Starting phenix.real_space_refine on Sun Mar 17 08:24:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8haj_34592/03_2024/8haj_34592_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8haj_34592/03_2024/8haj_34592.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8haj_34592/03_2024/8haj_34592.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8haj_34592/03_2024/8haj_34592.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8haj_34592/03_2024/8haj_34592_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8haj_34592/03_2024/8haj_34592_updated.pdb" } resolution = 4.8 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 326 5.49 5 S 47 5.16 5 C 9860 2.51 5 N 3138 2.21 5 O 3843 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 ARG 116": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "A ARG 131": "NH1" <-> "NH2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 23": "NH1" <-> "NH2" Residue "B ARG 35": "NH1" <-> "NH2" Residue "B ARG 36": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 40": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 55": "NH1" <-> "NH2" Residue "B ARG 67": "NH1" <-> "NH2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B ARG 92": "NH1" <-> "NH2" Residue "B ARG 95": "NH1" <-> "NH2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 17": "NH1" <-> "NH2" Residue "C ARG 20": "NH1" <-> "NH2" Residue "C ARG 29": "NH1" <-> "NH2" Residue "C ARG 32": "NH1" <-> "NH2" Residue "C ARG 35": "NH1" <-> "NH2" Residue "C ARG 42": "NH1" <-> "NH2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 30": "NH1" <-> "NH2" Residue "D PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 69": "NH1" <-> "NH2" Residue "D ARG 76": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D ARG 89": "NH1" <-> "NH2" Residue "D ARG 96": "NH1" <-> "NH2" Residue "E ARG 40": "NH1" <-> "NH2" Residue "E TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 42": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 52": "NH1" <-> "NH2" Residue "E ARG 53": "NH1" <-> "NH2" Residue "E ARG 63": "NH1" <-> "NH2" Residue "E ARG 69": "NH1" <-> "NH2" Residue "E ARG 72": "NH1" <-> "NH2" Residue "E ARG 83": "NH1" <-> "NH2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E ARG 116": "NH1" <-> "NH2" Residue "E ARG 128": "NH1" <-> "NH2" Residue "E ARG 129": "NH1" <-> "NH2" Residue "E ARG 131": "NH1" <-> "NH2" Residue "E ARG 134": "NH1" <-> "NH2" Residue "F ARG 19": "NH1" <-> "NH2" Residue "F ARG 23": "NH1" <-> "NH2" Residue "F ARG 35": "NH1" <-> "NH2" Residue "F ARG 36": "NH1" <-> "NH2" Residue "F ARG 39": "NH1" <-> "NH2" Residue "F ARG 40": "NH1" <-> "NH2" Residue "F ARG 45": "NH1" <-> "NH2" Residue "F ARG 55": "NH1" <-> "NH2" Residue "F ARG 67": "NH1" <-> "NH2" Residue "F 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 ARG 42": "NH1" <-> "NH2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "G ARG 71": "NH1" <-> "NH2" Residue "G ARG 77": "NH1" <-> "NH2" Residue "G ARG 81": "NH1" <-> "NH2" Residue "G ARG 88": "NH1" <-> "NH2" Residue "G ARG 99": "NH1" <-> "NH2" Residue "H TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 69": "NH1" <-> "NH2" Residue "H ARG 76": "NH1" <-> "NH2" Residue "H ARG 83": "NH1" <-> "NH2" Residue "H ARG 89": "NH1" <-> "NH2" Residue "H ARG 96": "NH1" <-> "NH2" Residue "H GLU 102": "OE1" <-> "OE2" Residue "H GLU 110": "OE1" <-> "OE2" Residue "K GLU 1150": "OE1" <-> "OE2" Residue "K TYR 1162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 1178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 1194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 1303": "OE1" <-> "OE2" Residue "K ASP 1308": "OD1" <-> "OD2" Residue "K ARG 1342": "NH1" <-> "NH2" Residue "K PHE 1353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 1397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 1430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 