Starting phenix.real_space_refine on Thu Aug 6 02:30:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u5h_41922/08_2026/8u5h_41922.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u5h_41922/08_2026/8u5h_41922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8u5h_41922/08_2026/8u5h_41922.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u5h_41922/08_2026/8u5h_41922.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u5h_41922/08_2026/8u5h_41922.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u5h_41922/08_2026/8u5h_41922.map" } resolution = 3.23 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= 0.004 sd= 2.051 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 314 5.49 5 S 15 5.16 5 C 7463 2.51 5 N 2514 2.21 5 O 3130 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 13436 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 281 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 3, 'TRANS': 37} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'ARG:plan': 3, 'GLU:plan': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 163 Classifications: {'peptide': 23} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 20} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 3200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 3200 Classifications: {'DNA': 157} Link IDs: {'rna3p': 156} Chain: "D" Number of atoms: 488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 488 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 3, 'TRANS': 62} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "H" Number of atoms: 3237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 3237 Classifications: {'DNA': 157} Link IDs: {'rna3p': 156} Chain: "I" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} 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: "J" Number of atoms: 676 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 84, 667 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} 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 Conformer: "B" Number of residues, atoms: 84, 667 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} 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 bond proxies already assigned to first conformer: 664 Chain: "K" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 824 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 104} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "M" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 731 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "O" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} 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: "Q" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 647 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 81} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "S" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 741 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ALYS J 20 " occ=0.77 ... (16 atoms not shown) pdb=" NZ BLYS J 20 " occ=0.23 Time building chain proxies: 2.63, per 1000 atoms: 0.20 Number of scatterers: 13436 At special positions: 0 Unit cell: (90.1331, 127.174, 122.235, 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 15 16.00 P 314 15.00 O 3130 8.00 N 2514 7.00 C 7463 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 485.9 milliseconds 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1694 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 10 sheets defined 64.7% alpha, 4.1% beta 153 base pairs and 259 stacking pairs defined. Time for finding SS restraints: 2.27 Creating SS restraints... Processing helix chain 'A' and resid 199 through 210 Processing helix chain 'B' and resid 173 through 177 removed outlier: 3.589A pdb=" N GLU B 177 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 35 removed outlier: 3.606A pdb=" N ILE D 30 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN D 31 " --> pdb=" O LYS D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'I' and resid 44 through 57 removed outlier: 4.226A pdb=" N LEU I 48 " --> pdb=" O GLY I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 79 removed outlier: 3.854A pdb=" N ASP I 77 " --> pdb=" O GLU I 73 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE I 78 " --> pdb=" O ILE I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 114 removed outlier: 3.638A pdb=" N MET I 90 " --> pdb=" O ARG I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 131 Processing helix chain 'J' and resid 25 through 29 Processing helix chain 'J' and resid 30 through 42 Processing helix chain 'J' and resid 49 through 76 removed outlier: 4.043A pdb=" N GLU J 53 " --> pdb=" O LEU J 49 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG J 55 " --> pdb=" O TYR J 51 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP J 68 " --> pdb=" O ASN J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 94 Processing helix chain 'K' and resid 16 through 22 Processing helix chain 'K' and resid 26 through 37 Processing helix chain 'K' and resid 45 through 73 removed outlier: 4.247A pdb=" N VAL K 49 " --> pdb=" O ALA K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 88 removed outlier: 3.722A pdb=" N