Starting phenix.real_space_refine on Fri Feb 16 20:57:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hai_34591/02_2024/8hai_34591_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hai_34591/02_2024/8hai_34591.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hai_34591/02_2024/8hai_34591.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hai_34591/02_2024/8hai_34591.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hai_34591/02_2024/8hai_34591_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hai_34591/02_2024/8hai_34591_updated.pdb" } resolution = 4.7 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 294 5.49 5 S 47 5.16 5 C 9542 2.51 5 N 3017 2.21 5 O 3647 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 TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 69": "NH1" <-> "NH2" Residue "A ARG 72": "NH1" <-> "NH2" Residue "A ARG 83": "NH1" <-> "NH2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A ASP 106": "OD1" <-> "OD2" 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 ASP 24": "OD1" <-> "OD2" 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 PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 42": "NH1" <-> "NH2" 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 ASP 90": "OD1" <-> "OD2" Residue "C ARG 99": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 72": "NH1" <-> "NH2" Residue "D ARG 79": "NH1" <-> "NH2" 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 TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 69": "NH1" <-> "NH2" Residue "E ARG 72": "NH1" <-> "NH2" Residue "E ARG 83": "NH1" <-> "NH2" 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 GLU 133": "OE1" <-> "OE2" 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 ARG 55": "NH1" <-> "NH2" Residue "F ARG 67": "NH1" <-> "NH2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "F ARG 78": "NH1" <-> "NH2" Residue "F TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 91": "OE1" <-> "OE2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "G ARG 99": "NH1" <-> "NH2" Residue "H ARG 33": "NH1" <-> "NH2" 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 "K ARG 1133": "NH1" <-> "NH2" Residue "K GLU 1147": "OE1" <-> "OE2" Residue "K TYR 1162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 1169": "OE1" <-> "OE2" Residue "K TYR 1192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 1273": "OD1" <-> "OD2" Residue "K PHE 1301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 1355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 1374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 1430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 1485": "OD1" <-> "OD2" Residue "K PHE 1487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 1503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 1523": "OE1" <-> "OE2" Residue "K ASP 1579": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16547 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 819 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 714 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 89} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'HIS:plan': 1, 'ALY:plan-2': 2, 'ALY:plan-1': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 801 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} 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: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 668 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 784 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 100} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "K" Number of atoms: 4381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4381 Classifications: {'peptide': 533} Link IDs: {'PCIS': 3, 'PTRANS': 32, 'TRANS': 497} Chain breaks: 2 Chain: "J" Number of atoms: 3012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3012 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "I" Number of atoms: 3015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3015 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} 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: 9.30, per 1000 atoms: 0.56 Number of scatterers: 16547 At special positions: 0 Unit cell: (107.31, 167.58, 138.18, 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 