Starting phenix.real_space_refine on Thu Aug 6 19:54:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ham_34596/08_2026/8ham_34596.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ham_34596/08_2026/8ham_34596.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ham_34596/08_2026/8ham_34596.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ham_34596/08_2026/8ham_34596.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ham_34596/08_2026/8ham_34596.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ham_34596/08_2026/8ham_34596.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8ham_34596/08_2026/8ham_34596.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ham_34596/08_2026/8ham_34596.cif" } resolution = 4.5 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= 0.004 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 330 5.49 5 S 46 5.16 5 C 9835 2.51 5 N 3130 2.21 5 O 3836 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 135 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17177 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 720 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 89} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ALY:plan-2': 2, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 673 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "G" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 730 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 3384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 3384 Classifications: {'DNA': 165} Link IDs: {'rna3p': 164} Chain: "J" Number of atoms: 3381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 3381 Classifications: {'DNA': 165} Link IDs: {'rna3p': 164} Chain: "K" Number of atoms: 4302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4302 Classifications: {'peptide': 517} Link IDs: {'PCIS': 3, 'PTRANS': 29, 'TRANS': 484} Chain breaks: 4 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: 3.45, per 1000 atoms: 0.20 Number of scatterers: 17177 At special positions: 0 Unit cell: (101.43, 161.7, 124.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 46 16.00 P 330 15.00 O 3836 8.00 N 3130 7.00 C 9835 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: 1.42 Conformation dependent library (CDL) restraints added in 593.4 milliseconds 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2428 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 14 sheets defined 62.0% alpha, 7.5% beta 129 base pairs and 248 stacking pairs defined. Time for finding SS restraints: 2.61 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.775A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.705A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.356A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.533A 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 Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.686A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) 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: 3.559A 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 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.561A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 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: 4.342A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.943A 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 Processing helix chain 'H' and resid 103 through 124 Processing helix chain 'K' and resid 1088 through 1104 Proline residue: K1096 - end of helix removed outlier: 3.514A pdb=" N GLN K1104 " --> pdb=" O ALA K1100 " (cutoff:3.500A) Processing helix chain 'K' and resid 1108 through 1112 Processing helix chain 'K' and resid 1124 through 1129 removed outlier: 3.510A pdb=" N ILE K1128 " --> pdb=" O ASP K1124 " (cutoff:3.500A) Processing helix chain 'K' and resid 1134 through 1145 Processing helix chain 'K' and resid 1149 through 1168 removed outlier: 4.061A pdb=" N TYR K1153 " --> pdb=" O GLU K1149 " (cutoff:3.500A) Processing helix chain 'K' and resid 1172 through 1197 removed outlier: 4.353A pdb=" N ASP K1190 " --> pdb=" O GLU K1186 " (cutoff:3.500A) Proline residue: K1191 - end of helix Processing helix chain 'K' and resid 1238 through 1244 Processing helix chain 'K' and resid 1292 through 1296 Processing helix chain 'K' and resid 1308 through 1316 Processing helix chain 'K' and resid 1332 through 1350 Processing helix chain 'K' and resid 1372 through 1380 Processing helix chain 'K' and resid 1443 through 1464 removed outlier: 4.474A pdb=" N THR K1447 " --> pdb=" O ARG K1443 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ALA K1448 " --> pdb=" O CYS K1444 " (cutoff:3.500A) Processing helix chain 'K' and resid 1495 through 1513 Processing helix chain 'K' and resid 1522 through 1530 Processing helix chain 'K' and resid 1533 through 1537 Processing helix chain 'K' and resid 1543 through 1554 removed outlier: 4.115A pdb=" N ASN K1547 " --> pdb=" O ASP K1543 " (cutoff:3.500A) Processing helix chain 'K' and