1448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 1482": "OD1" <-> "OD2" Residue "K ASP 1493": "OD1" <-> "OD2" Residue "K GLU 1500": "OE1" <-> "OE2" Residue "K GLU 1505": "OE1" <-> "OE2" Residue "K TYR 1585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 1596": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17214 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: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 735 Classifications: {'peptide': 92} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 90} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'ALY:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 673 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "G" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 730 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 3362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 3362 Classifications: {'DNA': 164} Link IDs: {'rna3p': 163} Chain: "J" Number of atoms: 3320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 3320 Classifications: {'DNA': 162} Link IDs: {'rna3p': 161} Chain: "K" Number of atoms: 4403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4403 Classifications: {'peptide': 533} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 499} Chain breaks: 3 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: 9.42, per 1000 atoms: 0.55 Number of scatterers: 17214 At special positions: 0 Unit cell: (107.31, 163.17, 122.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 47 16.00 P 326 15.00 O 3843 8.00 N 3138 7.00 C 9860 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: 8.83 Conformation dependent library (CDL) restraints added in 2.0 seconds 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2456 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 3 sheets defined 53.9% alpha, 5.1% beta 115 base pairs and 245 stacking pairs defined. Time for finding SS restraints: 8.50 Creating SS restraints... Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 64 through 78 removed outlier: 3.669A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) 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 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 31 through 40 Processing helix chain 'B' and resid 50 through 75 removed outlier: 4.423A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 removed outlier: 3.581A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 20 No H-bonds generated for 'chain 'C' and resid 17 through 20' Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.507A 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 35 through 45 Processing helix chain 'D' and resid 53 through 80 Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 102 through 119 Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 64 through 78 Processing helix chain 'E' and resid 86 through 113 Processing helix chain 'E' and resid 122 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 removed outlier: 4.259A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU F 74 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N HIS F 75 " --> pdb=" O THR F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 92 Processing helix chain 'G' and resid 17 through 20 No H-bonds generated for 'chain 'G' and resid 17 through 20' Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.367A 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 35 through 45 removed outlier: 3.552A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 80 Processing helix chain 'H' and resid 88 through 98 Processing helix chain 'H' and resid 101 through 120 Processing helix chain 'K' and resid 1051 through 1067 removed outlier: 4.161A pdb=" N GLN K1056 " --> pdb=" O GLU K1052 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ALA K1057 " --> pdb=" O GLU K1053 " (cutoff:3.500A) Proline residue: K1060 - end of helix Processing helix chain 'K' and resid 1071 through 1076 Proline residue: K1074 - end of helix No H-bonds generated for 'chain 'K' and resid 1071 through 1076' Processing helix chain 'K' and resid 1089 through 1092 No H-bonds generated for 'chain 'K' and resid 1089 through 1092' Processing helix chain 'K' and resid 1099 through 1108 Processing helix chain 'K' and resid 1114 through 1131 Processing helix chain 'K' and resid 1137 through 1158 removed outlier: 3.596A pdb=" N GLU K1152 " --> pdb=" O VAL K1148 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP K1154 " --> pdb=" O GLU K1150 " (cutoff:3.500A) Proline residue: K1155 - end of helix Processing helix chain 'K' and resid 1202 through 1207 removed outlier: 4.364A pdb=" N ASN K1206 " --> pdb=" O GLU K1202 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU K1207 " --> pdb=" O LYS K1203 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 1202 through 1207' Processing helix chain 'K' and resid 1257 through 1259 No H-bonds generated for 'chain 'K' and resid 1257 through 1259' Processing helix chain 'K' and resid 1273 through 1278 Processing helix chain 'K' and resid 1297 through 1313 Processing helix chain 'K' and resid 1337 through 1342 Processing helix chain 'K' and resid 1407 through 1428 removed outlier: 4.100A pdb=" N THR K1411 " --> pdb=" O LYS K1407 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ALA K1412 " --> pdb=" O CYS K1408 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS K1427 " --> pdb=" O GLU K1423 " (cutoff:3.500A) Processing helix chain 'K' and resid 1460 through 1476 Processing helix chain 'K' and resid 1486 through 1492 Processing helix chain 'K' and resid 1498 through 1500 No H-bonds generated for 'chain 'K' and resid 1498 through 1500' Processing helix chain 'K' and resid 1508 through 1518 Processing helix chain 'K' and resid 1579 through 1590 Processing helix chain 'K' and resid 1627 through 1637 Processing helix chain 'K' and resid 1644 through 1663 removed outlier: 4.048A pdb=" N GLN K1663 " --> pdb=" O HIS K1659 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'K' and resid 1192 through 1194 Processing sheet with id= B, first strand: chain 'K' and resid 1244 through 1246 Processing sheet with id= C, first strand: chain 'K' and resid 1482 through 1485 removed outlier: 4.471A pdb=" N TRP K1436 " --> pdb=" O ILE K1395 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N TYR K1397 " --> pdb=" O TRP K1436 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N HIS K1377 " --> pdb=" O SER K1396 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N LEU K1398 " --> pdb=" O GLY K1375 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLY K1375 " --> pdb=" O LEU K1398 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N SER K1400 " --> pdb=" O PHE K1373 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N PHE K1373 " --> pdb=" O SER K1400 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA K1362 " --> pdb=" O PHE K1373 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLY K1375 " --> pdb=" O LEU K1360 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU K1360 " --> pdb=" O GLY K1375 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N HIS K1377 " --> pdb=" O LYS K1358 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LYS K1358 " --> pdb=" O HIS K1377 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLN K1379 " --> pdb=" O ARG K1356 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ARG K1356 " --> pdb=" O GLN K1379 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N TYR K1381 " --> pdb=" O PRO K1354 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N HIS K1327 " --> pdb=" O ALA K1359 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N PHE K1361 " --> pdb=" O VAL K1325 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N VAL K1325 " --> pdb=" O PHE K1361 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N PHE K1363 " --> pdb=" O VAL K1323 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N VAL K1323 " --> pdb=" O PHE K1363 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N GLU K1365 " --> pdb=" O VAL K1321 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N VAL K1321 " --> pdb=" O GLU K1365 " (cutoff:3.500A) 499 hydrogen bonds defined for protein. 