Starting phenix.real_space_refine on Fri Jul 3 21:45:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hai_34591/07_2026/8hai_34591.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hai_34591/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8hai_34591/07_2026/8hai_34591.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hai_34591/07_2026/8hai_34591.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hai_34591/07_2026/8hai_34591.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hai_34591/07_2026/8hai_34591.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8hai_34591/07_2026/8hai_34591.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hai_34591/07_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-dev-6108/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: 3.14, 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: 1.12 Conformation dependent library (CDL) restraints added in 499.2 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: 2.22 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: 3.57 Time building geometry restraints manager: 1.60 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: 23631 1.64 - 3.28: 1185 3.28 - 4.92: 39 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: 1.030 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 17.000 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.830 ------------------------------------------------------------------------------- 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 : 0.713 8.197 24869 Z= 0.615 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 0.71328 / 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 : 0.342 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: 0.1057 time to fit residues: 16.9631 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 : 0.518 ------------------------------------------------------------------------------- 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 = 0.3592 r_free = 0.3592 target = 0.058456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.043399 restraints weight = 188424.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.043955 restraints weight = 111475.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.043955 restraints weight = 86682.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.044322 restraints weight = 78437.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.044433 restraints weight = 63460.617| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 17478 Z= 0.253 Angle : 0.737 7.715 24869 Z= 0.411 Chirality : 0.044 0.304 2772 Planarity : 0.005 0.043 2150 Dihedral : 28.890 177.983 4768 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.18 % Allowed : 3.56 % Favored : 96.26 % 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: 1.76 (0.23), residues: 1283 helix: 1.67 (0.18), residues: 788 sheet: 0.54 (0.69), residues: 59 loop : 0.49 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 67 TYR 0.030 0.002 TYR B 88 PHE 0.016 0.002 PHE K1361 TRP 0.010 0.002 TRP K1509 HIS 0.010 0.002 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.25 (17478) covalent geometry : angle 0.73728 / 0.41 (24869) hydrogen bonds : bond 0.08361 / 5.71 ( 860) hydrogen bonds : angle 3.89231 / 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 87 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8123 (mpp) cc_final: 0.7796 (mpp) REVERT: B 68 ASP cc_start: 0.9323 (m-30) cc_final: 0.8905 (m-30) REVERT: D 100 LEU cc_start: 0.9319 (mt) cc_final: 0.9054 (mt) REVERT: E 73 GLU cc_start: 0.8682 (tt0) cc_final: 0.8295 (mt-10) REVERT: E 120 MET cc_start: 0.8501 (mtm) cc_final: 0.7945 (ptp) REVERT: G 73 ASN cc_start: 0.8872 (t0) cc_final: 0.8482 (t0) REVERT: H 46 LYS cc_start: 0.9089 (mmpt) cc_final: 0.8548 (pttm) REVERT: H 69 ILE cc_start: 0.9124 (mm) cc_final: 0.8899 (mm) REVERT: K 1090 PHE cc_start: 0.8437 (m-10) cc_final: 0.7873 (m-80) REVERT: K 1094 LYS cc_start: 0.7855 (mtpt) cc_final: 0.7218 (mmmt) REVERT: K 1097 MET cc_start: 0.3241 (ppp) cc_final: 0.2772 (ppp) outliers start: 2 outliers final: 0 residues processed: 87 average time/residue: 0.1102 time to fit residues: 15.2737 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 : 0.310 ------------------------------------------------------------------------------- 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: 0.5980 chunk 22 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 154 optimal weight: 30.0000 chunk 49 optimal weight: 0.9990 chunk 140 optimal weight: 40.0000 chunk 117 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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** K1112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.057652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.041191 restraints weight = 175564.