Starting phenix.real_space_refine on Fri Feb 16 21:15:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hal_34595/02_2024/8hal_34595_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hal_34595/02_2024/8hal_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_34595/02_2024/8hal_34595.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hal_34595/02_2024/8hal_34595.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hal_34595/02_2024/8hal_34595_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hal_34595/02_2024/8hal_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-dev-5238/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: 9.85, per 1000 atoms: 0.59 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: 8.91 Conformation dependent library (CDL) restraints added in 2.1 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: 9.22 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: 7.64 Time building geometry restraints manager: 9.42 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: 1.090 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: 4.450 Check model and map are aligned: 0.260 Set scattering table: 0.180 Process input model: 56.650 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.550 ------------------------------------------------------------------------------- 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 : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 GLU cc_start: 0.7537 (mp0) cc_final: 0.7323 (mm-30) REVERT: E 110 CYS cc_start: 0.8206 (t) cc_final: 0.7997 (t) REVERT: E 120 MET cc_start: 0.7713 (ptp) cc_final: 0.7493 (mpp) REVERT: F 97 LEU cc_start: 0.8693 (tp) cc_final: 0.8338 (tp) REVERT: K 1148 GLN cc_start: 0.6269 (pp30) cc_final: 0.5746 (tp40) REVERT: K 1193 MET cc_start: -0.3248 (ttt) cc_final: -0.3778 (tpp) REVERT: K 1385 MET cc_start: -0.2374 (mtt) cc_final: -0.3087 (mpp) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.2613 time to fit residues: 38.7391 Evaluate side-chains 54 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.492 ------------------------------------------------------------------------------- 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: 0.7692 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 17537 Z= 0.312 Angle : 0.680 7.231 24975 Z= 0.390 Chirality : 0.040 0.176 2774 Planarity : 0.006 0.061 2132 Dihedral : 29.032 161.694 4825 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.36 % Allowed : 3.72 % Favored : 95.92 % 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: 1.12 (0.23), residues: 1261 helix: 1.18 (0.18), residues: 754 sheet: 0.16 (0.63), residues: 63 loop : 0.26 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP K1502 HIS 0.005 0.002 HIS E 113 PHE 0.011 0.002 PHE G 25 TYR 0.030 0.002 TYR H 83 ARG 0.011 0.001 ARG E 63 *********************** 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 74 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 70 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9548 (mt) cc_final: 0.9313 (mt) REVERT: B 58 LEU cc_start: 0.9430 (pp) cc_final: 0.9225 (pp) REVERT: B 84 MET cc_start: 0.7443 (ppp) cc_final: 0.7209 (ppp) REVERT: D 62 MET cc_start: 0.8721 (tpp) cc_final: 0.8411 (tpp) REVERT: F 58 LEU cc_start: 0.9515 (tp) cc_final: 0.9171 (pp) REVERT: F 97 LEU cc_start: 0.8826 (tp) cc_final: 0.8542 (tp) REVERT: K 1193 MET cc_start: -0.1622 (ttt) cc_final: -0.2535 (tpp) REVERT: K 1691 MET cc_start: 0.6373 (ppp) cc_final: 0.6168 (ppp) outliers start: 4 outliers final: 3 residues processed: 73 average time/residue: 0.2276 time to fit residues: 28.5629 Evaluate side-chains 49 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 46 time to evaluate : 1.509 ------------------------------------------------------------------------------- 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: 0.0770 chunk 95 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 141 optimal weight: 0.1980 chunk 152 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 chunk 139 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 113 optimal weight: 9.9990 overall best weight: 3.8544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1297 HIS ** K1638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1698 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17537 Z= 0.291 Angle : 0.676 7.940 24975 Z= 0.392 Chirality : 0.039 0.145 2774 Planarity : 0.005 0.063 2132 Dihedral : 29.759 171.080 4825 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 20.