Starting phenix.real_space_refine on Thu Aug 6 16:30:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hag_34588/08_2026/8hag_34588.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hag_34588/08_2026/8hag_34588.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8hag_34588/08_2026/8hag_34588.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hag_34588/08_2026/8hag_34588.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hag_34588/08_2026/8hag_34588.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hag_34588/08_2026/8hag_34588.map" model { file = "/net/cci-nas-00/data/ceres_data/8hag_34588/08_2026/8hag_34588.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hag_34588/08_2026/8hag_34588.cif" } resolution = 3.2 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= 0.001 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 9427 2.51 5 N 2985 2.21 5 O 3614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 129 residue(s): 0.02s 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: 16367 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} 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-2': 2, 'ALY:plan-1': 1, '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: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} 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: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 751 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 94} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 4260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4260 Classifications: {'peptide': 516} Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 486} Chain breaks: 3 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: 3.51, per 1000 atoms: 0.21 Number of scatterers: 16367 At special positions: 0 Unit cell: (106.112, 163.313, 137.614, 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 3614 8.00 N 2985 7.00 C 9427 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: 1.09 Conformation dependent library (CDL) restraints added in 633.6 milliseconds 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2418 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 14 sheets defined 62.4% alpha, 7.2% beta 114 base pairs and 231 stacking pairs defined. Time for finding SS restraints: 3.20 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.510A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.516A pdb=" N GLY A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.757A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N HIS B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.552A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.409A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 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: 3.651A 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 removed outlier: 3.584A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.636A 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 47 through 76 removed outlier: 4.379A pdb=" N TYR F 51 " --> pdb=" O SER F 47 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLU F 52 " --> pdb=" O GLY F 48 " (cutoff:3.500A) removed outlier: 3.987A 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: 4.184A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.816A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 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: 3.659A 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: 4.256A pdb=" N TYR K1117 " --> pdb=" O GLU K1113 " (cutoff:3.500A) Processing helix chain 'K' and resid 1136 through 1160 removed outlier: 4.031A pdb=" N ASP K1154 " --> pdb=" O GLU K1150 " (cutoff:3.500A) Proline residue: K1155 - end of helix removed outlier: 3.676A pdb=" N LEU K1160 " --> pdb=" O VAL K1156 " (cutoff:3.500A) 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 1344 through 1347 Processing helix chain 'K' and resid 1407 through 1429 removed outlier: 4.535A pdb=" N THR K1411 " --> pdb=" O LYS K1407 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ALA K1412 " --> pdb=" O CYS K1408 " (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 Processing helix chain 'K' and resid 1507 through 1523 removed outlier: 3.937A 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 1621 through 1625 Processing helix chain 'K' and resid 1626 through 1637 