Starting phenix.real_space_refine on Sun Mar 17 08:14:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ham_34596/03_2024/8ham_34596_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ham_34596/03_2024/8ham_34596.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ham_34596/03_2024/8ham_34596.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ham_34596/03_2024/8ham_34596.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ham_34596/03_2024/8ham_34596_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ham_34596/03_2024/8ham_34596_updated.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 330 5.49 5 S 46 5.16 5 C 9835 2.51 5 N 3130 2.21 5 O 3836 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 40": "NH1" <-> "NH2" Residue "A ARG 42": "NH1" <-> "NH2" Residue "A ARG 49": "NH1" <-> "NH2" Residue "A ARG 52": "NH1" <-> "NH2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A ARG 69": "NH1" <-> "NH2" Residue "A ARG 72": "NH1" <-> "NH2" Residue "A ARG 83": "NH1" <-> "NH2" 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 19": "NH1" <-> "NH2" Residue "B ARG 23": "NH1" <-> "NH2" Residue "B ARG 35": "NH1" <-> "NH2" Residue "B ARG 36": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 40": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 55": "NH1" <-> "NH2" Residue "B ARG 67": "NH1" <-> "NH2" Residue "B 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 ARG 29": "NH1" <-> "NH2" Residue "C ARG 32": "NH1" <-> "NH2" Residue "C ARG 35": "NH1" <-> "NH2" Residue "C ARG 42": "NH1" <-> "NH2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C ARG 71": "NH1" <-> "NH2" Residue "C ASP 72": "OD1" <-> "OD2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ARG 99": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D GLU 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 "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 ARG 69": "NH1" <-> "NH2" Residue "E ARG 72": "NH1" <-> "NH2" Residue "E ARG 83": "NH1" <-> "NH2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "E ARG 116": "NH1" <-> "NH2" Residue "E ARG 128": "NH1" <-> "NH2" Residue "E ARG 129": "NH1" <-> "NH2" Residue "E ARG 131": "NH1" <-> "NH2" Residue "E ARG 134": "NH1" <-> "NH2" Residue "F ARG 19": "NH1" <-> "NH2" Residue "F ARG 23": "NH1" <-> "NH2" Residue "F ARG 35": "NH1" <-> "NH2" Residue "F ARG 36": "NH1" <-> "NH2" Residue "F ARG 39": "NH1" <-> "NH2" Residue "F ARG 40": "NH1" <-> "NH2" Residue "F ARG 45": "NH1" <-> "NH2" Residue "F ARG 55": "NH1" <-> "NH2" Residue "F ARG 67": "NH1" <-> "NH2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "F ARG 78": "NH1" <-> "NH2" Residue "F ASP 85": "OD1" <-> "OD2" 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 GLU 41": "OE1" <-> "OE2" Residue "G ARG 42": "NH1" <-> "NH2" Residue "G GLU 61": "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 ARG 99": "NH1" <-> "NH2" Residue "H ARG 72": "NH1" <-> "NH2" Residue "H GLU 76": "OE1" <-> "OE2" 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 1091": "NH1" <-> "NH2" Residue "K ARG 1103": "NH1" <-> "NH2" Residue "K ARG 1112": "NH1" <-> "NH2" Residue "K ARG 1140": "NH1" <-> "NH2" Residue "K ARG 1169": "NH1" <-> "NH2" Residue "K ARG 1173": "NH1" <-> "NH2" Residue "K GLU 1183": "OE1" <-> "OE2" Residue "K GLU 1186": "OE1" <-> "OE2" Residue "K ARG 1202": "NH1" <-> "NH2" Residue "K TYR 1214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 1228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 1230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 1236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 1238": "OE1" <-> "OE2" Residue "K PHE 1241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 1243": "OE1" <-> "OE2" Residue "K GLU 1268": "OE1" <-> "OE2" Residue "K ARG 1288": "NH1" <-> "NH2" Residue "K ARG 1317": "NH1" <-> "NH2" Residue "K ARG 1319": "NH1" <-> "NH2" Residue "K ARG 1328": "NH1" <-> "NH2" Residue "K ARG 1333": "NH1" <-> "NH2" Residue "K ARG 1341": "NH1" <-> "NH2" Residue "K ARG 1347": "NH1" <-> "NH2" Residue "K ARG 1348": "NH1" <-> "NH2" Residue "K ARG 1360": "NH1" <-> "NH2" Residue "K ARG 1378": "NH1" <-> "NH2" Residue "K ARG 