Starting phenix.real_space_refine on Mon Dec 11 03:24:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hal_34595/12_2023/8hal_34595_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hal_34595/12_2023/8hal_34595.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hal_34595/12_2023/8hal_34595.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hal_34595/12_2023/8hal_34595.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hal_34595/12_2023/8hal_34595_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hal_34595/12_2023/8hal_34595_updated.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 302 5.49 5 S 46 5.16 5 C 9551 2.51 5 N 3022 2.21 5 O 3664 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 GLU 94": "OE1" <-> "OE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 17": "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 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 ARG 99": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 72": "NH1" <-> "NH2" Residue "D ARG 79": "NH1" <-> "NH2" Residue "D ARG 86": "NH1" <-> "NH2" Residue "D ARG 92": "NH1" <-> "NH2" Residue "D ARG 99": "NH1" <-> "NH2" Residue "E ARG 40": "NH1" <-> "NH2" Residue "E ARG 42": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E GLU 50": "OE1" <-> "OE2" 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 GLU 73": "OE1" <-> "OE2" Residue "E ARG 83": "NH1" <-> "NH2" Residue "E PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 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 GLU 35": "OE1" <-> "OE2" Residue "H TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "H GLU 113": "OE1" <-> "OE2" Residue "K GLU 1089": "OE1" <-> "OE2" Residue "K GLU 1107": "OE1" <-> "OE2" Residue "K GLU 1188": "OE1" <-> "OE2" Residue "K TYR 1198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 1236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 1241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 1319": "NH1" <-> "NH2" Residue "K GLU 1321": "OE1" <-> "OE2" Residue "K PHE 1397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 1410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 1513": "OE1" <-> "OE2" Residue "K TYR 1519": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 16585 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 819 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 728 Classifications: {'peptide': 92} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 90} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ALY:plan-2': 2, 'ALY:plan-1': 1} Unresolved non-hydrogen planarities: 7 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: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 764 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 98} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "I" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 3094 Classifications: {'DNA': 151} Link IDs: {'rna3p': 150} Chain: "J" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 3097 Classifications: {'DNA': 151} Link IDs: {'rna3p': 150} Chain: "K" Number of atoms: 4238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4238 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 28, 'TRANS': 481} Chain breaks: 4 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 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: 8.66, per 1000 atoms: 0.52 Number of scatterers: 16585 At special positions: 0 Unit cell: (110.25, 170.52, 136.71, 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 302 15.00 O 3664 8.00 N 3022 7.00 C 9551 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: 8.37 Conformation dependent library (CDL) restraints added in 1.8 seconds 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 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 53.8% alpha, 5.3% beta 117 base pairs and 228 stacking pairs defined. Time for finding SS restraints: 7.95 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 86 through 114 Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'B' and resid 26 through 29 removed outlier: 3.730A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 26 through 29' Processing helix chain 'B' and resid 31 through 40 Processing helix chain 'B' and resid 50 through 75 removed outlier: 4.281A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU B 74 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N HIS B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 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: 4.289A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'D' and resid 38 through 48 Processing helix chain 'D' and resid 56 through 83 Processing helix chain 'D' and resid 91 through 101 Processing helix chain 'D' and resid 105 through 122 Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 64 through 78 Processing helix chain 'E' and resid 86 through 114 removed outlier: 3.605A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 40 Processing helix chain 'F' and resid 50 through 76 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: 4.376A 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 1087 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 1117 through 1120 No H-bonds generated for 'chain 'K' and resid 1117 through 1120' 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 1143 Processing helix chain 'K' and resid 