sheet: 0.55 (0.73), residues: 54 loop : -0.44 (0.26), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP N1129 HIS 0.005 0.001 HIS D 109 PHE 0.047 0.002 PHE E 67 TYR 0.022 0.001 TYR C 50 ARG 0.008 0.000 ARG D 99 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8492 (mt-10) REVERT: A 106 ASP cc_start: 0.8794 (m-30) cc_final: 0.8572 (m-30) REVERT: B 63 GLU cc_start: 0.9155 (pm20) cc_final: 0.8665 (pm20) REVERT: D 68 ASP cc_start: 0.9087 (m-30) cc_final: 0.8875 (m-30) REVERT: D 95 GLN cc_start: 0.9339 (mt0) cc_final: 0.9049 (mp10) REVERT: D 108 LYS cc_start: 0.9620 (mtpp) cc_final: 0.9390 (mmmt) REVERT: E 77 ASP cc_start: 0.8590 (m-30) cc_final: 0.8219 (t0) REVERT: E 90 MET cc_start: 0.9021 (mmp) cc_final: 0.8524 (mmp) REVERT: E 120 MET cc_start: 0.8273 (tpt) cc_final: 0.8053 (mmm) REVERT: F 62 LEU cc_start: 0.9690 (mt) cc_final: 0.9389 (mt) REVERT: F 93 GLN cc_start: 0.8752 (tt0) cc_final: 0.8184 (tm-30) REVERT: G 24 GLN cc_start: 0.8919 (mp10) cc_final: 0.8692 (mp10) REVERT: G 38 ASN cc_start: 0.8572 (m-40) cc_final: 0.8264 (p0) REVERT: G 51 LEU cc_start: 0.9515 (tp) cc_final: 0.9256 (tp) REVERT: G 68 ASN cc_start: 0.8798 (m-40) cc_final: 0.8256 (t0) REVERT: G 72 ASP cc_start: 0.9130 (m-30) cc_final: 0.8781 (m-30) REVERT: H 41 VAL cc_start: 0.9328 (t) cc_final: 0.9099 (t) REVERT: N 1349 MET cc_start: -0.2944 (tpt) cc_final: -0.3440 (tpt) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.2558 time to fit residues: 70.4290 Evaluate side-chains 123 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 7.9990 chunk 115 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 119 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 138 optimal weight: 0.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN ** N1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N1236 ASN ** N1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 17266 Z= 0.270 Angle : 0.615 6.827 24572 Z= 0.362 Chirality : 0.038 0.158 2738 Planarity : 0.005 0.066 2114 Dihedral : 28.633 171.321 4715 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.09 % Allowed : 4.24 % Favored : 95.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.16 (0.22), residues: 1256 helix: 1.50 (0.18), residues: 748 sheet: 0.60 (0.74), residues: 55 loop : -0.37 (0.26), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP N1122 HIS 0.007 0.001 HIS D 109 PHE 0.033 0.002 PHE N1149 TYR 0.017 0.001 TYR C 50 ARG 0.007 0.001 ARG F 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 155 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 PHE cc_start: 0.8464 (m-10) cc_final: 0.8118 (m-10) REVERT: A 106 ASP cc_start: 0.8986 (m-30) cc_final: 0.8755 (m-30) REVERT: B 84 MET cc_start: 0.8692 (tpt) cc_final: 0.8470 (tpp) REVERT: B 97 LEU cc_start: 0.9119 (tp) cc_final: 0.8893 (tp) REVERT: C 38 ASN cc_start: 0.8206 (t0) cc_final: 0.7003 (t0) REVERT: D 68 ASP cc_start: 0.9083 (m-30) cc_final: 0.8874 (m-30) REVERT: D 121 TYR cc_start: 0.8409 (t80) cc_final: 0.8065 (t80) REVERT: E 77 ASP cc_start: 0.8705 (m-30) cc_final: 0.8438 (t0) REVERT: E 90 MET cc_start: 0.9025 (mmp) cc_final: 0.8803 (mmm) REVERT: E 97 GLU cc_start: 0.9355 (mt-10) cc_final: 0.8597 (mm-30) REVERT: E 120 MET cc_start: 0.8464 (tpt) cc_final: 0.8084 (mmm) REVERT: F 93 GLN cc_start: 0.8851 (tt0) cc_final: 0.8288 (tm-30) REVERT: