Starting phenix.real_space_refine on Sat Jul 4 00:04:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ham_34596/07_2026/8ham_34596.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ham_34596/07_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_34596/07_2026/8ham_34596.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ham_34596/07_2026/8ham_34596.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ham_34596/07_2026/8ham_34596.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ham_34596/07_2026/8ham_34596.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8ham_34596/07_2026/8ham_34596.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ham_34596/07_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-dev-6108/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: 3.49, 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 490.9 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: 2.43 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: 4.09 Time building geometry restraints manager: 1.95 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: 25148 2.07 - 4.14: 823 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: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.470 Find NCS groups from input model: 0.230 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.350 ------------------------------------------------------------------------------- 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 : 0.710 10.362 25994 Z= 0.619 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 0.70965 / 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 : 0.589 Fit side-chains REVERT: A 97 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7867 (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: 0.3669 (t60) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1320 time to fit residues: 11.7594 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 : 0.516 ------------------------------------------------------------------------------- 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: 0.7980 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: 9.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 30.0000 chunk 149 optimal weight: 5.9990 overall best weight: 6.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.061137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.040587 restraints weight = 166693.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.040506 restraints weight = 90792.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.040859 restraints weight = 61017.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.041117 restraints weight = 50731.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.041295 restraints weight = 46264.081| |-----------------------------------------------------------------------------| r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 18201 Z= 0.352 Angle : 0.895 12.026 25994 Z= 0.480 Chirality : 0.049 0.440 2886 Planarity : 0.007 0.063 2162 Dihedral : 29.831 177.520 5132 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.27 % Allowed : 3.06 % Favored : 96.67 % 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: 1.39 (0.23), residues: 1258 helix: 1.31 (0.18), residues: 783 sheet: 0.37 (0.59), residues: 79 loop : 0.46 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 35 TYR 0.034 0.002 TYR C 50 PHE 0.036 0.003 PHE G 25 TRP 0.017 0.002 TRP K1545 HIS 0.011 0.003 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00691 / 0.35 (18201) covalent geometry : angle 0.89495 / 0.48 (25994) hydrogen bonds : bond 0.09097 / 6.13 ( 915) hydrogen bonds : angle 4.47315 / 3.27 ( 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 43 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.528 Fit side-chains REVERT: A 120 MET cc_start: 0.8689 (mtm) cc_final: 0.8112 (mtp) REVERT: E 97 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7429 (mt-10) REVERT: H 61 ILE cc_start: 0.9532 (mm) cc_final: 0.9299 (mm) REVERT: K 1502 TRP cc_start: 0.4358 (t60) cc_final: 0.4040 (t60) outliers start: 3 outliers final: 1 residues processed: 43 average time/residue: 0.1287 time to fit residues: 9.4257 Evaluate side-chains 32 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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: 5.9990 chunk 74 optimal weight: 30.0000 chunk 121 optimal weight: 30.0000 chunk 128 optimal weight: 6.9990 chunk 107 optimal weight: 30.0000 chunk 61 optimal weight: 1.9990 chunk 78 optimal weight: 20.0000 chunk 60 optimal weight: 3.9990 chunk 96 optimal weight: 20.0000 chunk 21 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.3547 r_free = 0.3547 target = 0.061421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.040719 restraints weight = 165955.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.040674 restraints weight = 87937.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.041163 restraints weight = 59296.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.041357 restraints weight = 47776.