Starting phenix.real_space_refine on Thu Aug 6 17:20:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hai_34591/08_2026/8hai_34591.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hai_34591/08_2026/8hai_34591.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hai_34591/08_2026/8hai_34591.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hai_34591/08_2026/8hai_34591.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8hai_34591/08_2026/8hai_34591.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hai_34591/08_2026/8hai_34591.cif" model { file = "/net/cci-nas-00/data/ceres_data/8hai_34591/08_2026/8hai_34591.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hai_34591/08_2026/8hai_34591.cif" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 294 5.49 5 S 47 5.16 5 C 9542 2.51 5 N 3017 2.21 5 O 3647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 115 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16547 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: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 714 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 89} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ALY:plan-1': 1, 'ALY:plan-2': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 801 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 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: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 668 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} 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: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 784 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 100} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "K" Number of atoms: 4381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4381 Classifications: {'peptide': 533} Link IDs: {'PCIS': 3, 'PTRANS': 32, 'TRANS': 497} Chain breaks: 2 Chain: "J" Number of atoms: 3012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3012 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "I" Number of atoms: 3015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3015 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ALA C 14 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA C 14 " occ=0.00 Time building chain proxies: 3.12, per 1000 atoms: 0.19 Number of scatterers: 16547 At special positions: 0 Unit cell: (107.31, 167.58, 138.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 47 16.00 P 294 15.00 O 3647 8.00 N 3017 7.00 C 9542 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 - 3.00 Amino acid : True - 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: 0.78 Conformation dependent library (CDL) restraints added in 332.0 milliseconds 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2468 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 14 sheets defined 61.3% alpha, 7.2% beta 112 base pairs and 219 stacking pairs defined. Time for finding SS restraints: 2.02 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.540A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.594A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.766A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.637A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.394A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.582A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.560A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.587A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.677A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.407A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 26 through 30 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.658A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 124 Processing helix chain 'K' and resid 1052 through 1067 Proline residue: K1060 - end of helix Processing helix chain 'K' and resid 1072 through 1076 Processing helix chain 'K' and resid 1080 through 1085 Processing helix chain 'K' and resid 1088 through 1093 Processing helix chain 'K' and resid 1098 through 1108 Processing helix chain 'K' and resid 1113 through 1132 removed outlier: 4.212A pdb=" N TYR K1117 " --> pdb=" O GLU K1113 " (cutoff:3.500A) Processing helix chain 'K' and resid 1136 through 1160 removed outlier: 3.543A pdb=" N LYS K1140 " --> pdb=" O SER K1136 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASP K1154 " --> pdb=" O GLU K1150 " (cutoff:3.500A) Proline residue: K1155 - end of helix Processing helix chain 'K' and resid 1256 through 1260 Processing helix chain 'K' and resid 1272 through 1279 Processing helix chain 'K' and resid 1296 through 1314 Processing helix chain 'K' and resid 1336 through 1343 Processing helix chain 'K' and resid 1406 through 1429 removed outlier: 4.225A pdb=" N THR K1411 " --> pdb=" O LYS K1407 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ALA K1412 " --> pdb=" O CYS K1408 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY K1420 " --> pdb=" O GLU K1416 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS