Starting phenix.real_space_refine on Sun Mar 17 01:34:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hag_34588/03_2024/8hag_34588_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hag_34588/03_2024/8hag_34588.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hag_34588/03_2024/8hag_34588.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hag_34588/03_2024/8hag_34588.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hag_34588/03_2024/8hag_34588_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hag_34588/03_2024/8hag_34588_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 294 5.49 5 S 47 5.16 5 C 9427 2.51 5 N 2985 2.21 5 O 3614 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 ARG 69": "NH1" <-> "NH2" Residue "A ARG 72": "NH1" <-> "NH2" Residue "A ASP 77": "OD1" <-> "OD2" Residue "A ARG 83": "NH1" <-> "NH2" Residue "A GLU 97": "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 GLU 53": "OE1" <-> "OE2" Residue "B ARG 55": "NH1" <-> "NH2" Residue "B ARG 67": "NH1" <-> "NH2" Residue "B ASP 68": "OD1" <-> "OD2" Residue "B GLU 74": "OE1" <-> "OE2" 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 PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 91": "OE1" <-> "OE2" Residue "C ARG 99": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D ASP 51": "OD1" <-> "OD2" Residue "D GLU 71": "OE1" <-> "OE2" 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 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 ASP 77": "OD1" <-> "OD2" Residue "E ARG 83": "NH1" <-> "NH2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 105": "OE1" <-> "OE2" 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 GLU 133": "OE1" <-> "OE2" Residue "E ARG 134": "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 TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 55": "NH1" <-> "NH2" Residue "F ARG 67": "NH1" <-> "NH2" 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 TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 42": "NH1" <-> "NH2" Residue "G GLU 56": "OE1" <-> "OE2" 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 ARG 99": "NH1" <-> "NH2" Residue "H ARG 33": "NH1" <-> "NH2" Residue "H TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 71": "OE1" <-> "OE2" 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 GLU 93": "OE1" <-> "OE2" Residue "H ARG 99": "NH1" <-> "NH2" Residue "K PHE 1090": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 1133": "NH1" <-> "NH2" Residue "K GLU 1147": "OE1" <-> "OE2" Residue "K GLU 1169": "OE1" <-> "OE2" Residue "K TYR 1192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 1194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 1301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 1353": "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 TYR 1483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 1485": "OD1" <-> "OD2" Residue "K PHE 1487": "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-5265/modules/chem_data/mon_lib" Total number of atoms: 16367 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} 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: 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: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} 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: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 751 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 94} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 4260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4260 Classifications: {'peptide': 516} Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 486} Chain breaks: 3 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: 8.65, per 1000 atoms: 0.53 Number of scatterers: 16367 At special positions: 0 Unit cell: (106.112, 163.313, 137.614, 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 3614 8.00 N 2985 7.00 C 9427 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: 8.31 Conformation dependent library (CDL) restraints added in 2.0 seconds 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2418 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 3 sheets defined 54.9% alpha, 5.5% beta 114 base pairs and 231 stacking pairs defined. Time for finding SS restraints: 8.29 Creating SS restraints... Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 64 through 78 removed outlier: 3.749A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 113 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 76 removed outlier: 3.912A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N HIS B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.409A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 88 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 104 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 48 through 75 removed outlier: 4.566A pdb=" N GLU F 52 " --> pdb=" O GLY F 48 " (cutoff:3.500A) removed outlier: 3.987A 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: 4.184A 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 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: 4.031A pdb=" N ASP K1154 " --> pdb=" O GLU K1150 " (cutoff:3.500A) Proline residue: K1155 - end of helix removed outlier: 3.676A pdb=" N LEU K1160 " --> pdb=" O VAL K1156 " (cutoff:3.500A) 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 1344 through 1346 No H-bonds generated for 'chain 'K' and resid 1344 through 1346' Processing helix chain 'K' and resid 1408 through 1428 removed outlier: 4.459A pdb=" N ALA K1412 " --> pdb=" O CYS K1408 " (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 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: 4.150A pdb=" N ASP K1482 " --> pdb=" O ARG K1599 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG K1599 " --> pdb=" O ASP K1482 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N TRP K1436 " --> pdb=" O ILE K1395 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N TYR K1397 " --> pdb=" O TRP K1436 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG K1392 " --> pdb=" O TYR K1381 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N HIS K1377 " --> pdb=" O SER K1396 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N LEU K1398 " --> pdb=" O GLY K1375 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLY K1375 " --> pdb=" O LEU K1398 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N SER K1400 " --> pdb=" O PHE K1373 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N PHE K1373 " --> pdb=" O SER K1400 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ALA K1362 " --> pdb=" O PHE K1373 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLY K1375 " --> pdb=" O LEU K1360 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU K1360 " --> pdb=" O GLY K1375 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N HIS K1377 " --> pdb=" O LYS K1358 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LYS K1358 " --> pdb=" O HIS K1377 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLN K1379 " --> pdb=" O ARG K1356 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ARG K1356 " --> pdb=" O GLN K1379 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N TYR K1381 " --> pdb=" O PRO K1354 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N PHE K1361 " --> pdb=" O VAL K1325 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N VAL K1325 " --> pdb=" O PHE K1361 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N PHE K1363 " --> pdb=" O VAL K1323 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N VAL K1323 " --> pdb=" O PHE K1363 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N GLU K1365 " --> pdb=" O VAL K1321 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL K1321 " --> pdb=" O GLU K1365 " (cutoff:3.500A) 510 hydrogen bonds defined for protein. 1524 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 270 hydrogen bonds 536 hydrogen bond angles 0 basepair planarities 114 basepair parallelities 231 stacking parallelities Total time for adding SS restraints: 7.43 Time building geometry restraints manager: 8.74 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: 4033 1.34 - 1.46: 4652 1.46 - 1.58: 7950 1.58 - 1.70: 586 1.70 - 1.81: 70 Bond restraints: 17291 Sorted by residual: bond pdb=" NZ ALY B 12 " pdb=" CH ALY B 12 " ideal model delta sigma weight residual 1.343 1.385 -0.042 2.00e-02 2.50e+03 4.39e+00 bond pdb=" C3' DT I 136 " pdb=" O3' DT I 136 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.65e+00 bond pdb=" CB PRO E 38 " pdb=" CG PRO E 38 " ideal model delta sigma weight residual 1.492 1.554 -0.062 5.00e-02 4.00e+02 1.53e+00 bond pdb=" CH ALY B 12 " pdb=" OH ALY B 12 " ideal model delta sigma weight residual 1.225 1.247 -0.022 2.00e-02 2.50e+03 