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.041443 restraints weight = 44842.902| |-----------------------------------------------------------------------------| r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 18201 Z= 0.192 Angle : 0.617 10.096 25994 Z= 0.361 Chirality : 0.041 0.360 2886 Planarity : 0.004 0.053 2162 Dihedral : 29.815 178.610 5132 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % 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: 2.11 (0.23), residues: 1258 helix: 1.98 (0.18), residues: 785 sheet: 0.38 (0.59), residues: 77 loop : 0.57 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 35 TYR 0.015 0.001 TYR C 50 PHE 0.013 0.002 PHE K1410 TRP 0.008 0.001 TRP K1545 HIS 0.005 0.001 HIS K1451 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.19 (18201) covalent geometry : angle 0.61665 / 0.36 (25994) hydrogen bonds : bond 0.05172 / 3.46 ( 915) hydrogen bonds : angle 3.73537 / 2.76 ( 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 : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8656 (mtm) cc_final: 0.7978 (mtp) REVERT: F 84 MET cc_start: 0.8398 (tpp) cc_final: 0.8105 (tpp) REVERT: H 61 ILE cc_start: 0.9497 (mm) cc_final: 0.9229 (mm) REVERT: H 62 MET cc_start: 0.9424 (tpt) cc_final: 0.9133 (tpp) REVERT: K 1502 TRP cc_start: 0.4329 (t60) cc_final: 0.3998 (t60) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1377 time to fit residues: 10.0515 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 : 0.498 ------------------------------------------------------------------------------- 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: 8.9990 chunk 133 optimal weight: 7.9990 chunk 89 optimal weight: 50.0000 chunk 25 optimal weight: 0.0980 chunk 30 optimal weight: 5.9990 chunk 154 optimal weight: 40.0000 chunk 6 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 152 optimal weight: 40.0000 chunk 1 optimal weight: 1.9990 chunk 9 optimal weight: 20.0000 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K1146 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.060978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.040192 restraints weight = 166119.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.040063 restraints weight = 88891.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.040408 restraints weight = 59948.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.040680 restraints weight = 49350.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.040690 restraints weight = 45222.175| |-----------------------------------------------------------------------------| r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 18201 Z= 0.184 Angle : 0.617 9.855 25994 Z= 0.357 Chirality : 0.040 0.358 2886 Planarity : 0.004 0.055 2162 Dihedral : 29.845 179.980 5132 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % 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: 2.24 (0.23), residues: 1258 helix: 2.10 (0.18), residues: 785 sheet: 0.30 (0.58), residues: 77 loop : 0.61 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 99 TYR 0.013 0.001 TYR K1147 PHE 0.024 0.002 PHE A 104 TRP 0.007 0.001 TRP K1545 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.18 (18201) covalent geometry : angle 0.61675 / 0.36 (25994) hydrogen bonds : bond 0.05294 / 3.57 ( 915) hydrogen bonds : angle 3.60731 / 2.67 ( 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 47 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8762 (mtm) cc_final: 0.7993 (mtp) REVERT: D 94 ILE cc_start: 0.9460 (tp) cc_final: 0.9138 (tt) REVERT: F 84 MET cc_start: 0.8297 (tpp) cc_final: 0.8094 (tpp) REVERT: H 61 ILE cc_start: 0.9461 (mm) cc_final: 0.9177 (mm) REVERT: H 62 MET cc_start: 0.9391 (tpt) cc_final: 0.9088 (tpp) REVERT: K 1502 TRP cc_start: 0.4698 (t60) cc_final: 0.4201 (t60) REVERT: K 1691 MET cc_start: 0.4995 (ppp) cc_final: 0.4746 (ppp) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1235 time to fit residues: 9.7893 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 : 0.505 ------------------------------------------------------------------------------- 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: 20.0000 chunk 46 optimal weight: 0.9980 chunk 129 optimal weight: 20.0000 chunk 154 optimal weight: 50.0000 chunk 2 optimal weight: 0.8980 chunk 27 optimal weight: 9.9990 chunk 12 optimal weight: 0.8980 chunk 96 optimal weight: 20.0000 chunk 58 optimal weight: 0.7980 overall best weight: 2.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN K1413 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.060330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.039376 restraints weight = 164843.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.039290 restraints weight = 88878.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.039657 restraints weight = 59562.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.039863 restraints weight = 50321.