1392": "NH1" <-> "NH2" Residue "K ARG 1427": "NH1" <-> "NH2" Residue "K ARG 1428": "NH1" <-> "NH2" Residue "K ARG 1441": "NH1" <-> "NH2" Residue "K ARG 1443": "NH1" <-> "NH2" Residue "K ARG 1446": "NH1" <-> "NH2" Residue "K ARG 1498": "NH1" <-> "NH2" Residue "K ARG 1514": "NH1" <-> "NH2" Residue "K ARG 1530": "NH1" <-> "NH2" Residue "K ARG 1664": "NH1" <-> "NH2" Residue "K ARG 1672": "NH1" <-> "NH2" Residue "K ARG 1682": "NH1" <-> "NH2" Residue "K ARG 1683": "NH1" <-> "NH2" 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: 17177 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 720 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 89} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ALY:plan-2': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} 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: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 673 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} 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: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 730 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 3384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 3384 Classifications: {'DNA': 165} Link IDs: {'rna3p': 164} Chain: "J" Number of atoms: 3381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 3381 Classifications: {'DNA': 165} Link IDs: {'rna3p': 164} Chain: "K" Number of atoms: 4302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4302 Classifications: {'peptide': 517} Link IDs: {'PCIS': 3, 'PTRANS': 29, 'TRANS': 484} Chain breaks: 4 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: 9.18, per 1000 atoms: 0.53 Number of scatterers: 17177 At special positions: 0 Unit cell: (101.43, 161.7, 124.95, 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 46 16.00 P 330 15.00 O 3836 8.00 N 3130 7.00 C 9835 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: 8.00 Conformation dependent library (CDL) restraints added in 2.1 seconds 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2428 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 3 sheets defined 54.8% alpha, 5.6% beta 129 base pairs and 248 stacking pairs defined. Time for finding SS restraints: 8.59 Creating SS restraints... Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 64 through 78 Processing helix chain 'A' and resid 86 through 113 Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'B' and resid 25 through 28 No H-bonds generated for 'chain 'B' and resid 25 through 28' Processing helix chain 'B' and resid 31 through 40 Processing helix chain 'B' and resid 50 through 75 removed outlier: 3.691A pdb=" N GLU B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'C' and resid 17 through 20 No H-bonds generated for 'chain 'C' and resid 17 through 20' Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.356A 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 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 41 Processing helix chain 'F' and resid 48 through 75 removed outlier: 4.892A pdb=" N GLU F 52 " --> pdb=" O GLY F 48 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 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: 4.342A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 89 Processing helix chain 'G' and resid 91 through 96 Processing helix chain 'H' and resid 38 through 48 Processing helix chain 'H' and resid 56 through 83 Processing helix chain 'H' and resid 91 through 101 Processing helix chain 'H' and resid 104 through 123 Processing helix chain 'K' and resid 1088 through 1103 Proline residue: K1096 - end of helix Processing helix chain 'K' and resid 1109 through 1111 No H-bonds generated for 'chain 'K' and resid 1109 through 1111' Processing helix chain 'K' and resid 1125 through 1128 No H-bonds generated for 'chain 'K' and resid 1125 through 1128' Processing helix chain 'K' and resid 1135 through 1144 Processing helix chain 'K' and resid 1150 through 1167 Processing helix chain 'K' and resid 1173 through 1196 removed outlier: 4.353A pdb=" N ASP K1190 " --> pdb=" O GLU K1186 " (cutoff:3.500A) Proline residue: K1191 - end of helix Processing helix