294 15.00 O 3647 8.00 N 3017 7.00 C 9542 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: 8.99 Conformation dependent library (CDL) restraints added in 2.2 seconds 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2468 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 55 helices and 3 sheets defined 53.9% alpha, 5.3% beta 112 base pairs and 219 stacking pairs defined. Time for finding SS restraints: 8.74 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 31 through 40 Processing helix chain 'B' and resid 50 through 75 removed outlier: 3.644A pdb=" N GLU B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 removed outlier: 3.616A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) 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: 4.394A 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 '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 122 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 50 through 75 removed outlier: 4.378A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 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 36 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.407A 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 27 through 29 No H-bonds generated for 'chain 'H' and resid 27 through 29' 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 123 Processing helix chain 'K' and resid 1052 through 1066 Proline residue: K1060 - end of helix Processing helix chain 'K' and resid 1073 through 1075 No H-bonds generated for 'chain 'K' and resid 1073 through 1075' Processing helix chain 'K' and resid 1081 through 1084 No H-bonds generated for 'chain 'K' and resid 1081 through 1084' Processing helix chain 'K' and resid 1089 through 1092 No H-bonds generated for 'chain 'K' and resid 1089 through 1092' Processing helix chain 'K' and resid 1099 through 1107 Processing helix chain 'K' and resid 1114 through 1131 Processing helix chain 'K' and resid 1137 through 1160 removed outlier: 4.154A pdb=" N ASP K1154 " --> pdb=" O GLU K1150 " (cutoff:3.500A) Proline residue: K1155 - end of helix Processing helix chain 'K' and resid 1256 through 1259 No H-bonds generated for 'chain 'K' and resid 1256 through 1259' Processing helix chain 'K' and resid 1273 through 1278 Processing helix chain 'K' and resid 1297 through 1313 Processing helix chain 'K' and resid 1337 through 1342 Processing helix chain 'K' and resid 1407 through 1428 removed outlier: 4.225A pdb=" N THR K1411 " --> pdb=" O LYS K1407 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ALA K1412 " --> pdb=" O CYS K1408 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY K1420 " --> pdb=" O GLU K1416 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS K1426 " --> pdb=" O LEU K1422 " (cutoff:3.500A) Processing helix chain 'K' and resid 1460 through 1477 Processing helix chain 'K' and resid 1486 through 1492 Processing helix chain 'K' and resid 1498 through 1500 No H-bonds generated for 'chain 'K' and resid 1498 through 1500' Processing helix chain 'K' and resid 1508 through 1522 Processing helix chain 'K' and resid 1579 through 1590 Processing helix chain 'K' and resid 1603 through 1606 Processing helix chain 'K' and resid 1622 through 1624 No H-bonds generated for 'chain 'K' and resid 1622 through 1624' Processing helix chain 'K' and resid 1627 through 1636 Processing helix chain 'K' and resid 1644 through 1662 Processing sheet with id= A, first strand: chain 'K' and resid 1233 through 1235 Processing sheet with id= B, first strand: chain 'K' and resid 1244 through 1246 Processing sheet with id= C, first strand: chain 'K' and resid 1482 through 1485 removed outlier: 3.755A pdb=" N ASP K1482 " --> pdb=" O ARG K1599 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TRP K1436 " --> pdb=" O ILE K1395 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N TYR K1397 " --> pdb=" O TRP K1436 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N HIS K1377 " --> pdb=" O SER K1396 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU K1398 " --> pdb=" O GLY K1375 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLY K1375 " --> pdb=" O LEU K1398 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N SER K1400 " --> pdb=" O PHE K1373 