K1426 " --> pdb=" O LEU K1422 " (cutoff:3.500A) Processing helix chain 'K' and resid 1459 through 1477 Processing helix chain 'K' and resid 1486 through 1493 Processing helix chain 'K' and resid 1497 through 1501 removed outlier: 3.582A pdb=" N LEU K1501 " --> pdb=" O ALA K1498 " (cutoff:3.500A) Processing helix chain 'K' and resid 1507 through 1523 removed outlier: 3.963A pdb=" N ASN K1511 " --> pdb=" O ASP K1507 " (cutoff:3.500A) Processing helix chain 'K' and resid 1579 through 1591 Processing helix chain 'K' and resid 1602 through 1607 removed outlier: 4.200A pdb=" N ALA K1605 " --> pdb=" O ALA K1602 " (cutoff:3.500A) Processing helix chain 'K' and resid 1621 through 1625 Processing helix chain 'K' and resid 1627 through 1638 Processing helix chain 'K' and resid 1643 through 1663 removed outlier: 3.588A pdb=" N GLN K1663 " --> pdb=" O HIS K1659 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.644A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.588A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.510A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.188A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.849A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.194A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 1169 through 1170 removed outlier: 3.736A pdb=" N ASP K1240 " --> pdb=" O PHE K1170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 1198 through 1200 Processing sheet with id=AB4, first strand: chain 'K' and resid 1244 through 1246 Processing sheet with id=AB5, first strand: chain 'K' and resid 1321 through 1334 removed outlier: 6.465A pdb=" N ALA K1359 " --> pdb=" O VAL K1326 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA K1328 " --> pdb=" O THR K1357 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR K1357 " --> pdb=" O ALA K1328 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASP K1330 " --> pdb=" O TYR K1355 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TYR K1355 " --> pdb=" O ASP K1330 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N THR K1332 " --> pdb=" O PHE K1353 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE K1353 " --> pdb=" O THR K1332 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU K1360 " --> pdb=" O MET K1376 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE K1374 " --> pdb=" O ALA K1362 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLU K1364 " --> pdb=" O CYS K1372 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N CYS K1372 " --> pdb=" O GLU K1364 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ILE K1366 " --> pdb=" O ASP K1370 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ASP K1370 " --> pdb=" O ILE K1366 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLN K1379 " --> pdb=" O ILE K1395 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ILE K1395 " --> pdb=" O GLN K1379 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N TYR K1381 " --> pdb=" O VAL K1393 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N VAL K1393 " --> pdb=" O TYR K1381 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TRP K1436 " --> pdb=" O ILE K1395 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N TYR K1397 " --> pdb=" O TRP K1436 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP K1482 " --> pdb=" O ARG K1599 " (cutoff:3.500A) 594 hydrogen bonds defined for protein. 1746 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 266 hydrogen bonds 532 hydrogen bond angles 0 basepair planarities 112 basepair parallelities 219 stacking parallelities Total time for adding SS restraints: 4.43 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3938 1.34 - 1.46: 4891 1.46 - 1.58: 7993 1.58 - 1.70: 586 1.70 - 1.82: 70 Bond restraints: 17478 Sorted by residual: bond pdb=" C3' DT I 136 " pdb=" C2' DT I 136 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 bond pdb=" C3' DT J 145 " pdb=" C2' DT J 145 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.84e+00 bond pdb=" C3' DT I 53 " pdb=" C2' DT I 53 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.79e+00 bond pdb=" C3' DT I 157 " pdb=" C2' DT I 157 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.02e+00 bond pdb=" C3' DA J 90 " pdb=" C2' DA J 90 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.01e+00 ... (remaining 17473 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 23620 1.64 - 3.28: 1195 3.28 - 4.92: 40 4.92 - 6.56: 11 6.56 - 8.20: 3 Bond angle restraints: 24869 Sorted by residual: angle pdb=" O4' DC I 66 " pdb=" C1' DC I 66 " pdb=" N1 DC I 66 " ideal model delta sigma weight residual 108.00 111.30 -3.30 7.00e-01 2.04e+00 2.22e+01 angle pdb=" N3 DT I 65 " pdb=" C4 DT I 65 " pdb=" O4 DT I 65 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 angle pdb=" N3 DT J 82 " pdb=" C4 DT J 82 " pdb=" O4 DT J 82 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.96e+01 angle pdb=" N3 DT J 134 " pdb=" C4 DT J 134 " pdb=" O4 DT J 134 