1.16e+00 bond pdb=" CA ASP B 24 " pdb=" CB ASP B 24 " ideal model delta sigma weight residual 1.524 1.538 -0.014 1.31e-02 5.83e+03 1.16e+00 ... (remaining 17286 not shown) Histogram of bond angle deviations from ideal: 98.64 - 105.71: 1600 105.71 - 112.77: 9397 112.77 - 119.84: 5716 119.84 - 126.90: 7030 126.90 - 133.97: 864 Bond angle restraints: 24607 Sorted by residual: angle pdb=" N VAL B 21 " pdb=" CA VAL B 21 " pdb=" C VAL B 21 " ideal model delta sigma weight residual 113.20 109.24 3.96 9.60e-01 1.09e+00 1.70e+01 angle pdb=" N ASP K1098 " pdb=" CA ASP K1098 " pdb=" C ASP K1098 " ideal model delta sigma weight residual 108.34 113.26 -4.92 1.31e+00 5.83e-01 1.41e+01 angle pdb=" CB MET K1059 " pdb=" CG MET K1059 " pdb=" SD MET K1059 " ideal model delta sigma weight residual 112.70 122.20 -9.50 3.00e+00 1.11e-01 1.00e+01 angle pdb=" CB MET A 90 " pdb=" CG MET A 90 " pdb=" SD MET A 90 " ideal model delta sigma weight residual 112.70 120.71 -8.01 3.00e+00 1.11e-01 7.13e+00 angle pdb=" CA ARG K1494 " pdb=" CB ARG K1494 " pdb=" CG ARG K1494 " ideal model delta sigma weight residual 114.10 118.92 -4.82 2.00e+00 2.50e-01 5.82e+00 ... (remaining 24602 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.97: 8378 34.97 - 69.93: 1349 69.93 - 104.90: 27 104.90 - 139.86: 1 139.86 - 174.83: 2 Dihedral angle restraints: 9757 sinusoidal: 6011 harmonic: 3746 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 220.00 45.17 174.83 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 73.41 146.59 1 3.50e+01 8.16e-04 1.44e+01 dihedral pdb=" CG ARG C 77 " pdb=" CD ARG C 77 " pdb=" NE ARG C 77 " pdb=" CZ ARG C 77 " ideal model delta sinusoidal sigma weight residual 90.00 134.38 -44.38 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 9754 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2048 0.032 - 0.064: 533 0.064 - 0.096: 108 0.096 - 0.129: 51 0.129 - 0.161: 2 Chirality restraints: 2742 Sorted by residual: chirality pdb=" CA LEU A 65 " pdb=" N LEU A 65 " pdb=" C LEU A 65 " pdb=" CB LEU A 65 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CA MET K1059 " pdb=" N MET K1059 " pdb=" C MET K1059 " pdb=" CB MET K1059 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CA ILE B 46 " pdb=" N ILE B 46 " pdb=" C ILE B 46 " pdb=" CB ILE B 46 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.11e-01 ... (remaining 2739 not shown) Planarity restraints: 2112 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT J 108 " -0.031 2.00e-02 2.50e+03 1.58e-02 6.20e+00 pdb=" N1 DT J 108 " 0.034 2.00e-02 2.50e+03 pdb=" C2 DT J 108 " -0.003 2.00e-02 2.50e+03 pdb=" O2 DT J 108 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DT J 108 " 0.009 2.00e-02 2.50e+03 pdb=" C4 DT J 108 " -0.009 2.00e-02 2.50e+03 pdb=" O4 DT J 108 " -0.013 2.00e-02 2.50e+03 pdb=" C5 DT J 108 " -0.001 2.00e-02 2.50e+03 pdb=" C7 DT J 108 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DT J 108 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 83 " -0.010 2.00e-02 2.50e+03 1.15e-02 2.62e+00 pdb=" CG TYR D 83 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR D 83 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR D 83 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR D 83 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR D 83 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR D 83 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 83 " -0.000 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 3.96e-02 2.51e+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 2109 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1882 2.76 - 3.29: 15593 3.29 - 3.83: 31774 3.83 - 4.36: 35496 4.36 - 4.90: 53235 Nonbonded interactions: 137980 Sorted by model distance: nonbonded pdb=" OG1 THR C 16 " pdb=" OP1 DG I 48 " model vdw 2.220 2.440 nonbonded pdb=" NE2 HIS A 113 " pdb=" OD1 ASP E 123 " model vdw 2.244 2.520 nonbonded pdb=" NH2 ARG K1133 " pdb=" OP1 DG J 114 " model vdw 2.259 2.520 nonbonded pdb=" O TYR C 39 " pdb=" OG SER D 78 " model vdw 2.259 2.440 nonbonded pdb=" O LEU C 115 " pdb=" NZ LYS F 44 " model vdw 2.263 2.520 ... (remaining 137975 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' } ncs_group { reference = (chain 'B' and resid 20 through 101) selection = (chain 'F' and ((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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.310 