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.040004 restraints weight = 46512.074| |-----------------------------------------------------------------------------| r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 18201 Z= 0.175 Angle : 0.598 8.048 25994 Z= 0.350 Chirality : 0.040 0.337 2886 Planarity : 0.004 0.053 2162 Dihedral : 29.920 177.900 5132 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % 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: 2.38 (0.24), residues: 1258 helix: 2.23 (0.18), residues: 785 sheet: 0.11 (0.57), residues: 79 loop : 0.70 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 92 TYR 0.009 0.001 TYR C 57 PHE 0.015 0.001 PHE K1410 TRP 0.006 0.001 TRP K1545 HIS 0.008 0.001 HIS K1451 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.18 (18201) covalent geometry : angle 0.59781 / 0.35 (25994) hydrogen bonds : bond 0.04811 / 3.26 ( 915) hydrogen bonds : angle 3.50214 / 2.61 ( 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 47 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8705 (mtm) cc_final: 0.8171 (mtp) REVERT: C 72 ASP cc_start: 0.9062 (m-30) cc_final: 0.8804 (m-30) REVERT: E 106 ASP cc_start: 0.9175 (m-30) cc_final: 0.8898 (m-30) REVERT: F 84 MET cc_start: 0.8159 (tpp) cc_final: 0.7938 (tpp) REVERT: G 78 ILE cc_start: 0.9081 (mt) cc_final: 0.8510 (tp) REVERT: H 61 ILE cc_start: 0.9494 (mm) cc_final: 0.9192 (mm) REVERT: K 1502 TRP cc_start: 0.4764 (t60) cc_final: 0.4119 (t60) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1229 time to fit residues: 9.7813 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 : 0.481 ------------------------------------------------------------------------------- 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: 7.9990 chunk 31 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 19 optimal weight: 0.3980 chunk 98 optimal weight: 20.0000 chunk 90 optimal weight: 40.0000 chunk 79 optimal weight: 20.0000 chunk 86 optimal weight: 20.0000 chunk 37 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.3525 r_free = 0.3525 target = 0.060539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.039761 restraints weight = 164108.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 76)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.039585 restraints weight = 90125.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.039958 restraints weight = 60191.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.040222 restraints weight = 49829.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.040267 restraints weight = 45663.809| |-----------------------------------------------------------------------------| r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3520 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= 0.139 Angle : 0.575 8.339 25994 Z= 0.336 Chirality : 0.039 0.326 2886 Planarity : 0.004 0.052 2162 Dihedral : 29.878 178.018 5132 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % 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: 2.46 (0.24), residues: 1258 helix: 2.30 (0.18), residues: 785 sheet: 0.18 (0.58), residues: 79 loop : 0.68 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 99 TYR 0.021 0.001 TYR G 50 PHE 0.017 0.001 PHE H 65 TRP 0.005 0.001 TRP K1158 HIS 0.007 0.001 HIS K1451 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.14 (18201) covalent geometry : angle 0.57521 / 0.34 (25994) hydrogen bonds : bond 0.04448 / 3.01 ( 915) hydrogen bonds : angle 3.34399 / 2.48 ( 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 45 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8800 (mtm) cc_final: 0.8201 (mtp) REVERT: D 59 MET cc_start: 0.9303 (tpp) cc_final: 0.9092 (tpp) REVERT: E 106 ASP cc_start: 0.9223 (m-30) cc_final: 0.8909 (m-30) REVERT: F 84 MET cc_start: 0.8199 (tpp) cc_final: 0.7919 (tpp) REVERT: H 61 ILE cc_start: 0.9415 (mm) cc_final: 0.9116 (mm) REVERT: K 1290 MET cc_start: -0.0530 (mmt) cc_final: -0.0730 (mmm) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1218 time to fit residues: 9.3151 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 : 0.525 ------------------------------------------------------------------------------- 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: 6.9990 chunk 137 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 40.0000 chunk 38 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 95 optimal weight: 20.0000 chunk 68 optimal weight: 0.7980 chunk 145 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.059589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.038841 restraints weight = 164328.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.038764 restraints weight = 88705.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.039101 restraints weight = 60239.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.039365 restraints weight = 50089.