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N PHE K1373 " --> pdb=" O SER K1400 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ALA K1362 " --> pdb=" O PHE K1373 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLY K1375 " --> pdb=" O LEU K1360 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU K1360 " --> pdb=" O GLY K1375 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N HIS K1377 " --> pdb=" O LYS K1358 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LYS K1358 " --> pdb=" O HIS K1377 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLN K1379 " --> pdb=" O ARG K1356 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ARG K1356 " --> pdb=" O GLN K1379 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N TYR K1381 " --> pdb=" O PRO K1354 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N PHE K1361 " --> pdb=" O VAL K1325 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N VAL K1325 " --> pdb=" O PHE K1361 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N PHE K1363 " --> pdb=" O VAL K1323 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N VAL K1323 " --> pdb=" O PHE K1363 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N GLU K1365 " --> pdb=" O VAL K1321 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL K1321 " --> pdb=" O GLU K1365 " (cutoff:3.500A) 509 hydrogen bonds defined for protein. 1515 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 266 hydrogen bonds 532 hydrogen bond angles 0 basepair planarities 112 basepair parallelities 219 stacking parallelities Total time for adding SS restraints: 7.55 Time building geometry restraints manager: 9.33 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: 3938 1.34 - 1.46: 4891 1.46 - 1.58: 7993 1.58 - 1.70: 586 1.70 - 1.82: 70 Bond restraints: 17478 Sorted by residual: bond pdb=" NZ ALY B 16 " pdb=" CH ALY B 16 " ideal model delta sigma weight residual 1.343 1.385 -0.042 2.00e-02 2.50e+03 4.46e+00 bond pdb=" C3' DA J 59 " pdb=" O3' DA J 59 " ideal model delta sigma weight residual 1.422 1.463 -0.041 3.00e-02 1.11e+03 1.89e+00 bond pdb=" C LEU D 101 " pdb=" N LEU D 102 " ideal model delta sigma weight residual 1.326 1.351 -0.024 1.84e-02 2.95e+03 1.76e+00 bond pdb=" C3' DT I 136 " pdb=" O3' DT I 136 " ideal model delta sigma weight residual 1.422 1.458 -0.036 3.00e-02 1.11e+03 1.43e+00 bond pdb=" CH ALY B 16 " pdb=" OH ALY B 16 " ideal model delta sigma weight residual 1.225 1.247 -0.022 2.00e-02 2.50e+03 1.23e+00 ... (remaining 17473 not shown) Histogram of bond angle deviations from ideal: 98.35 - 105.47: 1432 105.47 - 112.59: 9503 112.59 - 119.71: 5511 119.71 - 126.83: 7478 126.83 - 133.95: 945 Bond angle restraints: 24869 Sorted by residual: angle pdb=" C ASN B 64 " pdb=" N VAL B 65 " pdb=" CA VAL B 65 " ideal model delta sigma weight residual 122.97 119.57 3.40 9.80e-01 1.04e+00 1.20e+01 angle pdb=" N ILE K1479 " pdb=" CA ILE K1479 " pdb=" C ILE K1479 " ideal model delta sigma weight residual 111.45 108.33 3.12 9.30e-01 1.16e+00 1.12e+01 angle pdb=" CB MET H 62 " pdb=" CG MET H 62 " pdb=" SD MET H 62 " ideal model delta sigma weight residual 112.70 120.90 -8.20 3.00e+00 1.11e-01 7.47e+00 angle pdb=" CA ARG K1494 " pdb=" CB ARG K1494 " pdb=" CG ARG K1494 " ideal model delta sigma weight residual 114.10 119.37 -5.27 2.00e+00 2.50e-01 6.93e+00 angle pdb=" CB ARG E 52 " pdb=" CG ARG E 52 " pdb=" CD ARG E 52 " ideal model delta sigma weight residual 111.30 117.32 -6.02 2.30e+00 1.89e-01 6.85e+00 ... (remaining 24864 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.34: 8559 35.34 - 70.67: 1299 70.67 - 106.01: 22 106.01 - 141.34: 0 141.34 - 176.68: 2 Dihedral angle restraints: 9882 sinusoidal: 6059 harmonic: 3823 Sorted by residual: dihedral pdb=" C4' DT I 136 " pdb=" C3' DT I 136 " pdb=" O3' DT I 136 " pdb=" P DT I 137 " ideal model delta sinusoidal sigma weight residual -140.00 36.68 -176.68 1 3.50e+01 8.16e-04 1.57e+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 53.71 166.29 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" CA ILE B 50 " pdb=" C ILE B 50 " pdb=" N TYR B 51 " pdb=" CA TYR B 51 " ideal model delta harmonic sigma weight residual 180.00 -163.72 -16.28 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 