LEU K 83 " --> pdb=" O ILE K 79 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN K 84 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 97 Processing helix chain 'M' and resid 34 through 46 Processing helix chain 'M' and resid 52 through 81 removed outlier: 3.853A pdb=" N ASN M 81 " --> pdb=" O LEU M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 99 Processing helix chain 'M' and resid 101 through 119 removed outlier: 3.887A pdb=" N SER M 109 " --> pdb=" O LYS M 105 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR M 118 " --> pdb=" O ALA M 114 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 57 removed outlier: 3.577A pdb=" N ARG O 49 " --> pdb=" O THR O 45 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 76 Processing helix chain 'O' and resid 85 through 114 Processing helix chain 'O' and resid 120 through 132 removed outlier: 3.507A pdb=" N ILE O 124 " --> pdb=" O MET O 120 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 29 removed outlier: 3.507A pdb=" N ILE Q 29 " --> pdb=" O ILE Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 30 through 42 Processing helix chain 'Q' and resid 49 through 76 removed outlier: 3.580A pdb=" N GLU Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ARG Q 55 " --> pdb=" O TYR Q 51 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP Q 68 " --> pdb=" O ASN Q 64 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 93 Processing helix chain 'R' and resid 16 through 22 Processing helix chain 'R' and resid 26 through 37 Processing helix chain 'R' and resid 45 through 73 removed outlier: 4.346A pdb=" N VAL R 49 " --> pdb=" O ALA R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 89 Processing helix chain 'R' and resid 90 through 97 Processing helix chain 'S' and resid 34 through 46 Processing helix chain 'S' and resid 52 through 81 removed outlier: 4.154A pdb=" N ASN S 81 " --> pdb=" O LEU S 77 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 99 Processing helix chain 'S' and resid 101 through 121 removed outlier: 3.578A pdb=" N LYS S 105 " --> pdb=" O GLY S 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 13 through 16 removed outlier: 3.759A pdb=" N LEU D 15 " --> pdb=" O ILE D 3 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 83 through 84 removed outlier: 6.851A pdb=" N ARG I 83 " --> pdb=" O VAL J 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'I' and resid 118 through 119 Processing sheet with id=AA4, first strand: chain 'J' and resid 96 through 98 removed outlier: 6.848A pdb=" N THR J 96 " --> pdb=" O THR R 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'K' and resid 42 through 43 removed outlier: 7.109A pdb=" N ARG K 42 " --> pdb=" O ILE M 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'K' and resid 77 through 78 Processing sheet with id=AA7, first strand: chain 'K' and resid 100 through 102 Processing sheet with id=AA8, first strand: chain 'O' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'R' and resid 42 through 43 removed outlier: 7.880A pdb=" N ARG R 42 " --> pdb=" O ILE S 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'R' and resid 77 through 78 424 hydrogen bonds defined for protein. 1251 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 385 hydrogen bonds 750 hydrogen bond angles 0 basepair planarities 153 basepair parallelities 259 stacking parallelities Total time for adding SS restraints: 2.84 Time building geometry restraints manager: 1.18 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: 2494 1.33 - 1.45: 4642 1.45 - 1.57: 6525 1.57 - 1.69: 626 1.69 - 1.81: 26 Bond restraints: 14313 Sorted by residual: bond pdb=" C3' DA C 211 " pdb=" C2' DA C 211 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" C3' DG H 40 " pdb=" C2' DG H 40 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DA H 13 " pdb=" C2' DA H 13 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C3' DT H 98 " pdb=" C2' DT H 98 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.91e+00 bond pdb=" C3' DT C 285 " pdb=" C2' DT C 285 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.82e+00 ... (remaining 14308 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 19492 1.81 - 3.62: 1088 3.62 - 5.43: 82 5.43 - 7.24: 32 7.24 - 9.05: 5 Bond angle restraints: 20699 Sorted by residual: angle pdb=" O4' DG C 208 " pdb=" C4' DG C 208 " pdb=" C3' DG C 208 " ideal model delta sigma weight residual 106.00 103.08 2.92 6.00e-01 2.78e+00 2.37e+01 angle pdb=" N3 DT C 280 " pdb=" C4 DT C 280 " pdb=" O4 DT C 280 " ideal model delta sigma weight residual 119.90 122.71 -2.81 6.00e-01 2.78e+00 2.19e+01 angle pdb=" O4' DG C 187 " pdb=" C4' DG C 187 " pdb=" C3' DG C 187 " ideal model delta sigma weight residual 106.00 103.27 2.73 6.00e-01 2.78e+00 2.07e+01 angle pdb=" N3 DT H 82 " pdb=" C4 DT H 82 " pdb=" O4 DT H 82 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.01e+01 angle pdb=" N3 DT H 34 " pdb=" C4 DT H 34 " pdb=" O4 DT H 34 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 2.00e+01 ... (remaining 20694 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 6275 35.81 - 71.62: 1468 71.62 - 107.43: 29 107.43 - 143.24: 6 143.24 - 179.05: 21 Dihedral