chain 'K' and resid 1238 through 1243 Processing helix chain 'K' and resid 1292 through 1295 No H-bonds generated for 'chain 'K' and resid 1292 through 1295' Processing helix chain 'K' and resid 1309 through 1315 Processing helix chain 'K' and resid 1333 through 1349 Processing helix chain 'K' and resid 1373 through 1379 Processing helix chain 'K' and resid 1444 through 1463 removed outlier: 4.562A pdb=" N ALA K1448 " --> pdb=" O CYS K1444 " (cutoff:3.500A) Processing helix chain 'K' and resid 1496 through 1513 Processing helix chain 'K' and resid 1522 through 1529 Processing helix chain 'K' and resid 1534 through 1536 No H-bonds generated for 'chain 'K' and resid 1534 through 1536' Processing helix chain 'K' and resid 1544 through 1553 Processing helix chain 'K' and resid 1617 through 1631 removed outlier: 5.848A pdb=" N GLU K1630 " --> pdb=" O GLU K1626 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL K1631 " --> pdb=" O LYS K1627 " (cutoff:3.500A) Processing helix chain 'K' and resid 1665 through 1674 Processing helix chain 'K' and resid 1681 through 1697 Processing sheet with id= A, first strand: chain 'K' and resid 1268 through 1271 Processing sheet with id= B, first strand: chain 'K' and resid 1280 through 1282 Processing sheet with id= C, first strand: chain 'K' and resid 1518 through 1521 removed outlier: 3.715A pdb=" N ASP K1518 " --> pdb=" O HIS K1636 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N TRP K1472 " --> pdb=" O ILE K1431 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N TYR K1433 " --> pdb=" O TRP K1472 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N HIS K1413 " --> pdb=" O SER K1432 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LEU K1434 " --> pdb=" O GLY K1411 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY K1411 " --> pdb=" O LEU K1434 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N SER K1436 " --> pdb=" O PHE K1409 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N PHE K1409 " --> pdb=" O SER K1436 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA K1398 " --> pdb=" O PHE K1409 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLY K1411 " --> pdb=" O LEU K1396 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU K1396 " --> pdb=" O GLY K1411 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N HIS K1413 " --> pdb=" O LYS K1394 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LYS K1394 " --> pdb=" O HIS K1413 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLN K1415 " --> pdb=" O ARG K1392 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ARG K1392 " --> pdb=" O GLN K1415 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N TYR K1417 " --> pdb=" O PRO K1390 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N PHE K1397 " --> pdb=" O VAL K1361 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N VAL K1361 " --> pdb=" O PHE K1397 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N PHE K1399 " --> pdb=" O VAL K1359 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N VAL K1359 " --> pdb=" O PHE K1399 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N GLU K1401 " --> pdb=" O VAL K1357 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N VAL K1357 " --> pdb=" O GLU K1401 " (cutoff:3.500A) 516 hydrogen bonds defined for protein. 1536 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 310 hydrogen bonds 620 hydrogen bond angles 0 basepair planarities 129 basepair parallelities 248 stacking parallelities Total time for adding SS restraints: 7.68 Time building geometry restraints manager: 8.