G 24 GLN cc_start: 0.8964 (mp10) cc_final: 0.8662 (mp10) REVERT: G 38 ASN cc_start: 0.8928 (m-40) cc_final: 0.8090 (t0) REVERT: G 64 GLU cc_start: 0.9276 (mm-30) cc_final: 0.8967 (mm-30) REVERT: G 68 ASN cc_start: 0.8966 (m-40) cc_final: 0.8668 (t0) REVERT: G 72 ASP cc_start: 0.9164 (m-30) cc_final: 0.8687 (m-30) outliers start: 1 outliers final: 0 residues processed: 155 average time/residue: 0.2813 time to fit residues: 65.5269 Evaluate side-chains 114 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 77 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 115 optimal weight: 20.0000 chunk 94 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 139 optimal weight: 20.0000 chunk 150 optimal weight: 40.0000 chunk 123 optimal weight: 8.9990 chunk 138 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS ** G 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN H 67 ASN ** N1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N1236 ASN N1261 HIS ** N1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 17266 Z= 0.386 Angle : 0.731 13.533 24572 Z= 0.421 Chirality : 0.041 0.161 2738 Planarity : 0.006 0.080 2114 Dihedral : 29.804 177.707 4715 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 23.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.18 % Allowed : 5.05 % Favored : 94.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.49 (0.22), residues: 1256 helix: 0.88 (0.18), residues: 749 sheet: -0.04 (0.67), residues: 64 loop : -0.44 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP N1509 HIS 0.008 0.002 HIS H 49 PHE 0.021 0.002 PHE D 70 TYR 0.025 0.002 TYR G 57 ARG 0.012 0.001 ARG G 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 135 time to evaluate : 1.435 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9488 (mm-30) cc_final: 0.9176 (mm-30) REVERT: A 97 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8425 (pt0) REVERT: A 106 ASP cc_start: 0.9051 (m-30) cc_final: 0.8829 (m-30) REVERT: B 74 GLU cc_start: 0.9271 (pp20) cc_final: 0.8982 (pp20) REVERT: B 84 MET cc_start: 0.8476 (tpt) cc_final: 0.8211 (tpp) REVERT: D 68 ASP cc_start: 0.9164 (m-30) cc_final: 0.8955 (m-30) REVERT: E 97 GLU cc_start: 0.9406 (mt-10) cc_final: 0.8854 (mm-30) REVERT: E 110 CYS cc_start: 0.9788 (m) cc_final: 0.9159 (t) REVERT: F 62 LEU cc_start: 0.9598 (mt) cc_final: 0.9377 (mt) REVERT: F 84 MET cc_start: 0.8785 (tpp) cc_final: 0.8565 (tpp) REVERT: F 88 TYR cc_start: 0.8437 (m-10) cc_final: 0.7814 (m-10) REVERT: F 93 GLN cc_start: 0.8784 (tt0) cc_final: 0.8580 (tm-30) REVERT: G 24 GLN cc_start: 0.8937 (mp10) cc_final: 0.8643 (mp10) REVERT: G 38 ASN cc_start: 0.9183 (m-40) cc_final: 0.8903 (m-40) REVERT: G 74 LYS cc_start: 0.9572 (tptp) cc_final: 0.9369 (mmmm) REVERT: G 90 ASP cc_start: 0.9244 (t70) cc_final: 0.9001 (t0) REVERT: G 99 ARG cc_start: 0.7753 (tpt90) cc_final: 0.7256 (mmm160) REVERT: H 83 TYR cc_start: 0.8981 (m-10) cc_final: 0.8713 (m-80) REVERT: N 1349 MET cc_start: 0.0832 (tpt) cc_final: 0.0206 (tpt) outliers start: 2 outliers final: 1 residues processed: 136 average time/residue: 0.2781 time to fit residues: 56.6036 Evaluate side-chains 92 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 10.0000 chunk 104 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 139 optimal weight: 9.9990 chunk 147 optimal weight: 20.0000 chunk 132 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 chunk 123 optimal weight: 8.9990 overall best weight: 2.