removed outlier: 4.335A pdb=" N PHE K1630 " --> pdb=" O GLY K1626 " (cutoff:3.500A) Processing helix chain 'K' and resid 1643 through 1663 removed outlier: 3.524A 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: 6.886A 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 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.535A 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: 7.470A 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: 6.633A 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: 7.471A 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: 3.697A 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: 6.676A pdb=" N ALA K1359 " --> pdb=" O VAL K1326 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA K1328 " --> pdb=" O THR K1357 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR K1357 " --> pdb=" O ALA K1328 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ASP K1330 " --> pdb=" O TYR K1355 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N TYR K1355 " --> pdb=" O ASP K1330 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N THR K1332 " --> pdb=" O PHE K1353 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N PHE K1353 " --> pdb=" O THR K1332 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE K1374 " --> pdb=" O ALA K1362 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLU K1364 " --> pdb=" O CYS K1372 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N CYS K1372 " --> pdb=" O GLU K1364 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE K1366 " --> pdb=" O ASP K1370 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ASP K1370 " --> pdb=" O ILE K1366 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N PHE K1373 " --> pdb=" O SER K1400 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N SER K1400 " --> pdb=" O PHE K1373 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLY K1375 " --> pdb=" O LEU K1398 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N LEU K1398 " --> pdb=" O GLY K1375 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N HIS K1377 " --> pdb=" O SER K1396 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG K1392 " --> pdb=" O TYR K1381 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N TRP K1436 " --> pdb=" O ILE K1395 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N TYR K1397 " --> pdb=" O TRP K1436 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG K1599 " --> pdb=" O ASP K1482 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASP K1482 " --> pdb=" O ARG K1599 " (cutoff:3.500A) 596 hydrogen bonds defined for protein. 1758 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 270 hydrogen bonds 536 hydrogen bond angles 0 basepair planarities 114 basepair parallelities 231 stacking parallelities Total time for adding SS restraints: 3.76 Time building geometry restraints manager: 1.62 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: 4033 1.34 - 1.46: 4652 1.46 - 1.58: 7950 1.58 - 1.70: 586 1.70 - 1.81: 70 Bond restraints: 17291 Sorted by residual: bond pdb=" C3' DA J 60 " pdb=" C2' DA J 60 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.20e+01 bond pdb=" C3' DG I 111 " pdb=" C2' DG I 111 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.16e+01 bond pdb=" C3' DG J 138 " pdb=" C2' DG J 138 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.10e+01 bond pdb=" C3' DT J 91 " pdb=" C2' DT J 91 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" C3' DT I 110 " pdb=" C2' DT I 110 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 ... (remaining 17286 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 23661 1.90 - 3.80: 907 3.80 - 5.70: 35 5.70 - 7.60: 2 7.60 - 9.50: 2 Bond angle restraints: 24607 Sorted by residual: angle pdb=" N3 DT I 157 " pdb=" C4 DT I 157 " pdb=" O4 DT I 157 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" N3 DT I 122 " pdb=" C4 DT I 122 " pdb=" O4 DT I 122 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT I 81 " pdb=" C4 DT I 81 " pdb=" O4 DT I 81 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 angle pdb=" N3 DT J 49 " pdb=" C4 DT J 49 " pdb=" O4 DT J 49 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.84e+01 angle pdb=" N3 DT I 23 " pdb=" C4 DT I 23 " pdb=" O4 DT I 23 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.84e+01 ... (remaining 24602 