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: 9.570 Check model and map are aligned: 0.250 Set scattering table: 0.140 Process input model: 52.980 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.090 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 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 0.062 17291 Z= 0.158 Angle : 0.560 9.502 24607 Z= 0.342 Chirality : 0.033 0.161 2742 Planarity : 0.003 0.040 2112 Dihedral : 24.831 174.830 7339 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 2.13 (0.23), residues: 1255 helix: 1.98 (0.19), residues: 759 sheet: 1.13 (0.60), residues: 83 loop : 0.51 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP K1115 HIS 0.012 0.001 HIS K1415 PHE 0.008 0.001 PHE K1090 TYR 0.028 0.001 TYR D 83 ARG 0.006 0.000 ARG H 79 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 1.449 Fit side-chains REVERT: A 41 TYR cc_start: 0.7741 (m-80) cc_final: 0.7497 (m-80) REVERT: H 62 MET cc_start: 0.8981 (tpp) cc_final: 0.8334 (tpt) REVERT: K 1124 MET cc_start: 0.6849 (mmp) cc_final: 0.6475 (mmm) REVERT: K 1349 MET cc_start: 0.5182 (ttp) cc_final: 0.4886 (ttm) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.2728 time to fit residues: 42.5877 Evaluate side-chains 70 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 7.9990 chunk 115 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 77 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 119 optimal weight: 20.0000 chunk 46 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 88 optimal weight: 20.0000 chunk 138 optimal weight: 20.0000 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 49 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 17291 Z= 0.399 Angle : 0.704 10.913 24607 Z= 0.396 Chirality : 0.042 0.183 2742 Planarity : 0.005 0.051 2112 Dihedral : 29.119 174.561 4739 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.27 % Allowed : 6.06 % Favored : 92.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 1.43 (0.23), residues: 1255 helix: 1.43 (0.18), residues: 774 sheet: 0.66 (0.57), residues: 72 loop : 0.24 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K1466 HIS 0.008 0.002 HIS K1255 PHE 0.032 0.002 PHE K1200 TYR 0.040 0.002 TYR D 83 ARG 0.007 0.001 ARG F 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 79 time to evaluate : 1.337 Fit side-chains revert: symmetry clash REVERT: B 63 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7958 (mm-30) REVERT: K 1097 MET cc_start: 0.6915 (ppp) cc_final: 0.5980 (ppp) REVERT: K 1124 MET cc_start: 0.6865 (mmp) cc_final: 0.6482 (mmm) REVERT: K 1349 MET cc_start: 0.5693 (ttp) cc_final: 0.5269 (ttm) outliers start: 14 outliers final: 8 residues processed: 89 average time/residue: 0.3147 time to fit residues: 41.3605 Evaluate side-chains 64 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 108 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 93 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 138 optimal weight: 20.0000 chunk 149 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 chunk 137 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 110 optimal weight: 0.0870 overall best weight: 1.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17291 Z= 0.201 Angle : 0.534 9.131 24607 Z= 0.311 Chirality : 0.034 0.135 2742 Planarity : 0.004 0.039 2112 Dihedral : 28.871 174.444 4739 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.63 % Allowed : 8.96 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 1.98 (0.23), residues: 1255 helix: 1.92 (0.19), residues: 775 sheet: 0.69 (0.58), residues: 72 loop : 0.36 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K1466 HIS 0.006 0.001 HIS K1415 PHE 0.008 0.001 PHE A 67 TYR 0.018 0.001 TYR D 83 ARG 0.008 0.000 ARG K1055 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 1.525 Fit side-chains revert: symmetry clash REVERT: G 64 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8311 (tm-30) REVERT: H 54 ILE cc_start: 0.8957 (mm) cc_final: 0.8613 (mm) REVERT: K 1097 MET cc_start: 0.6825 (ppp) cc_final: 0.5991 (ppp) REVERT: K 1124 MET cc_start: 0.6822 (mmp) cc_final: 0.6398 (mmm) REVERT: K 1349 MET cc_start: 0.5803 (ttp) cc_final: 0.5383 (ttm) outliers start: 7 outliers final: 4 residues processed: 73 average time/residue: 0.2472 time to fit residues: 29.2309 Evaluate side-chains 63 