1150 through 1167 Processing helix chain 'K' and resid 1173 through 1195 removed outlier: 4.198A pdb=" N ASP K1190 " --> pdb=" O GLU K1186 " (cutoff:3.500A) Proline residue: K1191 - end of helix removed outlier: 3.762A pdb=" N SER K1195 " --> pdb=" O PRO K1191 " (cutoff:3.500A) 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 1314 Processing helix chain 'K' and resid 1333 through 1349 Processing helix chain 'K' and resid 1373 through 1379 Processing helix chain 'K' and resid 1443 through 1464 removed outlier: 4.135A pdb=" N THR K1447 " --> pdb=" O ARG K1443 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ALA K1448 " --> pdb=" O CYS K1444 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU K1452 " --> pdb=" O ALA K1448 " (cutoff:3.500A) Processing helix chain 'K' and resid 1496 through 1512 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 1554 Processing helix chain 'K' and resid 1621 through 1627 Processing helix chain 'K' and resid 1664 through 1674 Processing helix chain 'K' and resid 1681 through 1697 Processing sheet with id= A, first strand: chain 'K' and resid 1226 through 1229 removed outlier: 3.740A pdb=" N LYS K1270 " --> pdb=" O TYR K1227 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER K1229 " --> pdb=" O GLU K1268 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU K1268 " --> pdb=" O SER K1229 " (cutoff:3.500A) 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: 4.239A pdb=" N TRP K1472 " --> pdb=" O ILE K1431 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N TYR K1433 " --> pdb=" O TRP K1472 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N HIS K1413 " --> pdb=" O SER K1432 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LEU K1434 " --> pdb=" O GLY K1411 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N GLY K1411 " --> pdb=" O LEU K1434 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N SER K1436 " --> pdb=" O PHE K1409 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N PHE K1409 " --> pdb=" O SER K1436 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA K1398 " --> pdb=" O PHE K1409 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLY K1411 " --> pdb=" O LEU K1396 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N LEU K1396 " --> pdb=" O GLY K1411 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N HIS K1413 " --> pdb=" O LYS K1394 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LYS K1394 " --> pdb=" O HIS K1413 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLN K1415 " --> pdb=" O ARG K1392 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ARG K1392 " --> pdb=" O GLN K1415 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N TYR K1417 " --> pdb=" O PRO K1390 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA K1363 " --> pdb=" O ALA K1395 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N PHE K1397 " --> pdb=" O VAL K1361 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N VAL K1361 " --> pdb=" O PHE K1397 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N PHE K1399 " --> pdb=" O VAL K1359 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N VAL K1359 " --> pdb=" O PHE K1399 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLU K1401 " --> pdb=" O VAL K1357 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL K1357 " --> pdb=" O GLU K1401 " (cutoff:3.500A) 499 hydrogen bonds defined for protein. 1488 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 280 hydrogen bonds 560 hydrogen bond angles 0 basepair planarities 117 basepair parallelities 228 stacking parallelities Total time for adding SS restraints: 6.99 Time building geometry restraints manager: 8.69 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: 2780 1.33 - 1.45: 5676 1.45 - 1.57: 8411 1.57 - 1.69: 602 1.69 - 1.81: 68 Bond restraints: 17537 Sorted by residual: bond pdb=" NZ ALY B 16 " pdb=" CH ALY B 16 " ideal model delta sigma weight residual 1.343 1.384 -0.041 2.00e-02 2.50e+03 4.25e+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 2.71e+00 bond pdb=" CG GLU F 63 " pdb=" CD GLU F 63 " ideal model delta sigma weight residual 1.516 1.484 0.032 2.50e-02 1.60e+03 1.62e+00 bond pdb=" C3' DA J 59 " pdb=" O3' DA J 59 " ideal model delta sigma weight residual 1.422 1.460 -0.038 3.00e-02 1.11e+03 1.56e+00 bond pdb=" CD GLU F 63 " pdb=" OE1 GLU F 63 " ideal model delta sigma weight residual 1.249 1.226 0.023 1.90e-02 2.77e+03 1.44e+00 ... (remaining 17532 not shown) Histogram of bond angle deviations from ideal: 98.39 - 105.51: 1466 105.51 - 112.62: 9542 112.62 - 119.74: 5609 119.74 - 126.85: 7427 126.85 - 133.96: 931 Bond angle restraints: 24975 Sorted by residual: angle pdb=" C LEU H 101 " pdb=" N LEU H 102 " pdb=" CA LEU H 102 " ideal model delta sigma weight residual 122.70 113.52 9.18 1.98e+00 2.55e-01 2.15e+01 angle pdb=" N GLU F 63 " pdb=" CA GLU F 63 " pdb=" CB GLU F 63 " ideal model delta sigma weight residual 110.28 117.11 -6.83 1.55e+00 4.16e-01 1.94e+01 angle pdb=" N GLU A 105 " pdb=" CA GLU A 105 " pdb=" CB GLU A 105 " ideal model delta sigma weight residual 110.12 115.86 -5.74 1.47e+00 4.63e-01 1.52e+01 angle pdb=" N GLY D 104 " pdb=" CA GLY D 104 " pdb=" C GLY D 104 " ideal model delta sigma weight residual 111.02 118.05 -7.03 1.86e+00 2.89e-01 1.43e+01 angle pdb=" N GLU K1186 " pdb=" CA GLU K1186 " pdb=" CB