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.042211 restraints weight = 104265.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.042844 restraints weight = 74673.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.043230 restraints weight = 61067.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.043386 restraints weight = 54599.994| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17478 Z= 0.133 Angle : 0.561 6.151 24869 Z= 0.333 Chirality : 0.039 0.305 2772 Planarity : 0.004 0.036 2150 Dihedral : 28.948 179.638 4768 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.45 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: 2.16 (0.23), residues: 1283 helix: 2.05 (0.18), residues: 784 sheet: 0.41 (0.67), residues: 64 loop : 0.56 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 52 TYR 0.014 0.001 TYR G 50 PHE 0.013 0.001 PHE K1343 TRP 0.007 0.001 TRP K1509 HIS 0.003 0.001 HIS K1199 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.13 (17478) covalent geometry : angle 0.56092 / 0.33 (24869) hydrogen bonds : bond 0.04847 / 3.40 ( 860) hydrogen bonds : angle 3.35943 / 2.43 ( 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 93 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8177 (mpp) cc_final: 0.7805 (mpp) REVERT: B 68 ASP cc_start: 0.9196 (m-30) cc_final: 0.8794 (m-30) REVERT: B 88 TYR cc_start: 0.8558 (m-10) cc_final: 0.8306 (m-80) REVERT: B 97 LEU cc_start: 0.9208 (tp) cc_final: 0.8995 (tp) REVERT: D 100 LEU cc_start: 0.9243 (mt) cc_final: 0.9023 (mt) REVERT: E 73 GLU cc_start: 0.8677 (tt0) cc_final: 0.8303 (mt-10) REVERT: E 120 MET cc_start: 0.8478 (mtm) cc_final: 0.7989 (ptp) REVERT: F 88 TYR cc_start: 0.8221 (m-80) cc_final: 0.7702 (m-80) REVERT: G 73 ASN cc_start: 0.8911 (t0) cc_final: 0.8568 (t0) REVERT: H 46 LYS cc_start: 0.9106 (mmpt) cc_final: 0.8543 (pttm) REVERT: H 69 ILE cc_start: 0.9095 (mm) cc_final: 0.8885 (mm) REVERT: K 1090 PHE cc_start: 0.8405 (m-10) cc_final: 0.7696 (m-80) REVERT: K 1094 LYS cc_start: 0.7806 (mtpt) cc_final: 0.7145 (mmmt) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.1027 time to fit residues: 15.0551 Evaluate side-chains 64 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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: 20.0000 chunk 94 optimal weight: 4.9990 chunk 143 optimal weight: 20.0000 chunk 80 optimal weight: 5.9990 chunk 128 optimal weight: 40.0000 chunk 17 optimal weight: 6.9990 chunk 149 optimal weight: 20.0000 chunk 127 optimal weight: 50.0000 chunk 137 optimal weight: 20.0000 chunk 93 optimal weight: 6.9990 chunk 132 optimal weight: 20.0000 overall best weight: 8.9992 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** G 104 GLN ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1255 HIS ** 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 = 0.3383 r_free = 0.3383 target = 0.049657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.033750 restraints weight = 191502.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.034656 restraints weight = 114403.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.035214 restraints weight = 82137.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.035550 restraints weight = 67253.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.035695 restraints weight = 59993.002| |-----------------------------------------------------------------------------| r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.088 17478 Z= 0.444 Angle : 1.097 15.704 24869 Z= 0.582 Chirality : 0.055 0.353 2772 Planarity : 0.010 0.111 2150 Dihedral : 30.387 179.431 4768 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 30.