angle restraints: 7799 sinusoidal: 5181 harmonic: 2618 Sorted by residual: dihedral pdb=" C4' DA H 5 " pdb=" C3' DA H 5 " pdb=" O3' DA H 5 " pdb=" P DT H 6 " ideal model delta sinusoidal sigma weight residual 220.00 40.95 179.05 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC C 224 " pdb=" C3' DC C 224 " pdb=" O3' DC C 224 " pdb=" P DT C 225 " ideal model delta sinusoidal sigma weight residual -140.00 37.49 -177.49 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DA C 309 " pdb=" C3' DA C 309 " pdb=" O3' DA C 309 " pdb=" P DT C 310 " ideal model delta sinusoidal sigma weight residual -140.00 34.44 -174.44 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 7796 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 2308 0.124 - 0.247: 40 0.247 - 0.371: 0 0.371 - 0.494: 0 0.494 - 0.618: 19 Chirality restraints: 2367 Sorted by residual: chirality pdb=" P DG H 136 " pdb=" OP1 DG H 136 " pdb=" OP2 DG H 136 " pdb=" O5' DG H 136 " both_signs ideal model delta sigma weight residual True 2.34 -2.95 -0.62 2.00e-01 2.50e+01 9.55e+00 chirality pdb=" P DC C 221 " pdb=" OP1 DC C 221 " pdb=" OP2 DC C 221 " pdb=" O5' DC C 221 " both_signs ideal model delta sigma weight residual True 2.34 -2.93 -0.60 2.00e-01 2.50e+01 8.91e+00 chirality pdb=" P DC H 48 " pdb=" OP1 DC H 48 " pdb=" OP2 DC H 48 " pdb=" O5' DC H 48 " both_signs ideal model delta sigma weight residual True 2.34 -2.93 -0.59 2.00e-01 2.50e+01 8.70e+00 ... (remaining 2364 not shown) Planarity restraints: 1540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG I 42 " 0.036 5.00e-02 4.00e+02 5.41e-02 4.69e+00 pdb=" N PRO I 43 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO I 43 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO I 43 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG C 202 " 0.001 2.00e-02 2.50e+03 1.17e-02 4.09e+00 pdb=" N9 DG C 202 " 0.008 2.00e-02 2.50e+03 pdb=" C8 DG C 202 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DG C 202 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DG C 202 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG C 202 " -0.013 2.00e-02 2.50e+03 pdb=" O6 DG C 202 " 0.012 2.00e-02 2.50e+03 pdb=" N1 DG C 202 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DG C 202 " -0.030 2.00e-02 2.50e+03 pdb=" N2 DG C 202 " 0.019 2.00e-02 2.50e+03 pdb=" N3 DG C 202 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DG C 202 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE R 79 " -0.032 5.00e-02 4.00e+02 4.79e-02 3.68e+00 pdb=" N PRO R 80 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO R 80 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO R 80 " -0.027 5.00e-02 4.00e+02 ... (remaining 1537 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1301 2.74 - 3.28: 12529 3.28 - 3.82: 27024 3.82 - 4.36: 30349 4.36 - 4.90: 44242 Nonbonded interactions: 115445 Sorted by model distance: nonbonded pdb=" N2 DG C 262 " pdb=" O2 DC H 53 " model vdw 2.200 2.496 nonbonded pdb=" N2 DG C 181 " pdb=" O2 DC H 134 " model vdw 2.201 2.496 nonbonded pdb=" OG SER I 57 " pdb=" OE1 GLU I 59 " model vdw 2.209 3.040 nonbonded pdb=" OP2 DG C 187 " pdb=" OG SER S 53 " model vdw 2.225 3.040 nonbonded pdb=" O2 DC C 180 " pdb=" N2 DG H 135 " model vdw 2.227 2.496 ... (remaining 115440 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 'I' selection = (chain 'O' and resid 38 through 135) } ncs_group { reference = (chain 'J' and ((resid 21 through 23 and (name N or name CA or name C or name O \ or name CB )) or resid 24 through 102)) selection = (chain 'Q' and resid 21 through 102) } ncs_group { reference = (chain 'K' and resid 12 through 119) selection = (chain 'R' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 56 or (resid 57 and (name N or name CA or name \ C or name O or name CB )) or resid 58 through 61 or (resid 62 and (name N or na \ me CA or name C or name O or name CB )) or resid 63 through 93 or (resid 94 and \ (name N or name CA or name C or name O or name CB )) or resid 95 through 119)) } ncs_group { reference = chain 'M' selection = (chain 'S' and (resid 28 through 105 or (resid 106 through 107 and (name N or na \ me CA or name C or name O or name CB )) or resid 108 through 122)) } 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=0.23 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 14.460 Find NCS groups from input model: 0.150 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: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 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 : 0.006 0.045 14313 Z= 0.522 Angle : 0.849 9.048 20699 Z= 0.684 Chirality : 0.068 0.618 2367 Planarity : 0.004 0.054 1540 Dihedral : 30.149 179.048 6105 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.85 % Allowed : 30.31 % Favored : 68.