1482 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 278 hydrogen bonds 548 hydrogen bond angles 0 basepair planarities 115 basepair parallelities 245 stacking parallelities Total time for adding SS restraints: 7.33 Time building geometry restraints manager: 9.36 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: 3161 1.33 - 1.45: 5678 1.45 - 1.57: 8664 1.57 - 1.69: 650 1.69 - 1.81: 70 Bond restraints: 18223 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 4.31e+00 bond pdb=" NZ ALY B 12 " pdb=" CH ALY B 12 " ideal model delta sigma weight residual 1.343 1.383 -0.040 2.00e-02 2.50e+03 4.09e+00 bond pdb=" C LEU K1073 " pdb=" N PRO K1074 " ideal model delta sigma weight residual 1.335 1.352 -0.017 1.19e-02 7.06e+03 2.15e+00 bond pdb=" C3' DT I 136 " pdb=" O3' DT I 136 " ideal model delta sigma weight residual 1.422 1.466 -0.044 3.00e-02 1.11e+03 2.13e+00 bond pdb=" CG GLU D 68 " pdb=" CD GLU D 68 " ideal model delta sigma weight residual 1.516 1.484 0.032 2.50e-02 1.60e+03 1.69e+00 ... (remaining 18218 not shown) Histogram of bond angle deviations from ideal: 98.05 - 105.24: 1458 105.24 - 112.44: 9933 112.44 - 119.64: 5645 119.64 - 126.83: 7959 126.83 - 134.03: 1010 Bond angle restraints: 26005 Sorted by residual: angle pdb=" N GLU D 68 " pdb=" CA GLU D 68 " pdb=" CB GLU D 68 " ideal model delta sigma weight residual 110.28 116.27 -5.99 1.55e+00 4.16e-01 1.49e+01 angle pdb=" N GLY D 101 " pdb=" CA GLY D 101 " pdb=" C GLY D 101 " ideal model delta sigma weight residual 110.77 118.16 -7.39 1.93e+00 2.68e-01 1.47e+01 angle pdb=" C ASN B 64 " pdb=" N VAL B 65 " pdb=" CA VAL B 65 " ideal model delta sigma weight residual 123.08 119.54 3.54 1.01e+00 9.80e-01 1.23e+01 angle pdb=" CA MET K1254 " pdb=" CB MET K1254 " pdb=" CG MET K1254 " ideal model delta sigma weight residual 114.10 120.70 -6.60 2.00e+00 2.50e-01 1.09e+01 angle pdb=" CA GLU D 68 " pdb=" CB GLU D 68 " pdb=" CG GLU D 68 " ideal model delta sigma weight residual 114.10 120.17 -6.07 2.00e+00 2.50e-01 9.22e+00 ... (remaining 26000 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.76: 8594 32.76 - 65.53: 1586 65.53 - 98.29: 38 98.29 - 131.05: 0 131.05 - 163.82: 2 Dihedral angle restraints: 10220 sinusoidal: 6415 harmonic: 3805 Sorted by residual: dihedral pdb=" CA PRO H 100 " pdb=" C PRO H 100 " pdb=" N GLY H 101 " pdb=" CA GLY H 101 " ideal model delta harmonic sigma weight residual -180.00 -160.22 -19.78 0 5.00e+00 4.00e-02 1.56e+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 220.00 56.18 163.82 1 3.50e+01 8.16e-04 1.54e+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 66.76 153.24 1 3.50e+01 8.16e-04 1.48e+01 ... (remaining 10217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2064 0.030 - 0.060: 608 0.060 - 0.091: 149 0.091 - 0.121: 61 0.121 - 0.151: 11 Chirality restraints: 2893 Sorted by residual: chirality pdb=" CA PRO E 121 " pdb=" N PRO E 121 " pdb=" C PRO E 121 " pdb=" CB PRO E 121 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.71e-01 chirality pdb=" CA ILE B 46 " pdb=" N ILE B 46 " pdb=" C ILE B 46 " pdb=" CB ILE B 46 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" P DA J 60 " pdb=" OP1 DA J 60 " pdb=" OP2 DA J 60 " pdb=" O5' DA J 60 " both_signs ideal model delta sigma weight residual True 2.35 -2.48 -0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 2890 not shown) Planarity restraints: 2182 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS K1336 " -0.040 5.00e-02 4.00e+02 6.12e-02 5.99e+00 pdb=" N PRO K1337 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO K1337 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO K1337 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 99 " 0.030 5.00e-02 4.00e+02 4.61e-02 3.41e+00 pdb=" N PRO H 100 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO H 100 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 100 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET K1059 " 0.030 5.00e-02 4.00e+02 4.58e-02 3.35e+00 pdb=" N PRO K1060 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO K1060 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO K1060 " 0.026 5.00e-02 4.00e+02 ... (remaining 2179 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1776 2.75 - 3.29: 16565 3.29 - 3.83: 33737 3.83 - 4.36: 38254 4.36 - 4.90: 56000 Nonbonded interactions: 146332 Sorted by model distance: nonbonded pdb=" OE1 GLN K1379 " pdb=" OG SER K1396 " model vdw 2.213 2.440 nonbonded pdb=" OH TYR G 50 " pdb=" OE1 GLN H 92 " model vdw 2.230 2.440 nonbonded pdb=" O THR K1496 " pdb=" OG SER K1581 " model vdw 2.231 2.440 nonbonded pdb=" O ALA E 75 " pdb=" N LYS E 79 " model vdw 2.270 2.520 nonbonded pdb=" O GLU F 74 " pdb=" NH2 ARG H 89 " model vdw 2.277 2.520 ... (remaining 146327 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 28 and (name N or name CA or name C or name O or name CB \ )) or resid 29 through 121)) selection = chain 'H' } ncs_group { reference = (chain 'I' and resid 10 through 169) selection = (chain 'J' and resid 10 through 169) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.630 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: 0.250 Set scattering table: 0.160 Process input model: 53.870 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 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 0.044 18223 Z= 0.163 Angle : 0.604 8.661 26005 Z= 0.369 Chirality : 0.034 0.151 2893 Planarity : 0.004 0.061 2182 Dihedral : 24.856 163.816 7764 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 1.21 (0.23), residues: 1276 helix: 1.37 (0.19), residues: 761 sheet: 0.14 (0.61), residues: 65 loop : 0.06 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K1466 HIS 0.004 0.001 HIS E 113 PHE 0.020 0.001 PHE K1508 TYR 0.011 0.001 TYR K1117 ARG 0.012 0.000 ARG D 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9156 (tp30) cc_final: 0.8689 (tt0) REVERT: D 34 TYR cc_start: 0.9157 (m-10) cc_final: 0.8885 (m-80) REVERT: G 78 ILE cc_start: 0.9124 (mt) cc_final: 0.8806 (mm) REVERT: K 1129 TRP cc_start: 0.7371 (m-10) cc_final: 0.7169 (m-10) REVERT: K 1478 ARG cc_start: 0.4409 (mmp-170) cc_final: 0.3607 (tpm170) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.2443 time to fit residues: 36.9255 Evaluate side-chains 63 residues out of total 1129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 9.9990 chunk 119 optimal weight: 5.9990 chunk 66 optimal weight: 20.0000 chunk 40 optimal weight: 8.9990 chunk 80 optimal weight: 8.9990 chunk 63 optimal weight: 20.0000 chunk 123 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 92 optimal weight: 7.9990 chunk 143 optimal weight: 6.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1132 ASN K1227 ASN K1236 ASN ** K1415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1659 HIS K1661 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.091 18223 Z= 0.429 Angle : 0.803 12.972 26005 Z= 0.453 Chirality : 0.044 0.226 2893 Planarity : 0.007 0.071 2182 Dihedral : 29.094 168.964 5103 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 23.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.27 % Allowed : 4.43 % Favored : 95.