GLU K1186 " ideal model delta sigma weight residual 110.12 115.43 -5.31 1.47e+00 4.63e-01 1.30e+01 ... (remaining 24970 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.55: 8491 35.55 - 71.11: 1338 71.11 - 106.66: 23 106.66 - 142.21: 1 142.21 - 177.77: 2 Dihedral angle restraints: 9855 sinusoidal: 6092 harmonic: 3763 Sorted by residual: dihedral pdb=" CA ARG E 63 " pdb=" C ARG E 63 " pdb=" N LYS E 64 " pdb=" CA LYS E 64 " ideal model delta harmonic sigma weight residual -180.00 -153.34 -26.66 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" C4' DT I 136 " pdb=" C3' DT I 136 " pdb=" O3' DT I 136 " pdb=" P DT I 137 " ideal model delta sinusoidal sigma weight residual -140.00 37.77 -177.77 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DA J 59 " pdb=" C3' DA J 59 " pdb=" O3' DA J 59 " pdb=" P DA J 60 " ideal model delta sinusoidal sigma weight residual 220.00 61.88 158.12 1 3.50e+01 8.16e-04 1.51e+01 ... (remaining 9852 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2205 0.039 - 0.079: 440 0.079 - 0.118: 109 0.118 - 0.157: 19 0.157 - 0.196: 1 Chirality restraints: 2774 Sorted by residual: chirality pdb=" CA GLU G 61 " pdb=" N GLU G 61 " pdb=" C GLU G 61 " pdb=" CB GLU G 61 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.64e-01 chirality pdb=" CA MET K1095 " pdb=" N MET K1095 " pdb=" C MET K1095 " pdb=" CB MET K1095 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.37e-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 -2.49 -0.14 2.00e-01 2.50e+01 5.02e-01 ... (remaining 2771 not shown) Planarity restraints: 2132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU H 102 " 0.037 5.00e-02 4.00e+02 5.56e-02 4.95e+00 pdb=" N PRO H 103 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO H 103 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO H 103 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 69 " 0.011 2.00e-02 2.50e+03 2.11e-02 4.46e+00 pdb=" C ARG A 69 " -0.037 2.00e-02 2.50e+03 pdb=" O ARG A 69 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU A 70 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 102 " 0.032 5.00e-02 4.00e+02 4.77e-02 3.65e+00 pdb=" N PRO D 103 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.026 5.00e-02 4.00e+02 ... (remaining 2129 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1051 2.73 - 3.27: 16039 3.27 - 3.81: 32646 3.81 - 4.36: 37899 4.36 - 4.90: 55156 Nonbonded interactions: 142791 Sorted by model distance: nonbonded pdb=" O2 DT J 140 " pdb=" N6 DA J 141 " model vdw 2.187 2.520 nonbonded pdb=" OD2 ASP F 68 " pdb=" NE2 GLN F 93 " model vdw 2.223 2.520 nonbonded pdb=" O ILE E 62 " pdb=" NE2 GLN E 93 " model vdw 2.224 2.520 nonbonded pdb=" O2 DT I 107 " pdb=" N2 DG J 75 " model vdw 2.237 2.520 nonbonded pdb=" N THR D 90 " pdb=" OE2 GLU D 93 " model vdw 2.258 2.520 ... (remaining 142786 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' and resid 31 through 124) } ncs_group { reference = (chain 'I' and resid 16 through 165) selection = (chain 'J' and resid 16 through 165) } 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: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.370 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 52.400 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 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 17537 Z= 0.171 Angle : 0.631 9.177 24975 Z= 0.383 Chirality : 0.035 0.196 2774 Planarity : 0.004 0.056 2132 Dihedral : 24.758 177.765 7427 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.23), residues: 1261 helix: 1.26 (0.19), residues: 749 sheet: 0.06 (0.66), residues: 58 loop : 0.41 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP K1502 HIS 0.003 0.001 HIS B 75 PHE 0.015 0.001 PHE A 104 TYR 0.019 0.001 TYR G 57 ARG 0.019 0.001 ARG E 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.2578 time to fit residues: 37.8255 Evaluate side-chains 52 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.581 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 30.0000 chunk 117 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 chunk 79 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 121 optimal weight: 9.9990 chunk 47 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 140 optimal weight: 30.0000 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN B 25 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN H 109 HIS K1343 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 17537 Z= 0.321 Angle : 0.700 7.761 24975 Z= 0.401 Chirality : 0.041 0.195 2774 Planarity : 0.006 0.068 2132 Dihedral : 29.095 161.988 4825 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.63 % Allowed : 4.08 % Favored : 95.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.22), residues: 1261 helix: 1.14 (0.18), residues: 748 sheet: 0.17 (0.63), residues: 63 loop : 0.30 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP K1502 HIS 0.007 0.002 HIS K1451 PHE 0.011 0.002 PHE D 65 TYR 0.030 0.002 TYR H 83 ARG 0.009 0.001 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 74 average time/residue: 0.2261 time to fit residues: 28.8700 Evaluate side-chains 47 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 1.435 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1439 time to fit residues: 2.5924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 141 optimal weight: 7.9990 chunk 152 optimal weight: 20.0000 chunk 125 optimal weight: 10.0000 chunk 139 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1272 ASN K1297 HIS ** K1638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1698 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 17537 Z= 0.369 Angle : 0.746 9.121 24975 Z= 0.430 Chirality : 0.042 0.214 2774 Planarity : 0.006 0.067 2132 Dihedral : 30.095 171.629 4825 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 25.