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3318 1.33 - 1.45: 5725 1.45 - 1.57: 8432 1.57 - 1.69: 658 1.69 - 1.81: 68 Bond restraints: 18201 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 4.45e+00 bond pdb=" NZ ALY B 12 " pdb=" CH ALY B 12 " ideal model delta sigma weight residual 1.343 1.384 -0.041 2.00e-02 2.50e+03 4.19e+00 bond pdb=" C3' DT I 136 " pdb=" O3' DT I 136 " ideal model delta sigma weight residual 1.422 1.471 -0.049 3.00e-02 1.11e+03 2.70e+00 bond pdb=" C LEU D 101 " pdb=" N LEU D 102 " ideal model delta sigma weight residual 1.329 1.352 -0.024 1.60e-02 3.91e+03 2.20e+00 bond pdb=" C3' DA J 59 " pdb=" O3' DA J 59 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.69e+00 ... (remaining 18196 not shown) Histogram of bond angle deviations from ideal: 98.47 - 105.58: 1652 105.58 - 112.68: 9983 112.68 - 119.79: 5891 119.79 - 126.90: 7504 126.90 - 134.00: 964 Bond angle restraints: 25994 Sorted by residual: angle pdb=" CA LEU K1507 " pdb=" CB LEU K1507 " pdb=" CG LEU K1507 " ideal model delta sigma weight residual 116.30 105.94 10.36 3.50e+00 8.16e-02 8.76e+00 angle pdb=" C ASN B 64 " pdb=" N VAL B 65 " pdb=" CA VAL B 65 " ideal model delta sigma weight residual 122.97 120.31 2.66 9.80e-01 1.04e+00 7.38e+00 angle pdb=" C PHE K1544 " pdb=" N TRP K1545 " pdb=" CA TRP K1545 " ideal model delta sigma weight residual 120.09 123.41 -3.32 1.25e+00 6.40e-01 7.04e+00 angle pdb=" CB MET K1290 " pdb=" CG MET K1290 " pdb=" SD MET K1290 " ideal model delta sigma weight residual 112.70 120.41 -7.71 3.00e+00 1.11e-01 6.60e+00 angle pdb=" C LEU D 101 " pdb=" N LEU D 102 " pdb=" CA LEU D 102 " ideal model delta sigma weight residual 120.49 116.91 3.58 1.42e+00 4.96e-01 6.35e+00 ... (remaining 25989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.73: 8639 34.73 - 69.46: 1510 69.46 - 104.19: 30 104.19 - 138.92: 2 138.92 - 173.65: 2 Dihedral angle restraints: 10183 sinusoidal: 6423 harmonic: 3760 Sorted by residual: dihedral pdb=" CA LYS B 20 " pdb=" C LYS B 20 " pdb=" N VAL B 21 " pdb=" CA VAL B 21 " ideal model delta harmonic sigma weight residual -180.00 -151.44 -28.56 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA MET K1412 " pdb=" C MET K1412 " pdb=" N HIS K1413 " pdb=" CA HIS K1413 " ideal model delta harmonic sigma weight residual 180.00 159.34 20.66 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA ILE F 29 " pdb=" C ILE F 29 " pdb=" N THR F 30 " pdb=" CA THR F 30 " ideal model delta harmonic sigma weight residual -180.00 -159.83 -20.17 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 10180 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2234 0.034 - 0.069: 512 0.069 - 0.103: 98 0.103 - 0.137: 41 0.137 - 0.172: 1 Chirality restraints: 2886 Sorted by residual: chirality pdb=" CA ILE K1635 " pdb=" N ILE K1635 " pdb=" C ILE K1635 " pdb=" CB ILE K1635 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.36e-01 chirality pdb=" P DA J 60 " pdb=" OP1 DA J 60 " pdb=" OP2 DA J 60 " pdb=" O5' DA J 60 " both_signs ideal model delta sigma weight residual True 2.35 -2.48 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CB VAL B 43 " pdb=" CA VAL B 43 " pdb=" CG1 VAL B 43 " pdb=" CG2 VAL B 43 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 3.99e-01 ... (remaining 2883 not shown) Planarity restraints: 2162 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 102 " -0.031 5.00e-02 4.00e+02 4.70e-02 3.53e+00 pdb=" N PRO D 103 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET E 120 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.90e+00 pdb=" N PRO E 121 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO E 121 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 121 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 30 " -0.007 2.00e-02 2.50e+03 1.12e-02 2.84e+00 pdb=" N1 DC J 30 " 0.007 2.00e-02 2.50e+03 pdb=" C2 DC J 30 " -0.026 2.00e-02 2.50e+03 pdb=" O2 DC J 30 " 0.013 2.00e-02 2.50e+03 pdb=" N3 DC J 30 " 0.011 2.00e-02 2.50e+03 pdb=" C4 DC J 30 " -0.002 2.00e-02 2.50e+03 pdb=" N4 DC J 30 " -0.006 2.00e-02 2.50e+03 pdb=" C5 DC J 30 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DC J 30 " 0.006 2.00e-02 2.50e+03 ... (remaining 2159 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3244 2.79 - 3.32: 16362 3.32 - 3.84: 34129 3.84 - 4.37: 38749 4.37 - 4.90: 55670 Nonbonded interactions: 148154 Sorted by model distance: nonbonded pdb=" ND2 ASN E 108 " pdb=" O GLY F 42 " model vdw 2.260 2.520 nonbonded pdb=" N GLY C 44 " pdb=" O ILE D 89 " model vdw 2.268 2.520 nonbonded pdb=" NE2 HIS A 113 " pdb=" OD1 ASP E 123 " model vdw 2.296 2.520 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.304 2.440 nonbonded