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" N3 DT J 135 " pdb=" C4 DT J 135 " pdb=" O4 DT J 135 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 ... (remaining 24864 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.34: 8559 35.34 - 70.67: 1299 70.67 - 106.01: 22 106.01 - 141.34: 0 141.34 - 176.68: 2 Dihedral angle restraints: 9882 sinusoidal: 6059 harmonic: 3823 Sorted by residual: dihedral pdb=" C4' DT I 136 " pdb=" C3' DT I 136 " pdb=" O3' DT I 136 " pdb=" P DT I 137 " ideal model delta sinusoidal sigma weight residual -140.00 36.68 -176.68 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 53.71 166.29 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" CA ILE B 50 " pdb=" C ILE B 50 " pdb=" N TYR B 51 " pdb=" CA TYR B 51 " ideal model delta harmonic sigma weight residual 180.00 -163.72 -16.28 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 9879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1647 0.033 - 0.066: 772 0.066 - 0.099: 265 0.099 - 0.131: 83 0.131 - 0.164: 5 Chirality restraints: 2772 Sorted by residual: chirality pdb=" C3' DA J 59 " pdb=" C4' DA J 59 " pdb=" O3' DA J 59 " pdb=" C2' DA J 59 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.74e-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 2.34 -2.47 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA TYR B 88 " pdb=" N TYR B 88 " pdb=" C TYR B 88 " pdb=" CB TYR B 88 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.73e-01 ... (remaining 2769 not shown) Planarity restraints: 2150 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 88 " 0.020 2.00e-02 2.50e+03 1.63e-02 5.31e+00 pdb=" CG TYR B 88 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR B 88 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR B 88 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 88 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 88 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 88 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 88 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 59 " 0.009 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" C LYS B 59 " -0.030 2.00e-02 2.50e+03 pdb=" O LYS B 59 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL B 60 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 102 " 0.026 5.00e-02 4.00e+02 3.95e-02 2.49e+00 pdb=" N PRO D 103 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.022 5.00e-02 4.00e+02 ... (remaining 2147 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2774 2.78 - 3.31: 16057 3.31 - 3.84: 32438 3.84 - 4.37: 36547 4.37 - 4.90: 53996 Nonbonded interactions: 141812 Sorted by model distance: nonbonded pdb=" NH1 ARG C 29 " pdb=" O SER D 36 " model vdw 2.249 3.120 nonbonded pdb=" N GLN G 24 " pdb=" OE2 GLU G 56 " model vdw 2.264 3.120 nonbonded pdb=" N THR H 90 " pdb=" OE2 GLU H 93 " model vdw 2.277 3.120 nonbonded pdb=" NE2 HIS A 113 " pdb=" OD1 ASP E 123 " model vdw 2.286 3.120 nonbonded pdb=" O TYR B 51 " pdb=" OG1 THR B 54 " model vdw 2.309 3.040 ... (remaining 141807 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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 101) selection = (chain 'F' and (resid 19 or (resid 20 and (name N or name CA or name C or name O \ or name CB )) or resid 21 through 101)) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 14 through 117) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 31 through 124) } ncs_group { reference = (chain 'I' and resid 18 through 163) selection = (chain 'J' and resid 18 through 163) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.390 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: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.290 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 20.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 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 : 0.005 0.042 17478 Z= 0.444 Angle : 0.718 8.197 24869 Z= 0.619 Chirality : 0.043 0.164 2772 Planarity : 0.004 0.039 2150 Dihedral : 24.523 176.680 7414 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.24), residues: 1283 helix: 1.61 (0.19), residues: 777 sheet: 0.55 (0.65), residues: 68 loop : 0.60 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 53 TYR 0.039 0.001 TYR B 88 PHE 0.011 0.001 PHE G 25 TRP 0.009 0.001 TRP K1509 HIS 0.004 0.000 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.44 (17478) covalent geometry : angle 0.71796 / 0.62 (24869) hydrogen bonds : bond 0.12563 / 8.79 ( 860) hydrogen bonds : angle 5.03596 / 3.75 ( 2278) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 ASP cc_start: 0.9049 (m-30) cc_final: 0.8814 (m-30) REVERT: D 100 LEU cc_start: 0.9459 (mt) cc_final: 0.9232 (mt) REVERT: G 73 ASN cc_start: 0.8705 (t0) cc_final: 0.8365 (t0) REVERT: K 1094 LYS cc_start: 0.7492 (mtpt) cc_final: 0.6648 (mmmt) REVERT: K 1097 MET cc_start: 0.3273 (ppp) cc_final: 0.2525 (tmm) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.1064 time to fit residues: 17.3583 Evaluate side-chains 67 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 20.0000 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN C 38 ASN C 104 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 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** K1379 GLN K1451 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.058296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.042460 restraints weight = 184356.