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.18 % Allowed : 5.71 % Favored : 94.11 % 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: 1.08 (0.23), residues: 1261 helix: 1.17 (0.18), residues: 755 sheet: 0.16 (0.64), residues: 63 loop : 0.19 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K1545 HIS 0.012 0.002 HIS D 109 PHE 0.020 0.002 PHE K1484 TYR 0.013 0.002 TYR D 40 ARG 0.020 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: 2 poor density : 69 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9556 (mt) cc_final: 0.9329 (mt) REVERT: B 84 MET cc_start: 0.7713 (ppp) cc_final: 0.7472 (ppp) REVERT: B 88 TYR cc_start: 0.8593 (m-10) cc_final: 0.8103 (m-10) REVERT: C 41 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7891 (mp0) REVERT: F 68 ASP cc_start: 0.8159 (m-30) cc_final: 0.7826 (m-30) REVERT: G 91 GLU cc_start: 0.8935 (pp20) cc_final: 0.8724 (pm20) outliers start: 2 outliers final: 0 residues processed: 71 average time/residue: 0.2492 time to fit residues: 29.5130 Evaluate side-chains 46 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 1.534 ------------------------------------------------------------------------------- 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: 9.9990 chunk 106 optimal weight: 7.9990 chunk 73 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 141 optimal weight: 30.0000 chunk 149 optimal weight: 20.0000 chunk 134 optimal weight: 7.9990 chunk 40 optimal weight: 0.6980 chunk 124 optimal weight: 6.9990 overall best weight: 4.3386 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1168 ASN K1272 ASN K1292 GLN K1547 ASN ** K1638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.5282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 17537 Z= 0.334 Angle : 0.708 8.189 24975 Z= 0.407 Chirality : 0.040 0.160 2774 Planarity : 0.006 0.092 2132 Dihedral : 30.188 170.411 4825 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 23.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % 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: 0.71 (0.23), residues: 1261 helix: 0.87 (0.18), residues: 744 sheet: 0.21 (0.68), residues: 63 loop : 0.04 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K1158 HIS 0.008 0.002 HIS D 109 PHE 0.017 0.002 PHE E 104 TYR 0.012 0.002 TYR K1298 ARG 0.019 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 67 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 1.428 Fit side-chains REVERT: A 92 LEU cc_start: 0.9568 (mt) cc_final: 0.9345 (mt) REVERT: A 105 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8279 (tm-30) REVERT: B 88 TYR cc_start: 0.8698 (m-10) cc_final: 0.8293 (m-10) REVERT: F 68 ASP cc_start: 0.8347 (m-30) cc_final: 0.8058 (m-30) REVERT: G 91 GLU cc_start: 0.8826 (pp20) cc_final: 0.8527 (pm20) REVERT: K 1158 TRP cc_start: 0.8592 (m100) cc_final: 0.8374 (m100) REVERT: K 1193 MET cc_start: -0.0009 (ttt) cc_final: -0.0569 (ttm) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.2513 time to fit residues: 27.9538 Evaluate side-chains 47 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 1.538 ------------------------------------------------------------------------------- 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: 2.9990 chunk 111 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 127 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 134 optimal weight: 5.9990 chunk 37 optimal weight: 0.0770 chunk 50 optimal weight: 0.8980 overall best weight: 0.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** K1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1272 ASN K1292 GLN K1638 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.5004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17537 Z= 0.174 Angle : 0.594 6.956 24975 Z= 0.344 Chirality : 0.036 0.166 2774 Planarity : 0.004 0.052 2132 Dihedral : 29.990 172.707 4825 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.09 % Allowed : 3.54 % Favored : 96.37 % 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: 1.38 (0.23), residues: 1261 helix: 1.45 (0.19), residues: 750 sheet: 0.28 (0.65), residues: 63 loop : 0.24 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K1472 HIS 0.007 0.001 HIS B 75 PHE 0.014 0.001 PHE G 25 TYR 0.010 0.001 TYR B 88 ARG 0.018 0.001 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 79 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9539 (mt) cc_final: 0.9321 (mt) REVERT: A 105 GLU cc_start: 0.8676 (tm-30) cc_final: 0.8308 (tm-30) REVERT: B 88 TYR cc_start: 0.8550 (m-10) cc_final: 0.8250 (m-10) REVERT: F 63 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8063 (pm20) REVERT: F 68 ASP cc_start: 0.8179 (m-30) cc_final: 0.7922 (m-30) REVERT: K 1193 MET cc_start: -0.1102 (ttt) cc_final: -0.1304 (ttt) outliers start: 1 outliers final: 0 residues processed: 79 average time/residue: 0.2542 time to fit residues: 33.0622 Evaluate side-chains 54 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 1.487 ------------------------------------------------------------------------------- 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: 8.9990 chunk 29 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 chunk 69 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 144 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- 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** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1272 ASN K1292 GLN K1336 ASN ** K1351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1638 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.5880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 17537 Z= 0.341 Angle : 0.693 7.309 24975 Z= 0.399 Chirality : 0.040 0.185 2774 Planarity : 0.005 0.052 2132 Dihedral : 30.329 169.404 4825 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 24.