Starting phenix.real_space_refine on Wed Aug 5 23:22:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vmn_43360/08_2026/8vmn_43360.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vmn_43360/08_2026/8vmn_43360.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vmn_43360/08_2026/8vmn_43360.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vmn_43360/08_2026/8vmn_43360.map" model { file = "/net/cci-nas-00/data/ceres_data/8vmn_43360/08_2026/8vmn_43360.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vmn_43360/08_2026/8vmn_43360.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.034 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 14 5.16 5 C 6889 2.51 5 N 2355 2.21 5 O 2968 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 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: 12540 Number of models: 1 Model: "" Number of chains: 10 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: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 825 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "J" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "K" 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: "M" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 736 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "O" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "Q" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 667 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 85} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "R" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} 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 Chain: "D" Number of atoms: 3202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 3202 Classifications: {'DNA': 157} Link IDs: {'rna3p': 156} Time building chain proxies: 2.79, per 1000 atoms: 0.22 Number of scatterers: 12540 At special positions: 0 Unit cell: (106.64, 141.04, 122.12, 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 14 16.00 P 314 15.00 O 2968 8.00 N 2355 7.00 C 6889 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: 0.64 Conformation dependent library (CDL) restraints added in 326.6 milliseconds 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1452 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 7 sheets defined 69.2% alpha, 1.8% beta 156 base pairs and 255 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'I' and resid 45 through 55 Processing helix chain 'I' and resid 63 through 75 removed outlier: 3.547A pdb=" N PHE I 67 " --> pdb=" O ARG I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 114 removed outlier: 3.676A pdb=" N VAL I 89 " --> pdb=" O GLN I 85 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET I 90 " --> pdb=" O SER I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 131 removed outlier: 3.535A pdb=" N ILE I 124 " --> pdb=" O MET I 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 29 removed outlier: 3.526A pdb=" N ILE J 29 " --> pdb=" O ILE J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 42 Processing helix chain 'J' and resid 49 through 76 removed outlier: 3.915A pdb=" N GLU J 53 " --> pdb=" O LEU J 49 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG J 55 " --> pdb=" O TYR J 51 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL J 65 " --> pdb=" O PHE J 61 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASP J 68 " --> pdb=" O ASN J 64 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA J 76 " --> pdb=" O TYR J 72 " (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: 4.577A pdb=" N VAL K 49 " --> pdb=" O ALA K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 88 Processing helix chain 'K' and resid 90 through 97 removed outlier: 3.587A pdb=" N LEU K 96 " --> pdb=" O GLU K 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 34 through 46 Processing helix chain 'M' and resid 53 through 81 removed outlier: 3.869A pdb=" N MET M 59 " --> pdb=" O ALA M 55 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU M 68 " --> pdb=" O ASN M 64 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU M 73 " --> pdb=" O ARG M 69 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN M 81 " --> pdb=" O LEU M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 99 removed outlier: 3.624A pdb=" N ILE M 91 " --> pdb=" O THR M 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 101 through 121 removed outlier: 4.461A pdb=" N SER M 109 " --> pdb=" O LYS M 105 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU M 110 " --> pdb=" O HIS M 106 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N TYR M 118 " --> pdb=" O ALA M 114 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER M 120 " --> pdb=" O THR M 116 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 55 removed outlier: 3.565A pdb=" N LEU O 48 " --> pdb=" O GLY O 44 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 76 removed outlier: 3.622A pdb=" N PHE O 67 " --> pdb=" O ARG O 63 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN O 76 " --> pdb=" O ARG O 72 " (cutoff:3.500A) Processing helix chain 'O' and resid 85 through 114 Processing helix chain 'O' and resid 120 through 131 removed outlier: 3.633A pdb=" N ILE O 124 " --> pdb=" O MET O 120 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 29 Processing helix chain 'Q' and resid 30 through 42 Processing helix chain 'Q' and resid 49 through 77 removed outlier: 4.254A pdb=" N GLU Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG Q 55 " --> pdb=" O TYR Q 51 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP Q 68 " --> pdb=" O ASN Q 64 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR Q 73 " --> pdb=" O ALA Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 93 removed outlier: 3.830A pdb=" N VAL Q 86 " --> pdb=" O THR Q 82 " (cutoff:3.500A) 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: 4.413A pdb=" N VAL R 49 " --> pdb=" O ALA R 45 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA R 69 " --> pdb=" O LEU R 65 " (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 44 Processing helix chain 'S' and resid 52 through 81 Processing helix chain 'S' and resid 87 through 99 Processing helix chain 'S' and resid 101 through 121 Processing sheet with id=AA1, first strand: chain 'I' and resid 83 through 84 removed outlier: 7.836A pdb=" N ARG I 83 " --> pdb=" O VAL J 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'I' and resid 118 through 119 removed outlier: 3.810A pdb=" N ILE I 119 " --> pdb=" O ARG J 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'J' and resid 97 through 98 removed outlier: 3.618A pdb=" N TYR J 98 " --> pdb=" O THR R 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'K' and resid 42 through 43 removed outlier: 7.732A pdb=" N ARG K 42 " --> pdb=" O ILE M 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'K' and resid 101 through 102 removed outlier: 6.804A pdb=" N THR K 101 " --> pdb=" O TYR Q 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'R' and resid 42 through 43 removed outlier: 7.328A pdb=" N ARG R 42 " --> pdb=" O ILE S 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'R' and resid 77 through 78 372 hydrogen bonds defined for protein. 1104 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 396 hydrogen bonds 756 hydrogen bond angles 0 basepair planarities 156 basepair parallelities 255 stacking parallelities Total time for adding SS restraints: 2.06 Time building geometry restraints manager: 0.96 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: 2483 1.33 - 1.45: 4422 1.45 - 1.57: 5848 1.57 - 1.69: 626 1.69 - 1.81: 24 Bond restraints: 13403 Sorted by residual: bond pdb=" C3' DC D 261 " pdb=" C2' DC D 261 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.44e+01 bond pdb=" C3' DT D 255 " pdb=" C2' DT D 255 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.25e+01 bond pdb=" C3' DC D 162 " pdb=" C2' DC D 162 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.20e+01 bond pdb=" C3' DT H 16 " pdb=" C2' DT H 16 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.19e+01 bond pdb=" C3' DT H 57 " pdb=" C2' DT H 57 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.18e+01 ... (remaining 13398 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 18656 2.08 - 4.16: 768 4.16 - 6.24: 30 6.24 - 8.33: 3 8.33 - 10.41: 2 Bond angle restraints: 19459 Sorted by residual: angle pdb=" O4' DA H 18 " pdb=" C4' DA H 18 " pdb=" C3' DA H 18 " ideal model delta sigma weight residual 106.00 102.97 3.03 6.00e-01 2.78e+00 2.54e+01 angle pdb=" O4' DG H 54 " pdb=" C1' DG H 54 " pdb=" N9 DG H 54 " ideal model delta sigma weight residual 108.00 111.51 -3.51 7.00e-01 2.04e+00 2.51e+01 angle pdb=" O4' DA H 35 " pdb=" C4' DA H 35 " pdb=" C3' DA H 35 " ideal model delta sigma weight residual 106.00 103.13 2.87 6.00e-01 2.78e+00 2.29e+01 angle pdb=" O4' DC H 48 " pdb=" C4' DC H 48 " pdb=" C3' DC H 48 " ideal model delta sigma weight residual 106.00 103.23 2.77 6.00e-01 2.78e+00 2.13e+01 angle pdb=" O4' DT H 95 " pdb=" C4' DT H 95 " pdb=" C3' DT H 95 " ideal model delta sigma weight residual 106.00 103.23 2.77 6.00e-01 2.78e+00 2.13e+01 ... (remaining 19454 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 5750 35.96 - 71.92: 1411 71.92 - 107.87: 28 107.87 - 143.83: 8 143.83 - 179.79: 25 Dihedral angle