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.09 % Allowed : 4.54 % Favored : 95.37 % 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: 0.10 (0.22), residues: 1283 helix: 0.18 (0.17), residues: 786 sheet: 0.75 (0.77), residues: 57 loop : 0.06 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG E 52 TYR 0.038 0.004 TYR K1089 PHE 0.032 0.004 PHE A 104 TRP 0.015 0.003 TRP K1509 HIS 0.019 0.003 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00864 / 0.44 (17478) covalent geometry : angle 1.09660 / 0.58 (24869) hydrogen bonds : bond 0.15750 / 10.64 ( 860) hydrogen bonds : angle 5.18580 / 3.78 ( 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: 1 poor density : 65 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8543 (mpp) cc_final: 0.8146 (mpp) REVERT: B 63 GLU cc_start: 0.8781 (pm20) cc_final: 0.8470 (pm20) REVERT: E 120 MET cc_start: 0.9032 (mtm) cc_final: 0.8777 (mtm) REVERT: F 88 TYR cc_start: 0.8249 (m-80) cc_final: 0.7471 (m-80) REVERT: H 69 ILE cc_start: 0.9221 (mm) cc_final: 0.8998 (mm) REVERT: K 1090 PHE cc_start: 0.8522 (m-10) cc_final: 0.7979 (m-80) REVERT: K 1094 LYS cc_start: 0.8211 (mtpt) cc_final: 0.7821 (mmmt) outliers start: 1 outliers final: 0 residues processed: 66 average time/residue: 0.1108 time to fit residues: 11.7425 Evaluate side-chains 48 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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: 6.9990 chunk 142 optimal weight: 30.0000 chunk 77 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 64 optimal weight: 30.0000 chunk 117 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 150 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS A 108 ASN B 64 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN G 89 ASN ** K1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1449 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.052382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.036851 restraints weight = 196861.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.037837 restraints weight = 113190.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.038453 restraints weight = 78788.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.038752 restraints weight = 63267.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.039004 restraints weight = 56230.406| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17478 Z= 0.232 Angle : 0.729 9.020 24869 Z= 0.410 Chirality : 0.045 0.386 2772 Planarity : 0.005 0.063 2150 Dihedral : 30.548 177.619 4768 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % 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: 0.96 (0.23), residues: 1283 helix: 1.05 (0.18), residues: 777 sheet: 0.57 (0.75), residues: 58 loop : 0.10 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 72 TYR 0.022 0.002 TYR K1089 PHE 0.013 0.002 PHE H 65 TRP 0.008 0.001 TRP K1122 HIS 0.010 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.23 (17478) covalent geometry : angle 0.72873 / 0.41 (24869) hydrogen bonds : bond 0.07133 / 4.95 ( 860) hydrogen bonds : angle 4.19070 / 3.03 ( 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 74 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.471 Fit side-chains REVERT: A 120 MET cc_start: 0.8409 (mpp) cc_final: 0.8000 (mpp) REVERT: B 68 ASP cc_start: 0.9509 (m-30) cc_final: 0.9183 (m-30) REVERT: D 100 LEU cc_start: 0.8792 (mt) cc_final: 0.8540 (mt) REVERT: E 120 MET cc_start: 0.8892 (mtm) cc_final: 0.8387 (mtp) REVERT: F 88 TYR cc_start: 0.8291 (m-80) cc_final: 0.7837 (m-80) REVERT: G 73 ASN cc_start: 0.9046 (t0) cc_final: 0.8719 (t0) REVERT: H 69 ILE cc_start: 0.9271 (mm) cc_final: 0.9028 (mm) REVERT: K 1090 PHE cc_start: 0.8602 (m-10) cc_final: 0.8081 (m-80) REVERT: K 1094 LYS cc_start: 0.8182 (mtpt) cc_final: 0.7812 (mmmt) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1077 time to fit residues: 13.0352 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 : 0.350 ------------------------------------------------------------------------------- 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: 20.0000 chunk 104 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 120 optimal weight: 20.0000 chunk 76 optimal weight: 0.5980 chunk 93 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 130 optimal weight: 20.