9879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1895 0.028 - 0.055: 612 0.055 - 0.082: 168 0.082 - 0.110: 70 0.110 - 0.137: 27 Chirality restraints: 2772 Sorted by residual: chirality pdb=" CA TYR B 88 " pdb=" N TYR B 88 " pdb=" C TYR B 88 " pdb=" CB TYR B 88 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA ILE K1598 " pdb=" N ILE K1598 " pdb=" C ILE K1598 " pdb=" CB ILE K1598 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.68e-01 chirality pdb=" CA ILE F 46 " pdb=" N ILE F 46 " pdb=" C ILE F 46 " pdb=" CB ILE F 46 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 2769 not shown) Planarity restraints: 2150 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 88 " 0.020 2.00e-02 2.50e+03 1.63e-02 5.31e+00 pdb=" CG TYR B 88 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR B 88 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR B 88 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 88 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 88 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 88 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 88 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 59 " 0.009 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" C LYS B 59 " -0.030 2.00e-02 2.50e+03 pdb=" O LYS B 59 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL B 60 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 102 " 0.026 5.00e-02 4.00e+02 3.95e-02 2.49e+00 pdb=" N PRO D 103 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.022 5.00e-02 4.00e+02 ... (remaining 2147 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2796 2.78 - 3.31: 16108 3.31 - 3.84: 32560 3.84 - 4.37: 36673 4.37 - 4.90: 54015 Nonbonded interactions: 142152 Sorted by model distance: nonbonded pdb=" NH1 ARG C 29 " pdb=" O SER D 36 " model vdw 2.249 2.520 nonbonded pdb=" N GLN G 24 " pdb=" OE2 GLU G 56 " model vdw 2.264 2.520 nonbonded pdb=" N THR H 90 " pdb=" OE2 GLU H 93 " model vdw 2.277 2.520 nonbonded pdb=" NE2 HIS A 113 " pdb=" OD1 ASP E 123 " model vdw 2.286 2.520 nonbonded pdb=" O TYR B 51 " pdb=" OG1 THR B 54 " model vdw 2.309 2.440 ... (remaining 142147 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' and resid 38 through 134) selection = (chain 'E' and resid 38 through 134) } ncs_group { reference = (chain 'B' and resid 19 through 101) selection = (chain 'F' and (resid 19 or (resid 20 and (name N or name CA or name C or name O \ or name CB )) or resid 21 through 101)) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 14 through 117) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 31 through 124) } ncs_group { reference = (chain 'I' and resid 18 through 163) selection = (chain 'J' and resid 18 through 163) } 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: 0.700 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: 0.020 Extract box with map and model: 4.310 Check model and map are aligned: 0.280 Set scattering table: 0.190 Process input model: 55.320 Find NCS groups from input model: 0.690 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 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 0.042 17478 Z= 0.164 Angle : 0.578 8.197 24869 Z= 0.359 Chirality : 0.033 0.137 2772 Planarity : 0.004 0.039 2150 Dihedral : 24.523 176.680 7414 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 1.74 (0.24), residues: 1283 helix: 1.61 (0.19), residues: 777 sheet: 0.55 (0.65), residues: 68 loop : 0.60 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K1509 HIS 0.004 0.000 HIS A 39 PHE 0.011 0.001 PHE G 25 TYR 0.039 0.001 TYR B 88 ARG 0.006 0.001 ARG E 53 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 ASP cc_start: 0.9049 (m-30) cc_final: 0.8814 (m-30) REVERT: D 100 LEU cc_start: 0.9459 (mt) cc_final: 0.9232 (mt) REVERT: G 73 ASN cc_start: 0.8705 (t0) cc_final: 0.8365 (t0) REVERT: K 1094 LYS cc_start: 0.7492 (mtpt) cc_final: 0.6648 (mmmt) REVERT: K 1097 MET cc_start: 0.3272 (ppp) cc_final: 0.2525 (tmm) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.2663 time to fit residues: 42.3503 Evaluate side-chains 67 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 7.9990 chunk 117 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 40 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 