resid 1617 through 1629 Processing helix chain 'K' and resid 1664 through 1675 Processing helix chain 'K' and resid 1680 through 1698 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.712A 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: 6.768A 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: 7.294A 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 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.540A 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: 7.122A 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 1205 through 1206 removed outlier: 3.526A pdb=" N ASP K1276 " --> pdb=" O PHE K1206 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 1234 through 1237 Processing sheet with id=AB4, first strand: chain 'K' and resid 1280 through 1282 Processing sheet with id=AB5, first strand: chain 'K' and resid 1357 through 1370 removed outlier: 6.529A pdb=" N ALA K1395 " --> pdb=" O VAL K1362 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER K1364 " --> pdb=" O THR K1393 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR K1393 " --> pdb=" O SER K1364 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ASP K1366 " --> pdb=" O TYR K1391 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N TYR K1391 " --> pdb=" O ASP K1366 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N THR K1368 " --> pdb=" O PHE K1389 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE K1389 " --> pdb=" O THR K1368 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU K1396 " --> pdb=" O MET K1412 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE K1410 " --> pdb=" O ALA K1398 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLU K1400 " --> pdb=" O CYS K1408 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N CYS K1408 " --> pdb=" O GLU K1400 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE K1402 " --> pdb=" O ASP K1406 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ASP K1406 " --> pdb=" O ILE K1402 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLN K1415 " --> pdb=" O ILE K1431 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N ILE K1431 " --> pdb=" O GLN K1415 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N TYR K1417 " --> pdb=" O VAL K1429 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VAL K1429 " --> pdb=" O TYR K1417 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N TRP K1472 " --> pdb=" O ILE K1431 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N TYR K1433 " --> pdb=" O TRP K1472 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP K1518 " --> pdb=" O HIS K1636 " (cutoff:3.500A) 605 hydrogen bonds defined for protein. 1785 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 310 hydrogen bonds 620 hydrogen bond angles 0 basepair planarities 129 basepair parallelities 248 stacking parallelities Total time for adding SS restraints: 4.41 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3318 1.33 - 1.45: 5725 1.45 - 1.57: 8432 1.57 - 1.69: 658 1.69 - 1.81: 68 Bond restraints: 18201 Sorted by residual: bond pdb=" C3' DA I 18 " pdb=" C2' DA I 18 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DT J 135 " pdb=" C2' DT J 135 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DA I 41 " pdb=" C2' DA I 41 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DG I 164 " pdb=" C2' DG I 164 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DT J 145 " pdb=" C2' DT J 145 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 ... (remaining 18196 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 25145 2.07 - 4.14: 826 4.14 - 6.22: 18 6.22 - 8.29: 4 8.29 - 10.36: 1 Bond angle restraints: 25994 Sorted by residual: angle pdb=" N3 DT I 65 " pdb=" C4 DT I 65 " pdb=" O4 DT I 65 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 2.00e+01 angle pdb=" N3 DT I 40 " pdb=" C4 DT I 40 " pdb=" O4 DT I 40 " 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 J 109 " pdb=" C4 DT J 109 " pdb=" O4 DT J 109 " 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 I 136 " pdb=" C4 DT I 136 " pdb=" O4 DT I 136 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT J 135 " pdb=" C4 DT J 135 " pdb=" O4 DT J 135 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 ... (remaining 25989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.73: 8639 34.73 - 69.46: 1510 69.46 - 104.19: 30 104.19 - 138.92: 2 138.92 - 173.65: 2 Dihedral angle restraints: 10183 sinusoidal: 6423 harmonic: 3760 Sorted by residual: dihedral pdb=" CA LYS B 20 " pdb=" C LYS B 20 " pdb=" N VAL B 21 " pdb=" CA VAL B 21 " ideal model delta harmonic sigma weight residual -180.00 -151.44 -28.56 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA MET K1412 " pdb=" C MET K1412 " pdb=" N HIS K1413 " pdb=" CA HIS K1413 " ideal model delta harmonic sigma weight residual 180.00 159.34 20.66 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA ILE F 29 " pdb=" C ILE F 29 " pdb=" N THR F 30 " pdb=" CA THR F 30 " ideal model delta harmonic sigma weight residual -180.00 -159.83 -20.17 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 10180 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1813 0.036 - 0.072: 761 0.072 - 0.107: 266 0.107 - 0.143: 42 0.143 - 0.179: 4 Chirality restraints: 2886 Sorted by residual: 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 -2.55 -0.18 2.00e-01 2.50e+01 7.99e-01 chirality pdb=" CA ILE K1635 " pdb=" N ILE K1635 " pdb=" C ILE K1635 " pdb=" CB ILE K1635 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.36e-01 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 -2.58 -0.15 2.00e-01 2.50e+01 5.89e-01 ... (remaining 2883 not shown) Planarity restraints: 2162 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 102 " -0.031 5.00e-02 4.00e+02 4.70e-02 3.53e+00 pdb=" N PRO D 103 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET E 120 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.90e+00 pdb=" N PRO E 121 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO E 121 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 121 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 30 " -0.007 2.00e-02 2.50e+03 1.12e-02 2.84e+00 pdb=" N1 DC J 30 " 0.007 2.00e-02 2.50e+03 pdb=" C2 DC J 30 " -0.026 2.00e-02 2.50e+03 pdb=" O2 DC J 30 " 0.013 2.00e-02 2.50e+03 pdb=" N3 DC J 30 " 0.011 2.00e-02 2.50e+03 pdb=" C4 DC J 30 " -0.002 2.00e-02 2.50e+03 pdb=" N4 DC J 30 " -0.006 2.00e-02 2.50e+03 pdb=" C5 DC J 30 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DC J 30 " 0.006 2.00e-02 2.50e+03 ... (remaining 2159 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3218 2.79 - 3.32: 16302 3.32 - 3.84: 34004 3.84 - 4.37: 38628 4.37 - 4.90: 55646 Nonbonded interactions: 147798 Sorted by model distance: nonbonded pdb=" ND2 ASN E 108 " pdb=" O GLY F 42 " model vdw 2.260 3.120 nonbonded pdb=" N GLY C 44 " pdb=" O ILE D 89 " model vdw 2.268 3.120 nonbonded pdb=" NE2 HIS A 113 " pdb=" OD1 ASP E 123 " model vdw 2.296 3.120 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.304 3.040 nonbonded pdb=" NH2 ARG G 35 " pdb=" OP2 DT I 129 " model vdw 2.309 3.120 ... (remaining 147793 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 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 14 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and ((resid 31 and (name N or name CA or name C or name O or name CB \ )) or resid 32 through 124)) selection = chain 'H' } ncs_group { reference = (chain 'I' and resid 10 through 171) selection = (chain 'J' and resid 10 through 171) } 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: 1.020 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.520 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 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 18201 Z= 0.456 Angle : 0.715 10.362 25994 Z= 0.624 Chirality : 0.043 0.179 2886 Planarity : 0.004 0.047 2162 Dihedral : 25.163 173.648 7755 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 2.08 (0.23), residues: 1258 helix: 1.94 (0.18), residues: 772 sheet: 0.25 (0.61), residues: 77 loop : 0.68 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 129 TYR 0.016 0.001 TYR K1227 PHE 0.024 0.001 PHE K1410 TRP 0.007 0.001 TRP K1472 HIS 0.009 0.001 HIS K1451 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.46 (18201) covalent geometry : angle 0.71487 / 0.62 (25994) hydrogen bonds : bond 0.12581 / 8.21 ( 915) hydrogen bonds : angle 5.04066 / 3.68 ( 2405) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.478 Fit side-chains REVERT: A 97 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7868 (mt-10) REVERT: A 124 ILE cc_start: 0.9712 (mt) cc_final: 0.9507 (tp) REVERT: B 84 MET cc_start: 0.7405 (tpp) cc_final: 0.7030 (mmm) REVERT: D 59 MET cc_start: 0.9014 (tpp) cc_final: 0.8581 (tpp) REVERT: K 1502 TRP cc_start: 0.4260 (t60) cc_final: 0.3670 (t60) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1274 time to fit residues: 11.3650 Evaluate side-chains 42 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 30.0000 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 30.0000 chunk 149 optimal weight: 5.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS C 104 GLN E 39 HIS ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1291 HIS K1415 GLN ** K1487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.060425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.039979 restraints weight = 167417.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.039879 restraints weight = 90351.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.040233 restraints weight = 61177.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.040504 restraints weight = 50747.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.040587 restraints weight = 46659.918| |-----------------------------------------------------------------------------| r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 18201 Z= 0.394 Angle : 0.978 13.612 25994 Z= 0.516 Chirality : 0.052 0.507 2886 Planarity : 0.008 0.080 2162 Dihedral : 29.812 175.266 5132 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.36 % Allowed : 3.51 % Favored : 96.