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.28), residues: 879 helix: 1.55 (0.22), residues: 553 sheet: 1.21 (1.16), residues: 21 loop : -1.17 (0.33), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 95 TYR 0.020 0.002 TYR J 88 PHE 0.009 0.001 PHE J 100 TRP 0.007 0.001 TRP A 176 HIS 0.004 0.001 HIS S 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00620 / 0.52 (14313) covalent geometry : angle 0.84926 / 0.68 (20699) hydrogen bonds : bond 0.13680 / 12.37 ( 809) hydrogen bonds : angle 5.46606 / 6.35 ( 2001) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 138 time to evaluate : 0.371 Fit side-chains REVERT: I 59 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7419 (pm20) REVERT: M 61 SER cc_start: 0.9096 (m) cc_final: 0.8864 (m) REVERT: Q 91 LYS cc_start: 0.8994 (ttpt) cc_final: 0.8785 (ttmm) outliers start: 6 outliers final: 2 residues processed: 140 average time/residue: 0.1353 time to fit residues: 25.6956 Evaluate side-chains 140 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 137 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain M residue 44 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 0.0030 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.4980 chunk 100 optimal weight: 0.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 84 GLN ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 108 ASN Q 25 ASN Q 93 GLN ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.179181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.120339 restraints weight = 38400.548| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.42 r_work: 0.3100 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3097 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3097 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.0686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14313 Z= 0.166 Angle : 0.692 8.912 20699 Z= 0.405 Chirality : 0.049 0.337 2367 Planarity : 0.005 0.053 1540 Dihedral : 32.714 178.359 4442 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.12 % Allowed : 28.61 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.28), residues: 879 helix: 1.71 (0.22), residues: 573 sheet: 0.35 (1.06), residues: 21 loop : -1.24 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 95 TYR 0.015 0.001 TYR J 88 PHE 0.008 0.001 PHE J 100 TRP 0.005 0.001 TRP B 176 HIS 0.005 0.001 HIS O 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.17 (14313) covalent geometry : angle 0.69188 / 0.41 (20699) hydrogen bonds : bond 0.06986 / 5.13 ( 809) hydrogen bonds : angle 3.66809 / 4.18 ( 2001) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.226 Fit side-chains REVERT: J 78 ARG cc_start: 0.8774 (ptp90) cc_final: 0.8233 (ptt-90) REVERT: M 61 SER cc_start: 0.8997 (m) cc_final: 0.8742 (m) REVERT: O 73 GLU cc_start: 0.9170 (tm-30) cc_final: 0.8756 (tt0) REVERT: Q 91 LYS cc_start: 0.8999 (ttpt) cc_final: 0.8739 (ttmm) REVERT: S 65 ASP cc_start: 0.8893 (t0) cc_final: 0.8681 (t0) outliers start: 22 outliers final: 10 residues processed: 160 average time/residue: 0.1374 time to fit residues: 29.8173 Evaluate side-chains 148 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 138 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain M residue 90 GLU Chi-restraints excluded: chain R residue 102 ILE Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 43 LYS Chi-restraints excluded: chain S residue 98 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 56 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 26 optimal weight: 20.0000 chunk 112 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 2 GLN ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 44 GLN ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 25 ASN Q 93 GLN ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.179426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.119930 restraints weight = 42689.358| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.68 r_work: 0.3077 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14313 Z= 0.156 Angle : 0.669 9.121 20699 Z= 0.390 Chirality : 0.049 0.370 2367 Planarity : 0.004 0.054 1540 Dihedral : 32.731 177.300 4434 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.82 % Allowed : 26.77 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.33 (0.28), residues: 879 helix: 1.87 (0.22), residues: 574 sheet: 0.13 (1.14), residues: 21 loop : -1.14 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 95 TYR 0.014 0.002 TYR K 39 PHE 0.009 0.001 PHE J 100 TRP 0.004 0.001 TRP B 176 HIS 0.004 0.001 HIS O 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.16 (14313) covalent geometry : angle 0.66870 / 0.39 (20699) hydrogen bonds : bond 0.06180 / 4.42 ( 809) hydrogen bonds : angle 3.26583 / 3.66 ( 2001) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 0.254 Fit side-chains REVERT: J 78 ARG cc_start: 0.8832 (ptp90) cc_final: 0.8249 (ptt-90) REVERT: M 61 SER cc_start: 0.8960 (m) cc_final: 0.8722 (m) REVERT: O 59 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7699 (pm20) REVERT: O 73 GLU cc_start: 0.9234 (tm-30) cc_final: 0.8819 (tt0) REVERT: Q 91 LYS cc_start: 0.8972 (ttpt) cc_final: 0.8725 (ttmm) REVERT: R 23 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8276 (mp) REVERT: R 89 ASN cc_start: 0.8683 (m-40) cc_final: 0.8050 (m-40) REVERT: S 65 ASP cc_start: 0.8949 (t0) cc_final: 0.8647 (t0) REVERT: S 90 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7469 (mm-30) REVERT: S 96 ARG cc_start: 0.8526 (ttm-80) cc_final: 0.8197 (ttm-80) REVERT: S 118 TYR cc_start: 0.8360 (t80) cc_final: 0.8049 (t80) outliers start: 27 outliers final: 16 residues processed: 180 average time/residue: 0.1373 time to fit residues: 33.5148 Evaluate side-chains 167 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain M residue 44 GLN Chi-restraints excluded: chain M residue 90 GLU Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain R residue 19 SER Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 43 LYS Chi-restraints excluded: chain S residue 77 LEU Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain S residue 90 GLU Chi-restraints excluded: chain S residue 98 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 49 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 30 optimal weight: 20.0000 chunk 7 optimal weight: 40.0000 chunk 113 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 27 optimal weight: 50.0000 chunk 99 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 25 ASN ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.178097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.119541 restraints weight = 32985.996| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.41 r_work: 0.3083 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14313 Z= 0.169 Angle : 0.684 10.355 20699 Z= 0.392 Chirality : 0.049 0.363 2367 Planarity : 0.004 0.055 1540 Dihedral : 32.789 177.974 4434 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.82 % Allowed : 27.05 % Favored : 68.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.28), residues: 879 helix: 1.90 (0.22), residues: 576 sheet: 0.36 (1.19), residues: 21 loop : -1.12 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 95 TYR 0.021 0.002 TYR M 118 PHE 0.011 0.001 PHE K 25 TRP 0.012 0.003 TRP B 176 HIS 0.004 0.001 HIS D 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.17 (14313) covalent geometry : angle 0.68374 / 0.39 (20699) hydrogen bonds : bond 0.06174 / 4.41 ( 809) hydrogen bonds : angle 3.19472 / 3.54 ( 2001) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 149 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: M 44 GLN cc_start: 0.8257 (tt0) cc_final: 0.7936 (tt0) REVERT: M 61 SER cc_start: 0.8995 (m) cc_final: 0.8744 (m) REVERT: O 51 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8436 (mt) REVERT: O 59 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7724 (pm20) REVERT: Q 91 LYS cc_start: 0.9004 (ttpt) cc_final: 0.8742 (ttmm) REVERT: S 65 ASP cc_start: 0.8929 (t0) cc_final: 0.8660 (t0) REVERT: S 90 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7448 (mm-30) REVERT: S 96 ARG cc_start: 0.8478 (ttm-80) cc_final: 0.8144 (ttm-80) outliers start: 34 outliers final: 15 residues processed: 171 average time/residue: 0.1388 time to fit residues: 32.0898 Evaluate side-chains 160 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain K residue 110 ASN Chi-restraints excluded: chain M residue 90 GLU Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 43 LYS Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain S residue 90 GLU Chi-restraints excluded: chain S residue 98 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 60 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 30 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.176112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.117157 restraints weight = 51129.389| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.99 r_work: 0.2984 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2984 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2984 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 14313 Z= 0.192 Angle : 0.700 10.295 20699 Z= 0.396 Chirality : 0.050 0.386 2367 Planarity : 0.005 0.054 1540 Dihedral : 32.876 178.527 4434 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 4.82 % Allowed : 27.76 % Favored : 67.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.33 (0.28), residues: 879 helix: 1.86 (0.22), residues: 577 sheet: -0.18 (1.17), residues: 22 loop : -1.14 (0.34), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 95 TYR 0.025 0.002 TYR Q 88 PHE 0.010 0.001 PHE J 100 TRP 0.013 0.002 TRP A 176 HIS 0.008 0.002 HIS M 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.19 (14313) covalent geometry : angle 0.69961 / 0.40 (20699) hydrogen bonds : bond 0.06247 / 4.52 ( 809) hydrogen bonds : angle 3.18969 / 3.55 ( 2001) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 0.287 Fit side-chains REVERT: D 1 MET cc_start: 0.6180 (mtt) cc_final: 0.4559 (tmm) REVERT: D 12 THR cc_start: 0.2370 (OUTLIER) cc_final: 0.2145 (t) REVERT: K 25 PHE cc_start: 0.8965 (OUTLIER) cc_final: 0.7875 (t80) REVERT: M 98 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8092 (mm) REVERT: O 51 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8086 (mt) REVERT: O 59 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7727 (pm20) REVERT: Q 91 LYS cc_start: 0.9043 (ttpt) cc_final: 0.8716 (ttmm) REVERT: Q 97 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8741 (tp) REVERT: S 65 ASP cc_start: 0.8999 (t0) cc_final: 0.8692 (t0) REVERT: S 90 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7633 (mm-30) outliers start: 34 outliers final: 19 residues processed: 176 average time/residue: 0.1249 