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.97: 8378 34.97 - 69.93: 1349 69.93 - 104.90: 27 104.90 - 139.86: 1 139.86 - 174.83: 2 Dihedral angle restraints: 9757 sinusoidal: 6011 harmonic: 3746 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 220.00 45.17 174.83 1 3.50e+01 8.16e-04 1.56e+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 73.41 146.59 1 3.50e+01 8.16e-04 1.44e+01 dihedral pdb=" CG ARG C 77 " pdb=" CD ARG C 77 " pdb=" NE ARG C 77 " pdb=" CZ ARG C 77 " ideal model delta sinusoidal sigma weight residual 90.00 134.38 -44.38 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 9754 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1585 0.032 - 0.064: 810 0.064 - 0.096: 265 0.096 - 0.129: 78 0.129 - 0.161: 4 Chirality restraints: 2742 Sorted by residual: chirality pdb=" CA LEU A 65 " pdb=" N LEU A 65 " pdb=" C LEU A 65 " pdb=" CB LEU A 65 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CA MET K1059 " pdb=" N MET K1059 " pdb=" C MET K1059 " pdb=" CB MET K1059 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" C3' DT I 136 " pdb=" C4' DT I 136 " pdb=" O3' DT I 136 " pdb=" C2' DT I 136 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.41e-01 ... (remaining 2739 not shown) Planarity restraints: 2112 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT J 108 " -0.031 2.00e-02 2.50e+03 1.58e-02 6.20e+00 pdb=" N1 DT J 108 " 0.034 2.00e-02 2.50e+03 pdb=" C2 DT J 108 " -0.003 2.00e-02 2.50e+03 pdb=" O2 DT J 108 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DT J 108 " 0.009 2.00e-02 2.50e+03 pdb=" C4 DT J 108 " -0.009 2.00e-02 2.50e+03 pdb=" O4 DT J 108 " -0.013 2.00e-02 2.50e+03 pdb=" C5 DT J 108 " -0.001 2.00e-02 2.50e+03 pdb=" C7 DT J 108 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DT J 108 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 83 " -0.010 2.00e-02 2.50e+03 1.15e-02 2.62e+00 pdb=" CG TYR D 83 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR D 83 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR D 83 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR D 83 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR D 83 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR D 83 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 83 " -0.000 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 3.96e-02 2.51e+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 2109 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1867 2.76 - 3.29: 15531 3.29 - 3.83: 31676 3.83 - 4.36: 35346 4.36 - 4.90: 53216 Nonbonded interactions: 137636 Sorted by model distance: nonbonded pdb=" OG1 THR C 16 " pdb=" OP1 DG I 48 " model vdw 2.220 3.040 nonbonded pdb=" NE2 HIS A 113 " pdb=" OD1 ASP E 123 " model vdw 2.244 3.120 nonbonded pdb=" NH2 ARG K1133 " pdb=" OP1 DG J 114 " model vdw 2.259 3.120 nonbonded pdb=" O TYR C 39 " pdb=" OG SER D 78 " model vdw 2.259 3.040 nonbonded pdb=" O LEU C 115 " pdb=" NZ LYS F 44 " model vdw 2.263 3.120 ... (remaining 137631 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' } ncs_group { reference = (chain 'B' and resid 20 through 101) selection = (chain 'F' and ((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 individual isotropic 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: 3.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.650 Find NCS groups from input model: 0.210 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: 0.000 Load rotamer database and sin/cos tables:1.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 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 0.062 17291 Z= 0.438 Angle : 0.706 9.502 24607 Z= 0.610 Chirality : 0.042 0.161 2742 Planarity : 0.003 0.040 2112 Dihedral : 24.831 174.830 7339 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 2.13 (0.23), residues: 1255 helix: 1.98 (0.19), residues: 759 sheet: 1.13 (0.60), residues: 83 loop : 0.51 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 79 TYR 0.028 0.001 TYR D 83 PHE 0.008 0.001 PHE K1090 TRP 0.003 0.000 TRP K1115 HIS 0.012 0.001 HIS K1415 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.44 (17291) covalent geometry : angle 0.70605 / 0.61 (24607) hydrogen bonds : bond 0.12109 / 7.81 ( 866) hydrogen bonds : angle 4.38763 / 3.15 ( 2294) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.434 Fit side-chains REVERT: A 41 TYR cc_start: 0.7741 (m-80) cc_final: 0.7497 (m-80) REVERT: H 62 MET cc_start: 0.8981 (tpp) cc_final: 0.8334 (tpt) REVERT: K 1124 MET cc_start: 0.6849 (mmp) cc_final: 0.6475 (mmm) REVERT: K 1349 MET cc_start: 0.5182 (ttp) cc_final: 0.4886 (ttm) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1051 time to fit residues: 16.7547 Evaluate side-chains 70 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 30.0000 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 40.0000 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 50.0000 chunk 91 optimal weight: 20.0000 chunk 149 optimal weight: 10.0000 overall best weight: 6.