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain F residue 49 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 9.9990 chunk 103 optimal weight: 50.0000 chunk 71 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 92 optimal weight: 50.0000 chunk 138 optimal weight: 20.0000 chunk 146 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 ASN H 63 ASN H 109 HIS K1126 ASN ** K1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.5565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 17291 Z= 0.417 Angle : 0.665 13.303 24607 Z= 0.377 Chirality : 0.041 0.165 2742 Planarity : 0.005 0.051 2112 Dihedral : 29.391 175.416 4739 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.26 % Allowed : 8.96 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 1.58 (0.23), residues: 1255 helix: 1.59 (0.18), residues: 776 sheet: 0.74 (0.63), residues: 66 loop : 0.19 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K1509 HIS 0.012 0.002 HIS K1415 PHE 0.013 0.002 PHE E 104 TYR 0.022 0.002 TYR D 83 ARG 0.024 0.001 ARG K1055 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 58 time to evaluate : 1.385 Fit side-chains revert: symmetry clash REVERT: C 64 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8329 (tm-30) REVERT: D 51 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7758 (p0) REVERT: G 64 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8396 (tm-30) REVERT: K 1097 MET cc_start: 0.6803 (ppp) cc_final: 0.6425 (ppp) REVERT: K 1124 MET cc_start: 0.7025 (mmp) cc_final: 0.6548 (mmm) REVERT: K 1349 MET cc_start: 0.6060 (ttp) cc_final: 0.5606 (ttm) outliers start: 25 outliers final: 12 residues processed: 80 average time/residue: 0.2875 time to fit residues: 35.2115 Evaluate side-chains 61 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 48 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 63 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 40.0000 chunk 83 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 60 optimal weight: 0.8980 chunk 125 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 63 ASN K1236 ASN ** K1415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.5749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17291 Z= 0.252 Angle : 0.560 5.894 24607 Z= 0.326 Chirality : 0.036 0.149 2742 Planarity : 0.004 0.045 2112 Dihedral : 29.228 175.146 4739 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.36 % Allowed : 10.68 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 1.90 (0.24), residues: 1255 helix: 1.89 (0.19), residues: 774 sheet: 0.84 (0.65), residues: 66 loop : 0.25 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K1509 HIS 0.003 0.001 HIS H 49 PHE 0.008 0.001 PHE G 25 TYR 0.012 0.001 TYR D 83 ARG 0.007 0.000 ARG G 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 62 time to evaluate : 1.478 Fit side-chains REVERT: D 54 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8933 (tp) REVERT: G 64 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8305 (tm-30) REVERT: K 1097 MET cc_start: 0.6779 (ppp) cc_final: 0.6073 (ppp) REVERT: K 1124 MET cc_start: 0.7203 (mmp) cc_final: 0.6696 (mmm) REVERT: K 1349 MET cc_start: 0.6130 (ttp) cc_final: 0.5654 (ttm) REVERT: K 1466 TRP cc_start: 0.4754 (t60) cc_final: 0.4215 (t60) outliers start: 15 outliers final: 8 residues processed: 74 average time/residue: 0.2472 time to fit residues: 29.8981 Evaluate side-chains 63 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 54 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain K residue 1156 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 0.7980 chunk 132 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 86 optimal weight: 0.0370 chunk 36 optimal weight: 0.9980 chunk 147 optimal weight: 7.9990 chunk 122 optimal weight: 50.0000 chunk 68 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 overall best weight: 0.7658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 63 ASN H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.5685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17291 Z= 0.161 Angle : 0.518 6.274 24607 Z= 0.304 Chirality : 0.033 0.150 2742 Planarity : 0.003 0.043 2112 Dihedral : 28.904 176.624 4739 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.09 % Allowed : 11.40 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 2.26 (0.24), residues: 1255 helix: 2.22 (0.19), residues: 