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS A 108 ASN B 64 ASN E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1415 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.053126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.037580 restraints weight = 190082.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.038622 restraints weight = 107139.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.039240 restraints weight = 73590.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.039643 restraints weight = 58669.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.039804 restraints weight = 51202.206| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17478 Z= 0.156 Angle : 0.650 12.361 24869 Z= 0.369 Chirality : 0.042 0.380 2772 Planarity : 0.005 0.063 2150 Dihedral : 30.387 177.306 4768 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % 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: 1.60 (0.23), residues: 1283 helix: 1.64 (0.18), residues: 774 sheet: 0.57 (0.75), residues: 58 loop : 0.24 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 72 TYR 0.039 0.002 TYR K1139 PHE 0.009 0.001 PHE A 104 TRP 0.007 0.001 TRP K1122 HIS 0.008 0.001 HIS K1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.16 (17478) covalent geometry : angle 0.65040 / 0.37 (24869) hydrogen bonds : bond 0.05651 / 3.94 ( 860) hydrogen bonds : angle 3.70269 / 2.67 ( 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 78 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8988 (tp30) cc_final: 0.8639 (tp30) REVERT: A 120 MET cc_start: 0.8455 (mpp) cc_final: 0.8041 (mpp) REVERT: B 68 ASP cc_start: 0.9421 (m-30) cc_final: 0.9101 (m-30) REVERT: D 100 LEU cc_start: 0.8877 (mt) cc_final: 0.8652 (mt) REVERT: E 120 MET cc_start: 0.8867 (mtm) cc_final: 0.8294 (mtp) REVERT: F 88 TYR cc_start: 0.8301 (m-80) cc_final: 0.7982 (m-80) REVERT: G 61 GLU cc_start: 0.8955 (tm-30) cc_final: 0.8655 (tm-30) REVERT: G 73 ASN cc_start: 0.9054 (t0) cc_final: 0.8804 (t0) REVERT: H 69 ILE cc_start: 0.9267 (mm) cc_final: 0.9041 (mm) REVERT: H 71 GLU cc_start: 0.9278 (tp30) cc_final: 0.9040 (tp30) REVERT: K 1090 PHE cc_start: 0.8639 (m-10) cc_final: 0.8052 (m-80) REVERT: K 1094 LYS cc_start: 0.8153 (mtpt) cc_final: 0.7854 (mmmt) REVERT: K 1097 MET cc_start: 0.1084 (ppp) cc_final: 0.0798 (ppp) REVERT: K 1254 MET cc_start: 0.0206 (ttt) cc_final: -0.0819 (mmt) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1029 time to fit residues: 13.0838 Evaluate side-chains 54 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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: 10.0000 chunk 131 optimal weight: 20.0000 chunk 34 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 85 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 148 optimal weight: 20.0000 chunk 14 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN E 108 ASN G 38 ASN H 109 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.052785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.037267 restraints weight = 190306.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.038320 restraints weight = 106739.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.038972 restraints weight = 72820.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.039333 restraints weight = 57465.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.039489 restraints weight = 50449.519| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.4908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17478 Z= 0.167 Angle : 0.641 8.500 24869 Z= 0.364 Chirality : 0.041 0.367 2772 Planarity : 0.004 0.041 2150 Dihedral : 30.285 176.408 4768 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % 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: 1.86 (0.18), residues: 772 sheet: 0.41 (0.69), residues: 68 loop : 0.07 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 72 TYR 0.027 0.002 TYR B 88 PHE 0.011 0.001 PHE A 104 TRP 0.007 0.001 