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS C 104 GLN D 49 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS K1415 HIS K1451 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.087764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.051935 restraints weight = 86769.002| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 4.04 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.095 17291 Z= 0.388 Angle : 0.986 10.707 24607 Z= 0.519 Chirality : 0.058 0.440 2742 Planarity : 0.008 0.083 2112 Dihedral : 29.663 177.984 4739 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.18 % Allowed : 7.51 % Favored : 91.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 0.79 (0.22), residues: 1255 helix: 0.92 (0.18), residues: 773 sheet: 0.92 (0.68), residues: 58 loop : -0.08 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG K1055 TYR 0.049 0.003 TYR K1194 PHE 0.027 0.003 PHE C 25 TRP 0.012 0.002 TRP K1466 HIS 0.012 0.003 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00865 / 0.39 (17291) covalent geometry : angle 0.98555 / 0.52 (24607) hydrogen bonds : bond 0.09318 / 6.23 ( 866) hydrogen bonds : angle 4.23247 / 3.08 ( 2294) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.378 Fit side-chains REVERT: F 84 MET cc_start: 0.8884 (tpp) cc_final: 0.8570 (tpt) REVERT: H 62 MET cc_start: 0.9224 (tpp) cc_final: 0.9020 (mmt) REVERT: K 1124 MET cc_start: 0.6718 (mmp) cc_final: 0.6458 (mmm) REVERT: K 1349 MET cc_start: 0.6810 (ttp) cc_final: 0.6497 (ttm) outliers start: 13 outliers final: 6 residues processed: 77 average time/residue: 0.1112 time to fit residues: 13.3620 Evaluate side-chains 58 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 100 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 125 optimal weight: 40.0000 chunk 7 optimal weight: 3.9990 chunk 115 optimal weight: 0.2980 chunk 42 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 145 optimal weight: 20.0000 chunk 131 optimal weight: 20.0000 chunk 104 optimal weight: 20.0000 chunk 18 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.088392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.052741 restraints weight = 85335.381| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 3.95 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17291 Z= 0.158 Angle : 0.607 10.013 24607 Z= 0.346 Chirality : 0.041 0.282 2742 Planarity : 0.004 0.057 2112 Dihedral : 29.334 177.560 4739 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.45 % Allowed : 8.33 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 1.54 (0.23), residues: 1255 helix: 1.66 (0.18), residues: 775 sheet: 0.62 (0.61), residues: 68 loop : -0.03 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K1055 TYR 0.021 0.001 TYR C 39 PHE 0.011 0.001 PHE G 25 TRP 0.009 0.001 TRP K1466 HIS 0.007 0.001 HIS K1415 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.16 (17291) covalent geometry : angle 0.60712 / 0.35 (24607) hydrogen bonds : bond 0.05442 / 3.61 ( 866) hydrogen bonds : angle 3.45705 / 2.52 ( 2294) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.321 Fit side-chains REVERT: A 81 ASP cc_start: 0.8257 (t0) cc_final: 0.8052 (t0) REVERT: A 92 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9280 (mm) REVERT: B 63 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8254 (mm-30) REVERT: G 64 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8524 (tm-30) REVERT: K 1097 MET cc_start: 0.7283 (ppp) cc_final: 0.6285 (ppp) REVERT: K 1124 MET cc_start: 0.6839 (mmp) cc_final: 0.6446 (mmm) REVERT: K 1349 MET cc_start: 0.5667 (ttp) cc_final: 0.5240 (ttm) outliers start: 16 outliers final: 10 residues processed: 77 average time/residue: 0.1041 time to fit residues: 12.7658 Evaluate side-chains 65 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 120 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 145 optimal weight: 20.0000 chunk 117 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 151 optimal weight: 40.0000 chunk 89 optimal weight: 0.3980 chunk 107 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 104 optimal weight: 8.9990 chunk 146 optimal weight: 20.0000 chunk 29 optimal weight: 1.