Starting phenix.real_space_refine (version: 1.21rc1) on Sun Oct 8 06:25:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hak_34594/10_2023/8hak_34594_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hak_34594/10_2023/8hak_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_34594/10_2023/8hak_34594.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hak_34594/10_2023/8hak_34594.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hak_34594/10_2023/8hak_34594_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hak_34594/10_2023/8hak_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-1.21rc1-5097/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: 8.78, per 1000 atoms: 0.54 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: 8.88 Conformation dependent library (CDL) restraints added in 1.5 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: 8.10 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: 7.55 Time building geometry restraints manager: 9.24 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: 8018 34.08 - 68.16: 1337 68.16 - 102.24: 34 102.24 - 136.32: 0 136.32 - 170.40: 2 Dihedral angle restraints: 9391 sinusoidal: 5640 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 9388 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: 0.890 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: 4.410 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 53.290 Find NCS groups from input model: 0.600 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.430 ------------------------------------------------------------------------------- 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 : 24.836 170.401 6969 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 *********************** 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 : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.2668 time to fit residues: 73.7434 Evaluate side-chains 114 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.420 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7595 ------------------------------------------------------------------------------- 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: 1.9990 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: 1.9990 chunk 72 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 138 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 17266 Z= 0.240 Angle : 0.585 6.384 24572 Z= 0.347 Chirality : 0.036 0.148 2738 Planarity : 0.005 0.064 2114 Dihedral : 29.049 170.813 4367 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.27 % Allowed : 3.25 % Favored : 96.48 % 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: 1.19 (0.22), residues: 1256 helix: 1.54 (0.18), residues: 746 sheet: 0.65 (0.74), residues: 55 loop : -0.39 (0.26), residues: 455 *********************** 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 161 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 158 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 159 average time/residue: 0.2790 time to fit residues: 67.3946 Evaluate side-chains 109 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.400 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7626 ------------------------------------------------------------------------------- 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: 5.9990 chunk 43 optimal weight: 6.9990 chunk 115 optimal weight: 20.0000 chunk 94 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 139 optimal weight: 30.0000 chunk 150 optimal weight: 20.0000 chunk 123 optimal weight: 10.0000 chunk 138 optimal weight: 7.9990 chunk 47 optimal weight: 0.6980 chunk 111 optimal weight: 5.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS ** G 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN ** N1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N1236 ASN ** N1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N1591 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 17266 Z= 0.410 Angle : 0.744 10.320 24572 Z= 0.429 Chirality : 0.042 0.173 2738 Planarity : 0.007 0.121 2114 Dihedral : 30.355 179.384 4367 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 23.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.55 % Favored : 97.37 % Rotamer: Outliers : 0.09 % Allowed : 5.77 % Favored : 94.14 % 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: 0.47 (0.22), residues: 1256 helix: 0.84 (0.18), residues: 755 sheet: 0.12 (0.69), residues: 64 loop : -0.42 (0.27), residues: 437 *********************** 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 138 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 138 average time/residue: 0.2984 time to fit residues: 61.6676 Evaluate side-chains 85 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 84 time to evaluate : 1.448 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1589 time to fit residues: 2.1667 ------------------------------------------------------------------------------- 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: 0.1980 chunk 104 optimal weight: 0.0870 chunk 72 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 139 optimal weight: 20.0000 chunk 147 optimal weight: 9.9990 chunk 132 optimal weight: 0.0030 chunk 39 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 overall best weight: 0.3970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN E 55 GLN E 68 GLN E 93 GLN E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 ASN ** N1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N1236 ASN ** N1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17266 Z= 0.179 Angle : 0.589 6.278 24572 Z= 0.343 Chirality : 0.036 0.171 2738 Planarity : 0.005 0.063 2114 Dihedral : 30.223 178.258 4367 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.27 % Allowed : 2.34 % Favored : 97.39 % 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: 0.99 (0.22), residues: 1256 helix: 1.33 (0.18), residues: 748 sheet: 0.35 (0.74), residues: 55 loop : -0.33 (0.27), residues: 453 *********************** 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 165 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 162 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 165 average time/residue: 0.3485 time to fit residues: 85.3901 Evaluate side-chains 108 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 107 time to evaluate : 1.471 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2030 time to fit residues: 2.1871 ------------------------------------------------------------------------------- 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: 1.9990 chunk 110 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 126 optimal weight: 40.0000 chunk 102 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 75 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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** N1261 HIS ** N1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.4790 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= 0.299 Angle : 0.634 8.478 24572 Z= 0.367 Chirality : 0.037 0.147 2738 Planarity : 0.005 0.066 2114 Dihedral : 30.383 178.598 4367 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % 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: 0.97 (0.22), residues: 1256 helix: 1.33 (0.18), residues: 755 sheet: 0.37 (0.69), residues: 60 loop : -0.43 (0.27), residues: 441 *********************** 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 134 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.2777 time to fit residues: 57.0240 Evaluate side-chains 91 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.409 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6949 ------------------------------------------------------------------------------- 