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.27 % Allowed : 6.35 % Favored : 93.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.23), residues: 1261 helix: 0.77 (0.18), residues: 747 sheet: 0.19 (0.66), residues: 63 loop : 0.06 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP K1502 HIS 0.028 0.002 HIS D 109 PHE 0.025 0.003 PHE K1161 TYR 0.027 0.003 TYR K1482 ARG 0.028 0.001 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 1.444 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 71 average time/residue: 0.2445 time to fit residues: 29.2154 Evaluate side-chains 42 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.541 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 141 optimal weight: 30.0000 chunk 149 optimal weight: 5.9990 chunk 134 optimal weight: 7.9990 chunk 40 optimal weight: 0.6980 chunk 124 optimal weight: 10.0000 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN ** K1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1292 GLN K1336 ASN ** K1638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.5464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 17537 Z= 0.325 Angle : 0.697 7.685 24975 Z= 0.403 Chirality : 0.040 0.191 2774 Planarity : 0.005 0.082 2132 Dihedral : 30.356 171.637 4825 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 22.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.09 % Allowed : 4.35 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.23), residues: 1261 helix: 0.79 (0.18), residues: 743 sheet: 0.28 (0.68), residues: 63 loop : -0.01 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP K1545 HIS 0.007 0.002 HIS K1451 PHE 0.020 0.002 PHE E 104 TYR 0.012 0.002 TYR K1298 ARG 0.011 0.001 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 72 average time/residue: 0.2559 time to fit residues: 30.3578 Evaluate side-chains 43 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 1.542 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 85 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 127 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 134 optimal weight: 2.9990 chunk 37 optimal weight: 0.0060 chunk 50 optimal weight: 1.9990 overall best weight: 1.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** K1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1272 ASN K1292 GLN ** K1638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.5399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17537 Z= 0.199 Angle : 0.614 6.915 24975 Z= 0.357 Chirality : 0.037 0.155 2774 Planarity : 0.004 0.053 2132 Dihedral : 30.273 172.314 4825 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.23), residues: 1261 helix: 1.26 (0.19), residues: 743 sheet: 0.24 (0.66), residues: 63 loop : 0.13 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K1502 HIS 0.006 0.001 HIS B 75 PHE 0.017 0.001 PHE E 104 TYR 0.009 0.001 TYR K1460 ARG 0.007 0.000 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.534 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.2511 time to fit residues: 30.7107 Evaluate side-chains 46 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 1.575 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 20.0000 chunk 29 optimal weight: 0.5980 chunk 87 optimal weight: 10.0000 chunk 36 optimal weight: 0.7980 chunk 149 optimal weight: 0.0470 chunk 124 optimal weight: 20.0000 chunk 69 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 overall best weight: 0.8480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN K1163 ASN ** K1168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1272 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.5329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17537 Z= 0.168 Angle : 0.590 10.075 24975 Z= 0.341 Chirality : 0.035 0.155 2774 Planarity : 0.004 0.054 2132 Dihedral : 29.907 169.305 4825 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.18 % Allowed : 2.54 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.24), residues: 1261 helix: 1.50 (0.19), residues: 749 sheet: 0.24 (0.65), residues: 63 loop : 0.17 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP K1472 HIS 0.005 0.001 HIS K1451 PHE 0.011 0.001 PHE E 104 TYR 0.009 0.001 TYR G 57 ARG 0.005 0.000 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 79 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 80 average time/residue: 0.2763 time to fit residues: 35.5391 Evaluate side-chains 52 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 51 time to evaluate : 1.413 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2041 time to fit residues: 2.1589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 126 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 149 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN ** K1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1292 GLN ** K1351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1547 ASN ** K1638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.6215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 17537 Z= 0.389 Angle : 0.725 7.923 24975 Z= 0.415 Chirality : 0.041 0.162 2774 Planarity : 0.006 0.160 2132 Dihedral : 30.398 169.147 4825 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 25.