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.043553 restraints weight = 104882.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.044235 restraints weight = 72483.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.044658 restraints weight = 57735.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.044826 restraints weight = 50412.500| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 17478 Z= 0.254 Angle : 0.752 7.860 24869 Z= 0.421 Chirality : 0.044 0.344 2772 Planarity : 0.006 0.043 2150 Dihedral : 28.841 178.209 4768 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.18 % Allowed : 3.38 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.23), residues: 1283 helix: 1.64 (0.18), residues: 788 sheet: 0.51 (0.69), residues: 59 loop : 0.47 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 67 TYR 0.032 0.002 TYR B 88 PHE 0.015 0.002 PHE F 61 TRP 0.010 0.002 TRP K1509 HIS 0.009 0.002 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.25 (17478) covalent geometry : angle 0.75196 / 0.42 (24869) hydrogen bonds : bond 0.08453 / 5.77 ( 860) hydrogen bonds : angle 3.89200 / 2.83 ( 2278) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8121 (mpp) cc_final: 0.7812 (mpp) REVERT: B 68 ASP cc_start: 0.9327 (m-30) cc_final: 0.8904 (m-30) REVERT: D 100 LEU cc_start: 0.9284 (mt) cc_final: 0.9007 (mt) REVERT: E 73 GLU cc_start: 0.8683 (tt0) cc_final: 0.8303 (mt-10) REVERT: E 120 MET cc_start: 0.8512 (mtm) cc_final: 0.7977 (ptp) REVERT: G 73 ASN cc_start: 0.8928 (t0) cc_final: 0.8578 (t0) REVERT: H 46 LYS cc_start: 0.9114 (mmpt) cc_final: 0.8549 (pttm) REVERT: H 69 ILE cc_start: 0.9104 (mm) cc_final: 0.8887 (mm) REVERT: K 1090 PHE cc_start: 0.8331 (m-10) cc_final: 0.7738 (m-80) REVERT: K 1094 LYS cc_start: 0.7879 (mtpt) cc_final: 0.7175 (mmmt) REVERT: K 1097 MET cc_start: 0.3086 (ppp) cc_final: 0.2636 (ppp) outliers start: 2 outliers final: 0 residues processed: 88 average time/residue: 0.1214 time to fit residues: 17.2929 Evaluate side-chains 60 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 60 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 154 optimal weight: 30.0000 chunk 49 optimal weight: 5.9990 chunk 140 optimal weight: 40.0000 chunk 117 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS A 108 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN K1112 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.056925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.040470 restraints weight = 175198.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.041474 restraints weight = 104084.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.042099 restraints weight = 74648.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.042482 restraints weight = 60843.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.042568 restraints weight = 54150.133| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17478 Z= 0.150 Angle : 0.583 6.259 24869 Z= 0.342 Chirality : 0.039 0.331 2772 Planarity : 0.004 0.037 2150 Dihedral : 28.977 179.860 4768 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.23), residues: 1283 helix: 2.01 (0.18), residues: 784 sheet: 0.42 (0.68), residues: 64 loop : 0.54 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 52 TYR 0.018 0.001 TYR F 88 PHE 0.008 0.001 PHE D 65 TRP 0.008 0.001 TRP K1509 HIS 0.003 0.001 HIS K1199 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.15 (17478) covalent geometry : angle 0.58332 / 0.34 (24869) hydrogen bonds : bond 0.05055 / 3.54 ( 860) hydrogen bonds : angle 3.41094 / 2.47 ( 2278) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.485 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.8211 (mpp) cc_final: 0.7830 (mpp) REVERT: B 68 ASP cc_start: 0.9241 (m-30) cc_final: 0.8839 (m-30) REVERT: B 88 TYR cc_start: 0.8541 (m-10) cc_final: 0.8297 (m-80) REVERT: D 100 LEU cc_start: 0.9219 (mt) cc_final: 0.8997 (mt) REVERT: E 73 GLU cc_start: 0.8700 (tt0) cc_final: 0.8365 (mt-10) REVERT: E 120 MET cc_start: 0.8552 (mtm) cc_final: 0.8028 (ptp) REVERT: G 73 ASN cc_start: 0.8922 (t0) cc_final: 0.8579 (t0) REVERT: H 69 ILE cc_start: 0.9101 (mm) cc_final: 0.8885 (mm) REVERT: H 80 LEU cc_start: 0.8789 (tp) cc_final: 0.8589 (tp) REVERT: K 1090 PHE cc_start: 0.8433 (m-10) cc_final: 0.7722 (m-80) REVERT: K 1094 LYS cc_start: 0.7831 (mtpt) cc_final: 0.7175 (mmmt) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1200 time to fit residues: 17.6194 Evaluate side-chains 61 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 84 optimal weight: 6.9990 chunk 94 optimal weight: 8.9990 chunk 143 optimal weight: 30.0000 chunk 80 optimal weight: 4.9990 chunk 128 optimal weight: 40.0000 chunk 17 optimal weight: 9.9990 chunk 149 optimal weight: 20.0000 chunk 127 optimal weight: 50.0000 chunk 137 optimal weight: 30.0000 chunk 93 optimal weight: 3.9990 chunk 132 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 ASN C 73 ASN D 109 HIS E 39 HIS ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1481 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.052306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.036965 restraints weight = 197520.