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 1.07 (0.23), residues: 1258 helix: 1.04 (0.17), residues: 783 sheet: 0.33 (0.59), residues: 79 loop : 0.39 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 35 TYR 0.035 0.003 TYR C 50 PHE 0.040 0.003 PHE G 25 TRP 0.020 0.002 TRP K1545 HIS 0.012 0.003 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00774 / 0.39 (18201) covalent geometry : angle 0.97768 / 0.52 (25994) hydrogen bonds : bond 0.10096 / 6.82 ( 915) hydrogen bonds : angle 4.70326 / 3.44 ( 2405) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.467 Fit side-chains REVERT: A 120 MET cc_start: 0.8705 (mtm) cc_final: 0.8071 (mtp) REVERT: C 56 GLU cc_start: 0.8210 (tt0) cc_final: 0.7336 (tt0) REVERT: E 97 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7531 (mt-10) REVERT: H 61 ILE cc_start: 0.9570 (mm) cc_final: 0.9345 (mm) REVERT: K 1502 TRP cc_start: 0.4585 (t60) cc_final: 0.4287 (t60) outliers start: 4 outliers final: 1 residues processed: 45 average time/residue: 0.1288 time to fit residues: 9.3748 Evaluate side-chains 34 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 48 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 74 optimal weight: 40.0000 chunk 121 optimal weight: 10.0000 chunk 128 optimal weight: 8.9990 chunk 107 optimal weight: 0.3980 chunk 61 optimal weight: 0.9990 chunk 78 optimal weight: 20.0000 chunk 60 optimal weight: 4.9990 chunk 96 optimal weight: 20.0000 chunk 21 optimal weight: 2.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K1266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.061669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.040791 restraints weight = 166166.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.040812 restraints weight = 87045.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.041194 restraints weight = 58935.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.041389 restraints weight = 49162.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.041510 restraints weight = 45624.533| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18201 Z= 0.162 Angle : 0.617 9.858 25994 Z= 0.358 Chirality : 0.041 0.384 2886 Planarity : 0.004 0.044 2162 Dihedral : 29.767 179.609 5132 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 2.05 (0.23), residues: 1258 helix: 1.92 (0.18), residues: 784 sheet: 0.39 (0.59), residues: 77 loop : 0.56 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 116 TYR 0.018 0.001 TYR C 50 PHE 0.013 0.001 PHE K1410 TRP 0.007 0.001 TRP K1158 HIS 0.004 0.001 HIS K1451 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.16 (18201) covalent geometry : angle 0.61651 / 0.36 (25994) hydrogen bonds : bond 0.05078 / 3.39 ( 915) hydrogen bonds : angle 3.68942 / 2.72 ( 2405) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.8712 (mtm) cc_final: 0.7905 (mtp) REVERT: H 61 ILE cc_start: 0.9488 (mm) cc_final: 0.9215 (mm) REVERT: H 62 MET cc_start: 0.9404 (tpt) cc_final: 0.9121 (tpp) REVERT: K 1502 TRP cc_start: 0.4412 (t60) cc_final: 0.4099 (t60) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1256 time to fit residues: 9.2326 Evaluate side-chains 34 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 0.9980 chunk 133 optimal weight: 6.9990 chunk 89 optimal weight: 50.0000 chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 154 optimal weight: 40.0000 chunk 6 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 152 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 9 optimal weight: 20.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K1146 GLN K1413 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.061450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.040514 restraints weight = 165584.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 79)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.040469 restraints weight = 88158.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.040792 restraints weight = 59229.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.041066 restraints weight = 49562.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.041134 restraints weight = 45828.163| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18201 Z= 0.150 Angle : 0.598 9.450 25994 Z= 0.345 Chirality : 0.040 0.378 2886 Planarity : 0.004 0.051 2162 Dihedral : 29.703 178.493 5132 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 2.40 (0.24), residues: 1258 helix: 2.24 (0.18), residues: 785 sheet: 0.33 (0.58), residues: 77 loop : 0.64 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 99 TYR 0.016 0.001 TYR K1147 PHE 0.029 0.002 PHE A 104 TRP 0.006 0.001 TRP K1545 HIS 0.004 0.001 HIS K1451 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.15 (18201) covalent geometry : angle 0.59796 / 0.34 (25994) hydrogen bonds : bond 0.04842 / 3.25 ( 915) hydrogen bonds : angle 3.45895 / 2.56 ( 2405) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8011 (mt-10) REVERT: A 120 MET cc_start: 0.8798 (mtm) cc_final: 0.8043 (mtp) REVERT: H 61 ILE cc_start: 0.9470 (mm) cc_final: 0.9212 (mm) REVERT: K 1502 TRP cc_start: 0.4478 (t60) cc_final: 0.3977 (t60) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1134 time to fit residues: 9.6262 Evaluate side-chains 35 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 20.0000 chunk 127 optimal weight: 40.0000 chunk 119 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 chunk 154 optimal weight: 0.0050 chunk 2 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 96 optimal weight: 20.0000 chunk 58 optimal weight: 6.9990 overall best weight: 3.