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % 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: 0.98 (0.23), residues: 1261 helix: 1.14 (0.18), residues: 750 sheet: 0.24 (0.68), residues: 63 loop : 0.04 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K1545 HIS 0.006 0.002 HIS A 39 PHE 0.017 0.002 PHE K1484 TYR 0.015 0.002 TYR K1482 ARG 0.007 0.001 ARG C 17 *********************** 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 73 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9571 (mt) cc_final: 0.9347 (mt) REVERT: A 105 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8235 (tm-30) REVERT: B 88 TYR cc_start: 0.8629 (m-10) cc_final: 0.8262 (m-10) REVERT: D 37 TYR cc_start: 0.9187 (m-80) cc_final: 0.8896 (m-10) REVERT: F 68 ASP cc_start: 0.8168 (m-30) cc_final: 0.7924 (m-30) REVERT: K 1158 TRP cc_start: 0.8746 (m100) cc_final: 0.8527 (m100) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.2613 time to fit residues: 31.2628 Evaluate side-chains 49 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 1.579 ------------------------------------------------------------------------------- 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: 3.9990 chunk 85 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 149 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1628 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.6447 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= 0.328 Angle : 0.704 8.497 24975 Z= 0.404 Chirality : 0.040 0.160 2774 Planarity : 0.006 0.160 2132 Dihedral : 30.723 173.831 4825 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 24.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % 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: 0.64 (0.23), residues: 1261 helix: 0.88 (0.18), residues: 744 sheet: 0.18 (0.68), residues: 63 loop : -0.12 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K1158 HIS 0.007 0.002 HIS K1628 PHE 0.015 0.002 PHE E 78 TYR 0.014 0.002 TYR K1298 ARG 0.012 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 73 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9571 (mt) cc_final: 0.9357 (mt) REVERT: A 105 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8213 (tm-30) REVERT: B 88 TYR cc_start: 0.8700 (m-10) cc_final: 0.8305 (m-10) REVERT: E 105 GLU cc_start: 0.8595 (pm20) cc_final: 0.8330 (pm20) REVERT: F 68 ASP cc_start: 0.8123 (m-30) cc_final: 0.7817 (m-30) REVERT: K 1158 TRP cc_start: 0.8687 (m100) cc_final: 0.8436 (m100) REVERT: K 1193 MET cc_start: 0.0608 (ttt) cc_final: -0.0119 (ttm) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.2551 time to fit residues: 30.6328 Evaluate side-chains 48 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 1.516 ------------------------------------------------------------------------------- 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: 7.9990 chunk 89 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 94 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 135 optimal weight: 0.0870 overall best weight: 1.0760 ------------------------------------------------------------------------------- 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 24 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1292 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.6192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17537 Z= 0.185 Angle : 0.625 8.874 24975 Z= 0.358 Chirality : 0.037 0.177 2774 Planarity : 0.004 0.074 2132 Dihedral : 30.439 172.969 4825 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % 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: 1.04 (0.23), residues: 1261 helix: 1.24 (0.19), residues: 750 sheet: 0.11 (0.69), residues: 63 loop : -0.01 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K1151 HIS 0.010 0.001 HIS D 109 PHE 0.010 0.001 PHE H 70 TYR 0.020 0.001 TYR A 41 ARG 0.009 0.001 ARG E 52 *********************** 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 74 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9534 (mt) cc_final: 0.9318 (mt) REVERT: A 105 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8197 (tm-30) REVERT: B 88 TYR cc_start: 0.8548 (m-10) cc_final: 0.8219 (m-10) REVERT: D 102 LEU cc_start: 0.8749 (mm) cc_final: 0.8521 (tp) REVERT: E 105 GLU cc_start: 0.8705 (pm20) cc_final: 0.8463 (pm20) REVERT: F 68 ASP cc_start: 0.8075 (m-30) cc_final: 0.7824 (m-30) REVERT: K 1203 LYS cc_start: 0.4798 (tptp) cc_final: 0.4317 (ttmm) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.2709 time to fit residues: 32.2758 Evaluate side-chains 53 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 139 optimal weight: 20.0000 chunk 83 optimal weight: 5.9990 chunk 60 optimal weight: 0.0370 chunk 109 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 138 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 overall best weight: 2.6066 ------------------------------------------------------------------------------- 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** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.6444 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= 0.238 Angle : 0.640 7.608 24975 Z= 0.367 Chirality : 0.037 0.148 2774 Planarity : 0.005 0.078 2132 Dihedral : 30.417 171.382 4825 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 20.