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.037928 restraints weight = 114914.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.038515 restraints weight = 80700.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.038782 restraints weight = 65065.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.039051 restraints weight = 58002.700| |-----------------------------------------------------------------------------| r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.163 17478 Z= 0.378 Angle : 0.996 13.243 24869 Z= 0.531 Chirality : 0.051 0.370 2772 Planarity : 0.009 0.098 2150 Dihedral : 30.099 178.806 4768 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 26.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.22), residues: 1283 helix: 0.68 (0.17), residues: 774 sheet: 0.79 (0.76), residues: 57 loop : 0.15 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.002 ARG E 52 TYR 0.035 0.004 TYR K1089 PHE 0.023 0.003 PHE A 104 TRP 0.014 0.003 TRP K1509 HIS 0.015 0.003 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00731 / 0.38 (17478) covalent geometry : angle 0.99563 / 0.53 (24869) hydrogen bonds : bond 0.13536 / 9.17 ( 860) hydrogen bonds : angle 4.74587 / 3.45 ( 2278) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.500 Fit side-chains REVERT: A 120 MET cc_start: 0.8440 (mpp) cc_final: 0.8064 (mpp) REVERT: B 63 GLU cc_start: 0.8815 (pm20) cc_final: 0.8391 (pm20) REVERT: E 120 MET cc_start: 0.9093 (mtm) cc_final: 0.8249 (mtm) REVERT: H 69 ILE cc_start: 0.9183 (mm) cc_final: 0.8961 (mm) REVERT: K 1090 PHE cc_start: 0.8431 (m-10) cc_final: 0.7885 (m-80) REVERT: K 1094 LYS cc_start: 0.8212 (mtpt) cc_final: 0.7776 (mmmt) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1152 time to fit residues: 12.4342 Evaluate side-chains 49 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 15 optimal weight: 0.8980 chunk 142 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 112 optimal weight: 9.9990 chunk 64 optimal weight: 0.0570 chunk 117 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 150 optimal weight: 20.0000 chunk 72 optimal weight: 0.9980 overall best weight: 1.1900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS A 108 ASN B 64 ASN E 39 HIS E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 ASN K1262 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.054510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.038742 restraints weight = 188029.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.039811 restraints weight = 104692.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.040468 restraints weight = 71556.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.040779 restraints weight = 56537.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.041068 restraints weight = 49956.411| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17478 Z= 0.147 Angle : 0.648 8.557 24869 Z= 0.368 Chirality : 0.042 0.386 2772 Planarity : 0.005 0.055 2150 Dihedral : 30.055 178.697 4768 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.23), residues: 1283 helix: 1.63 (0.18), residues: 783 sheet: 0.78 (0.75), residues: 58 loop : 0.25 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 72 TYR 0.044 0.002 TYR F 88 PHE 0.009 0.001 PHE E 67 TRP 0.007 0.001 TRP K1122 HIS 0.004 0.001 HIS K1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.15 (17478) covalent geometry : angle 0.64799 / 0.37 (24869) hydrogen bonds : bond 0.05279 / 3.70 ( 860) hydrogen bonds : angle 3.65274 / 2.64 ( 2278) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.493 Fit side-chains REVERT: A 94 GLU cc_start: 0.8559 (tp30) cc_final: 0.8334 (tp30) REVERT: A 105 GLU cc_start: 0.9010 (tp30) cc_final: 0.8652 (tp30) REVERT: A 120 MET cc_start: 0.8397 (mpp) cc_final: 0.8008 (mpp) REVERT: B 68 ASP cc_start: 0.9371 (m-30) cc_final: 0.9038 (m-30) REVERT: B 88 TYR cc_start: 0.8465 (m-10) cc_final: 0.8220 (m-80) REVERT: C 62 ILE cc_start: 0.9586 (mp) cc_final: 0.9364 (tt) REVERT: D 100 LEU cc_start: 0.8782 (mt) cc_final: 0.8526 (mt) REVERT: E 81 ASP cc_start: 0.8505 (t70) cc_final: 0.8251 (t0) REVERT: E 120 MET cc_start: 0.8757 (mtm) cc_final: 0.8469 (mtm) REVERT: F 84 MET cc_start: 0.9224 (tpp) cc_final: 0.8896 (tpp) REVERT: F 88 TYR cc_start: 0.8200 (m-80) cc_final: 0.7929 (m-80) REVERT: G 73 ASN cc_start: 0.9060 (t0) cc_final: 0.8816 (t0) REVERT: H 69 ILE cc_start: 0.9256 (mm) cc_final: 0.8977 (mm) REVERT: K 1090 PHE cc_start: 0.8604 (m-10) cc_final: 0.8003 (m-80) REVERT: K 1094 LYS cc_start: 0.7988 (mtpt) cc_final: 0.7518 (mmmt) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.0978 time to fit residues: 13.7978 Evaluate side-chains 56 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 83 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 120 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 chunk 130 optimal weight: 30.0000 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS A 108 ASN B 64 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** K1415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.050027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.034068 restraints weight = 184095.