pdb=" NH2 ARG G 35 " pdb=" OP2 DT I 129 " model vdw 2.309 2.520 ... (remaining 148149 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 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 14 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and ((resid 31 and (name N or name CA or name C or name O or name CB \ )) or resid 32 through 124)) selection = chain 'H' } ncs_group { reference = (chain 'I' and resid 10 through 171) selection = (chain 'J' and resid 10 through 171) } 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: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.340 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 54.840 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.080 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 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 0.049 18201 Z= 0.157 Angle : 0.565 10.362 25994 Z= 0.351 Chirality : 0.033 0.172 2886 Planarity : 0.004 0.047 2162 Dihedral : 25.163 173.648 7755 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 2.08 (0.23), residues: 1258 helix: 1.94 (0.18), residues: 772 sheet: 0.25 (0.61), residues: 77 loop : 0.68 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K1472 HIS 0.009 0.001 HIS K1451 PHE 0.024 0.001 PHE K1410 TYR 0.016 0.001 TYR K1227 ARG 0.006 0.000 ARG E 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.372 Fit side-chains REVERT: A 97 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7867 (mt-10) REVERT: A 124 ILE cc_start: 0.9712 (mt) cc_final: 0.9507 (tp) REVERT: B 84 MET cc_start: 0.7405 (tpp) cc_final: 0.7030 (mmm) REVERT: D 59 MET cc_start: 0.9014 (tpp) cc_final: 0.8581 (tpp) REVERT: K 1502 TRP cc_start: 0.4260 (t60) cc_final: 0.3669 (t60) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.2816 time to fit residues: 24.6822 Evaluate side-chains 42 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 79 optimal weight: 7.9990 chunk 63 optimal weight: 8.9990 chunk 122 optimal weight: 0.0870 chunk 47 optimal weight: 0.0770 chunk 74 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 141 optimal weight: 7.9990 overall best weight: 3.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN E 39 HIS F 64 ASN K1291 HIS K1415 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18201 Z= 0.278 Angle : 0.630 9.161 25994 Z= 0.362 Chirality : 0.037 0.167 2886 Planarity : 0.005 0.049 2162 Dihedral : 29.301 171.758 5132 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.09 % Allowed : 2.61 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 2.34 (0.23), residues: 1258 helix: 2.14 (0.18), residues: 773 sheet: 0.29 (0.60), residues: 78 loop : 0.81 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K1545 HIS 0.010 0.001 HIS B 75 PHE 0.021 0.002 PHE G 25 TYR 0.018 0.002 TYR C 50 ARG 0.007 0.001 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 1.536 Fit side-chains REVERT: A 124 ILE cc_start: 0.9719 (mt) cc_final: 0.9491 (tp) REVERT: H 61 ILE cc_start: 0.9520 (mm) cc_final: 0.9270 (mm) REVERT: K 1502 TRP cc_start: 0.4257 (t60) cc_final: 0.3951 (t60) outliers start: 1 outliers final: 0 residues processed: 47 average time/residue: 0.2682 time to fit residues: 21.1417 Evaluate side-chains 33 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 117 optimal weight: 40.0000 chunk 96 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 141 optimal weight: 9.9990 chunk 153 optimal weight: 3.9990 chunk 126 optimal weight: 0.0040 chunk 140 optimal weight: 30.0000 chunk 48 optimal weight: 0.9990 chunk 113 optimal weight: 7.9990 overall best weight: 2.8000 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** K1113 GLN K1146 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18201 Z= 0.235 Angle : 0.572 8.067 25994 Z= 0.334 Chirality : 0.035 0.145 2886 Planarity : 0.004 0.041 2162 Dihedral : 29.470 171.134 5132 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.09 % Allowed : 2.79 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 2.39 (0.24), residues: 1258 helix: 2.23 (0.19), residues: 770 sheet: 0.52 (0.61), residues: 76 loop : 0.69 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K1545 HIS 0.007 0.001 HIS