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN H 109 HIS K1236 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.085724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.049462 restraints weight = 84526.386| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 3.90 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 17291 Z= 0.224 Angle : 0.671 7.874 24607 Z= 0.372 Chirality : 0.043 0.285 2742 Planarity : 0.005 0.061 2112 Dihedral : 29.470 176.122 4739 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.81 % Allowed : 9.05 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 1.71 (0.23), residues: 1255 helix: 1.72 (0.18), residues: 783 sheet: 1.02 (0.69), residues: 57 loop : 0.13 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 33 TYR 0.023 0.002 TYR F 88 PHE 0.011 0.001 PHE C 25 TRP 0.014 0.001 TRP K1466 HIS 0.005 0.001 HIS K1415 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.22 (17291) covalent geometry : angle 0.67145 / 0.37 (24607) hydrogen bonds : bond 0.05996 / 3.94 ( 866) hydrogen bonds : angle 3.46177 / 2.50 ( 2294) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.501 Fit side-chains REVERT: A 81 ASP cc_start: 0.8338 (t0) cc_final: 0.8120 (t0) REVERT: A 92 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9286 (mm) REVERT: C 64 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8674 (tm-30) REVERT: G 64 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8557 (tm-30) REVERT: H 54 ILE cc_start: 0.9008 (mm) cc_final: 0.8659 (mm) REVERT: K 1097 MET cc_start: 0.7269 (ppp) cc_final: 0.6473 (ppp) REVERT: K 1124 MET cc_start: 0.6841 (mmp) cc_final: 0.6413 (mmm) REVERT: K 1349 MET cc_start: 0.5868 (ttp) cc_final: 0.5461 (ttm) outliers start: 20 outliers final: 13 residues processed: 76 average time/residue: 0.0968 time to fit residues: 12.0221 Evaluate side-chains 65 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 120 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 28 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 102 optimal weight: 20.0000 chunk 145 optimal weight: 20.0000 chunk 129 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS B 64 ASN ** H 63 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 = 0.4104 r_free = 0.4104 target = 0.083673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.047000 restraints weight = 84537.049| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 4.00 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.5526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 17291 Z= 0.248 Angle : 0.697 9.406 24607 Z= 0.387 Chirality : 0.046 0.295 2742 Planarity : 0.005 0.052 2112 Dihedral : 29.651 177.600 4739 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.26 % Allowed : 9.50 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 1.47 (0.23), residues: 1255 helix: 1.58 (0.18), residues: 781 sheet: 0.84 (0.70), residues: 58 loop : -0.04 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K1055 TYR 0.016 0.002 TYR H 83 PHE 0.015 0.002 PHE E 78 TRP 0.075 0.003 TRP K1466 HIS 0.014 0.002 HIS K1415 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.25 (17291) covalent geometry : angle 0.69727 / 0.39 (24607) hydrogen bonds : bond 0.06037 / 3.94 ( 866) hydrogen bonds : angle 3.55469 / 2.58 ( 2294) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 54 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9533 (OUTLIER) cc_final: 0.9281 (mm) REVERT: C 64 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8420 (tm-30) REVERT: G 64 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8490 (tm-30) REVERT: H 54 ILE cc_start: 0.9038 (mm) cc_final: 0.8742 (mm) REVERT: H 93 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8392 (mp0) REVERT: K 1097 MET cc_start: 0.7297 (ppp) cc_final: 0.6752 (ppp) REVERT: K 1124 MET cc_start: 0.6939 (mmp) cc_final: 0.6527 (mmm) REVERT: K 1349 MET cc_start: 0.6727 (ttp) cc_final: 0.6344 (ttm) REVERT: K 1466 TRP cc_start: 0.4708 (t60) cc_final: 0.4404 (t60) outliers start: 25 outliers final: 16 residues processed: 77 average time/residue: 0.0932 time to fit residues: 11.8283 Evaluate side-chains 66 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 48 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 111 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 79 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 123 optimal weight: 10.0000 chunk 141 optimal weight: 20.0000 chunk 96 optimal weight: 30.0000 chunk 50 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 149 optimal weight: 20.0000 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.084463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.048039 restraints weight = 84668.560| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 3.95 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.5522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17291 Z= 0.138 Angle : 0.590 6.848 24607 Z= 0.337 Chirality : 0.041 0.277 2742 Planarity : 0.004 0.041 2112 Dihedral : 29.449 175.692 4739 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.54 % Allowed : 10.68 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 1.98 (0.23), residues: 1255 helix: 1.99 (0.18), residues: 783 sheet: 0.93 (0.71), residues: 58 loop : 0.13 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 35 TYR 0.011 0.001 TYR D 83 PHE 0.010 0.001 PHE H 70 TRP 0.038 0.002 TRP K1466 HIS 0.008 0.001 HIS K1415 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.14 (17291) covalent geometry : angle 0.58962 / 0.34 (24607) hydrogen bonds : bond 0.04748 / 3.12 ( 866) hydrogen bonds : angle 3.20950 / 2.33 ( 2294) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9253 (mm) REVERT: A 131 ARG cc_start: 0.9142 (OUTLIER) cc_final: 0.8867 (mtt180) REVERT: C 64 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8494 (tm-30) REVERT: D 54 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8810 (tp) REVERT: H 54 ILE cc_start: 0.9057 (mm) cc_final: 0.8797 (mm) REVERT: H 93 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8302 (mp0) REVERT: K 1097 MET cc_start: 0.7267 (ppp) cc_final: 0.6786 (ppp) REVERT: K 1124 MET cc_start: 0.7128 (mmp) cc_final: 0.6639 (mmm) REVERT: K 1349 MET cc_start: 0.6869 (ttp) cc_final: 0.6499 (ttm) REVERT: K 1466 TRP cc_start: 0.4733 (t60) cc_final: 0.4515 (t60) outliers start: 17 outliers final: 9 residues processed: 73 average time/residue: 0.1039 time to fit residues: 12.1251 Evaluate side-chains 66 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 93 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 55 optimal weight: 0.8980 chunk 117 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 10 optimal weight: 0.0570 chunk 114 optimal weight: 20.0000 chunk 6 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 96 optimal weight: 40.0000 chunk 108 optimal weight: 30.0000 chunk 20 optimal weight: 2.9990 overall best weight: 1.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.084207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.047913 restraints weight = 84321.196| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 3.96 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.5633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 17291 Z= 0.151 Angle : 0.590 6.848 24607 Z= 0.336 Chirality : 0.040 0.278 2742 Planarity : 0.004 0.040 2112 Dihedral : 29.404 177.380 4739 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.36 % Allowed : 10.95 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 1255 helix: 2.12 (0.19), residues: 777 sheet: 1.03 (0.72), residues: 58 loop : 0.16 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 35 TYR 0.010 0.001 TYR C 57 PHE 0.017 0.001 PHE K1090 TRP 0.026 0.001 TRP K1466 HIS 0.008 0.001 HIS K1415 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.15 (17291) covalent geometry : angle 0.58967 / 0.34 (24607) hydrogen bonds : bond 0.04709 / 3.09 ( 866) hydrogen bonds : angle 3.17107 / 2.30 ( 2294) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9266 (mm) REVERT: C 64 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8485 (tm-30) REVERT: G 64 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8537 (tm-30) REVERT: H 54 ILE cc_start: 0.9041 (mm) cc_final: 0.8768 (mm) REVERT: H 93 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8293 (mp0) REVERT: K 1097 MET cc_start: 0.7299 (ppp) cc_final: 0.6797 (ppp) REVERT: K 1124 MET cc_start: 0.7066 (mmp) cc_final: 0.6579 (mmm) REVERT: K 1349 MET cc_start: 0.6859 (ttp) cc_final: 0.6501 (ttm) REVERT: K 1466 TRP cc_start: 0.4788 (t60) cc_final: 0.4302 (t60) REVERT: K 1470 MET cc_start: -0.1503 (mmp) cc_final: -0.1705 (mmp) outliers start: 15 outliers final: 12 residues processed: 67 average time/residue: 0.0972 time to fit residues: 10.8088 Evaluate side-chains 66 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 93 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 1.9990 chunk 101 optimal weight: 20.0000 chunk 118 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 139 optimal weight: 40.0000 chunk 111 optimal weight: 8.9990 chunk 23 optimal weight: 0.7980 chunk 135 optimal weight: 20.0000 chunk 149 optimal weight: 20.0000 chunk 60 optimal weight: 0.7980 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.083355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.046807 restraints weight = 84423.989| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.98 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.5888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17291 Z= 0.201 Angle : 0.631 7.665 24607 Z= 0.353 Chirality : 0.042 0.285 2742 Planarity : 0.004 0.047 2112 Dihedral : 29.533 177.771 4739 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.54 % Allowed : 11.13 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 2.01 (0.23), residues: 1255 helix: 2.02 (0.18), residues: 783 sheet: 0.97 (0.71), residues: 58 loop : 0.14 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K1055 TYR 0.009 0.001 TYR H 121 PHE 0.011 0.001 PHE E 78 TRP 0.015 0.001 TRP K1466 HIS 0.006 0.001 HIS K1415 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.20 (17291) covalent geometry : angle 0.63063 / 0.35 (24607) hydrogen bonds : bond 0.05190 / 3.40 ( 866) hydrogen bonds : angle 3.30188 / 2.41 ( 2294) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9273 (mm) REVERT: A 131 ARG cc_start: 0.9162 (OUTLIER) cc_final: 0.8925 (mtt180) REVERT: C 64 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8460 (tm-30) REVERT: G 64 GLU cc_start: 0.8823 (tm-30) cc_final: 0.8589 (tm-30) REVERT: H 93 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8309 (mp0) REVERT: K 1097 MET cc_start: 0.7246 (ppp) cc_final: 0.6773 (ppp) REVERT: K 1124 MET cc_start: 0.7052 (mmp) cc_final: 0.6576 (mmm) REVERT: K 1349 MET cc_start: 0.7082 (ttp) cc_final: 0.6768 (ttm) REVERT: K 1466 TRP cc_start: 0.4732 (t60) cc_final: 0.4248 (t60) outliers start: 17 outliers final: 13 residues processed: 66 average time/residue: 0.1046 time to fit residues: 11.0356 Evaluate side-chains 65 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 93 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 97 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 120 optimal weight: 20.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.084078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.048120 restraints weight = 85304.085| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 3.91 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.5843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 17291 Z= 0.123 Angle : 0.570 10.954 24607 Z= 0.329 Chirality : 0.040 0.273 2742 Planarity : 0.004 0.044 2112 Dihedral : 29.390 178.218 4739 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.45 % Allowed : 11.31 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 2.22 (0.24), residues: 1255 helix: 2.21 (0.19), residues: 777 sheet: 1.07 (0.72), residues: 58 loop : 0.19 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 35 TYR 0.009 0.001 TYR C 57 PHE 0.010 0.001 PHE H 70 TRP 0.014 0.001 TRP K1466 HIS 0.007 0.001 HIS K1415 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.12 (17291) covalent geometry : angle 0.57017 / 0.33 (24607) hydrogen bonds : bond 0.04327 / 2.82 ( 866) hydrogen bonds : angle 3.10282 / 2.26 ( 2294) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.9270 (mm) REVERT: A 131 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8843 (mtt180) REVERT: C 64 GLU cc_start: 0.8597 (tm-30) cc_final: 0.8395 (tm-30) REVERT: G 64 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8422 (tm-30) REVERT: H 54 ILE cc_start: 0.9037 (mm) cc_final: 0.8803 (mm) REVERT: H 93 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8268 (mp0) REVERT: K 1097 MET cc_start: 0.7230 (ppp) cc_final: 0.6735 (ppp) REVERT: K 1124 MET cc_start: 0.7083 (mmp) cc_final: 0.6588 (mmm) REVERT: K 1349 MET cc_start: 0.6473 (ttp) cc_final: 0.6078 (ttm) REVERT: K 1466 TRP cc_start: 0.4709 (t60) cc_final: 0.4264 (t60) outliers start: 16 outliers final: 10 residues processed: 71 average time/residue: 0.0982 time to fit residues: 11.2549 Evaluate side-chains 68 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 93 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 124 optimal weight: 50.0000 chunk 80 optimal weight: 6.9990 chunk 9 optimal weight: 50.0000 chunk 64 optimal weight: 20.0000 chunk 47 optimal weight: 1.9990 chunk 88 optimal weight: 0.0870 chunk 146 optimal weight: 20.0000 chunk 137 optimal weight: 40.0000 chunk 79 optimal weight: 7.9990 chunk 148 optimal weight: 20.0000 chunk 99 optimal weight: 20.0000 overall best weight: 7.4168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.081181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.044961 restraints weight = 86392.316| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.78 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.6494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.089 17291 Z= 0.380 Angle : 0.804 13.181 24607 Z= 0.431 Chirality : 0.050 0.303 2742 Planarity : 0.006 0.064 2112 Dihedral : 29.917 178.966 4739 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.36 % Allowed : 11.40 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 1.53 (0.23), residues: 1255 helix: 1.65 (0.18), residues: 781 sheet: 0.88 (0.70), residues: 58 loop : -0.08 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 42 TYR 0.014 0.002 TYR H 121 PHE 0.023 0.002 PHE E 78 TRP 0.012 0.002 TRP K1129 HIS 0.010 0.002 HIS K1415 Details of bonding type rmsd/Z covalent geometry : bond 0.00838 / 0.38 (17291) covalent geometry : angle 0.80412 / 0.43 (24607) hydrogen bonds : bond 0.07469 / 4.89 ( 866) hydrogen bonds : angle 3.77577 / 2.76 ( 2294) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: C 64 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8480 (tm-30) REVERT: G 64 GLU cc_start: 0.8881 (tm-30) cc_final: 0.8659 (tm-30) REVERT: H 93 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8344 (mp0) REVERT: K 1097 MET cc_start: 0.6994 (ppp) cc_final: 0.6390 (ppp) REVERT: K 1124 MET cc_start: 0.7219 (mmp) cc_final: 0.6728 (mmm) REVERT: K 1349 MET cc_start: 0.5893 (ttp) cc_final: 0.5410 (ttm) REVERT: K 1466 TRP cc_start: 0.4664 (t60) cc_final: 0.4216 (t60) outliers start: 15 outliers final: 12 residues processed: 66 average time/residue: 0.0942 time to fit residues: 9.8810 Evaluate side-chains 63 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 93 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 105 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 9 optimal weight: 50.0000 chunk 144 optimal weight: 20.0000 chunk 110 optimal weight: 6.9990 chunk 87 optimal weight: 0.0000 chunk 93 optimal weight: 8.9990 chunk 124 optimal weight: 40.0000 chunk 140 optimal weight: 30.0000 overall best weight: 2.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.082289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.047374 restraints weight = 85082.436| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 4.52 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.6504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17291 Z= 0.184 Angle : 0.648 14.492 24607 Z= 0.363 Chirality : 0.043 0.286 2742 Planarity : 0.004 0.062 2112 Dihedral : 29.782 179.146 4739 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.27 % Allowed : 11.67 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 1255 helix: 1.88 (0.18), residues: 783 sheet: 0.89 (0.71), residues: 58 loop : 0.03 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 42 TYR 0.010 0.001 TYR D 83 PHE 0.013 0.001 PHE E 78 TRP 0.009 0.001 TRP K1509 HIS 0.008 0.001 HIS K1415 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.18 (17291) covalent geometry : angle 0.64771 / 0.36 (24607) hydrogen bonds : bond 0.05038 / 3.31 ( 866) hydrogen bonds : angle 3.35043 / 2.45 ( 2294) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3902.17 seconds wall clock time: 67 minutes 16.81 seconds (4036.81 seconds total)