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.034931 restraints weight = 110668.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.035465 restraints weight = 79717.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.035805 restraints weight = 65491.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.035986 restraints weight = 58454.300| |-----------------------------------------------------------------------------| r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 17478 Z= 0.292 Angle : 0.814 9.566 24869 Z= 0.442 Chirality : 0.045 0.381 2772 Planarity : 0.006 0.060 2150 Dihedral : 30.236 177.495 4768 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 19.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.23), residues: 1283 helix: 1.24 (0.18), residues: 770 sheet: 0.48 (0.70), residues: 67 loop : 0.08 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 20 TYR 0.024 0.002 TYR K1089 PHE 0.022 0.002 PHE E 78 TRP 0.009 0.002 TRP K1509 HIS 0.011 0.002 HIS K1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.29 (17478) covalent geometry : angle 0.81393 / 0.44 (24869) hydrogen bonds : bond 0.09930 / 6.79 ( 860) hydrogen bonds : angle 4.25612 / 3.08 ( 2278) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.486 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.8502 (mpp) cc_final: 0.8088 (mpp) REVERT: B 68 ASP cc_start: 0.9532 (m-30) cc_final: 0.9205 (m-30) REVERT: D 100 LEU cc_start: 0.8913 (mt) cc_final: 0.8599 (mt) REVERT: G 73 ASN cc_start: 0.9020 (t0) cc_final: 0.8708 (t0) REVERT: H 69 ILE cc_start: 0.9292 (mm) cc_final: 0.9056 (mm) REVERT: K 1090 PHE cc_start: 0.8587 (m-10) cc_final: 0.8040 (m-80) REVERT: K 1094 LYS cc_start: 0.8227 (mtpt) cc_final: 0.7919 (mmmt) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.1065 time to fit residues: 12.0142 Evaluate side-chains 53 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 15 optimal weight: 9.9990 chunk 131 optimal weight: 30.0000 chunk 34 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 101 optimal weight: 8.9990 chunk 148 optimal weight: 20.0000 chunk 14 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN B 64 ASN E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS ** K1255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1415 HIS K1449 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.053063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.037521 restraints weight = 190056.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.038572 restraints weight = 106287.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.039224 restraints weight = 72270.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.039609 restraints weight = 56946.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.039766 restraints weight = 49754.721| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17478 Z= 0.160 Angle : 0.642 7.949 24869 Z= 0.365 Chirality : 0.042 0.380 2772 Planarity : 0.004 0.043 2150 Dihedral : 30.254 177.650 4768 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.23), residues: 1283 helix: 1.74 (0.18), residues: 777 sheet: 0.43 (0.73), residues: 58 loop : 0.10 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 72 TYR 0.018 0.002 TYR B 88 PHE 0.009 0.001 PHE K1343 TRP 0.008 0.001 TRP K1122 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.16 (17478) covalent geometry : angle 0.64166 / 0.37 (24869) hydrogen bonds : bond 0.05260 / 3.68 ( 860) hydrogen bonds : angle 3.64081 / 2.63 ( 2278) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8537 (tp30) cc_final: 0.8292 (tp30) REVERT: A 105 GLU cc_start: 0.8908 (tp30) cc_final: 0.8557 (tp30) REVERT: A 120 MET cc_start: 0.8571 (mpp) cc_final: 0.8126 (mpp) REVERT: B 68 ASP cc_start: 0.9423 (m-30) cc_final: 0.9044 (m-30) REVERT: B 88 TYR cc_start: 0.8338 (m-80) cc_final: 0.8042 (m-80) REVERT: D 59 MET cc_start: 0.8931 (tpt) cc_final: 0.8656 (tpp) REVERT: D 100 LEU cc_start: 0.8900 (mt) cc_final: 0.8658 (mt) REVERT: E 81 ASP cc_start: 0.8466 (t70) cc_final: 0.8209 (t0) REVERT: E 120 MET cc_start: 0.8797 (mtm) cc_final: 0.7809 (ptp) REVERT: G 73 ASN cc_start: 0.9043 (t0) cc_final: 0.8773 (t0) REVERT: H 69 ILE cc_start: 0.9293 (mm) cc_final: 0.9029 (mm) REVERT: K 1090 PHE cc_start: 0.8628 (m-10) cc_final: 