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: 6.9990 chunk 86 optimal weight: 8.9990 chunk 36 optimal weight: 0.0470 chunk 148 optimal weight: 30.0000 chunk 122 optimal weight: 0.0000 chunk 68 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 142 optimal weight: 10.0000 overall best weight: 1.9886 ------------------------------------------------------------------------------- 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** ** N1638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17266 Z= 0.204 Angle : 0.592 7.860 24572 Z= 0.345 Chirality : 0.036 0.147 2738 Planarity : 0.005 0.066 2114 Dihedral : 30.495 179.118 4367 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.10 (0.23), residues: 1256 helix: 1.41 (0.18), residues: 754 sheet: 0.43 (0.70), residues: 60 loop : -0.34 (0.27), residues: 442 *********************** 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 146 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.3058 time to fit residues: 66.6733 Evaluate side-chains 92 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.414 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7242 ------------------------------------------------------------------------------- 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: 2.9990 chunk 84 optimal weight: 6.9990 chunk 108 optimal weight: 30.0000 chunk 83 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 147 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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** ** N1638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.5498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 17266 Z= 0.276 Angle : 0.629 10.896 24572 Z= 0.363 Chirality : 0.037 0.145 2738 Planarity : 0.005 0.068 2114 Dihedral : 30.567 179.000 4367 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % 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: 1.09 (0.23), residues: 1256 helix: 1.43 (0.18), residues: 748 sheet: 0.16 (0.67), residues: 64 loop : -0.32 (0.28), residues: 444 *********************** 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 : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.2999 time to fit residues: 61.0590 Evaluate side-chains 86 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.412 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7026 ------------------------------------------------------------------------------- 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: 0.7980 chunk 93 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 115 optimal weight: 9.9990 chunk 134 optimal weight: 10.0000 chunk 141 optimal weight: 0.0040 overall best weight: 0.8996 ------------------------------------------------------------------------------- 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** N1638 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.5425 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= 0.185 Angle : 0.605 10.576 24572 Z= 0.348 Chirality : 0.036 0.191 2738 Planarity : 0.004 0.068 2114 Dihedral : 30.480 179.587 4367 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % 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: 1.03 (0.23), residues: 1256 helix: 1.35 (0.18), residues: 754 sheet: 0.19 (0.72), residues: 59 loop : -0.29 (0.28), residues: 443 *********************** 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 148 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.3077 time to fit residues: 67.7114 Evaluate side-chains 90 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.523 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7645 ------------------------------------------------------------------------------- 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: 0.0980 chunk 137 optimal weight: 0.7980 chunk 141 optimal weight: 0.1980 chunk 82 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 129 optimal weight: 8.9990 chunk 136 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 HIS ** 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: 0.7995 moved from start: 0.5523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17266 Z= 0.191 Angle : 0.614 10.798 24572 Z= 0.351 Chirality : 0.036 0.187 2738 Planarity : 0.004 0.069 2114 Dihedral : 30.266 178.874 4367 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.97 (0.23), residues: 1256 helix: 1.24 (0.18), residues: 754 sheet: 0.18 (0.72), residues: 59 loop : -0.20 (0.28), residues: 443 *********************** 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 147 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.2922 time to fit residues: 65.2439 Evaluate side-chains 93 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 1.537 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9426 ------------------------------------------------------------------------------- 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: 8.9990 chunk 88 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 chunk 152 optimal weight: 10.0000 chunk 140 optimal weight: 8.9990 chunk 121 optimal weight: 9.9990 chunk 12 optimal weight: 0.6980 chunk 93 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 96 optimal weight: 8.9990 overall best weight: 4.5186 ------------------------------------------------------------------------------- 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** ** N1151 GLN ** 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: 0.8122 moved from start: 0.6501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 17266 Z= 0.368 Angle : 0.725 13.492 24572 Z= 0.414 Chirality : 0.041 0.164 2738 Planarity : 0.006 0.078 2114 Dihedral : 30.793 178.757 4367 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 24.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % 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: 0.52 (0.22), residues: 1256 helix: 0.86 (0.18), residues: 755 sheet: -0.47 (0.62), residues: 69 loop : -0.26 (0.28), residues: 432 ********************** 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 128 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.2876 time to fit residues: 55.5407 Evaluate side-chains 81 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 1.435 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7279 ------------------------------------------------------------------------------- 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: 0.9980 chunk 111 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 106 optimal weight: 8.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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** ** 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 = 0.3490 r_free = 0.3490 target = 0.055808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.033874 restraints weight = 143484.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.034822 restraints weight = 76634.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.035366 restraints weight = 53013.718| |-----------------------------------------------------------------------------| r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.6453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17266 Z= 0.224 Angle : 0.646 12.056 24572 Z= 0.369 Chirality : 0.038 0.171 2738 Planarity : 0.005 0.071 2114 Dihedral : 30.845 177.453 4367 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % 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: 0.56 (0.22), residues: 1256 helix: 0.92 (0.18), residues: 756 sheet: -0.47 (0.62), residues: 69 loop : -0.29 (0.28), residues: 431 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2534.33 seconds wall clock time: 48 minutes 4.27 seconds (2884.27 seconds total)