K1451 PHE 0.022 0.002 PHE E 104 TYR 0.015 0.002 TYR C 50 ARG 0.004 0.000 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 1.460 Fit side-chains REVERT: A 124 ILE cc_start: 0.9746 (mt) cc_final: 0.9537 (tp) REVERT: E 97 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7010 (mt-10) REVERT: F 84 MET cc_start: 0.8170 (tpp) cc_final: 0.7931 (tpp) REVERT: H 61 ILE cc_start: 0.9528 (mm) cc_final: 0.9179 (mm) REVERT: H 62 MET cc_start: 0.9008 (tpt) cc_final: 0.8723 (tpp) REVERT: K 1502 TRP cc_start: 0.4321 (t60) cc_final: 0.3638 (t60) outliers start: 1 outliers final: 0 residues processed: 46 average time/residue: 0.3019 time to fit residues: 22.6044 Evaluate side-chains 36 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 0.0970 chunk 106 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 chunk 142 optimal weight: 30.0000 chunk 150 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 134 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1266 GLN K1698 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18201 Z= 0.239 Angle : 0.567 7.545 25994 Z= 0.332 Chirality : 0.035 0.178 2886 Planarity : 0.004 0.045 2162 Dihedral : 29.471 168.132 5132 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.09 % Allowed : 1.26 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 2.45 (0.24), residues: 1258 helix: 2.28 (0.18), residues: 768 sheet: 0.33 (0.59), residues: 78 loop : 0.75 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K1545 HIS 0.006 0.001 HIS F 75 PHE 0.032 0.002 PHE A 104 TYR 0.015 0.001 TYR C 50 ARG 0.003 0.000 ARG C 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 1.211 Fit side-chains REVERT: C 72 ASP cc_start: 0.9041 (m-30) cc_final: 0.8784 (m-30) REVERT: F 84 MET cc_start: 0.8163 (tpp) cc_final: 0.7914 (tpp) REVERT: H 61 ILE cc_start: 0.9525 (mm) cc_final: 0.9218 (mm) REVERT: K 1502 TRP cc_start: 0.3852 (t60) cc_final: 0.3496 (t60) outliers start: 1 outliers final: 0 residues processed: 49 average time/residue: 0.2920 time to fit residues: 23.4642 Evaluate side-chains 33 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 112 optimal weight: 20.0000 chunk 62 optimal weight: 8.9990 chunk 128 optimal weight: 7.9990 chunk 104 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 135 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1628 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.5404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 18201 Z= 0.460 Angle : 0.747 11.572 25994 Z= 0.425 Chirality : 0.042 0.159 2886 Planarity : 0.005 0.038 2162 Dihedral : 30.382 169.348 5132 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 21.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 1.45 (0.23), residues: 1258 helix: 1.44 (0.18), residues: 761 sheet: 0.51 (0.64), residues: 66 loop : 0.34 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K1545 HIS 0.011 0.002 HIS F 75 PHE 0.029 0.003 PHE B 61 TYR 0.014 0.002 TYR C 39 ARG 0.008 0.001 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 1.414 Fit side-chains REVERT: D 59 MET cc_start: 0.9189 (tpp) cc_final: 0.8976 (tpp) REVERT: F 84 MET cc_start: 0.8263 (tpp) cc_final: 0.7695 (tpp) REVERT: H 61 ILE cc_start: 0.9583 (mm) cc_final: 0.9295 (mm) REVERT: K 1290 MET cc_start: -0.0098 (mmt) cc_final: -0.0326 (mmt) REVERT: K 1502 TRP cc_start: 0.4794 (t60) cc_final: 0.4374 (t60) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.2814 time to fit residues: 18.1376 Evaluate side-chains 32 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.9980 chunk 135 optimal weight: 20.0000 chunk 29 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 150 optimal weight: 8.9990 chunk 125 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.5239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18201 Z= 0.204 Angle : 0.571 7.230 25994 Z= 0.338 Chirality : 0.035 0.146 2886 Planarity : 0.004 0.045 2162 Dihedral : 30.273 172.295 5132 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 2.10 (0.24), residues: 1258 helix: 2.05 (0.19), residues: 769 sheet: 0.09 (0.59), residues: 76 loop : 0.52 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K1502 HIS 0.006 0.001 HIS B 75 PHE 0.012 0.001 PHE K1410 TYR 0.014 0.001 TYR K1102 ARG 0.006 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 1.