121 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 ASN C 104 GLN ** E 68 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 24 GLN K1112 GLN K1379 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 17478 Z= 0.297 Angle : 0.651 7.822 24869 Z= 0.370 Chirality : 0.037 0.142 2772 Planarity : 0.005 0.047 2150 Dihedral : 28.681 169.532 4768 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.18 % Allowed : 3.56 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 2.02 (0.23), residues: 1283 helix: 1.92 (0.18), residues: 785 sheet: 0.76 (0.74), residues: 60 loop : 0.48 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K1509 HIS 0.010 0.001 HIS B 75 PHE 0.013 0.002 PHE G 25 TYR 0.033 0.002 TYR B 88 ARG 0.008 0.001 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 87 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8229 (mpp) cc_final: 0.7904 (mpp) REVERT: B 68 ASP cc_start: 0.9410 (m-30) cc_final: 0.8986 (m-30) REVERT: D 100 LEU cc_start: 0.9330 (mt) cc_final: 0.9127 (mt) REVERT: E 73 GLU cc_start: 0.8160 (tt0) cc_final: 0.7948 (tt0) REVERT: G 73 ASN cc_start: 0.8897 (t0) cc_final: 0.8488 (t0) REVERT: H 69 ILE cc_start: 0.9162 (mm) cc_final: 0.8959 (mm) REVERT: H 106 LEU cc_start: 0.9400 (mt) cc_final: 0.9197 (mt) REVERT: K 1090 PHE cc_start: 0.7870 (m-10) cc_final: 0.7317 (m-80) REVERT: K 1094 LYS cc_start: 0.7896 (mtpt) cc_final: 0.7133 (mmmt) REVERT: K 1097 MET cc_start: 0.1823 (ppp) cc_final: 0.0879 (ppp) REVERT: K 1349 MET cc_start: 0.1249 (mmt) cc_final: 0.0935 (mtt) REVERT: K 1607 ASN cc_start: 0.8041 (m-40) cc_final: 0.7803 (p0) outliers start: 2 outliers final: 0 residues processed: 88 average time/residue: 0.2682 time to fit residues: 37.9841 Evaluate side-chains 59 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 0.0060 chunk 43 optimal weight: 0.9990 chunk 117 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 141 optimal weight: 10.0000 chunk 152 optimal weight: 7.9990 chunk 125 optimal weight: 9.9990 chunk 139 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 overall best weight: 4.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 ASN C 38 ASN C 89 ASN E 39 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN ** K1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1262 HIS K1307 ASN K1481 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.119 17478 Z= 0.349 Angle : 0.694 6.604 24869 Z= 0.393 Chirality : 0.039 0.242 2772 Planarity : 0.005 0.061 2150 Dihedral : 29.742 178.894 4768 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 20.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.36 % Allowed : 3.12 % Favored : 96.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 1.47 (0.23), residues: 1283 helix: 1.43 (0.18), residues: 779 sheet: 0.94 (0.77), residues: 58 loop : 0.32 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K1509 HIS 0.007 0.001 HIS K1199 PHE 0.019 0.002 PHE G 25 TYR 0.043 0.002 TYR B 88 ARG 0.011 0.001 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 77 time to evaluate : 1.562 Fit side-chains REVERT: A 120 MET cc_start: 0.8346 (mpp) cc_final: 0.8116 (mpp) REVERT: B 63 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7720 (pm20) REVERT: B 68 ASP cc_start: 0.9524 (m-30) cc_final: 0.9206 (m-30) REVERT: D 100 LEU cc_start: 0.8777 (mt) cc_final: 0.8444 (mt) REVERT: G 73 ASN cc_start: 0.8980 (t0) cc_final: 0.8674 (t0) REVERT: K 1090 PHE cc_start: 0.8188 (m-10) cc_final: 0.7500 (m-80) REVERT: K 1094 LYS cc_start: 0.8014 (mtpt) cc_final: 0.7580 (mmmt) REVERT: K 1097 MET cc_start: 0.1400 (ppp) cc_final: 0.0130 (ptt) REVERT: K 1349 MET cc_start: 0.3145 (mmt) cc_final: 0.2916 (mtt) outliers start: 4 outliers final: 1 residues processed: 81 average time/residue: 0.2631 time to fit residues: 34.2256 Evaluate side-chains 49 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 94 optimal weight: 9.9990 chunk 141 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 chunk 134 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 124 optimal weight: 9.