767 sheet: 0.88 (0.65), residues: 66 loop : 0.33 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K1466 HIS 0.004 0.000 HIS K1415 PHE 0.010 0.001 PHE H 70 TYR 0.010 0.001 TYR G 57 ARG 0.013 0.000 ARG K1055 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 63 time to evaluate : 1.456 Fit side-chains revert: symmetry clash REVERT: G 91 GLU cc_start: 0.7829 (pp20) cc_final: 0.7549 (tm-30) REVERT: H 93 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.8015 (mp0) REVERT: K 1097 MET cc_start: 0.6710 (ppp) cc_final: 0.6084 (ppp) REVERT: K 1124 MET cc_start: 0.7210 (mmp) cc_final: 0.6668 (mmm) REVERT: K 1349 MET cc_start: 0.6244 (ttp) cc_final: 0.5677 (ttm) outliers start: 12 outliers final: 5 residues processed: 73 average time/residue: 0.2289 time to fit residues: 27.5968 Evaluate side-chains 63 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 57 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 93 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 8.9990 chunk 16 optimal weight: 0.1980 chunk 83 optimal weight: 20.0000 chunk 107 optimal weight: 20.0000 chunk 123 optimal weight: 30.0000 chunk 82 optimal weight: 6.9990 chunk 146 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.6322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 17291 Z= 0.361 Angle : 0.623 8.148 24607 Z= 0.356 Chirality : 0.038 0.148 2742 Planarity : 0.004 0.050 2112 Dihedral : 29.292 176.235 4739 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.45 % Allowed : 11.40 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 1.87 (0.24), residues: 1255 helix: 1.84 (0.19), residues: 777 sheet: 0.73 (0.65), residues: 66 loop : 0.29 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP K1466 HIS 0.007 0.001 HIS K1415 PHE 0.012 0.001 PHE E 78 TYR 0.015 0.002 TYR D 83 ARG 0.007 0.001 ARG K1055 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 50 time to evaluate : 1.399 Fit side-chains revert: symmetry clash REVERT: K 1059 MET cc_start: 0.7842 (mmt) cc_final: 0.7640 (mmm) REVERT: K 1097 MET cc_start: 0.6630 (ppp) cc_final: 0.5911 (ppp) REVERT: K 1124 MET cc_start: 0.7232 (mmp) cc_final: 0.6725 (mmm) REVERT: K 1349 MET cc_start: 0.6289 (ttp) cc_final: 0.5831 (ttm) outliers start: 16 outliers final: 11 residues processed: 62 average time/residue: 0.2348 time to fit residues: 24.2108 Evaluate side-chains 59 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 48 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain K residue 1156 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 0.5980 chunk 87 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 99 optimal weight: 0.4980 chunk 72 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 115 optimal weight: 3.9990 chunk 133 optimal weight: 7.9990 chunk 140 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1415 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.6247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17291 Z= 0.167 Angle : 0.531 8.233 24607 Z= 0.310 Chirality : 0.034 0.168 2742 Planarity : 0.003 0.041 2112 Dihedral : 29.094 177.607 4739 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.90 % Allowed : 12.22 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 2.22 (0.24), residues: 1255 helix: 2.16 (0.19), residues: 770 sheet: 0.84 (0.65), residues: 65 loop : 0.37 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP K1466 HIS 0.008 0.001 HIS K1415 PHE 0.012 0.001 PHE K1090 TYR 0.010 0.001 TYR G 57 ARG 0.006 0.000 ARG G 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 56 time to evaluate : 1.444 Fit side-chains revert: symmetry clash REVERT: K 1097 MET cc_start: 0.6587 (ppp) cc_final: 0.5904 (ppp) REVERT: K 1124 MET cc_start: 0.7238 (mmp) cc_final: 0.6723 (mmm) REVERT: K 1349 MET cc_start: 0.6378 (ttp) cc_final: 0.5942 (ttm) REVERT: K 1466 TRP cc_start: 0.4422 (t60) cc_final: 0.4105 (t60) outliers start: 10 outliers final: 7 residues processed: 65 average time/residue: 0.2604 time to fit residues: 27.5190 Evaluate side-chains 59 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 52 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 108 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 8.9990 chunk 136 optimal weight: 10.0000 chunk 140 optimal weight: 7.9990 chunk 82 optimal weight: 20.0000 chunk 59 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 123 optimal weight: 10.0000 