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 72 ASP cc_start: 0.9140 (m-30) cc_final: 0.8845 (m-30) REVERT: D 59 MET cc_start: 0.9134 (tpp) cc_final: 0.8884 (tpp) REVERT: F 84 MET cc_start: 0.8021 (tpp) cc_final: 0.7305 (tpp) REVERT: H 61 ILE cc_start: 0.9586 (mm) cc_final: 0.9337 (mm) REVERT: H 71 GLU cc_start: 0.7910 (tp30) cc_final: 0.7609 (tp30) REVERT: K 1502 TRP cc_start: 0.4755 (t60) cc_final: 0.4479 (t60) REVERT: K 1691 MET cc_start: 0.5406 (ppp) cc_final: 0.5107 (ppp) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.3092 time to fit residues: 23.3670 Evaluate side-chains 34 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 0.0050 chunk 17 optimal weight: 0.4980 chunk 85 optimal weight: 7.9990 chunk 110 optimal weight: 3.9990 chunk 127 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 chunk 150 optimal weight: 6.9990 chunk 94 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 overall best weight: 2.5000 ------------------------------------------------------------------------------- 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** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.5431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18201 Z= 0.236 Angle : 0.577 8.045 25994 Z= 0.340 Chirality : 0.035 0.141 2886 Planarity : 0.004 0.046 2162 Dihedral : 30.168 170.003 5132 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 2.12 (0.24), residues: 1258 helix: 2.07 (0.19), residues: 771 sheet: 0.35 (0.63), residues: 66 loop : 0.45 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K1502 HIS 0.005 0.001 HIS F 75 PHE 0.018 0.001 PHE H 65 TYR 0.010 0.001 TYR K1102 ARG 0.004 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 59 MET cc_start: 0.9122 (tpp) cc_final: 0.8900 (tpp) REVERT: F 84 MET cc_start: 0.8087 (tpp) cc_final: 0.7346 (tpp) REVERT: H 61 ILE cc_start: 0.9557 (mm) cc_final: 0.9240 (mm) REVERT: K 1502 TRP cc_start: 0.4750 (t60) cc_final: 0.4438 (t60) REVERT: K 1661 MET cc_start: 0.2902 (mmt) cc_final: 0.2491 (mmm) REVERT: K 1691 MET cc_start: 0.5417 (ppp) cc_final: 0.5115 (ppp) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.2807 time to fit residues: 20.0668 Evaluate side-chains 32 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 5.9990 chunk 89 optimal weight: 20.0000 chunk 45 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 102 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 118 optimal weight: 9.9990 chunk 136 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.5929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 18201 Z= 0.285 Angle : 0.618 7.977 25994 Z= 0.360 Chirality : 0.036 0.153 2886 Planarity : 0.004 0.045 2162 Dihedral : 30.347 169.849 5132 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 1258 helix: 1.91 (0.19), residues: 772 sheet: 0.27 (0.63), residues: 66 loop : 0.33 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K1502 HIS 0.006 0.001 HIS F 75 PHE 0.020 0.002 PHE K1410 TYR 0.012 0.001 TYR H 40 ARG 0.004 0.000 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.392 Fit side-chains REVERT: F 84 MET cc_start: 0.8127 (tpp) cc_final: 0.7410 (tpp) REVERT: H 61 ILE cc_start: 0.9607 (mm) cc_final: 0.9301 (mm) REVERT: K 1661 MET cc_start: 0.3507 (mmt) cc_final: 0.3021 (mmm) REVERT: K 1691 MET cc_start: 0.5518 (ppp) cc_final: 0.5269 (ppp) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.2445 time to fit residues: 16.0276 Evaluate side-chains 31 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 6.9990 chunk 140 optimal weight: 20.0000 chunk 144 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 110 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 139 optimal weight: 8.9990 chunk 92 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.6398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 18201 Z= 0.331 Angle : 0.653 10.151 25994 Z= 0.376 Chirality : 0.037 0.169 2886 Planarity : 0.004 0.042 2162 Dihedral : 30.623 170.474 5132 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 19.