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.23), residues: 1261 helix: 0.97 (0.18), residues: 748 sheet: 0.25 (0.67), residues: 63 loop : -0.09 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K1545 HIS 0.010 0.002 HIS D 109 PHE 0.017 0.002 PHE E 78 TYR 0.014 0.002 TYR C 39 ARG 0.015 0.001 ARG E 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.2579 time to fit residues: 30.0246 Evaluate side-chains 42 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.488 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1292 GLN K1297 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.6158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17537 Z= 0.212 Angle : 0.634 8.875 24975 Z= 0.365 Chirality : 0.037 0.166 2774 Planarity : 0.005 0.091 2132 Dihedral : 30.422 172.350 4825 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 19.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.23), residues: 1261 helix: 1.23 (0.19), residues: 744 sheet: 0.33 (0.67), residues: 63 loop : -0.04 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K1472 HIS 0.009 0.001 HIS B 75 PHE 0.016 0.001 PHE G 25 TYR 0.014 0.001 TYR G 57 ARG 0.008 0.001 ARG K1427 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.543 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.2538 time to fit residues: 30.7807 Evaluate side-chains 46 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 1.334 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 139 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1168 ASN ** K1351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1628 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.6836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 17537 Z= 0.313 Angle : 0.700 7.484 24975 Z= 0.402 Chirality : 0.039 0.160 2774 Planarity : 0.006 0.087 2132 Dihedral : 30.666 170.200 4825 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 25.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.23), residues: 1261 helix: 0.99 (0.18), residues: 745 sheet: 0.27 (0.69), residues: 63 loop : -0.24 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP K1158 HIS 0.008 0.002 HIS D 109 PHE 0.021 0.002 PHE K1185 TYR 0.012 0.002 TYR K1298 ARG 0.005 0.001 ARG E 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.700 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.2571 time to fit residues: 30.8171 Evaluate side-chains 42 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.539 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 154 optimal weight: 9.9990 chunk 142 optimal weight: 0.0980 chunk 122 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 overall best weight: 4.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS ** K1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.7399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 17537 Z= 0.325 Angle : 0.724 9.665 24975 Z= 0.415 Chirality : 0.041 0.314 2774 Planarity : 0.005 0.065 2132 Dihedral : 30.979 176.224 4825 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 25.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.23), residues: 1261 helix: 0.66 (0.18), residues: 748 sheet: -0.14 (0.68), residues: 63 loop : -0.36 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP K1472 HIS 0.009 0.002 HIS D 109 PHE 0.032 0.002 PHE K1185 TYR 0.044 0.002 TYR K1153 ARG 0.006 0.001 ARG K1112 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.2603 time to fit residues: 29.0010 Evaluate side-chains 40 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 1.493 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 7.9990 chunk 37 optimal weight: 0.3980 chunk 113 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 123 optimal weight: 7.9990 chunk 51 optimal weight: 0.8980 chunk 126 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 108 optimal weight: 9.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN ** K1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.046605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.031972 restraints weight = 220332.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.032875 restraints weight = 113522.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.033393 restraints weight = 75122.811| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.7303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17537 Z= 0.222 Angle : 0.657 9.577 24975 Z= 0.378 Chirality : 0.038 0.200 2774 Planarity : 0.004 0.060 2132 Dihedral : 30.736 173.855 4825 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 20.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.23), residues: 1261 helix: 0.99 (0.19), residues: 737 sheet: -0.37 (0.66), residues: 63 loop : -0.26 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K1472 HIS 0.008 0.001 HIS D 109 PHE 0.020 0.002 PHE K1185 TYR 0.013 0.001 TYR K1298 ARG 0.004 0.000 ARG E 116 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2243.92 seconds wall clock time: 42 minutes 50.97 seconds (2570.97 seconds total)