chunk 129 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.6941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 17291 Z= 0.466 Angle : 0.677 13.388 24607 Z= 0.385 Chirality : 0.041 0.194 2742 Planarity : 0.005 0.069 2112 Dihedral : 29.588 176.877 4739 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.00 % Allowed : 12.31 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 1.70 (0.23), residues: 1255 helix: 1.75 (0.19), residues: 765 sheet: 0.57 (0.65), residues: 65 loop : 0.19 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP K1466 HIS 0.009 0.001 HIS K1415 PHE 0.016 0.002 PHE E 78 TYR 0.016 0.002 TYR D 83 ARG 0.007 0.001 ARG C 17 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 53 time to evaluate : 1.444 Fit side-chains REVERT: K 1059 MET cc_start: 0.7760 (mmt) cc_final: 0.7506 (mmm) REVERT: K 1097 MET cc_start: 0.6444 (ppp) cc_final: 0.5803 (ppp) REVERT: K 1124 MET cc_start: 0.7477 (mmp) cc_final: 0.6891 (mmt) REVERT: K 1349 MET cc_start: 0.6576 (ttp) cc_final: 0.6045 (ttm) outliers start: 11 outliers final: 7 residues processed: 63 average time/residue: 0.2537 time to fit residues: 25.8268 Evaluate side-chains 58 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 51 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 151 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 120 optimal weight: 30.0000 chunk 12 optimal weight: 0.3980 chunk 93 optimal weight: 0.0270 chunk 73 optimal weight: 20.0000 chunk 95 optimal weight: 6.9990 chunk 128 optimal weight: 7.9990 overall best weight: 3.8844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.7097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 17291 Z= 0.325 Angle : 0.603 9.771 24607 Z= 0.348 Chirality : 0.037 0.206 2742 Planarity : 0.004 0.064 2112 Dihedral : 29.576 177.832 4739 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.81 % Allowed : 12.40 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 1.73 (0.23), residues: 1255 helix: 1.83 (0.19), residues: 770 sheet: 0.06 (0.64), residues: 59 loop : 0.15 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.003 TRP K1466 HIS 0.008 0.001 HIS D 109 PHE 0.012 0.001 PHE E 78 TYR 0.010 0.001 TYR H 121 ARG 0.004 0.000 ARG G 35 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 54 time to evaluate : 1.500 Fit side-chains REVERT: H 93 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8179 (mp0) REVERT: K 1059 MET cc_start: 0.7724 (mmt) cc_final: 0.7490 (mmm) REVERT: K 1097 MET cc_start: 0.6374 (ppp) cc_final: 0.6104 (ppp) REVERT: K 1124 MET cc_start: 0.7537 (mmp) cc_final: 0.6966 (mmt) REVERT: K 1349 MET cc_start: 0.6737 (ttp) cc_final: 0.6243 (ttm) outliers start: 9 outliers final: 8 residues processed: 62 average time/residue: 0.2583 time to fit residues: 26.2181 Evaluate side-chains 62 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 53 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 93 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 0.9990 chunk 111 optimal weight: 0.4980 chunk 17 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 120 optimal weight: 40.0000 chunk 50 optimal weight: 1.9990 chunk 124 optimal weight: 20.0000 chunk 15 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 106 optimal weight: 30.0000 chunk 6 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 63 ASN ** 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 = 0.4105 r_free = 0.4105 target = 0.083541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.047463 restraints weight = 85618.934| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 3.95 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.6902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17291 Z= 0.156 Angle : 0.537 7.492 24607 Z= 0.314 Chirality : 0.033 0.192 2742 Planarity : 0.004 0.038 2112 Dihedral : 29.200 177.453 4739 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.00 % Allowed : 12.31 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 2.18 (0.24), residues: 1255 helix: 2.20 (0.19), residues: 767 sheet: 0.64 (0.64), residues: 65 loop : 0.25 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP K1466 HIS 0.005 0.001 HIS K1415 PHE 0.014 0.001 PHE K1090 TYR 0.013 0.001 TYR K1162 ARG 0.004 0.000 ARG G 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2938.94 seconds wall clock time: 53 minutes 58.35 seconds (3238.35 seconds total)