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.060495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.039698 restraints weight = 164809.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.039672 restraints weight = 88319.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.040083 restraints weight = 59529.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.040253 restraints weight = 49710.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.040393 restraints weight = 46307.020| |-----------------------------------------------------------------------------| r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 18201 Z= 0.184 Angle : 0.622 7.854 25994 Z= 0.358 Chirality : 0.040 0.371 2886 Planarity : 0.004 0.041 2162 Dihedral : 29.828 176.614 5132 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 2.35 (0.23), residues: 1258 helix: 2.21 (0.18), residues: 785 sheet: 0.09 (0.57), residues: 79 loop : 0.68 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 86 TYR 0.022 0.001 TYR G 50 PHE 0.013 0.002 PHE G 25 TRP 0.006 0.001 TRP K1545 HIS 0.007 0.001 HIS K1451 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.18 (18201) covalent geometry : angle 0.62190 / 0.36 (25994) hydrogen bonds : bond 0.05167 / 3.49 ( 915) hydrogen bonds : angle 3.54299 / 2.63 ( 2405) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.8774 (mtm) cc_final: 0.8058 (mtp) REVERT: D 94 ILE cc_start: 0.9506 (tp) cc_final: 0.9207 (tt) REVERT: E 97 GLU cc_start: 0.8142 (tt0) cc_final: 0.7282 (mt-10) REVERT: E 106 ASP cc_start: 0.9216 (m-30) cc_final: 0.8971 (m-30) REVERT: H 61 ILE cc_start: 0.9503 (mm) cc_final: 0.9221 (mm) REVERT: K 1502 TRP cc_start: 0.4752 (t60) cc_final: 0.4420 (t60) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.1151 time to fit residues: 8.4131 Evaluate side-chains 33 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 128 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 98 optimal weight: 20.0000 chunk 90 optimal weight: 50.0000 chunk 79 optimal weight: 20.0000 chunk 86 optimal weight: 30.0000 chunk 37 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** 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 = 0.3500 r_free = 0.3500 target = 0.059661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.038804 restraints weight = 165282.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.038799 restraints weight = 88445.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.039214 restraints weight = 59395.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.039334 restraints weight = 49473.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.039361 restraints weight = 46282.886| |-----------------------------------------------------------------------------| r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 18201 Z= 0.187 Angle : 0.635 7.047 25994 Z= 0.363 Chirality : 0.040 0.362 2886 Planarity : 0.004 0.040 2162 Dihedral : 29.965 174.784 5132 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 1258 helix: 2.11 (0.18), residues: 783 sheet: -0.02 (0.57), residues: 79 loop : 0.62 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 55 TYR 0.013 0.001 TYR H 42 PHE 0.016 0.002 PHE K1410 TRP 0.007 0.001 TRP K1545 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.19 (18201) covalent geometry : angle 0.63542 / 0.36 (25994) hydrogen bonds : bond 0.05255 / 3.56 ( 915) hydrogen bonds : angle 3.56627 / 2.65 ( 2405) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8662 (mtm) cc_final: 0.8169 (mtp) REVERT: H 61 ILE cc_start: 0.9461 (mm) cc_final: 0.9143 (mm) REVERT: K 1502 TRP cc_start: 0.4958 (t60) cc_final: 0.4337 (t60) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.1078 time to fit residues: 7.7922 Evaluate side-chains 32 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 144 optimal weight: 7.9990 chunk 137 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 40.0000 chunk 38 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 95 optimal weight: 30.0000 chunk 68 optimal weight: 0.8980 chunk 145 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS C 24 GLN ** E 93 GLN ** 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 = 0.3505 r_free = 0.3505 target = 0.059847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.039017 restraints weight = 163951.