TRP K1122 HIS 0.010 0.001 HIS K1415 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.17 (17478) covalent geometry : angle 0.64059 / 0.36 (24869) hydrogen bonds : bond 0.05802 / 4.04 ( 860) hydrogen bonds : angle 3.57536 / 2.57 ( 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 79 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.8518 (mpp) cc_final: 0.8110 (mpp) REVERT: B 63 GLU cc_start: 0.8896 (pm20) cc_final: 0.8517 (pm20) REVERT: B 68 ASP cc_start: 0.9407 (m-30) cc_final: 0.9045 (m-30) REVERT: C 90 ASP cc_start: 0.9067 (t0) cc_final: 0.8847 (t0) REVERT: D 59 MET cc_start: 0.8877 (tpt) cc_final: 0.8632 (tpp) REVERT: D 100 LEU cc_start: 0.8889 (mt) cc_final: 0.8638 (mt) REVERT: E 120 MET cc_start: 0.8894 (mtm) cc_final: 0.8307 (mtp) REVERT: F 88 TYR cc_start: 0.8135 (m-80) cc_final: 0.7839 (m-80) REVERT: G 61 GLU cc_start: 0.8973 (tm-30) cc_final: 0.8605 (tm-30) REVERT: G 73 ASN cc_start: 0.8998 (t0) cc_final: 0.8768 (t0) REVERT: H 69 ILE cc_start: 0.9289 (mm) cc_final: 0.9058 (mm) REVERT: K 1090 PHE cc_start: 0.8598 (m-10) cc_final: 0.8026 (m-80) REVERT: K 1094 LYS cc_start: 0.8159 (mtpt) cc_final: 0.7865 (mmmt) REVERT: K 1097 MET cc_start: 0.0959 (ppp) cc_final: -0.0086 (ptt) REVERT: K 1254 MET cc_start: 0.0351 (ttt) cc_final: -0.0911 (mmt) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1060 time to fit residues: 13.6967 Evaluate side-chains 57 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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: 2.9990 chunk 19 optimal weight: 5.9990 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: 20.0000 chunk 29 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN E 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.050677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.034675 restraints weight = 182664.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.035585 restraints weight = 108651.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.036140 restraints weight = 77734.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.036481 restraints weight = 63532.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.036674 restraints weight = 56817.236| |-----------------------------------------------------------------------------| r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 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 : 0.003 0.039 17478 Z= 0.178 Angle : 0.646 8.099 24869 Z= 0.368 Chirality : 0.041 0.347 2772 Planarity : 0.005 0.047 2150 Dihedral : 30.323 177.135 4768 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 14.13 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: 1.66 (0.23), residues: 1283 helix: 1.80 (0.18), residues: 771 sheet: 0.30 (0.73), residues: 58 loop : 0.09 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 49 TYR 0.027 0.002 TYR G 50 PHE 0.009 0.001 PHE A 104 TRP 0.010 0.001 TRP K1115 HIS 0.007 0.001 HIS K1415 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.18 (17478) covalent geometry : angle 0.64612 / 0.37 (24869) hydrogen bonds : bond 0.05975 / 4.16 ( 860) hydrogen bonds : angle 3.64812 / 2.61 ( 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 76 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.8640 (mpp) cc_final: 0.8102 (mpp) REVERT: B 68 ASP cc_start: 0.9443 (m-30) cc_final: 0.9071 (m-30) REVERT: C 90 ASP cc_start: 0.9057 (t0) cc_final: 0.8854 (t0) REVERT: D 59 MET cc_start: 0.8912 (tpt) cc_final: 0.8631 (tpp) REVERT: D 100 LEU cc_start: 0.8900 (mt) cc_final: 0.8630 (mt) REVERT: E 120 MET cc_start: 0.8920 (mtm) cc_final: 0.8384 (mtp) REVERT: F 88 TYR cc_start: 0.8020 (m-80) cc_final: 0.7687 (m-80) REVERT: G 61 GLU cc_start: 0.8939 (tm-30) cc_final: 0.8533 (tm-30) REVERT: G 73 ASN cc_start: 0.9009 (t0) cc_final: 0.8765 (t0) REVERT: H 69 ILE cc_start: 0.9303 (mm) cc_final: 0.9061 (mm) REVERT: H 94 ILE cc_start: 0.8757 (mt) cc_final: 0.8536 (mt) REVERT: K 1090 PHE cc_start: 0.8589 (m-10) cc_final: 0.8010 (m-80) REVERT: K 1094 LYS cc_start: 0.8183 (mtpt) cc_final: 0.7884 (mmmt) REVERT: K 1097 MET cc_start: 0.0796 (ppp) cc_final: -0.0402 (ptt) REVERT: K 1254 MET cc_start: 0.0750 (ttt) cc_final: -0.0359 (mmt) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1031 time to fit residues: 12.8438 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 : 0.407 ------------------------------------------------------------------------------- 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: 7.9990 chunk 33 optimal weight: 0.6980 chunk 141 optimal weight: 30.0000 chunk 65 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 127 optimal weight: 50.0000 chunk 122 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 139 optimal weight: 20.0000 chunk 92 optimal weight: 30.0000 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN E 108 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS K1659 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.052659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.037225 restraints weight = 190408.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.038269 restraints weight = 105299.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.038926 restraints weight = 71466.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.039206 restraints weight = 56228.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.039470 restraints weight = 49913.905| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.5249 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= 0.145 Angle : 0.613 8.071 24869 Z= 0.352 Chirality : 0.041 0.343 2772 Planarity : 0.004 0.044 2150 Dihedral : 30.285 176.260 4768 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % 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: 1.68 (0.23), residues: 1283 helix: 1.83 (0.18), residues: 778 sheet: 0.21 (0.73), residues: 58 loop : 0.07 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 72 TYR 0.023 0.002 TYR B 88 PHE 0.008 0.001 PHE E 67 TRP 0.007 0.001 TRP K1509 HIS 0.009 0.001 HIS K1415 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.14 (17478) covalent geometry : angle 0.61271 / 0.35 (24869) hydrogen bonds : bond 0.05133 / 3.58 ( 860) hydrogen bonds : angle 3.50735 / 2.50 ( 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 76 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.445 Fit side-chains REVERT: A 104 PHE cc_start: 0.9296 (m-10) cc_final: 0.9085 (m-80) REVERT: A 120 MET cc_start: 0.8686 (mpp) cc_final: 0.8176 (mpp) REVERT: B 68 ASP cc_start: 0.9418 (m-30) cc_final: 0.9068 (m-30) REVERT: C 90 ASP cc_start: 0.9062 (t0) cc_final: 0.8802 (t0) REVERT: D 100 LEU cc_start: 0.8843 (mt) cc_final: 0.8607 (mt) REVERT: E 81 ASP cc_start: 0.8559 (t70) cc_final: 0.8269 (t0) REVERT: E 120 MET cc_start: 0.8907 (mtm) cc_final: 0.8265 (mtp) REVERT: F 88 TYR cc_start: 0.8148 (m-80) cc_final: 0.7917 (m-80) REVERT: G 61 GLU cc_start: 0.8978 (tm-30) cc_final: 0.8566 (tm-30) REVERT: G 73 ASN cc_start: 0.8993 (t0) cc_final: 0.8731 (t0) REVERT: H 69 ILE cc_start: 0.9261 (mm) cc_final: 0.9016 (mm) REVERT: K 1090 PHE cc_start: 0.8619 (m-10) cc_final: 0.8094 (m-80) REVERT: K 1094 LYS cc_start: 0.8174 (mtpt) cc_final: 0.7887 (mmmt) REVERT: K 1097 MET cc_start: 0.0690 (ppp) cc_final: -0.0263 (ptt) REVERT: K 1254 MET cc_start: 0.0806 (ttt) cc_final: -0.0293 (mmt) REVERT: K 1349 MET cc_start: 0.4567 (mmt) cc_final: 0.4307 (mmt) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.0928 time to fit residues: 11.7977 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 : 0.399 ------------------------------------------------------------------------------- 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: 4.9990 chunk 7 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 125 optimal weight: 30.0000 chunk 72 optimal weight: 0.9980 chunk 138 optimal weight: 20.0000 chunk 50 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 134 optimal weight: 20.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN E 108 ASN H 109 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.050315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.034391 restraints weight = 182875.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.035282 restraints weight = 108493.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.035837 restraints weight = 77713.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.036170 restraints weight = 63560.