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS E 108 ASN F 25 ASN ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1307 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.4585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17478 Z= 0.245 Angle : 0.601 5.514 24869 Z= 0.346 Chirality : 0.036 0.151 2772 Planarity : 0.004 0.039 2150 Dihedral : 29.698 179.557 4768 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 1.71 (0.23), residues: 1283 helix: 1.73 (0.18), residues: 772 sheet: 0.77 (0.75), residues: 58 loop : 0.25 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K1509 HIS 0.005 0.001 HIS F 75 PHE 0.009 0.001 PHE A 104 TYR 0.025 0.002 TYR B 88 ARG 0.008 0.000 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.515 Fit side-chains REVERT: A 120 MET cc_start: 0.8412 (mpp) cc_final: 0.8132 (mpp) REVERT: B 68 ASP cc_start: 0.9487 (m-30) cc_final: 0.9198 (m-30) REVERT: D 100 LEU cc_start: 0.8744 (mt) cc_final: 0.8413 (mt) REVERT: G 73 ASN cc_start: 0.8946 (t0) cc_final: 0.8705 (t0) REVERT: K 1090 PHE cc_start: 0.8131 (m-10) cc_final: 0.7421 (m-80) REVERT: K 1094 LYS cc_start: 0.8014 (mtpt) cc_final: 0.7724 (mmmt) REVERT: K 1349 MET cc_start: 0.2573 (mmt) cc_final: 0.2072 (mtt) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.2778 time to fit residues: 35.1279 Evaluate side-chains 50 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 85 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 111 optimal weight: 30.0000 chunk 61 optimal weight: 2.9990 chunk 127 optimal weight: 10.0000 chunk 103 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 76 optimal weight: 3.9990 chunk 134 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1132 ASN K1255 HIS ** K1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1307 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.5419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17478 Z= 0.272 Angle : 0.626 9.341 24869 Z= 0.359 Chirality : 0.036 0.221 2772 Planarity : 0.005 0.082 2150 Dihedral : 29.926 179.479 4768 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 18.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 1.52 (0.23), residues: 1283 helix: 1.57 (0.18), residues: 773 sheet: 0.67 (0.76), residues: 57 loop : 0.20 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K1509 HIS 0.005 0.001 HIS B 75 PHE 0.024 0.002 PHE A 104 TYR 0.027 0.002 TYR B 88 ARG 0.012 0.001 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.562 Fit side-chains REVERT: B 68 ASP cc_start: 0.9549 (m-30) cc_final: 0.9298 (m-30) REVERT: D 100 LEU cc_start: 0.8797 (mt) cc_final: 0.8487 (mt) REVERT: G 38 ASN cc_start: 0.8284 (m-40) cc_final: 0.7221 (m-40) REVERT: G 73 ASN cc_start: 0.9072 (t0) cc_final: 0.8827 (t0) REVERT: K 1090 PHE cc_start: 0.8419 (m-10) cc_final: 0.7638 (m-80) REVERT: K 1094 LYS cc_start: 0.8104 (mtpt) cc_final: 0.7774 (mmmt) REVERT: K 1624 MET cc_start: -0.4170 (mpp) cc_final: -0.4390 (mtm) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.2604 time to fit residues: 33.5463 Evaluate side-chains 53 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 87 optimal weight: 0.0870 chunk 36 optimal weight: 9.9990 chunk 149 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 144 optimal weight: 7.9990 overall best weight: 2.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 HIS E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1307 ASN K1415 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.5611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17478 Z= 0.221 Angle : 0.588 5.643 24869 Z= 0.339 Chirality : 0.035 0.155 2772 Planarity : 0.004 0.034 2150 Dihedral : 29.892 178.590 4768 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 1.65 (0.23), residues: 1283 helix: 1.79 (0.18), residues: 769 sheet: 0.44 (0.75), residues: 57 loop : 0.08 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K1122 HIS 0.003 0.001 HIS B 75 PHE 0.022 0.001 PHE A 104 TYR 0.031 0.002 TYR F 88 ARG 0.004 0.000 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 1.556 Fit side-chains REVERT: B 68 ASP cc_start: 0.9529 (m-30) cc_final: 0.9237 (m-30) REVERT: D 100 LEU cc_start: 0.8775 (mt) cc_final: 0.8506 (mt) REVERT: F 85 ASP cc_start: 0.8223 (m-30) cc_final: 0.7967 (m-30) REVERT: G 73 ASN cc_start: 0.9098 (t0) cc_final: 0.8878 (t0) REVERT: K 1075 PHE cc_start: 0.9358 (t80) cc_final: 0.9094 (t80) REVERT: K 1090 PHE cc_start: 0.8418 (m-10) cc_final: 0.8184 (m-80) REVERT: K 1097 MET cc_start: 0.1868 (ppp) cc_final: 0.0109 (ptt) REVERT: K 1339 MET cc_start: -0.1265 (ttt) cc_final: -0.1991 (mtp) REVERT: K 1349 MET cc_start: 0.4106 (mtt) cc_final: 0.3254 (mtt) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.2502 time to fit residues: 31.1640 Evaluate side-chains 51 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 109 optimal weight: 9.9990 chunk 84 optimal weight: 8.9990 chunk 126 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 149 optimal weight: 7.9990 chunk 93 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 92 optimal weight: 9.