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.039443 restraints weight = 46220.573| |-----------------------------------------------------------------------------| r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 18201 Z= 0.192 Angle : 0.622 12.543 25994 Z= 0.357 Chirality : 0.040 0.335 2886 Planarity : 0.004 0.051 2162 Dihedral : 29.997 177.166 5132 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % 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: 2.32 (0.24), residues: 1258 helix: 2.19 (0.18), residues: 784 sheet: 0.09 (0.59), residues: 79 loop : 0.63 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 29 TYR 0.010 0.001 TYR H 40 PHE 0.016 0.002 PHE H 65 TRP 0.007 0.001 TRP K1545 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.19 (18201) covalent geometry : angle 0.62218 / 0.36 (25994) hydrogen bonds : bond 0.05256 / 3.56 ( 915) hydrogen bonds : angle 3.51753 / 2.61 ( 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 38 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.551 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.9004 (mmm) cc_final: 0.8801 (mmp) REVERT: A 120 MET cc_start: 0.8742 (mtm) cc_final: 0.8233 (mtp) REVERT: E 106 ASP cc_start: 0.9217 (m-30) cc_final: 0.8913 (m-30) REVERT: F 84 MET cc_start: 0.8245 (tpp) cc_final: 0.7982 (tpp) REVERT: H 61 ILE cc_start: 0.9463 (mm) cc_final: 0.9166 (mm) REVERT: K 1375 MET cc_start: -0.1644 (ttt) cc_final: -0.2441 (ttt) REVERT: K 1502 TRP cc_start: 0.4426 (t60) cc_final: 0.4110 (t60) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1365 time to fit residues: 8.5975 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 : 0.508 ------------------------------------------------------------------------------- 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: 0.7980 chunk 61 optimal weight: 4.9990 chunk 79 optimal weight: 20.0000 chunk 128 optimal weight: 7.9990 chunk 81 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 chunk 102 optimal weight: 20.0000 chunk 56 optimal weight: 6.9990 chunk 123 optimal weight: 20.0000 chunk 68 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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 = 0.3491 r_free = 0.3491 target = 0.059305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.038465 restraints weight = 165862.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.038460 restraints weight = 89430.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.038853 restraints weight = 59922.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.038974 restraints weight = 50140.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.039157 restraints weight = 46843.484| |-----------------------------------------------------------------------------| r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18201 Z= 0.200 Angle : 0.631 10.081 25994 Z= 0.362 Chirality : 0.040 0.330 2886 Planarity : 0.004 0.050 2162 Dihedral : 30.087 176.507 5132 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 12.12 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: 2.19 (0.24), residues: 1258 helix: 2.10 (0.18), residues: 784 sheet: 0.03 (0.58), residues: 79 loop : 0.55 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 92 TYR 0.025 0.001 TYR K1102 PHE 0.016 0.002 PHE H 65 TRP 0.007 0.001 TRP K1545 HIS 0.008 0.001 HIS K1451 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.20 (18201) covalent geometry : angle 0.63123 / 0.36 (25994) hydrogen bonds : bond 0.05269 / 3.58 ( 915) hydrogen bonds : angle 3.58872 / 2.67 ( 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 35 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8743 (mtm) cc_final: 0.8198 (mtp) REVERT: F 84 MET cc_start: 0.8135 (tpp) cc_final: 0.7906 (tpp) REVERT: H 61 ILE cc_start: 0.9486 (mm) cc_final: 0.9181 (mm) REVERT: K 1375 MET cc_start: -0.2231 (ttt) cc_final: -0.3013 (mmm) REVERT: K 1502 TRP cc_start: 0.4472 (t60) cc_final: 0.4076 (t60) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1321 time to fit residues: 7.9262 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 : 0.503 ------------------------------------------------------------------------------- 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: 6.9990 chunk 52 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 103 optimal weight: 30.0000 chunk 30 optimal weight: 0.9980 chunk 149 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.059300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.038399 restraints weight = 165931.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.038368 restraints weight = 88826.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.038733 restraints weight = 60088.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.038915 restraints weight = 50996.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.039038 restraints weight = 46906.433| |-----------------------------------------------------------------------------| r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18201 Z= 0.173 Angle : 0.608 9.814 25994 Z= 0.353 Chirality : 0.040 0.315 2886 Planarity : 0.004 0.049 2162 Dihedral : 30.174 176.708 5132 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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: 2.14 (0.24), residues: 1258 helix: 2.08 (0.18), residues: 784 sheet: -0.03 (0.57), residues: 79 loop : 0.51 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 92 TYR 0.024 0.001 TYR K1102 PHE 0.026 0.002 PHE D 65 TRP 0.008 0.001 TRP K1545 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.17 (18201) covalent geometry : angle 0.60782 / 0.35 (25994) hydrogen bonds : bond 0.04756 / 