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.036362 restraints weight = 56788.286| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.5516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17478 Z= 0.177 Angle : 0.641 8.130 24869 Z= 0.364 Chirality : 0.041 0.332 2772 Planarity : 0.005 0.047 2150 Dihedral : 30.335 176.232 4768 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % 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: 1.62 (0.23), residues: 1283 helix: 1.78 (0.18), residues: 777 sheet: 0.17 (0.74), residues: 57 loop : 0.03 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 42 TYR 0.024 0.002 TYR B 88 PHE 0.012 0.001 PHE A 104 TRP 0.009 0.001 TRP K1509 HIS 0.008 0.001 HIS K1415 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.18 (17478) covalent geometry : angle 0.64082 / 0.36 (24869) hydrogen bonds : bond 0.06263 / 4.35 ( 860) hydrogen bonds : angle 3.64343 / 2.61 ( 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 74 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.348 Fit side-chains REVERT: A 94 GLU cc_start: 0.8840 (tp30) cc_final: 0.8474 (tp30) REVERT: A 120 MET cc_start: 0.8686 (mpp) cc_final: 0.8102 (mpp) REVERT: B 68 ASP cc_start: 0.9474 (m-30) cc_final: 0.9083 (m-30) REVERT: C 90 ASP cc_start: 0.9049 (t0) cc_final: 0.8819 (t0) REVERT: D 100 LEU cc_start: 0.8885 (mt) cc_final: 0.8631 (mt) REVERT: E 120 MET cc_start: 0.8932 (mtm) cc_final: 0.8414 (mtp) REVERT: F 88 TYR cc_start: 0.8022 (m-80) cc_final: 0.7768 (m-80) REVERT: G 61 GLU cc_start: 0.8956 (tm-30) cc_final: 0.8543 (tm-30) REVERT: G 73 ASN cc_start: 0.8984 (t0) cc_final: 0.8743 (t0) REVERT: H 69 ILE cc_start: 0.9283 (mm) cc_final: 0.9021 (mm) REVERT: H 71 GLU cc_start: 0.9341 (tp30) cc_final: 0.9113 (tp30) REVERT: K 1090 PHE cc_start: 0.8633 (m-10) cc_final: 0.8110 (m-80) REVERT: K 1094 LYS cc_start: 0.8104 (mtpt) cc_final: 0.7809 (mmmt) REVERT: K 1097 MET cc_start: 0.0854 (ppp) cc_final: -0.0245 (ptt) REVERT: K 1254 MET cc_start: 0.0800 (ttt) cc_final: -0.0323 (mmt) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1068 time to fit residues: 13.1475 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 : 0.441 ------------------------------------------------------------------------------- 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: 4.9990 chunk 48 optimal weight: 1.9990 chunk 145 optimal weight: 30.0000 chunk 86 optimal weight: 50.0000 chunk 92 optimal weight: 20.0000 chunk 33 optimal weight: 2.9990 chunk 154 optimal weight: 30.0000 chunk 16 optimal weight: 0.4980 chunk 87 optimal weight: 0.9990 chunk 104 optimal weight: 7.9990 chunk 72 optimal weight: 0.5980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN E 108 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.052541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.037024 restraints weight = 191906.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.038117 restraints weight = 104087.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.038767 restraints weight = 69939.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.039178 restraints weight = 55058.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.039358 restraints weight = 47953.279| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.5509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 17478 Z= 0.136 Angle : 0.601 8.031 24869 Z= 0.345 Chirality : 0.041 0.322 2772 Planarity : 0.004 0.045 2150 Dihedral : 30.287 175.726 4768 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % 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: 1.96 (0.18), residues: 775 sheet: 0.10 (0.73), residues: 58 loop : 0.02 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 72 TYR 0.024 0.001 TYR B 88 PHE 0.038 0.001 PHE A 104 TRP 0.007 0.001 TRP K1122 HIS 0.009 0.001 HIS K1415 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.14 (17478) covalent geometry : angle 0.60087 / 0.34 (24869) hydrogen bonds : bond 0.04734 / 3.32 ( 860) hydrogen bonds : angle 3.45216 / 2.46 ( 2278) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2496.78 seconds wall clock time: 43 minutes 58.73 seconds (2638.73 seconds total)