time to fit residues: 29.9705 Evaluate side-chains 170 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 110 ASN Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain M residue 90 GLU Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain R residue 19 SER Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 43 LYS Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain S residue 90 GLU Chi-restraints excluded: chain S residue 98 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 111 optimal weight: 0.3980 chunk 26 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 24 optimal weight: 5.9990 chunk 77 optimal weight: 0.2980 chunk 35 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 25 ASN ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 79 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.177306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.118392 restraints weight = 42903.542| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.53 r_work: 0.3044 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14313 Z= 0.152 Angle : 0.671 10.349 20699 Z= 0.383 Chirality : 0.049 0.393 2367 Planarity : 0.004 0.056 1540 Dihedral : 32.844 178.341 4434 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.68 % Allowed : 29.32 % Favored : 67.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.28), residues: 879 helix: 1.98 (0.22), residues: 576 sheet: -0.25 (1.15), residues: 22 loop : -1.09 (0.34), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 83 TYR 0.016 0.002 TYR Q 88 PHE 0.007 0.001 PHE A 190 TRP 0.009 0.001 TRP A 176 HIS 0.004 0.001 HIS S 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.15 (14313) covalent geometry : angle 0.67150 / 0.38 (20699) hydrogen bonds : bond 0.05917 / 4.21 ( 809) hydrogen bonds : angle 3.05350 / 3.39 ( 2001) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.213 Fit side-chains REVERT: D 1 MET cc_start: 0.5861 (mtt) cc_final: 0.4365 (tmm) REVERT: D 6 LYS cc_start: 0.9120 (mmtm) cc_final: 0.6985 (tppt) REVERT: K 25 PHE cc_start: 0.8904 (OUTLIER) cc_final: 0.7892 (t80) REVERT: M 98 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8168 (mm) REVERT: O 51 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8126 (mt) REVERT: O 59 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7834 (pm20) REVERT: O 73 GLU cc_start: 0.9290 (tm-30) cc_final: 0.8811 (tt0) REVERT: O 81 ASP cc_start: 0.7997 (t0) cc_final: 0.7434 (t0) REVERT: Q 97 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8704 (tp) REVERT: R 89 ASN cc_start: 0.8636 (m-40) cc_final: 0.8008 (m-40) REVERT: S 65 ASP cc_start: 0.8925 (t0) cc_final: 0.8632 (t0) REVERT: S 90 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7675 (mm-30) outliers start: 26 outliers final: 14 residues processed: 169 average time/residue: 0.1174 time to fit residues: 27.4882 Evaluate side-chains 165 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 110 ASN Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 90 GLU Chi-restraints excluded: chain S residue 98 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 72 optimal weight: 0.7980 chunk 28 optimal weight: 50.0000 chunk 20 optimal weight: 30.0000 chunk 31 optimal weight: 20.0000 chunk 76 optimal weight: 0.7980 chunk 5 optimal weight: 20.0000 chunk 57 optimal weight: 0.6980 chunk 19 optimal weight: 30.0000 chunk 16 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 91 optimal weight: 0.3980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 25 ASN S 79 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.176814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.116843 restraints weight = 37590.518| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.41 r_work: 0.3046 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3049 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3049 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14313 Z= 0.167 Angle : 0.677 10.215 20699 Z= 0.384 Chirality : 0.049 0.398 2367 Planarity : 0.004 0.057 1540 Dihedral : 32.815 178.587 4434 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.11 % Allowed : 29.60 % Favored : 66.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.50 (0.29), residues: 879 helix: 2.00 (0.22), residues: 577 sheet: -0.38 (1.08), residues: 22 loop : -1.07 (0.34), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 95 TYR 0.016 0.002 TYR Q 88 PHE 0.009 0.001 PHE J 100 TRP 0.008 0.001 TRP A 176 HIS 0.004 0.001 HIS M 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.17 (14313) covalent geometry : angle 0.67733 / 0.38 (20699) hydrogen bonds : bond 0.05956 / 4.26 ( 809) hydrogen bonds : angle 3.04419 / 3.38 ( 2001) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.238 Fit side-chains REVERT: D 1 MET cc_start: 0.5778 (mtt) cc_final: 0.4224 (tmm) REVERT: D 6 LYS cc_start: 0.9153 (mmtm) cc_final: 0.7078 (tppt) REVERT: K 25 PHE cc_start: 0.8905 (OUTLIER) cc_final: 0.7891 (t80) REVERT: K 42 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.6890 (ptm160) REVERT: M 98 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8093 (mm) REVERT: O 51 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8136 (mt) REVERT: O 59 