restraints: 7222 sinusoidal: 4972 harmonic: 2250 Sorted by residual: dihedral pdb=" C4' DT D 236 " pdb=" C3' DT D 236 " pdb=" O3' DT D 236 " pdb=" P DA D 237 " ideal model delta sinusoidal sigma weight residual 220.00 40.21 179.79 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG D 167 " pdb=" C3' DG D 167 " pdb=" O3' DG D 167 " pdb=" P DG D 168 " ideal model delta sinusoidal sigma weight residual 220.00 41.08 178.92 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT D 195 " pdb=" C3' DT D 195 " pdb=" O3' DT D 195 " pdb=" P DC D 196 " ideal model delta sinusoidal sigma weight residual -140.00 38.06 -178.06 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 7219 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1381 0.037 - 0.075: 594 0.075 - 0.112: 183 0.112 - 0.149: 47 0.149 - 0.187: 13 Chirality restraints: 2218 Sorted by residual: chirality pdb=" C3' DC D 249 " pdb=" C4' DC D 249 " pdb=" O3' DC D 249 " pdb=" C2' DC D 249 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 8.73e-01 chirality pdb=" CA MET O 90 " pdb=" N MET O 90 " pdb=" C MET O 90 " pdb=" CB MET O 90 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.45e-01 chirality pdb=" C3' DT D 203 " pdb=" C4' DT D 203 " pdb=" O3' DT D 203 " pdb=" C2' DT D 203 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.18e-01 ... (remaining 2215 not shown) Planarity restraints: 1377 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC D 250 " 0.001 2.00e-02 2.50e+03 2.16e-02 1.05e+01 pdb=" N1 DC D 250 " -0.009 2.00e-02 2.50e+03 pdb=" C2 DC D 250 " 0.056 2.00e-02 2.50e+03 pdb=" O2 DC D 250 " -0.027 2.00e-02 2.50e+03 pdb=" N3 DC D 250 " -0.014 2.00e-02 2.50e+03 pdb=" C4 DC D 250 " -0.003 2.00e-02 2.50e+03 pdb=" N4 DC D 250 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DC D 250 " -0.009 2.00e-02 2.50e+03 pdb=" C6 DC D 250 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE R 25 " -0.051 5.00e-02 4.00e+02 7.51e-02 9.03e+00 pdb=" N PRO R 26 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO R 26 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO R 26 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC H 114 " -0.001 2.00e-02 2.50e+03 1.77e-02 7.02e+00 pdb=" N1 DC H 114 " -0.009 2.00e-02 2.50e+03 pdb=" C2 DC H 114 " 0.044 2.00e-02 2.50e+03 pdb=" O2 DC H 114 " -0.024 2.00e-02 2.50e+03 pdb=" N3 DC H 114 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DC H 114 " 0.008 2.00e-02 2.50e+03 pdb=" N4 DC H 114 " -0.010 2.00e-02 2.50e+03 pdb=" C5 DC H 114 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DC H 114 " -0.003 2.00e-02 2.50e+03 ... (remaining 1374 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 129 2.60 - 3.17: 9814 3.17 - 3.75: 22719 3.75 - 4.32: 28539 4.32 - 4.90: 41403 Nonbonded interactions: 102604 Sorted by model distance: nonbonded pdb=" N2 DG H 93 " pdb=" O2 DC D 222 " model vdw 2.024 2.496 nonbonded pdb=" OG SER M 109 " pdb=" OE1 GLU M 110 " model vdw 2.038 3.040 nonbonded pdb=" O2 DC H 154 " pdb=" N2 DG D 161 " model vdw 2.102 2.496 nonbonded pdb=" O2 DC H 110 " pdb=" N2 DG D 205 " model vdw 2.113 2.496 nonbonded pdb=" N2 DG H 94 " pdb=" O2 DC D 221 " model vdw 2.121 2.496 ... (remaining 102599 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' and resid 37 through 135) selection = chain 'O' } ncs_group { reference = (chain 'J' and ((resid 20 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 20 through 102) } ncs_group { reference = chain 'K' 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 119)) } ncs_group { reference = chain 'M' selection = (chain 'S' and resid 28 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.170 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: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 12.680 Find NCS groups from input model: 0.180 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:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 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 0.071 13403 Z= 0.531 Angle : 0.833 10.407 19459 Z= 0.715 Chirality : 0.047 0.187 2218 Planarity : 0.005 0.075 1377 Dihedral : 30.827 179.789 5770 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.63 % Allowed : 25.16 % Favored : 74.21 % 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: 0.74 (0.31), residues: 760 helix: 1.49 (0.23), residues: 520 sheet: None (None), residues: 0 loop : -1.82 (0.36), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 128 TYR 0.033 0.002 TYR M 80 PHE 0.015 0.001 PHE J 100 HIS 0.009 0.001 HIS R 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.53 (13403) covalent geometry : angle 0.83343 / 0.71 (19459) hydrogen bonds : bond 0.13450 / 