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.038971 restraints weight = 88423.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.039361 restraints weight = 60078.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.039547 restraints weight = 50471.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.039662 restraints weight = 46802.550| |-----------------------------------------------------------------------------| r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18201 Z= 0.151 Angle : 0.600 8.979 25994 Z= 0.345 Chirality : 0.040 0.347 2886 Planarity : 0.004 0.039 2162 Dihedral : 29.964 175.667 5132 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 2.30 (0.24), residues: 1258 helix: 2.19 (0.18), residues: 784 sheet: 0.00 (0.58), residues: 79 loop : 0.64 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 92 TYR 0.029 0.001 TYR K1102 PHE 0.020 0.001 PHE H 65 TRP 0.006 0.001 TRP K1502 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.15 (18201) covalent geometry : angle 0.59954 / 0.35 (25994) hydrogen bonds : bond 0.04674 / 3.17 ( 915) hydrogen bonds : angle 3.42000 / 2.53 ( 2405) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.443 Fit side-chains REVERT: A 120 MET cc_start: 0.8683 (mtm) cc_final: 0.8171 (mtp) REVERT: E 106 ASP cc_start: 0.9123 (m-30) cc_final: 0.8869 (m-30) REVERT: H 61 ILE cc_start: 0.9455 (mm) cc_final: 0.9138 (mm) REVERT: K 1502 TRP cc_start: 0.4940 (t60) cc_final: 0.4628 (t60) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.1215 time to fit residues: 7.7336 Evaluate side-chains 31 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 66 optimal weight: 1.9990 chunk 61 optimal weight: 0.3980 chunk 79 optimal weight: 20.0000 chunk 128 optimal weight: 10.0000 chunk 81 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 chunk 102 optimal weight: 20.0000 chunk 56 optimal weight: 4.9990 chunk 123 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 119 optimal weight: 9.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** 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 = 0.3508 r_free = 0.3508 target = 0.059866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.038941 restraints weight = 164862.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 76)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.038941 restraints weight = 87629.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.039248 restraints weight = 60123.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.039510 restraints weight = 50538.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.039634 restraints weight = 46559.961| |-----------------------------------------------------------------------------| r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 18201 Z= 0.142 Angle : 0.584 7.102 25994 Z= 0.338 Chirality : 0.039 0.340 2886 Planarity : 0.004 0.044 2162 Dihedral : 29.951 175.524 5132 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 2.37 (0.24), residues: 1258 helix: 2.24 (0.18), residues: 783 sheet: -0.01 (0.57), residues: 79 loop : 0.69 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 92 TYR 0.023 0.001 TYR K1102 PHE 0.014 0.001 PHE H 65 TRP 0.007 0.001 TRP K1502 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.14 (18201) covalent geometry : angle 0.58450 / 0.34 (25994) hydrogen bonds : bond 0.04419 / 3.00 ( 915) hydrogen bonds : angle 3.33136 / 2.46 ( 2405) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.504 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.8745 (mtm) cc_final: 0.8081 (mtp) REVERT: E 106 ASP cc_start: 0.9070 (m-30) cc_final: 0.8868 (m-30) REVERT: H 61 ILE cc_start: 0.9422 (mm) cc_final: 0.9087 (mm) REVERT: K 1502 TRP cc_start: 0.5022 (t60) cc_final: 0.4418 (t60) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.1342 time to fit residues: 8.6838 Evaluate side-chains 33 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 113 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 103 optimal weight: 30.0000 chunk 30 optimal weight: 0.1980 chunk 149 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 84 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** F 75 HIS ** 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 = 0.3515 r_free = 0.3515 target = 0.060024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.039162 restraints weight = 165259.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.039132 restraints weight = 88959.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.039528 restraints weight = 59547.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.039677 restraints weight = 49938.