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.5639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17478 Z= 0.175 Angle : 0.557 5.520 24869 Z= 0.322 Chirality : 0.034 0.163 2772 Planarity : 0.004 0.035 2150 Dihedral : 29.722 178.582 4768 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 1.84 (0.23), residues: 1283 helix: 1.97 (0.18), residues: 768 sheet: 0.37 (0.74), residues: 57 loop : 0.12 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K1509 HIS 0.007 0.001 HIS K1415 PHE 0.036 0.001 PHE A 104 TYR 0.015 0.001 TYR B 88 ARG 0.005 0.000 ARG G 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.663 Fit side-chains revert: symmetry clash REVERT: B 68 ASP cc_start: 0.9470 (m-30) cc_final: 0.9152 (m-30) REVERT: D 100 LEU cc_start: 0.8757 (mt) cc_final: 0.8443 (mt) REVERT: E 120 MET cc_start: 0.8945 (ptp) cc_final: 0.8213 (mpp) REVERT: G 73 ASN cc_start: 0.9092 (t0) cc_final: 0.8868 (t0) REVERT: K 1075 PHE cc_start: 0.9341 (t80) cc_final: 0.9040 (t80) REVERT: K 1090 PHE cc_start: 0.8389 (m-10) cc_final: 0.8174 (m-80) REVERT: K 1097 MET cc_start: 0.1642 (ppp) cc_final: 0.0033 (ptt) REVERT: K 1339 MET cc_start: -0.1655 (ttt) cc_final: -0.2040 (ttm) REVERT: K 1349 MET cc_start: 0.4108 (mtt) cc_final: 0.3507 (mtt) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.2586 time to fit residues: 33.4118 Evaluate side-chains 53 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 8.9990 chunk 89 optimal weight: 0.0370 chunk 45 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 94 optimal weight: 8.9990 chunk 101 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 117 optimal weight: 20.0000 chunk 135 optimal weight: 8.9990 overall best weight: 0.7262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1582 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.5611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17478 Z= 0.158 Angle : 0.545 8.177 24869 Z= 0.315 Chirality : 0.034 0.157 2772 Planarity : 0.003 0.033 2150 Dihedral : 29.467 178.372 4768 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 1.94 (0.23), residues: 1283 helix: 2.07 (0.18), residues: 764 sheet: 0.58 (0.73), residues: 56 loop : 0.13 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K1266 HIS 0.011 0.001 HIS K1415 PHE 0.039 0.001 PHE A 104 TYR 0.035 0.001 TYR B 88 ARG 0.003 0.000 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.525 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.7940 (tp30) cc_final: 0.7494 (tp30) REVERT: B 68 ASP cc_start: 0.9454 (m-30) cc_final: 0.9120 (m-30) REVERT: D 100 LEU cc_start: 0.8735 (mt) cc_final: 0.8429 (mt) REVERT: E 120 MET cc_start: 0.8622 (ptp) cc_final: 0.7991 (mpp) REVERT: G 73 ASN cc_start: 0.9032 (t0) cc_final: 0.8811 (t0) REVERT: K 1075 PHE cc_start: 0.9359 (t80) cc_final: 0.9111 (t80) REVERT: K 1097 MET cc_start: 0.1619 (ppp) cc_final: 0.0007 (ptt) REVERT: K 1339 MET cc_start: -0.1682 (ttt) cc_final: -0.2055 (ttm) REVERT: K 1349 MET cc_start: 0.3957 (mtt) cc_final: 0.3308 (mtt) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.2471 time to fit residues: 32.8044 Evaluate side-chains 50 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 5.9990 chunk 130 optimal weight: 8.9990 chunk 139 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 109 optimal weight: 20.0000 chunk 42 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 131 optimal weight: 7.9990 chunk 138 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 ASN ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1481 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.6364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 17478 Z= 0.316 Angle : 0.647 7.492 24869 Z= 0.368 Chirality : 0.037 0.149 2772 Planarity : 0.005 0.044 2150 Dihedral : 29.942 179.364 4768 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 21.