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7816 (pm20) REVERT: O 73 GLU cc_start: 0.9309 (tm-30) cc_final: 0.8915 (tt0) REVERT: O 81 ASP cc_start: 0.8110 (t0) cc_final: 0.7505 (t0) REVERT: Q 97 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8656 (tp) REVERT: S 65 ASP cc_start: 0.8956 (t0) cc_final: 0.8667 (t0) outliers start: 29 outliers final: 14 residues processed: 164 average time/residue: 0.1280 time to fit residues: 28.8037 Evaluate side-chains 165 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 42 ARG Chi-restraints excluded: chain K residue 110 ASN Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 98 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 54 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 19 optimal weight: 30.0000 chunk 111 optimal weight: 0.9980 chunk 21 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 59 optimal weight: 0.0970 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.178136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.118645 restraints weight = 31469.706| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.43 r_work: 0.3069 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14313 Z= 0.147 Angle : 0.665 9.263 20699 Z= 0.379 Chirality : 0.048 0.401 2367 Planarity : 0.004 0.058 1540 Dihedral : 32.753 178.500 4434 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.68 % Allowed : 29.60 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.29), residues: 879 helix: 2.07 (0.22), residues: 576 sheet: -0.52 (1.14), residues: 22 loop : -1.03 (0.34), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 83 TYR 0.016 0.001 TYR Q 88 PHE 0.008 0.001 PHE J 100 TRP 0.008 0.001 TRP A 176 HIS 0.005 0.001 HIS J 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.15 (14313) covalent geometry : angle 0.66472 / 0.38 (20699) hydrogen bonds : bond 0.05757 / 4.08 ( 809) hydrogen bonds : angle 2.96916 / 3.33 ( 2001) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.334 Fit side-chains REVERT: D 1 MET cc_start: 0.6180 (mtt) cc_final: 0.4627 (tmm) REVERT: D 6 LYS cc_start: 0.9141 (mmtm) cc_final: 0.7288 (tppt) REVERT: I 59 GLU cc_start: 0.8435 (pm20) cc_final: 0.8073 (pm20) REVERT: J 27 GLN cc_start: 0.9131 (mm-40) cc_final: 0.8883 (mp10) REVERT: K 25 PHE cc_start: 0.8860 (OUTLIER) cc_final: 0.7847 (t80) REVERT: M 98 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8175 (mt) REVERT: O 51 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8091 (mt) REVERT: O 59 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7842 (pm20) REVERT: O 73 GLU cc_start: 0.9287 (tm-30) cc_final: 0.8740 (tt0) REVERT: O 81 ASP cc_start: 0.8089 (t0) cc_final: 0.7496 (t0) REVERT: Q 97 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8656 (tp) REVERT: R 89 ASN cc_start: 0.8525 (m-40) cc_final: 0.8190 (m-40) REVERT: S 65 ASP cc_start: 0.8897 (t0) cc_final: 0.8630 (t0) REVERT: S 90 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7555 (mm-30) outliers start: 26 outliers final: 15 residues processed: 169 average time/residue: 0.1397 time to fit residues: 32.1679 Evaluate side-chains 168 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 90 GLU Chi-restraints excluded: chain S residue 98 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 102 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 103 optimal weight: 0.5980 chunk 9 optimal weight: 9.9990 chunk 29 optimal weight: 20.0000 chunk 85 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 98 optimal weight: 0.7980 chunk 40 optimal weight: 9.9990 chunk 96 optimal weight: 0.2980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 76 GLN ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.176942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.115611 restraints weight = 34176.084| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.47 r_work: 0.3044 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14313 Z= 0.166 Angle : 0.678 11.106 20699 Z= 0.383 Chirality : 0.049 0.401 2367 Planarity : 0.004 0.058 1540 Dihedral : 32.750 178.894 4434 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.11 % Allowed : 29.75 % Favored : 66.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.29), residues: 879 helix: 2.12 (0.22), residues: 571 sheet: -0.47 (1.13), residues: 22 loop : -0.91 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 83 TYR 0.018 0.002 TYR Q 88 PHE 0.016 0.001 PHE D 45 TRP 0.012 0.002 TRP A 176 HIS 0.004 0.001 HIS J 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.17 (14313) covalent geometry : angle 0.67804 / 0.38 (20699) hydrogen bonds : bond 0.05876 / 4.21 ( 809) hydrogen bonds : angle 3.00549 / 3.36 ( 2001) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.422 Fit side-chains REVERT: D 1 MET cc_start: 0.5897 (mtt) cc_final: 0.4097 (tmm) REVERT: D 6 LYS cc_start: 0.9141 (mmtm) cc_final: 0.7467 (tppt) REVERT: D 67 LEU cc_start: 0.8881 (mm) cc_final: 0.8247 (mm) REVERT: I 59 GLU cc_start: 0.8436 (pm20) cc_final: 0.8093 (pm20) REVERT: J 27 GLN cc_start: 0.9137 (mm-40) cc_final: 0.8892 (mp10) REVERT: K 25 PHE cc_start: 0.8882 (OUTLIER) cc_final: 0.7801 (t80) REVERT: K 42 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.6898 (ptm160) REVERT: M 98 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8201 (mt) REVERT: O 51 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8153 (mt) REVERT: O 59 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7882 (pm20) REVERT: O 73 GLU cc_start: 0.9322 (tm-30) cc_final: 0.8760 (tt0) REVERT: O 81 ASP cc_start: 0.8109 (t0) cc_final: 0.7519 (t0) REVERT: Q 97 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8672 (tp) REVERT: S 65 ASP cc_start: 0.8908 (t0) cc_final: 0.8633 (t0) REVERT: S 90 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7577 (mm-30) outliers start: 29 outliers final: 16 residues processed: 167 average time/residue: 0.1366 time to fit residues: 31.5858 Evaluate side-chains 169 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 76 GLN Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 42 ARG Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 90 GLU Chi-restraints excluded: chain S residue 98 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 72 optimal weight: 0.9990 chunk 98 optimal weight: 0.4980 chunk 50 optimal weight: 0.4980 chunk 1 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 18 optimal weight: 20.0000 chunk 57 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.178137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.119501 restraints weight = 47685.015| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.83 r_work: 0.3035 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14313 Z= 0.149 Angle : 0.671 11.137 20699 Z= 0.380 Chirality : 0.049 0.403 2367 Planarity : 0.004 0.058 1540 Dihedral : 32.739 178.787 4434 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.26 % Allowed : 30.17 % Favored : 66.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.29), residues: 879 helix: 2.17 (0.22), residues: 571 sheet: -0.34 (1.13), residues: 22 loop : -0.87 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 83 TYR 0.016 0.001 TYR K 39 PHE 0.010 0.001 PHE I 78 TRP 0.013 0.002 TRP A 176 HIS 0.005 0.001 HIS J 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.15 (14313) covalent geometry : angle 0.67141 / 0.38 (20699) hydrogen bonds : bond 0.05708 / 4.07 ( 809) hydrogen bonds : angle 2.95604 / 3.30 ( 2001) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 0.352 Fit side-chains REVERT: D 1 MET cc_start: 0.5972 (mtt) cc_final: 0.4278 (tmm) REVERT: D 6 LYS cc_start: 0.9115 (mmtm) cc_final: 0.7445 (tppt) REVERT: D 67 LEU cc_start: 0.8968 (mm) cc_final: 0.8400 (mm) REVERT: I 58 THR cc_start: 0.8932 (t) cc_final: 0.8730 (t) REVERT: I 59 GLU cc_start: 0.8365 (pm20) cc_final: 0.8061 (pm20) REVERT: J 27 GLN cc_start: 0.9147 (mm-40) cc_final: 0.8905 (mp10) REVERT: K 25 PHE cc_start: 0.8876 (OUTLIER) cc_final: 0.7787 (t80) REVERT: K 42 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.6891 (ptm160) REVERT: M 98 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8182 (mt) REVERT: O 51 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8093 (mt) REVERT: O 56 LYS cc_start: 0.8243 (ttpt) cc_final: 0.7635 (ttpp) REVERT: O 59 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7897 (pm20) REVERT: O 73 GLU cc_start: 0.9343 (tm-30) cc_final: 0.8790 (tt0) REVERT: O 81 ASP cc_start: 0.8143 (t0) cc_final: 0.7559 (t0) REVERT: Q 97 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8677 (tp) REVERT: S 65 ASP cc_start: 0.8917 (t0) cc_final: 0.8644 (t0) REVERT: S 90 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7605 (mm-30) outliers start: 23 outliers final: 13 residues processed: 165 average time/residue: 0.1530 time to fit residues: 34.1548 Evaluate side-chains 167 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 42 ARG Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 90 GLU Chi-restraints excluded: chain S residue 98 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 89 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 41 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 19 optimal weight: 30.0000 chunk 70 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 76 GLN ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.176508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.117386 restraints weight = 38373.280| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.40 r_work: 0.3044 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14313 Z= 0.169 Angle : 0.681 10.937 20699 Z= 0.383 Chirality : 0.049 0.403 2367 Planarity : 0.004 0.057 1540 Dihedral : 32.760 179.342 4434 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.26 % Allowed : 30.03 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.67 (0.29), residues: 879 helix: 2.10 (0.22), residues: 571 sheet: 0.09 (1.18), residues: 22 loop : -0.89 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 83 TYR 0.021 0.002 TYR Q 88 PHE 0.009 0.001 PHE J 100 TRP 0.017 0.002 TRP A 176 HIS 0.004 0.001 HIS M 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.17 (14313) covalent geometry : angle 0.68081 / 0.38 (20699) hydrogen bonds : bond 0.05856 / 4.22 ( 809) hydrogen bonds : angle 3.01572 / 3.36 ( 2001) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3213.99 seconds wall clock time: 55 minutes 29.24 seconds (3329.24 seconds total)