0.8052 (m-80) REVERT: K 1094 LYS cc_start: 0.8166 (mtpt) cc_final: 0.7852 (mmmt) REVERT: K 1097 MET cc_start: 0.0895 (ppp) cc_final: 0.0656 (ppp) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0988 time to fit residues: 13.2213 Evaluate side-chains 55 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 72 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 139 optimal weight: 20.0000 chunk 140 optimal weight: 30.0000 chunk 154 optimal weight: 30.0000 chunk 92 optimal weight: 6.9990 chunk 152 optimal weight: 30.0000 chunk 29 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS A 108 ASN E 108 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1132 ASN ** K1255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.053102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.037600 restraints weight = 190002.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.038660 restraints weight = 105242.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.039321 restraints weight = 71488.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.039657 restraints weight = 56256.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.039927 restraints weight = 49428.516| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17478 Z= 0.151 Angle : 0.628 8.463 24869 Z= 0.356 Chirality : 0.041 0.357 2772 Planarity : 0.004 0.044 2150 Dihedral : 30.098 176.472 4768 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.23), residues: 1283 helix: 1.89 (0.18), residues: 780 sheet: 0.53 (0.74), residues: 57 loop : 0.16 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 92 TYR 0.043 0.002 TYR F 88 PHE 0.011 0.001 PHE K1270 TRP 0.007 0.001 TRP K1122 HIS 0.011 0.001 HIS K1415 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.15 (17478) covalent geometry : angle 0.62837 / 0.36 (24869) hydrogen bonds : bond 0.05448 / 3.79 ( 860) hydrogen bonds : angle 3.49098 / 2.50 ( 2278) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.469 Fit side-chains REVERT: A 120 MET cc_start: 0.8577 (mpp) cc_final: 0.8122 (mpp) REVERT: B 68 ASP cc_start: 0.9386 (m-30) cc_final: 0.8993 (m-30) REVERT: D 59 MET cc_start: 0.8972 (tpt) cc_final: 0.8639 (tpp) REVERT: D 100 LEU cc_start: 0.8874 (mt) cc_final: 0.8628 (mt) REVERT: E 81 ASP cc_start: 0.8539 (t70) cc_final: 0.8246 (t0) REVERT: E 120 MET cc_start: 0.8701 (mtm) cc_final: 0.7681 (ptp) REVERT: G 73 ASN cc_start: 0.8997 (t0) cc_final: 0.8733 (t0) REVERT: H 69 ILE cc_start: 0.9278 (mm) cc_final: 0.9012 (mm) REVERT: K 1090 PHE cc_start: 0.8617 (m-10) cc_final: 0.8092 (m-80) REVERT: K 1094 LYS cc_start: 0.8152 (mtpt) cc_final: 0.7839 (mmmt) REVERT: K 1097 MET cc_start: 0.0600 (ppp) cc_final: -0.0549 (ptt) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1035 time to fit residues: 13.5323 Evaluate side-chains 55 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 105 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 141 optimal weight: 40.0000 chunk 65 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 91 optimal weight: 20.0000 chunk 127 optimal weight: 50.0000 chunk 122 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 139 optimal weight: 20.0000 chunk 92 optimal weight: 5.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN E 93 GLN E 108 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS ** K1255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1659 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.050239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.035008 restraints weight = 183232.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.035450 restraints weight = 110211.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.035638 restraints weight = 92395.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.035832 restraints weight = 74216.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.035898 restraints weight = 67892.289| |-----------------------------------------------------------------------------| r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.5415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17478 Z= 0.203 Angle : 0.683 8.808 24869 Z= 0.383 Chirality : 0.042 0.350 2772 Planarity : 0.005 0.046 2150 Dihedral : 30.243 178.218 4768 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.23), residues: 1283 helix: 1.75 (0.18), residues: 770 sheet: 0.32 (0.74), residues: 56 loop : 0.02 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 69 TYR 0.054 0.003 TYR B 88 PHE 0.013 0.002 PHE E 78 TRP 0.011 0.002 TRP K1509 HIS 0.007 0.001 HIS K1415 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.20 (17478) covalent geometry : angle 0.68279 / 0.38 (24869) hydrogen bonds : bond 0.06839 / 4.74 ( 860) hydrogen bonds : angle 3.79173 / 2.72 ( 2278) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8663 (mpp) cc_final: 0.8209 (mpp) REVERT: B 68 ASP cc_start: 0.9464 (m-30) cc_final: 0.9036 (m-30) REVERT: D 59 MET cc_start: 0.8897 (tpt) cc_final: 0.8548 (tpp) REVERT: D 100 LEU cc_start: 0.8942 (mt) cc_final: 0.8651 (mt) REVERT: G 73 ASN cc_start: 0.8978 (t0) cc_final: 0.8732 (t0) REVERT: H 69 ILE cc_start: 0.9301 (mm) cc_final: 0.9038 (mm) REVERT: K 1090 PHE cc_start: 0.8677 (m-10) cc_final: 0.8147 (m-80) REVERT: K 1094 LYS cc_start: 0.8183 (mtpt) cc_final: 0.7897 (mmmt) REVERT: K 1097 MET cc_start: 0.0661 (ppp) cc_final: -0.0625 (ptt) REVERT: K 1349 MET cc_start: 0.2476 (mmt) cc_final: 0.1761 (mmt) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.1060 time to fit residues: 12.6396 Evaluate side-chains 51 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 97 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 84 optimal weight: 0.0970 chunk 125 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 138 optimal weight: 30.0000 chunk 50 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 134 optimal weight: 20.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN E 108 ASN G 38 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.053152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.037690 restraints weight = 190051.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.038761 restraints weight = 104737.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.039434 restraints weight = 70715.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.039829 restraints weight = 55193.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.040011 restraints weight = 48064.541| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.5325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 17478 Z= 0.134 Angle : 0.619 9.095 24869 Z= 0.351 Chirality : 0.041 0.343 2772 Planarity : 0.004 0.043 2150 Dihedral : 30.126 176.127 4768 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.23), residues: 1283 helix: 1.91 (0.18), residues: 778 sheet: 0.30 (0.73), residues: 57 loop : 0.05 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 72 TYR 0.053 0.002 TYR B 88 PHE 0.010 0.001 PHE K1343 TRP 0.007 0.001 TRP K1122 HIS 0.010 0.001 HIS K1415 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.13 (17478) covalent geometry : angle 0.61938 / 0.35 (24869) hydrogen bonds : bond 0.04664 / 3.25 ( 860) hydrogen bonds : angle 3.47377 / 2.48 ( 2278) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: A 104 PHE cc_start: 0.9287 (m-10) cc_final: 0.9082 (m-80) REVERT: A 120 MET cc_start: 0.8560 (mpp) cc_final: 0.8182 (mpp) REVERT: B 53 GLU cc_start: 0.9040 (tp30) cc_final: 0.8774 (tm-30) REVERT: B 68 ASP cc_start: 0.9440 (m-30) cc_final: 0.9063 (m-30) REVERT: D 100 LEU cc_start: 0.8900 (mt) cc_final: 0.8630 (mt) REVERT: E 81 ASP cc_start: 0.8467 (t70) cc_final: 0.8176 (t0) REVERT: G 73 ASN cc_start: 0.8981 (t0) cc_final: 0.8698 (t0) REVERT: H 69 ILE cc_start: 0.9293 (mm) cc_final: 0.9011 (mm) REVERT: K 1090 PHE cc_start: 0.8630 (m-10) cc_final: 0.8116 (m-80) REVERT: K 1094 LYS cc_start: 0.8171 (mtpt) cc_final: 0.7882 (mmmt) REVERT: K 1097 MET cc_start: 0.0977 (ppp) cc_final: -0.0158 (ptt) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0991 time to fit residues: 12.9195 Evaluate side-chains 55 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 95 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 145 optimal weight: 30.0000 chunk 86 optimal weight: 0.0570 chunk 92 optimal weight: 40.0000 chunk 33 optimal weight: 7.9990 chunk 154 optimal weight: 30.0000 chunk 16 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 104 optimal weight: 0.0070 chunk 72 optimal weight: 3.9990 overall best weight: 1.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN E 108 ASN G 38 ASN H 84 ASN H 109 HIS ** K1255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.053080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.037658 restraints weight = 190207.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.038737 restraints weight = 104733.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.039406 restraints weight = 70505.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.039811 restraints weight = 55245.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.039978 restraints weight = 47887.630| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.5338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17478 Z= 0.133 Angle : 0.615 10.181 24869 Z= 0.347 Chirality : 0.040 0.331 2772 Planarity : 0.004 0.042 2150 Dihedral : 30.040 175.959 4768 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.23), residues: 1283 helix: 1.95 (0.18), residues: 777 sheet: 0.27 (0.65), residues: 67 loop : -0.09 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 92 TYR 0.056 0.002 TYR B 88 PHE 0.019 0.001 PHE E 67 TRP 0.006 0.001 TRP K1509 HIS 0.010 0.001 HIS K1415 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.13 (17478) covalent geometry : angle 0.61550 / 0.35 (24869) hydrogen bonds : bond 0.04797 / 3.35 ( 860) hydrogen bonds : angle 3.42815 / 2.45 ( 2278) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2602.33 seconds wall clock time: 45 minutes 44.14 seconds (2744.14 seconds total)