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN G 89 ASN ** N1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17266 Z= 0.246 Angle : 0.611 7.708 24572 Z= 0.358 Chirality : 0.037 0.152 2738 Planarity : 0.005 0.066 2114 Dihedral : 29.871 177.242 4715 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.90 (0.22), residues: 1256 helix: 1.28 (0.18), residues: 747 sheet: -0.06 (0.67), residues: 64 loop : -0.36 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N1115 HIS 0.006 0.001 HIS B 75 PHE 0.028 0.001 PHE E 104 TYR 0.019 0.002 TYR C 50 ARG 0.010 0.001 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9511 (mm-30) cc_final: 0.9179 (mm-30) REVERT: A 97 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8198 (pt0) REVERT: B 74 GLU cc_start: 0.9349 (pp20) cc_final: 0.9053 (pp20) REVERT: B 84 MET cc_start: 0.8572 (tpt) cc_final: 0.8175 (tpp) REVERT: C 61 GLU cc_start: 0.9337 (mm-30) cc_final: 0.8533 (mm-30) REVERT: C 101 THR cc_start: 0.9590 (p) cc_final: 0.9384 (p) REVERT: D 37 TYR cc_start: 0.9370 (m-80) cc_final: 0.8968 (m-80) REVERT: D 68 ASP cc_start: 0.9218 (m-30) cc_final: 0.8903 (m-30) REVERT: D 80 LEU cc_start: 0.9654 (mm) cc_final: 0.9444 (mm) REVERT: E 90 MET cc_start: 0.8996 (mmp) cc_final: 0.8743 (mmm) REVERT: E 97 GLU cc_start: 0.9367 (mt-10) cc_final: 0.8864 (mm-30) REVERT: E 110 CYS cc_start: 0.9772 (m) cc_final: 0.9119 (t) REVERT: E 120 MET cc_start: 0.9172 (tpt) cc_final: 0.8828 (mmm) REVERT: F 84 MET cc_start: 0.8668 (tpp) cc_final: 0.8257 (tpp) REVERT: F 87 VAL cc_start: 0.9410 (t) cc_final: 0.9194 (t) REVERT: F 88 TYR cc_start: 0.8649 (m-10) cc_final: 0.8117 (m-10) REVERT: F 93 GLN cc_start: 0.8833 (tt0) cc_final: 0.8619 (tm-30) REVERT: F 97 LEU cc_start: 0.9448 (tp) cc_final: 0.9223 (tp) REVERT: G 24 GLN cc_start: 0.9083 (mp10) cc_final: 0.8784 (mp10) REVERT: G 38 ASN cc_start: 0.9062 (m-40) cc_final: 0.8706 (p0) REVERT: G 39 TYR cc_start: 0.9260 (m-80) cc_final: 0.8824 (m-80) REVERT: G 90 ASP cc_start: 0.9310 (t70) cc_final: 0.9064 (t0) REVERT: N 1349 MET cc_start: 0.1604 (tpt) cc_final: 0.0635 (tpt) REVERT: N 1624 MET cc_start: -0.0948 (mmm) cc_final: -0.1350 (mmm) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.2955 time to fit residues: 62.4895 Evaluate side-chains 99 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 110 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 126 optimal weight: 0.0000 chunk 102 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 75 optimal weight: 7.9990 chunk 132 optimal weight: 30.0000 chunk 37 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N1591 HIS ** N1638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.5473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 17266 Z= 0.323 Angle : 0.655 9.238 24572 Z= 0.381 Chirality : 0.038 0.161 2738 Planarity : 0.005 0.068 2114 Dihedral : 30.066 179.664 4715 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 21.