3.24 ( 915) hydrogen bonds : angle 3.49388 / 2.59 ( 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 : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8740 (mtm) cc_final: 0.8294 (mtp) REVERT: F 84 MET cc_start: 0.7984 (tpp) cc_final: 0.7706 (tpp) REVERT: H 61 ILE cc_start: 0.9448 (mm) cc_final: 0.9131 (mm) REVERT: K 1502 TRP cc_start: 0.4922 (t60) cc_final: 0.4550 (t60) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.1358 time to fit residues: 8.8097 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 : 0.512 ------------------------------------------------------------------------------- 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: 7.9990 chunk 17 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 28 optimal weight: 0.1980 chunk 57 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 79 optimal weight: 20.0000 chunk 73 optimal weight: 50.0000 chunk 97 optimal weight: 20.0000 chunk 116 optimal weight: 7.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 = 0.3507 r_free = 0.3507 target = 0.059735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.038860 restraints weight = 164295.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.038782 restraints weight = 88154.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.039104 restraints weight = 59850.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.039386 restraints weight = 49886.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.039480 restraints weight = 46191.025| |-----------------------------------------------------------------------------| r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 18201 Z= 0.134 Angle : 0.593 8.999 25994 Z= 0.343 Chirality : 0.039 0.307 2886 Planarity : 0.004 0.049 2162 Dihedral : 30.143 177.149 5132 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % 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: 2.24 (0.24), residues: 1258 helix: 2.16 (0.18), residues: 784 sheet: 0.01 (0.58), residues: 79 loop : 0.52 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 92 TYR 0.020 0.001 TYR K1102 PHE 0.015 0.001 PHE D 65 TRP 0.004 0.001 TRP K1545 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.13 (18201) covalent geometry : angle 0.59282 / 0.34 (25994) hydrogen bonds : bond 0.04435 / 3.00 ( 915) hydrogen bonds : angle 3.35562 / 2.49 ( 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 42 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8796 (mtm) cc_final: 0.8277 (mtp) REVERT: B 97 LEU cc_start: 0.9377 (tp) cc_final: 0.9131 (tp) REVERT: D 59 MET cc_start: 0.9243 (tpp) cc_final: 0.8851 (tpp) REVERT: E 106 ASP cc_start: 0.9001 (m-30) cc_final: 0.8800 (m-30) REVERT: F 63 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8186 (mt-10) REVERT: F 84 MET cc_start: 0.7824 (tpp) cc_final: 0.7518 (tpp) REVERT: H 61 ILE cc_start: 0.9436 (mm) cc_final: 0.9113 (mm) REVERT: K 1375 MET cc_start: -0.2492 (ttt) cc_final: -0.2815 (mmm) REVERT: K 1385 MET cc_start: 0.7564 (tmm) cc_final: 0.7247 (ptm) REVERT: K 1502 TRP cc_start: 0.4920 (t60) cc_final: 0.4529 (t60) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1326 time to fit residues: 9.3578 Evaluate side-chains 36 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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: 3.9990 chunk 63 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 123 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 91 optimal weight: 30.0000 chunk 26 optimal weight: 3.9990 chunk 130 optimal weight: 30.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** 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 = 0.3486 r_free = 0.3486 target = 0.059358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.038547 restraints weight = 165279.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.038359 restraints weight = 90625.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.038742 restraints weight = 61653.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.038903 restraints weight = 51732.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.039071 restraints weight = 47887.623| |-----------------------------------------------------------------------------| r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.4594 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= 0.174 Angle : 0.617 8.998 25994 Z= 0.353 Chirality : 0.040 0.315 2886 Planarity : 0.004 0.047 2162 Dihedral : 30.238 176.224 5132 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % 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: 2.14 (0.24), residues: 1258 helix: 2.11 (0.18), residues: 784 sheet: -0.07 (0.57), residues: 79 loop : 0.45 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 35 TYR 0.019 0.001 TYR K1102 PHE 0.017 0.002 PHE D 65 TRP 0.008 0.001 TRP K1545 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.17 (18201) covalent geometry : angle 0.61717 / 0.35 (25994) hydrogen bonds : bond 0.05126 / 3.48 ( 915) hydrogen bonds : angle 3.49672 / 2.59 ( 2405) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3288.52 seconds wall clock time: 57 minutes 45.42 seconds (3465.42 seconds total)