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 1.07 (0.22), residues: 1276 helix: 1.21 (0.18), residues: 747 sheet: 1.35 (0.73), residues: 45 loop : -0.00 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP K1122 HIS 0.014 0.003 HIS A 113 PHE 0.021 0.003 PHE H 67 TYR 0.027 0.003 TYR B 51 ARG 0.042 0.001 ARG K1055 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 69 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9638 (tt) cc_final: 0.9349 (tt) REVERT: A 96 CYS cc_start: 0.9508 (m) cc_final: 0.9294 (m) REVERT: A 106 ASP cc_start: 0.9102 (t0) cc_final: 0.8707 (m-30) REVERT: E 41 TYR cc_start: 0.8196 (m-80) cc_final: 0.7757 (m-80) REVERT: K 1254 MET cc_start: -0.1075 (tpt) cc_final: -0.3600 (ptp) REVERT: K 1478 ARG cc_start: 0.4817 (mmp-170) cc_final: 0.4242 (tpm170) REVERT: K 1654 MET cc_start: 0.7000 (mtm) cc_final: 0.6685 (mtt) outliers start: 3 outliers final: 1 residues processed: 72 average time/residue: 0.2648 time to fit residues: 31.1680 Evaluate side-chains 52 residues out of total 1129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 51 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 chunk 119 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 143 optimal weight: 40.0000 chunk 155 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 142 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1230 GLN K1261 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18223 Z= 0.209 Angle : 0.586 9.164 26005 Z= 0.341 Chirality : 0.035 0.190 2893 Planarity : 0.004 0.060 2182 Dihedral : 29.212 170.092 5103 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.18 % Allowed : 2.22 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 1.63 (0.23), residues: 1276 helix: 1.82 (0.18), residues: 747 sheet: 0.43 (0.69), residues: 54 loop : 0.06 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K1122 HIS 0.005 0.001 HIS E 113 PHE 0.034 0.002 PHE E 104 TYR 0.013 0.001 TYR K1117 ARG 0.004 0.000 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 74 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9292 (tp30) cc_final: 0.8697 (tt0) REVERT: A 106 ASP cc_start: 0.9090 (t0) cc_final: 0.8863 (m-30) REVERT: B 63 GLU cc_start: 0.9012 (pm20) cc_final: 0.8410 (pm20) REVERT: B 97 LEU cc_start: 0.8940 (tp) cc_final: 0.8724 (tp) REVERT: D 56 MET cc_start: 0.9682 (tmm) cc_final: 0.9378 (tpp) REVERT: H 99 LEU cc_start: 0.8908 (tp) cc_final: 0.8569 (tp) REVERT: K 1157 MET cc_start: -0.0096 (ttt) cc_final: -0.0473 (ttt) REVERT: K 1254 MET cc_start: -0.0880 (tpt) cc_final: -0.2286 (ptp) REVERT: K 1478 ARG cc_start: 0.4942 (mmp-170) cc_final: 0.4351 (tpm170) outliers start: 2 outliers final: 1 residues processed: 76 average time/residue: 0.2735 time to fit residues: 33.4226 Evaluate side-chains 54 residues out of total 1129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 10.0000 chunk 108 optimal weight: 0.2980 chunk 74 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 152 optimal weight: 0.8980 chunk 75 optimal weight: 7.9990 chunk 136 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 overall best weight: 4.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN K1307 ASN K1591 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 18223 Z= 0.298 Angle : 0.634 8.791 26005 Z= 0.367 Chirality : 0.037 0.170 2893 Planarity : 0.005 0.057 2182 Dihedral : 29.355 169.893 5103 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 20.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.23), residues: 1276 helix: 1.78 (0.18), residues: 743 sheet: 0.15 (0.68), residues: 59 loop : -0.04 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K1122 HIS 0.009 0.002 HIS A 113 PHE 0.023 0.002 PHE E 104 TYR 0.018 0.002 TYR A 99 ARG 0.010 0.001 ARG E 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.439 Fit side-chains revert: symmetry clash REVERT: A 106 ASP cc_start: 0.9189 (t0) cc_final: 0.8860 (m-30) REVERT: B 63 GLU cc_start: 0.8996 (pm20) cc_final: 0.8434 (pm20) REVERT: K 1097 MET cc_start: 0.5960 (tpp) cc_final: 0.5429 (ppp) REVERT: K 1157 MET cc_start: -0.0016 (ttt) cc_final: -0.0398 (ttt) REVERT: K 1254 MET cc_start: -0.0418 (tpt) cc_final: -0.1914 (ptp) REVERT: K 1478 ARG cc_start: 0.5023 (mmp-170) cc_final: 0.4391 (tpm170) REVERT: K 1652 MET cc_start: 0.7491 (ppp) cc_final: 0.7282 (ppp) REVERT: K 1654 MET cc_start: 0.5615 (tpt) cc_final: 0.4977 (mtt) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.2744 time to fit residues: 29.4620 Evaluate side-chains 48 residues out of total 1129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 8.9990 chunk 86 optimal weight: 7.9990 chunk 2 optimal weight: 20.0000 chunk 113 optimal weight: 9.9990 chunk 63 optimal weight: 0.0980 chunk 130 optimal weight: 0.4980 chunk 105 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 77 optimal weight: 6.9990 chunk 137 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 overall best weight: 1.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1261 HIS K1307 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18223 Z= 0.188 Angle : 0.581 7.020 26005 Z= 0.337 Chirality : 0.036 0.202 2893 Planarity : 0.004 0.057 2182 Dihedral : 29.384 171.071 5103 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 1.69 (0.23), residues: 1276 helix: 1.96 (0.19), residues: 744 sheet: 0.60 (0.71), residues: 54 loop : -0.10 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K1122 HIS 0.006 0.001 HIS F 75 PHE 0.018 0.001 PHE K1508 TYR 0.019 0.001 TYR A 99 ARG 0.005 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 1.527 Fit side-chains revert: symmetry clash REVERT: A 106 ASP cc_start: 0.9138 (t0) cc_final: 0.8870 (m-30) REVERT: B 63 GLU cc_start: 0.8936 (pm20) cc_final: 0.8300 (pm20) REVERT: D 56 MET cc_start: 0.9628 (tmm) cc_final: 0.9265 (tpp) REVERT: H 99 LEU cc_start: 0.8877 (tp) cc_final: 0.8549 (tp) REVERT: K 1157 MET cc_start: 0.0191 (ttt) cc_final: -0.0279 (ttt) REVERT: K 1254 MET cc_start: -0.0446 (tpt) cc_final: -0.1862 (ptp) REVERT: K 1288 PHE cc_start: 0.6744 (m-80) cc_final: 0.6428 (m-80) REVERT: K 1478 ARG cc_start: 0.4978 (mmp-170) cc_final: 0.4400 (tpm170) REVERT: K 1654 MET cc_start: 0.5562 (tpt) cc_final: 0.4843 (mtt) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.2739 time to fit residues: 28.1712 Evaluate side-chains 50 residues out of total 1129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 9.9990 chunk 137 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 89 optimal weight: 20.0000 chunk 37 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN D 81 ASN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1261 HIS K1307 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18223 Z= 0.230 Angle : 0.586 6.668 26005 Z= 0.339 Chirality : 0.035 0.183 2893 Planarity : 0.004 0.057 2182 Dihedral : 29.389 170.397 5103 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.09 % Allowed : 1.77 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.23), residues: 1276 helix: 2.00 (0.19), residues: 745 sheet: 0.74 (0.72), residues: 54 loop : -0.06 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K1122 HIS 0.007 0.001 HIS F 75 PHE 0.018 0.001 PHE K1508 TYR 0.011 0.001 TYR E 41 ARG 0.004 0.000 ARG E 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 1.180 Fit side-chains REVERT: A 106 ASP cc_start: 0.9151 (t0) cc_final: 0.8850 (m-30) REVERT: K 1157 MET cc_start: 0.0604 (ttt) cc_final: 0.0007 (ttt) REVERT: K 1254 MET cc_start: -0.0125 (tpt) cc_final: -0.1619 (ptp) REVERT: K 1288 PHE cc_start: 0.6173 (m-80) cc_final: 0.5947 (m-80) REVERT: K 1478 ARG cc_start: 0.5107 (mmp-170) cc_final: 0.4551 (tpm170) outliers start: 1 outliers final: 0 residues processed: 60 average time/residue: 0.3096 time to fit residues: 30.6189 Evaluate side-chains 50 residues out of total 1129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 87 optimal weight: 8.9990 chunk 111 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 