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.82 (0.22), residues: 1256 helix: 1.22 (0.18), residues: 757 sheet: 0.01 (0.68), residues: 64 loop : -0.47 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP N1509 HIS 0.005 0.001 HIS F 75 PHE 0.011 0.002 PHE F 100 TYR 0.017 0.002 TYR H 40 ARG 0.014 0.001 ARG G 29 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9577 (mm-30) cc_final: 0.9213 (mm-30) REVERT: A 97 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8201 (mp0) REVERT: B 74 GLU cc_start: 0.9412 (pp20) cc_final: 0.9138 (pp20) REVERT: B 84 MET cc_start: 0.8512 (tpt) cc_final: 0.8182 (tpp) REVERT: C 64 GLU cc_start: 0.9591 (pt0) cc_final: 0.9339 (pt0) REVERT: C 72 ASP cc_start: 0.9176 (m-30) cc_final: 0.8586 (m-30) REVERT: C 99 ARG cc_start: 0.8366 (mmm-85) cc_final: 0.7995 (mmm-85) REVERT: D 37 TYR cc_start: 0.9387 (m-80) cc_final: 0.8973 (m-80) REVERT: D 68 ASP cc_start: 0.9173 (m-30) cc_final: 0.8815 (m-30) REVERT: E 90 MET cc_start: 0.9007 (mmp) cc_final: 0.8763 (mmm) REVERT: E 97 GLU cc_start: 0.9353 (mt-10) cc_final: 0.8911 (mm-30) REVERT: E 120 MET cc_start: 0.9024 (tpt) cc_final: 0.8632 (mmm) REVERT: F 84 MET cc_start: 0.8656 (tpp) cc_final: 0.8340 (tpp) REVERT: F 88 TYR cc_start: 0.8468 (m-10) cc_final: 0.7815 (m-10) REVERT: F 93 GLN cc_start: 0.8945 (tt0) cc_final: 0.8632 (tm-30) REVERT: G 24 GLN cc_start: 0.8932 (mp10) cc_final: 0.8679 (mp10) REVERT: G 38 ASN cc_start: 0.9024 (m-40) cc_final: 0.8823 (m-40) REVERT: G 39 TYR cc_start: 0.9282 (m-80) cc_final: 0.8933 (m-80) REVERT: G 90 ASP cc_start: 0.9284 (t70) cc_final: 0.8993 (t0) REVERT: H 41 VAL cc_start: 0.9529 (t) cc_final: 0.9323 (t) REVERT: N 1349 MET cc_start: 0.2706 (tpt) cc_final: 0.2040 (tpt) REVERT: N 1624 MET cc_start: -0.0914 (mmm) cc_final: -0.1216 (mmm) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.2971 time to fit residues: 59.6808 Evaluate side-chains 94 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 133 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 chunk 148 optimal weight: 20.0000 chunk 122 optimal weight: 0.0070 chunk 68 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 142 optimal weight: 9.9990 overall best weight: 2.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 HIS ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.5631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17266 Z= 0.236 Angle : 0.613 10.750 24572 Z= 0.358 Chirality : 0.036 0.145 2738 Planarity : 0.005 0.067 2114 Dihedral : 30.115 179.244 4715 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.01 (0.23), residues: 1256 helix: 1.38 (0.18), residues: 754 sheet: -0.06 (0.66), residues: 64 loop : -0.36 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP N1509 HIS 0.004 0.001 HIS D 109 PHE 0.012 0.001 PHE E 67 TYR 0.019 0.001 TYR N1394 ARG 0.007 0.000 ARG N1392 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9577 (mm-30) cc_final: 0.9213 (mm-30) REVERT: A 94 GLU cc_start: 0.8957 (tt0) cc_final: 0.8619 (tt0) REVERT: A 97 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8127 (mp0) REVERT: B 74 GLU cc_start: 0.9411 (pp20) cc_final: 0.9116 (pp20) REVERT: B 84 MET cc_start: 0.8467 (tpt) cc_final: 0.8140 (tpp) REVERT: C 68 ASN cc_start: 0.9517 (t0) cc_final: 0.9181 (t0) REVERT: C 101 THR cc_start: 0.9559 (p) cc_final: 0.9295 (p) REVERT: D 37 TYR cc_start: 0.9359 (m-80) cc_final: 0.8984 (m-80) REVERT: D 68 ASP cc_start: 0.9213 (m-30) cc_final: 0.8891 (m-30) REVERT: E 90 MET cc_start: 0.8994 (mmp) cc_final: 0.8764 (mmm) REVERT: E 97 GLU cc_start: 0.9347 (mt-10) cc_final: 0.8907 (mm-30) REVERT: E 110 CYS cc_start: 0.9788 (m) cc_final: 0.9117 (t) REVERT: E 120 MET cc_start: 0.9013 (tpt) cc_final: 0.8662 (mmm) REVERT: F 84 MET cc_start: 0.8671 (tpp) cc_final: 0.8297 (tpp) REVERT: F 87 VAL cc_start: 0.9377 (t) cc_final: 0.9150 (t) REVERT: F 93 GLN cc_start: 0.8963 (tt0) cc_final: 0.8628 (tm-30) REVERT: F 97 LEU cc_start: 0.9474 (tp) cc_final: 0.9249 (tp) REVERT: G 24 GLN cc_start: 0.9040 (mp10) cc_final: 0.8823 (mp10) REVERT: G 38 ASN cc_start: 0.8998 (m-40) cc_final: 0.8731 (p0) REVERT: G 39 TYR cc_start: 0.9308 (m-80) cc_final: 0.8837 (m-80) REVERT: G 90 ASP cc_start: 0.9277 (t70) cc_final: 0.9003 (t0) REVERT: N 1349 MET cc_start: 0.2827 (tpt) cc_final: 0.2336 (tpt) REVERT: N 1624 MET cc_start: -0.0864 (mmm) cc_final: -0.1190 (mmm) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.2747 time to fit residues: 56.9267 Evaluate side-chains 98 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 16 optimal weight: 0.4980 chunk 84 optimal weight: 6.9990 chunk 108 optimal weight: 30.0000 chunk 83 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 147 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N1158 GLN ** N1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.6011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 17266 Z= 0.251 Angle : 0.626 10.522 24572 Z= 0.361 Chirality : 0.036 0.145 2738 Planarity : 0.005 0.069 2114 Dihedral : 30.034 179.646 4715 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 18.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.01 (0.23), residues: 1256 helix: 1.37 (0.18), residues: 755 sheet: -0.26 (0.63), residues: 69 loop : -0.32 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP N1436 HIS 0.004 0.001 HIS F 75 PHE 0.012 0.002 PHE D 70 TYR 0.026 0.002 TYR N1446 ARG 0.006 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9574 (mm-30) cc_final: 0.9243 (mm-30) REVERT: A 94 GLU cc_start: 0.9021 (tt0) cc_final: 0.8621 (tt0) REVERT: A 97 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8271 (mp0) REVERT: B 74 GLU cc_start: 0.9424 (pp20) cc_final: 0.9107 (pp20) REVERT: B 84 MET cc_start: 0.8514 (tpt) cc_final: 0.8242 (tpp) REVERT: C 68 ASN cc_start: 0.9361 (t0) cc_final: 0.9024 (t0) REVERT: C 101 THR cc_start: 0.9545 (p) cc_final: 0.9268 (p) REVERT: D 33 ARG cc_start: 0.5971 (mtt180) cc_final: 0.3115 (mmm-85) REVERT: D 68 ASP cc_start: 0.9181 (m-30) cc_final: 0.8856 (m-30) REVERT: E 90 MET cc_start: 0.9003 (mmp) cc_final: 0.8767 (mmm) REVERT: E 97 GLU cc_start: 0.9352 (mt-10) cc_final: 0.8963 (mm-30) REVERT: E 110 CYS cc_start: 0.9766 (m) cc_final: 0.9168 (t) REVERT: E 120 MET cc_start: 0.9010 (tpt) cc_final: 0.8565 (mmm) REVERT: F 84 MET cc_start: 0.8508 (tpp) cc_final: 0.8203 (tpp) REVERT: F 93 GLN cc_start: 0.8867 (tt0) cc_final: 0.8411 (tm-30) REVERT: F 97 LEU cc_start: 0.9460 (tp) cc_final: 0.9238 (tp) REVERT: G 24 GLN cc_start: 0.9039 (mp10) cc_final: 0.8804 (mp10) REVERT: G 38 ASN cc_start: 0.8907 (m-40) cc_final: 0.8660 (p0) REVERT: G 39 TYR cc_start: 0.9296 (m-80) cc_final: 0.8549 (m-80) REVERT: G 90 ASP cc_start: 0.9300 (t70) cc_final: 0.9047 (t0) REVERT: H 41 VAL cc_start: 0.9479 (t) cc_final: 0.9266 (t) REVERT: N 1349 MET cc_start: 0.3780 (tpt) cc_final: 0.3227 (tpt) REVERT: N 1624 MET cc_start: -0.0702 (mmm) cc_final: -0.1037 (mmm) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.2865 time to fit residues: 59.2505 Evaluate side-chains 96 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 93 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 115 optimal weight: 9.9990 chunk 134 optimal weight: 9.9990 chunk 141 optimal weight: 0.0980 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 55 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.5968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17266 Z= 0.177 Angle : 0.590 7.215 24572 Z= 0.343 Chirality : 0.036 0.198 2738 Planarity : 0.004 0.068 2114 Dihedral : 29.853 179.803 4715 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.17 (0.23), residues: 1256 helix: 1.50 (0.18), residues: 756 sheet: 0.01 (0.74), residues: 59 loop : -0.29 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP N1436 HIS 0.003 0.001 HIS E 113 PHE 0.011 0.001 PHE E 67 TYR 0.044 0.001 TYR F 88 ARG 0.005 0.000 ARG H 79 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9578 (mm-30) cc_final: 0.9276 (mm-30) REVERT: A 94 GLU cc_start: 0.8962 (tt0) cc_final: 0.8574 (tt0) REVERT: A 97 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8346 (mp0) REVERT: A 133 GLU cc_start: 0.8089 (mp0) cc_final: 0.7560 (pm20) REVERT: B 63 GLU cc_start: 0.9194 (pm20) cc_final: 0.8846 (pm20) REVERT: B 74 GLU cc_start: 0.9378 (pp20) cc_final: 0.9018 (pp20) REVERT: B 84 MET cc_start: 0.8339 (tpt) cc_final: 0.8093 (tpp) REVERT: C 64 GLU cc_start: 0.9075 (pt0) cc_final: 0.8830 (pp20) REVERT: C 68 ASN cc_start: 0.9349 (t0) cc_final: 0.8952 (t0) REVERT: C 90 ASP cc_start: 0.9178 (t70) cc_final: 0.8921 (t0) REVERT: C 101 THR cc_start: 0.9516 (p) cc_final: 0.9230 (t) REVERT: D 33 ARG cc_start: 0.5451 (mtt180) cc_final: 0.3212 (mmm-85) REVERT: D 68 ASP cc_start: 0.9163 (m-30) cc_final: 0.8843 (m-30) REVERT: D 100 LEU cc_start: 0.9322 (mt) cc_final: 0.9095 (mp) REVERT: D 121 TYR cc_start: 0.9067 (t80) cc_final: 0.8773 (t80) REVERT: E 90 MET cc_start: 0.8985 (mmp) cc_final: 0.8693 (mmm) REVERT: E 97 GLU cc_start: 0.9349 (mt-10) cc_final: 0.8930 (mm-30) REVERT: E 110 CYS cc_start: 0.9762 (m) cc_final: 0.9145 (t) REVERT: E 120 MET cc_start: 0.8971 (tpt) cc_final: 0.8534 (mmm) REVERT: F 84 MET cc_start: 0.8494 (tpp) cc_final: 0.8237 (tpp) REVERT: F 88 TYR cc_start: 0.8453 (m-10) cc_final: 0.8238 (m-10) REVERT: F 93 GLN cc_start: 0.8993 (tt0) cc_final: 0.8396 (tm-30) REVERT: G 24 GLN cc_start: 0.9069 (mp10) cc_final: 0.8829 (mp10) REVERT: G 38 ASN cc_start: 0.8893 (m-40) cc_final: 0.8663 (p0) REVERT: G 39 TYR cc_start: 0.9272 (m-80) cc_final: 0.8472 (m-80) REVERT: G 90 ASP cc_start: 0.9259 (t70) cc_final: 0.9001 (t0) REVERT: G 118 LYS cc_start: 0.7595 (ptpp) cc_final: 0.6405 (ptmm) REVERT: H 62 MET cc_start: 0.9496 (tpp) cc_final: 0.9262 (tpp) REVERT: N 1349 MET cc_start: 0.3372 (tpt) cc_final: 0.2695 (tpt) REVERT: N 1624 MET cc_start: -0.0782 (mmm) cc_final: -0.1107 (mmm) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.2833 time to fit residues: 62.6567 Evaluate side-chains 108 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 128 optimal weight: 9.9990 chunk 137 optimal weight: 6.9990 chunk 141 optimal weight: 0.5980 chunk 82 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 chunk 136 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N1077 GLN ** N1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.6798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 17266 Z= 0.387 Angle : 0.708 12.346 24572 Z= 0.406 Chirality : 0.040 0.178 2738 Planarity : 0.006 0.072 2114 Dihedral : 30.226 179.451 4715 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 25.