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 1.75 (0.24), residues: 1258 helix: 1.84 (0.19), residues: 765 sheet: 0.11 (0.63), residues: 66 loop : 0.20 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K1545 HIS 0.007 0.001 HIS F 75 PHE 0.021 0.002 PHE H 65 TYR 0.011 0.002 TYR K1153 ARG 0.004 0.000 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.487 Fit side-chains REVERT: D 59 MET cc_start: 0.9175 (mmp) cc_final: 0.8961 (mmp) REVERT: E 120 MET cc_start: 0.8874 (tpp) cc_final: 0.8404 (mmm) REVERT: F 84 MET cc_start: 0.8163 (tpp) cc_final: 0.7412 (tpp) REVERT: H 61 ILE cc_start: 0.9510 (mm) cc_final: 0.9229 (mm) REVERT: K 1290 MET cc_start: 0.0466 (mmt) cc_final: 0.0234 (mmt) REVERT: K 1661 MET cc_start: 0.3910 (mmt) cc_final: 0.3406 (mmm) REVERT: K 1691 MET cc_start: 0.5661 (ppp) cc_final: 0.5411 (ppp) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.2412 time to fit residues: 15.8988 Evaluate side-chains 28 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 0.8980 chunk 90 optimal weight: 10.0000 chunk 70 optimal weight: 0.7980 chunk 102 optimal weight: 8.9990 chunk 155 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 chunk 75 optimal weight: 8.9990 chunk 98 optimal weight: 6.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- 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** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.6443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 18201 Z= 0.255 Angle : 0.608 8.881 25994 Z= 0.354 Chirality : 0.036 0.169 2886 Planarity : 0.004 0.045 2162 Dihedral : 30.558 170.914 5132 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 1.88 (0.24), residues: 1258 helix: 1.93 (0.19), residues: 768 sheet: 0.04 (0.62), residues: 67 loop : 0.29 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K1502 HIS 0.006 0.001 HIS F 75 PHE 0.017 0.002 PHE H 65 TYR 0.011 0.001 TYR H 40 ARG 0.004 0.000 ARG A 131 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.393 Fit side-chains revert: symmetry clash REVERT: F 84 MET cc_start: 0.7943 (tpp) cc_final: 0.7219 (tpp) REVERT: H 61 ILE cc_start: 0.9553 (mm) cc_final: 0.9256 (mm) REVERT: K 1290 MET cc_start: 0.0684 (mmt) cc_final: 0.0445 (mmt) REVERT: K 1385 MET cc_start: 0.4378 (ttt) cc_final: 0.4165 (ttt) REVERT: K 1661 MET cc_start: 0.3842 (mmt) cc_final: 0.3381 (mmm) REVERT: K 1691 MET cc_start: 0.5698 (ppp) cc_final: 0.5443 (ppp) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.2388 time to fit residues: 15.8098 Evaluate side-chains 29 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 34 optimal weight: 0.0010 chunk 123 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 127 optimal weight: 7.9990 chunk 15 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 108 optimal weight: 9.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- 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** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 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 = 0.3482 r_free = 0.3482 target = 0.059227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.038714 restraints weight = 169522.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 87)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.037984 restraints weight = 97049.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.038081 restraints weight = 73115.294| |-----------------------------------------------------------------------------| r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.6241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18201 Z= 0.155 Angle : 0.563 8.578 25994 Z= 0.330 Chirality : 0.035 0.175 2886 Planarity : 0.004 0.049 2162 Dihedral : 30.296 171.897 5132 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 2.16 (0.24), residues: 1258 helix: 2.18 (0.19), residues: 764 sheet: -0.26 (0.57), residues: 77 loop : 0.47 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K1472 HIS 0.004 0.001 HIS B 75 PHE 0.019 0.001 PHE D 65 TYR 0.012 0.001 TYR C 57 ARG 0.006 0.000 ARG B 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2284.02 seconds wall clock time: 43 minutes 6.22 seconds (2586.22 seconds total)