128 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 152 optimal weight: 7.9990 chunk 95 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN K1261 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.5201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18223 Z= 0.236 Angle : 0.600 8.035 26005 Z= 0.345 Chirality : 0.036 0.188 2893 Planarity : 0.004 0.055 2182 Dihedral : 29.529 171.135 5103 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 1.55 (0.23), residues: 1276 helix: 1.85 (0.19), residues: 746 sheet: 0.32 (0.69), residues: 59 loop : -0.16 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K1122 HIS 0.007 0.001 HIS F 75 PHE 0.022 0.002 PHE K1641 TYR 0.010 0.001 TYR K1117 ARG 0.004 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 1.538 Fit side-chains revert: symmetry clash REVERT: A 106 ASP cc_start: 0.9138 (t0) cc_final: 0.8841 (m-30) REVERT: H 99 LEU cc_start: 0.8960 (tp) cc_final: 0.8583 (tp) REVERT: K 1157 MET cc_start: 0.1086 (ttt) cc_final: 0.0352 (ttt) REVERT: K 1254 MET cc_start: 0.0420 (tpt) cc_final: -0.1071 (ptp) REVERT: K 1288 PHE cc_start: 0.6163 (m-80) cc_final: 0.5919 (m-10) REVERT: K 1478 ARG cc_start: 0.4936 (mmp-170) cc_final: 0.4444 (tpm170) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.2644 time to fit residues: 27.2839 Evaluate side-chains 51 residues out of total 1129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.6342 > 50: distance: 43 - 60: 4.009 distance: 47 - 67: 10.422 distance: 51 - 78: 12.093 distance: 56 - 60: 6.399 distance: 57 - 86: 17.117 distance: 60 - 61: 6.517 distance: 61 - 62: 4.517 distance: 61 - 64: 7.851 distance: 62 - 63: 4.538 distance: 62 - 67: 5.343 distance: 63 - 95: 21.369 distance: 64 - 65: 10.154 distance: 64 - 66: 3.811 distance: 67 - 68: 3.500 distance: 68 - 69: 5.199 distance: 68 - 71: 5.514 distance: 69 - 70: 5.514 distance: 69 - 78: 4.115 distance: 70 - 103: 14.043 distance: 71 - 72: 3.532 distance: 72 - 73: 3.769 distance: 72 - 74: 5.711 distance: 73 - 75: 3.205 distance: 74 - 76: 4.834 distance: 75 - 77: 4.346 distance: 76 - 77: 4.923 distance: 78 - 79: 3.184 distance: 79 - 80: 8.923 distance: 79 - 82: 5.400 distance: 80 - 81: 4.450 distance: 80 - 86: 10.570 distance: 81 - 110: 8.583 distance: 82 - 83: 3.932 distance: 83 - 84: 8.108 distance: 83 - 85: 8.920 distance: 86 - 87: 7.837 distance: 87 - 88: 4.051 distance: 87 - 90: 6.966 distance: 88 - 89: 14.206 distance: 88 - 95: 11.831 distance: 90 - 91: 16.580 distance: 91 - 92: 12.208 distance: 92 - 93: 12.719 distance: 92 - 94: 3.595 distance: 95 - 96: 24.726 distance: 96 - 97: 13.217 distance: 96 - 99: 27.261 distance: 97 - 98: 14.181 distance: 97 - 103: 10.887 distance: 99 - 100: 32.369 distance: 100 - 102: 7.517 distance: 103 - 104: 12.036 distance: 104 - 105: 7.877 distance: 104 - 107: 7.211 distance: 105 - 106: 10.465 distance: 105 - 110: 8.067 distance: 106 - 137: 21.672 distance: 107 - 108: 7.560 distance: 107 - 109: 9.116 distance: 110 - 111: 3.633 distance: 111 - 112: 9.335 distance: 111 - 114: 6.055 distance: 112 - 113: 4.971 distance: 112 - 118: 4.437 distance: 113 - 142: 6.784 distance: 114 - 115: 3.897 distance: 114 - 116: 18.373 distance: 115 - 117: 14.031 distance: 118 - 119: 7.621 distance: 119 - 120: 9.381 distance: 119 - 122: 7.477 distance: 120 - 121: 5.166 distance: 120 - 129: 4.656 distance: 121 - 149: 5.696 distance: 122 - 123: 5.831 distance: 123 - 124: 5.626 distance: 126 - 127: 6.287 distance: 126 - 128: 6.344 distance: 130 - 131: 7.303 distance: 130 - 133: 10.536 distance: 131 - 132: 4.211 distance: 131 - 137: 3.909 distance: 132 - 156: 3.955 distance: 133 - 134: 8.755 distance: 134 - 135: 10.570 distance: 134 - 136: 11.117 distance: 137 - 138: 5.262 distance: 138 - 139: 3.506 distance: 138 - 141: 8.993 distance: 139 - 140: 3.045 distance: 139 - 142: 3.021 distance: 140 - 165: 6.260