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.039812 restraints weight = 46776.660| |-----------------------------------------------------------------------------| r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18201 Z= 0.135 Angle : 0.585 8.871 25994 Z= 0.337 Chirality : 0.039 0.335 2886 Planarity : 0.004 0.042 2162 Dihedral : 29.970 175.521 5132 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 2.41 (0.24), residues: 1258 helix: 2.28 (0.18), residues: 784 sheet: 0.02 (0.58), residues: 79 loop : 0.67 (0.33), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 23 TYR 0.019 0.001 TYR K1102 PHE 0.023 0.001 PHE D 65 TRP 0.006 0.001 TRP K1158 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.13 (18201) covalent geometry : angle 0.58499 / 0.34 (25994) hydrogen bonds : bond 0.04354 / 2.95 ( 915) hydrogen bonds : angle 3.27284 / 2.43 ( 2405) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.8754 (mtm) cc_final: 0.8266 (mtp) REVERT: B 97 LEU cc_start: 0.9358 (tp) cc_final: 0.9060 (tp) REVERT: E 106 ASP cc_start: 0.9033 (m-30) cc_final: 0.8827 (m-30) REVERT: H 61 ILE cc_start: 0.9392 (mm) cc_final: 0.9013 (mm) REVERT: K 1502 TRP cc_start: 0.4972 (t60) cc_final: 0.4405 (t60) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.1225 time to fit residues: 8.2694 Evaluate side-chains 34 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 61 optimal weight: 2.9990 chunk 17 optimal weight: 0.0070 chunk 14 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 79 optimal weight: 20.0000 chunk 73 optimal weight: 50.0000 chunk 97 optimal weight: 30.0000 chunk 116 optimal weight: 5.9990 overall best weight: 1.3002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** 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 = 0.3519 r_free = 0.3519 target = 0.060166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.039288 restraints weight = 164358.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.039287 restraints weight = 88026.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.039634 restraints weight = 59120.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.039887 restraints weight = 49815.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.039932 restraints weight = 45779.780| |-----------------------------------------------------------------------------| r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 18201 Z= 0.129 Angle : 0.581 9.291 25994 Z= 0.334 Chirality : 0.039 0.333 2886 Planarity : 0.004 0.043 2162 Dihedral : 29.948 175.423 5132 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 2.45 (0.24), residues: 1258 helix: 2.33 (0.18), residues: 784 sheet: -0.12 (0.57), residues: 79 loop : 0.67 (0.33), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 23 TYR 0.018 0.001 TYR K1102 PHE 0.034 0.001 PHE K1410 TRP 0.007 0.001 TRP K1158 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.13 (18201) covalent geometry : angle 0.58092 / 0.33 (25994) hydrogen bonds : bond 0.04227 / 2.86 ( 915) hydrogen bonds : angle 3.22141 / 2.39 ( 2405) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.534 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.8726 (mtm) cc_final: 0.8060 (mtp) REVERT: B 97 LEU cc_start: 0.9350 (tp) cc_final: 0.9056 (tp) REVERT: E 106 ASP cc_start: 0.9029 (m-30) cc_final: 0.8729 (m-30) REVERT: H 61 ILE cc_start: 0.9390 (mm) cc_final: 0.9022 (mm) REVERT: K 1502 TRP cc_start: 0.5001 (t60) cc_final: 0.4433 (t60) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.1150 time to fit residues: 7.7258 Evaluate side-chains 34 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 87 optimal weight: 30.0000 chunk 41 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 123 optimal weight: 8.9990 chunk 114 optimal weight: 7.9990 chunk 138 optimal weight: 0.1980 chunk 91 optimal weight: 30.0000 chunk 26 optimal weight: 0.7980 chunk 130 optimal weight: 30.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 93 GLN ** 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 = 0.3516 r_free = 0.3516 target = 0.059989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.039211 restraints weight = 164929.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.039119 restraints weight = 89478.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.039461 restraints weight = 60094.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.039726 restraints weight = 49961.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.039803 restraints weight = 46561.582| |-----------------------------------------------------------------------------| r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18201 Z= 0.133 Angle : 0.585 9.985 25994 Z= 0.335 Chirality : 0.039 0.333 2886 Planarity : 0.004 0.042 2162 Dihedral : 29.963 175.298 5132 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 2.41 (0.24), residues: 1258 helix: 2.31 (0.18), residues: 784 sheet: -0.16 (0.56), residues: 79 loop : 0.62 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 35 TYR 0.015 0.001 TYR K1102 PHE 0.020 0.001 PHE K1410 TRP 0.006 0.001 TRP K1158 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.13 (18201) covalent geometry : angle 0.58464 / 0.33 (25994) hydrogen bonds : bond 0.04355 / 2.95 ( 915) hydrogen bonds : angle 3.22572 / 2.39 ( 2405) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2998.81 seconds wall clock time: 52 minutes 31.28 seconds (3151.28 seconds total)