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.09 % Allowed : 1.08 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.79 (0.23), residues: 1256 helix: 1.20 (0.18), residues: 748 sheet: -0.36 (0.69), residues: 64 loop : -0.38 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP N1436 HIS 0.006 0.002 HIS N1255 PHE 0.018 0.002 PHE D 70 TYR 0.034 0.002 TYR F 88 ARG 0.008 0.001 ARG H 79 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9566 (mm-30) cc_final: 0.9275 (mm-30) REVERT: A 94 GLU cc_start: 0.9033 (tt0) cc_final: 0.8591 (tt0) REVERT: A 97 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8056 (mp0) REVERT: A 106 ASP cc_start: 0.9008 (m-30) cc_final: 0.8681 (m-30) REVERT: B 63 GLU cc_start: 0.9172 (pm20) cc_final: 0.8957 (pm20) REVERT: B 74 GLU cc_start: 0.9486 (pp20) cc_final: 0.9196 (pp20) REVERT: B 84 MET cc_start: 0.8588 (tpt) cc_final: 0.8283 (tpp) REVERT: C 68 ASN cc_start: 0.9188 (t0) cc_final: 0.8785 (t0) REVERT: C 101 THR cc_start: 0.9476 (p) cc_final: 0.9213 (t) REVERT: C 112 GLN cc_start: 0.9099 (mp10) cc_final: 0.8778 (mp10) REVERT: D 33 ARG cc_start: 0.6806 (mtt180) cc_final: 0.3924 (tpp80) REVERT: D 68 ASP cc_start: 0.9107 (m-30) cc_final: 0.8645 (m-30) REVERT: E 90 MET cc_start: 0.9050 (mmp) cc_final: 0.8475 (mmp) REVERT: E 97 GLU cc_start: 0.9313 (mt-10) cc_final: 0.8974 (mm-30) REVERT: E 107 THR cc_start: 0.9629 (p) cc_final: 0.9414 (p) REVERT: E 120 MET cc_start: 0.9096 (tpt) cc_final: 0.8657 (mmm) REVERT: F 62 LEU cc_start: 0.9598 (mt) cc_final: 0.9329 (mt) REVERT: F 84 MET cc_start: 0.8719 (tpp) cc_final: 0.8449 (tpp) REVERT: F 87 VAL cc_start: 0.9411 (t) cc_final: 0.9202 (t) REVERT: F 88 TYR cc_start: 0.8442 (m-10) cc_final: 0.8215 (m-10) REVERT: F 93 GLN cc_start: 0.9029 (tt0) cc_final: 0.8646 (tm-30) REVERT: G 24 GLN cc_start: 0.9085 (mp10) cc_final: 0.8819 (mp10) REVERT: G 38 ASN cc_start: 0.8856 (m-40) cc_final: 0.8611 (m-40) REVERT: G 90 ASP cc_start: 0.9237 (t70) cc_final: 0.8934 (t0) REVERT: N 1349 MET cc_start: 0.4195 (tpt) cc_final: 0.3464 (tpt) REVERT: N 1624 MET cc_start: -0.0719 (mmm) cc_final: -0.0963 (mmm) outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.2837 time to fit residues: 55.6801 Evaluate side-chains 90 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 145 optimal weight: 20.0000 chunk 88 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 152 optimal weight: 20.0000 chunk 140 optimal weight: 20.0000 chunk 121 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 93 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 96 optimal weight: 6.9990 overall best weight: 3.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.6950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 17266 Z= 0.280 Angle : 0.661 12.455 24572 Z= 0.379 Chirality : 0.038 0.180 2738 Planarity : 0.005 0.071 2114 Dihedral : 30.398 176.772 4715 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 20.