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 1.53 (0.23), residues: 1283 helix: 1.66 (0.18), residues: 774 sheet: 0.46 (0.75), residues: 57 loop : 0.07 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K1509 HIS 0.009 0.001 HIS K1415 PHE 0.026 0.002 PHE A 104 TYR 0.040 0.002 TYR B 88 ARG 0.006 0.001 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 1.658 Fit side-chains revert: symmetry clash REVERT: B 68 ASP cc_start: 0.9564 (m-30) cc_final: 0.9309 (m-30) REVERT: D 100 LEU cc_start: 0.8801 (mt) cc_final: 0.8484 (mt) REVERT: E 120 MET cc_start: 0.8716 (ptp) cc_final: 0.7830 (mpp) REVERT: G 73 ASN cc_start: 0.9156 (t0) cc_final: 0.8938 (t0) REVERT: K 1075 PHE cc_start: 0.9347 (t80) cc_final: 0.9035 (t80) REVERT: K 1097 MET cc_start: 0.2373 (ppp) cc_final: 0.1284 (ppp) REVERT: K 1339 MET cc_start: -0.2069 (ttt) cc_final: -0.2325 (ttm) REVERT: K 1349 MET cc_start: 0.4812 (mtt) cc_final: 0.4342 (mtt) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.2802 time to fit residues: 33.1918 Evaluate side-chains 45 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 154 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 chunk 122 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 97 optimal weight: 0.0000 overall best weight: 2.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.6546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17478 Z= 0.248 Angle : 0.610 7.869 24869 Z= 0.348 Chirality : 0.036 0.169 2772 Planarity : 0.004 0.043 2150 Dihedral : 30.030 177.460 4768 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 1.61 (0.23), residues: 1283 helix: 1.75 (0.18), residues: 771 sheet: 0.38 (0.74), residues: 57 loop : 0.09 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K1509 HIS 0.010 0.001 HIS K1255 PHE 0.041 0.001 PHE A 104 TYR 0.040 0.002 TYR B 88 ARG 0.004 0.001 ARG F 92 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 1.477 Fit side-chains revert: symmetry clash REVERT: B 68 ASP cc_start: 0.9095 (m-30) cc_final: 0.8663 (m-30) REVERT: D 100 LEU cc_start: 0.8789 (mt) cc_final: 0.8474 (mt) REVERT: E 120 MET cc_start: 0.8641 (ptp) cc_final: 0.7842 (mpp) REVERT: F 84 MET cc_start: 0.8116 (ppp) cc_final: 0.7784 (ppp) REVERT: F 88 TYR cc_start: 0.7195 (m-80) cc_final: 0.6437 (m-80) REVERT: G 73 ASN cc_start: 0.9151 (t0) cc_final: 0.8945 (t0) REVERT: K 1075 PHE cc_start: 0.9382 (t80) cc_final: 0.9066 (t80) REVERT: K 1097 MET cc_start: 0.2577 (ppp) cc_final: 0.1558 (ppp) REVERT: K 1254 MET cc_start: 0.1356 (ttt) cc_final: -0.0174 (mmt) REVERT: K 1339 MET cc_start: -0.1747 (ttt) cc_final: -0.2021 (ttm) REVERT: K 1349 MET cc_start: 0.4898 (mtt) cc_final: 0.4468 (mtt) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.2242 time to fit residues: 28.1126 Evaluate side-chains 47 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 123 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 126 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 108 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1262 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.049957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.034262 restraints weight = 183674.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.035181 restraints weight = 108557.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.035770 restraints weight = 77323.161| |-----------------------------------------------------------------------------| r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.6589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17478 Z= 0.195 Angle : 0.573 7.677 24869 Z= 0.329 Chirality : 0.035 0.161 2772 Planarity : 0.004 0.038 2150 Dihedral : 29.857 177.741 4768 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 1.76 (0.23), residues: 1283 helix: 1.91 (0.18), residues: 768 sheet: 0.25 (0.72), residues: 57 loop : 0.10 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K1509 HIS 0.010 0.001 HIS K1415 PHE 0.038 0.001 PHE A 104 TYR 0.037 0.002 TYR B 88 ARG 0.008 0.000 ARG B 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2314.12 seconds wall clock time: 43 minutes 59.07 seconds (2639.07 seconds total)