15.13 ( 768) hydrogen bonds : angle 4.91494 / 6.57 ( 1860) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 122 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: J 82 THR cc_start: 0.8710 (m) cc_final: 0.8430 (p) REVERT: M 39 TYR cc_start: 0.7613 (t80) cc_final: 0.7008 (t80) REVERT: O 37 LYS cc_start: 0.8244 (tppt) cc_final: 0.7526 (mmmm) outliers start: 4 outliers final: 2 residues processed: 123 average time/residue: 0.1235 time to fit residues: 20.7587 Evaluate side-chains 109 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 107 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain R residue 74 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.0770 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 39 HIS R 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.125932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.097183 restraints weight = 32354.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.099366 restraints weight = 16691.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.100802 restraints weight = 11150.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.101707 restraints weight = 8866.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.102163 restraints weight = 7802.013| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13403 Z= 0.200 Angle : 0.759 8.760 19459 Z= 0.435 Chirality : 0.057 0.344 2218 Planarity : 0.005 0.051 1377 Dihedral : 34.010 179.823 4277 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.80 % Allowed : 18.20 % Favored : 78.01 % 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: 1.00 (0.30), residues: 760 helix: 1.64 (0.23), residues: 525 sheet: None (None), residues: 0 loop : -1.67 (0.37), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Q 55 TYR 0.027 0.002 TYR M 80 PHE 0.012 0.002 PHE S 62 HIS 0.007 0.001 HIS R 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.20 (13403) covalent geometry : angle 0.75861 / 0.44 (19459) hydrogen bonds : bond 0.09186 / 10.07 ( 768) hydrogen bonds : angle 3.49944 / 4.58 ( 1860) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.292 Fit side-chains REVERT: K 108 LEU cc_start: 0.9013 (tp) cc_final: 0.8811 (tp) REVERT: R 64 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7551 (tt0) REVERT: S 77 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7727 (mp) outliers start: 24 outliers final: 15 residues processed: 132 average time/residue: 0.1179 time to fit residues: 21.5762 Evaluate side-chains 125 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain O residue 39 HIS Chi-restraints excluded: chain Q residue 27 GLN Chi-restraints excluded: chain Q residue 50 ILE Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 77 LEU Chi-restraints excluded: chain S residue 87 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 77 optimal weight: 0.3980 chunk 83 optimal weight: 0.8980 chunk 8 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 9 optimal weight: 20.0000 chunk 79 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.121628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.092477 restraints weight = 32588.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.094467 restraints weight = 18061.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.095752 restraints weight = 12551.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.096505 restraints weight = 10181.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.097014 restraints weight = 9080.681| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 13403 Z= 0.240 Angle : 0.801 9.303 19459 Z= 0.460 Chirality : 0.059 0.398 2218 Planarity : 0.006 0.045 1377 Dihedral : 34.051 178.749 4273 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 5.06 % Allowed : 19.94 % Favored : 75.00 % 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: 0.54 (0.30), residues: 760 helix: 1.35 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -1.97 (0.37), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 88 TYR 0.053 0.003 TYR S 80 PHE 0.015 0.002 PHE S 62 HIS 0.013 0.002 HIS I 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.24 (13403) covalent geometry : angle 0.80076 / 0.46 (19459) hydrogen bonds : bond 0.09858 / 10.99 ( 768) hydrogen bonds : angle 3.72305 / 4.77 ( 1860) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 120 MET cc_start: 0.7012 (mtt) cc_final: 0.6793 (mtt) REVERT: J 88 TYR cc_start: 0.7763 (m-10) cc_final: 0.7556 (m-10) REVERT: M 76 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.8196 (ptp-170) REVERT: Q 35 ARG cc_start: 0.7469 (mtp85) cc_final: 0.7228 (mtp180) REVERT: R 64 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7626 (tt0) REVERT: S 77 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8256 (mp) outliers start: 32 outliers final: 22 residues processed: 141 average time/residue: 0.1288 time to fit residues: 24.6728 Evaluate side-chains 131 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 90 MET Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain O residue 39 HIS Chi-restraints excluded: chain O residue 50 GLU Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain Q residue 27 GLN Chi-restraints excluded: chain Q residue 50 ILE Chi-restraints excluded: chain Q residue 82 THR Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 38 ASN Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 77 LEU Chi-restraints excluded: chain S residue 87 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 10 optimal weight: 20.0000 chunk 67 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 100 optimal weight: 20.0000 chunk 21 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.124327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.095302 restraints weight = 32086.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.097454 restraints weight = 16603.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.098925 restraints weight = 11119.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.099802 restraints weight = 8794.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.100325 restraints weight = 7721.098| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13403 Z= 0.164 Angle : 0.707 9.202 19459 Z= 0.409 Chirality : 0.054 0.352 2218 Planarity : 0.004 0.046 1377 Dihedral : 33.919 179.993 4273 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.48 % Allowed : 21.84 % Favored : 74.68 % 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: 1.12 (0.31), residues: 760 helix: 1.78 (0.23), residues: 528 sheet: None (None), residues: 0 loop : -1.78 (0.38), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 30 TYR 0.057 0.002 TYR S 80 PHE 0.009 0.001 PHE S 62 HIS 0.004 0.001 HIS I 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.16 (13403) covalent geometry : angle 0.70729 / 0.41 (19459) hydrogen bonds : bond 0.08438 / 9.27 ( 768) hydrogen bonds : angle 3.27185 / 4.23 ( 1860) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: J 62 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8757 (mm) REVERT: M 39 TYR cc_start: 0.7910 (t80) cc_final: 0.7626 (t80) REVERT: M 76 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.8147 (ptp-170) REVERT: R 64 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7659 (tt0) REVERT: S 77 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7819 (mp) outliers start: 22 outliers final: 16 residues processed: 122 average time/residue: 0.1128 time to fit residues: 19.0740 Evaluate side-chains 123 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 90 MET Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain O residue 39 HIS Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain Q residue 27 GLN Chi-restraints excluded: chain Q residue 50 ILE Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 38 ASN Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 77 LEU Chi-restraints excluded: chain S residue 87 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 44 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 94 optimal weight: 20.0000 chunk 72 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 39 optimal weight: 0.0170 chunk 6 optimal weight: 9.9990 overall best weight: 1.1020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.122808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.094229 restraints weight = 32130.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.096230 restraints weight = 17502.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.097536 restraints weight = 12011.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.098350 restraints weight = 9663.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.098765 restraints weight = 8556.847| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13403 Z= 0.170 Angle : 0.704 9.268 19459 Z= 0.407 Chirality : 0.054 0.359 2218 Planarity : 0.004 0.047 1377 Dihedral : 33.823 179.913 4273 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.64 % Allowed : 22.78 % Favored : 73.58 % 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: 1.23 (0.31), residues: 760 helix: 1.88 (0.23), residues: 527 sheet: None (None), residues: 0 loop : -1.80 (0.38), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 35 TYR 0.044 0.002 TYR S 80 PHE 0.010 0.001 PHE S 62 HIS 0.006 0.001 HIS I 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.17 (13403) covalent geometry : angle 0.70351 / 0.41 (19459) hydrogen bonds : bond 0.08423 / 9.26 ( 768) hydrogen bonds : angle 3.25806 / 4.19 ( 1860) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: K 64 GLU cc_start: 0.8340 (tm-30) cc_final: 0.8119 (tm-30) REVERT: M 39 TYR cc_start: 0.7918 (t80) cc_final: 0.7690 (t80) REVERT: M 117 LYS cc_start: 0.8512 (tptm) cc_final: 0.8153 (mtpt) REVERT: R 64 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7722 (tt0) REVERT: S 77 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7907 (mp) outliers start: 23 outliers final: 16 residues processed: 127 average time/residue: 0.1042 time to fit residues: 18.4384 Evaluate side-chains 125 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 90 MET Chi-restraints excluded: chain I residue 108 ASN Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain O residue 39 HIS Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain Q residue 27 GLN Chi-restraints excluded: chain Q residue 50 ILE Chi-restraints excluded: chain Q residue 82 THR Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 38 ASN Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 77 LEU Chi-restraints excluded: chain S residue 87 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 2 optimal weight: 20.0000 chunk 96 optimal weight: 9.9990 chunk 81 optimal weight: 0.0570 chunk 51 optimal weight: 4.9990 chunk 72 optimal weight: 0.0570 chunk 7 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 36 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 9 optimal weight: 20.0000 chunk 22 optimal weight: 4.9990 overall best weight: 2.2220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.114956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.086109 restraints weight = 32009.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.088024 restraints weight = 17791.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.089303 restraints weight = 12429.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.090085 restraints weight = 10103.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.090488 restraints weight = 8996.305| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13403 Z= 0.234 Angle : 0.800 9.747 19459 Z= 0.452 Chirality : 0.059 0.418 2218 Planarity : 0.006 0.046 1377 Dihedral : 33.895 179.715 4271 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 5.22 % Allowed : 21.68 % Favored : 73.10 % 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: 0.57 (0.30), residues: 760 helix: 1.37 (0.22), residues: 527 sheet: None (None), residues: 0 loop : -1.99 (0.37), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O 129 TYR 0.060 0.003 TYR S 80 PHE 0.015 0.002 PHE S 62 HIS 0.014 0.002 HIS I 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.23 (13403) covalent geometry : angle 0.79992 / 0.45 (19459) hydrogen bonds : bond 0.10076 / 11.06 ( 768) hydrogen bonds : angle 3.67129 / 4.71 ( 1860) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 110 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 64 GLU cc_start: 0.8359 (tm-30) cc_final: 0.8036 (tm-30) REVERT: M 39 TYR cc_start: 0.8017 (OUTLIER) cc_final: 0.7744 (t80) REVERT: M 48 ASP cc_start: 0.8277 (p0) cc_final: 0.8059 (p0) REVERT: M 117 LYS cc_start: 0.8576 (tptm) cc_final: 0.8243 (mtpt) REVERT: R 64 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7664 (tt0) REVERT: S 77 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8042 (mp) outliers start: 33 outliers final: 25 residues processed: 134 average time/residue: 0.1092 time to fit residues: 20.5524 Evaluate side-chains 129 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 90 MET Chi-restraints excluded: chain I residue 108 ASN Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 39 TYR Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain O residue 39 HIS Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain Q residue 27 GLN Chi-restraints excluded: chain Q residue 49 LEU Chi-restraints excluded: chain Q residue 50 ILE Chi-restraints excluded: chain Q residue 82 THR Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 38 ASN Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 63 VAL Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 77 LEU Chi-restraints excluded: chain S residue 87 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 37 optimal weight: 0.9990 chunk 78 optimal weight: 0.1980 chunk 69 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.117171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.088801 restraints weight = 31929.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.090811 restraints weight = 17538.