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % 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: 1.01 (0.23), residues: 1261 helix: 1.23 (0.19), residues: 754 sheet: 0.12 (0.68), residues: 63 loop : -0.08 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP K1472 HIS 0.009 0.001 HIS D 109 PHE 0.013 0.001 PHE G 25 TYR 0.011 0.001 TYR G 57 ARG 0.007 0.001 ARG E 52 *********************** 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 72 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9547 (mt) cc_final: 0.9327 (mt) REVERT: A 105 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8216 (tm-30) REVERT: B 88 TYR cc_start: 0.8578 (m-10) cc_final: 0.8223 (m-10) REVERT: C 41 GLU cc_start: 0.8347 (pm20) cc_final: 0.8101 (pm20) REVERT: H 61 ILE cc_start: 0.8932 (mm) cc_final: 0.8679 (mm) REVERT: K 1193 MET cc_start: -0.0425 (ttt) cc_final: -0.0848 (ttm) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.2497 time to fit residues: 29.5818 Evaluate side-chains 51 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 154 optimal weight: 6.9990 chunk 142 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 12 optimal weight: 0.1980 chunk 94 optimal weight: 5.9990 chunk 75 optimal weight: 8.9990 chunk 97 optimal weight: 7.9990 overall best weight: 4.4388 ------------------------------------------------------------------------------- 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** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1292 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.7165 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= 0.341 Angle : 0.725 7.828 24975 Z= 0.415 Chirality : 0.041 0.189 2774 Planarity : 0.006 0.075 2132 Dihedral : 30.860 172.263 4825 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 27.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.23), residues: 1261 helix: 0.78 (0.18), residues: 740 sheet: 0.35 (0.70), residues: 58 loop : -0.23 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP K1158 HIS 0.007 0.002 HIS D 109 PHE 0.017 0.002 PHE E 78 TYR 0.012 0.002 TYR K1503 ARG 0.021 0.001 ARG E 52 ********************** 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 67 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 2.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9568 (mt) cc_final: 0.9349 (mt) REVERT: A 105 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8174 (tm-30) REVERT: B 88 TYR cc_start: 0.8650 (m-10) cc_final: 0.8269 (m-10) REVERT: C 41 GLU cc_start: 0.8608 (pm20) cc_final: 0.8222 (pm20) REVERT: F 68 ASP cc_start: 0.8258 (m-30) cc_final: 0.7952 (m-30) REVERT: K 1118 GLN cc_start: 0.8447 (mt0) cc_final: 0.7719 (pm20) REVERT: K 1193 MET cc_start: 0.0365 (ttt) cc_final: -0.0170 (ttm) REVERT: K 1203 LYS cc_start: 0.5228 (tptp) cc_final: 0.4944 (ttmm) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.2867 time to fit residues: 31.4641 Evaluate side-chains 47 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 1.489 ------------------------------------------------------------------------------- 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: 10.0000 chunk 37 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 126 optimal weight: 20.0000 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1292 GLN K1297 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.047386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.032724 restraints weight = 217344.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.033668 restraints weight = 110308.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.034187 restraints weight = 72791.421| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.6868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17537 Z= 0.190 Angle : 0.635 9.198 24975 Z= 0.364 Chirality : 0.037 0.150 2774 Planarity : 0.004 0.056 2132 Dihedral : 30.545 174.405 4825 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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: 0.87 (0.24), residues: 1261 helix: 1.12 (0.19), residues: 747 sheet: -0.11 (0.67), residues: 63 loop : -0.08 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP K1151 HIS 0.011 0.001 HIS B 75 PHE 0.010 0.001 PHE G 25 TYR 0.018 0.001 TYR K1298 ARG 0.010 0.001 ARG E 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2342.37 seconds wall clock time: 44 minutes 29.70 seconds (2669.70 seconds total)