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.69 (0.22), residues: 1256 helix: 1.11 (0.18), residues: 749 sheet: -0.53 (0.68), residues: 64 loop : -0.39 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP N1436 HIS 0.007 0.001 HIS E 113 PHE 0.031 0.002 PHE D 65 TYR 0.031 0.002 TYR F 88 ARG 0.005 0.000 ARG H 79 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9560 (mm-30) cc_final: 0.9273 (mm-30) REVERT: A 81 ASP cc_start: 0.8184 (t0) cc_final: 0.7957 (t70) REVERT: A 94 GLU cc_start: 0.8912 (tt0) cc_final: 0.8441 (pt0) REVERT: A 97 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8398 (mp0) REVERT: A 106 ASP cc_start: 0.8895 (m-30) cc_final: 0.8652 (m-30) REVERT: A 110 CYS cc_start: 0.8951 (t) cc_final: 0.8652 (t) REVERT: B 63 GLU cc_start: 0.9180 (pm20) cc_final: 0.8925 (pm20) REVERT: B 74 GLU cc_start: 0.9474 (pp20) cc_final: 0.9180 (pp20) REVERT: B 84 MET cc_start: 0.8370 (tpt) cc_final: 0.8032 (tpp) REVERT: B 97 LEU cc_start: 0.9199 (tp) cc_final: 0.8976 (tp) REVERT: C 68 ASN cc_start: 0.9131 (t0) cc_final: 0.8718 (t0) REVERT: D 59 MET cc_start: 0.9407 (tpt) cc_final: 0.9083 (tpt) REVERT: D 61 ILE cc_start: 0.9617 (mt) cc_final: 0.9403 (mt) REVERT: D 65 PHE cc_start: 0.9669 (t80) cc_final: 0.9259 (t80) REVERT: D 68 ASP cc_start: 0.9203 (m-30) cc_final: 0.8863 (m-30) REVERT: E 97 GLU cc_start: 0.9329 (mt-10) cc_final: 0.8968 (mm-30) REVERT: E 120 MET cc_start: 0.9097 (tpt) cc_final: 0.8673 (mmm) REVERT: F 84 MET cc_start: 0.8676 (tpp) cc_final: 0.8350 (tpp) REVERT: F 87 VAL cc_start: 0.9379 (t) cc_final: 0.9169 (t) REVERT: F 88 TYR cc_start: 0.8422 (m-10) cc_final: 0.8200 (m-10) REVERT: F 93 GLN cc_start: 0.9097 (tt0) cc_final: 0.8692 (tm-30) REVERT: G 24 GLN cc_start: 0.9104 (mp10) cc_final: 0.8833 (mp10) REVERT: N 1349 MET cc_start: 0.4033 (tpt) cc_final: 0.3494 (tpt) REVERT: N 1624 MET cc_start: -0.0728 (mmm) cc_final: -0.1010 (mmm) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.2685 time to fit residues: 52.1962 Evaluate side-chains 91 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 chunk 124 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1379 GLN ** 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 = 0.3526 r_free = 0.3526 target = 0.059892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.038254 restraints weight = 160995.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.039292 restraints weight = 81936.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 73)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.039976 restraints weight = 54812.091| |-----------------------------------------------------------------------------| r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.6788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17266 Z= 0.190 Angle : 0.619 10.245 24572 Z= 0.352 Chirality : 0.036 0.185 2738 Planarity : 0.004 0.068 2114 Dihedral : 30.053 178.091 4715 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.98 (0.23), residues: 1256 helix: 1.30 (0.18), residues: 757 sheet: -0.34 (0.66), residues: 69 loop : -0.23 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP N1436 HIS 0.005 0.001 HIS E 113 PHE 0.027 0.001 PHE D 65 TYR 0.027 0.001 TYR F 88 ARG 0.005 0.000 ARG H 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2575.32 seconds wall clock time: 48 minutes 3.60 seconds (2883.60 seconds total)