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.092125 restraints weight = 12112.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.092930 restraints weight = 9786.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.093347 restraints weight = 8696.153| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13403 Z= 0.161 Angle : 0.706 9.262 19459 Z= 0.408 Chirality : 0.054 0.362 2218 Planarity : 0.004 0.049 1377 Dihedral : 33.713 179.445 4271 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.80 % Allowed : 23.89 % Favored : 72.31 % 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: 1.18 (0.31), residues: 760 helix: 1.85 (0.23), residues: 527 sheet: None (None), residues: 0 loop : -1.82 (0.37), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 35 TYR 0.031 0.002 TYR S 80 PHE 0.008 0.001 PHE S 62 HIS 0.004 0.001 HIS M 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.16 (13403) covalent geometry : angle 0.70581 / 0.41 (19459) hydrogen bonds : bond 0.08399 / 9.23 ( 768) hydrogen bonds : angle 3.21315 / 4.14 ( 1860) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 64 GLU cc_start: 0.8363 (tm-30) cc_final: 0.8002 (tm-30) REVERT: M 92 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.8030 (tp-100) REVERT: M 117 LYS cc_start: 0.8577 (tptm) cc_final: 0.8161 (mtpt) REVERT: O 50 GLU cc_start: 0.8425 (mp0) cc_final: 0.8213 (mp0) REVERT: O 105 GLU cc_start: 0.7324 (mm-30) cc_final: 0.7001 (mm-30) REVERT: R 64 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7653 (tt0) REVERT: S 77 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7718 (mp) outliers start: 24 outliers final: 18 residues processed: 126 average time/residue: 0.1312 time to fit residues: 23.0017 Evaluate side-chains 125 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 90 MET Chi-restraints excluded: chain I residue 108 ASN Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 92 GLN Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain O residue 39 HIS Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain Q residue 49 LEU Chi-restraints excluded: chain Q residue 50 ILE Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 38 ASN Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 77 LEU Chi-restraints excluded: chain S residue 87 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 80 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 86 optimal weight: 0.3980 chunk 24 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 11 optimal weight: 9.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.117518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.089255 restraints weight = 31831.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.091281 restraints weight = 17527.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.092600 restraints weight = 12122.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.093427 restraints weight = 9795.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.093887 restraints weight = 8682.527| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13403 Z= 0.158 Angle : 0.696 9.263 19459 Z= 0.403 Chirality : 0.054 0.355 2218 Planarity : 0.004 0.050 1377 Dihedral : 33.655 179.095 4271 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.16 % Allowed : 24.68 % Favored : 72.15 % 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: 1.35 (0.31), residues: 760 helix: 1.97 (0.23), residues: 527 sheet: None (None), residues: 0 loop : -1.74 (0.38), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 35 TYR 0.043 0.002 TYR S 80 PHE 0.008 0.001 PHE S 62 HIS 0.006 0.001 HIS S 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.16 (13403) covalent geometry : angle 0.69634 / 0.40 (19459) hydrogen bonds : bond 0.08206 / 8.96 ( 768) hydrogen bonds : angle 3.15788 / 4.10 ( 1860) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 64 GLU cc_start: 0.8366 (tm-30) cc_final: 0.8037 (tm-30) REVERT: M 117 LYS cc_start: 0.8599 (tptm) cc_final: 0.8245 (mtpt) REVERT: O 50 GLU cc_start: 0.8424 (mp0) cc_final: 0.8167 (mp0) REVERT: R 64 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7661 (tt0) outliers start: 20 outliers final: 16 residues processed: 124 average time/residue: 0.1319 time to fit residues: 22.6041 Evaluate side-chains 122 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 90 MET Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain O residue 39 HIS Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain Q residue 49 LEU Chi-restraints excluded: chain Q residue 50 ILE Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 38 ASN Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 87 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 53 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 77 optimal weight: 0.0770 chunk 63 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 54 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 13 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 23 optimal weight: 0.0970 overall best weight: 0.5536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 82 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.118298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.090286 restraints weight = 32217.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.092336 restraints weight = 17637.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.093655 restraints weight = 12101.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.094490 restraints weight = 9736.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.094952 restraints weight = 8609.389| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13403 Z= 0.152 Angle : 0.684 9.182 19459 Z= 0.397 Chirality : 0.053 0.359 2218 Planarity : 0.004 0.051 1377 Dihedral : 33.600 178.682 4271 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.01 % Allowed : 25.00 % Favored : 71.99 % 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: 1.56 (0.32), residues: 760 helix: 2.08 (0.23), residues: 524 sheet: None (None), residues: 0 loop : -1.48 (0.38), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 35 TYR 0.030 0.002 TYR S 80 PHE 0.007 0.001 PHE S 62 HIS 0.006 0.001 HIS S 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.15 (13403) covalent geometry : angle 0.68361 / 0.40 (19459) hydrogen bonds : bond 0.07851 / 8.55 ( 768) hydrogen bonds : angle 3.07841 / 3.97 ( 1860) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: K 64 GLU cc_start: 0.8352 (tm-30) cc_final: 0.8025 (tm-30) REVERT: K 112 GLN cc_start: 0.7635 (mm110) cc_final: 0.7006 (mp10) REVERT: M 92 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.8053 (tp-100) REVERT: M 117 LYS cc_start: 0.8591 (tptm) cc_final: 0.8222 (mtpt) REVERT: R 64 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7632 (tt0) outliers start: 19 outliers final: 14 residues processed: 125 average time/residue: 0.1270 time to fit residues: 21.7641 Evaluate side-chains 122 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 92 GLN Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain Q residue 49 LEU Chi-restraints excluded: chain Q residue 50 ILE Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 38 ASN Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 87 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 50 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 55 optimal weight: 0.8980 chunk 100 optimal weight: 20.0000 chunk 98 optimal weight: 10.0000 chunk 1 optimal weight: 20.0000 chunk 87 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.118677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.090445 restraints weight = 31968.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.092456 restraints weight = 17594.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.093759 restraints weight = 12123.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.094615 restraints weight = 9780.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.095081 restraints weight = 8638.957| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13403 Z= 0.159 Angle : 0.695 9.199 19459 Z= 0.402 Chirality : 0.053 0.373 2218 Planarity : 0.004 0.050 1377 Dihedral : 33.604 178.804 4271 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.16 % Allowed : 25.16 % Favored : 71.68 % 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: 1.45 (0.31), residues: 760 helix: 2.03 (0.23), residues: 527 sheet: None (None), residues: 0 loop : -1.65 (0.38), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 35 TYR 0.031 0.002 TYR M 80 PHE 0.008 0.001 PHE S 62 HIS 0.005 0.001 HIS I 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.16 (13403) covalent geometry : angle 0.69527 / 0.40 (19459) hydrogen bonds : bond 0.08023 / 8.72 ( 768) hydrogen bonds : angle 3.12402 / 4.03 ( 1860) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: K 64 GLU cc_start: 0.8376 (tm-30) cc_final: 0.8058 (tm-30) REVERT: K 112 GLN cc_start: 0.7676 (mm110) cc_final: 0.7060 (mp10) REVERT: M 92 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7987 (tp-100) REVERT: M 117 LYS cc_start: 0.8589 (tptm) cc_final: 0.8246 (mtpt) REVERT: O 81 ASP cc_start: 0.7928 (p0) cc_final: 0.7346 (p0) REVERT: R 64 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7675 (tt0) REVERT: S 90 GLU cc_start: 0.7058 (mp0) cc_final: 0.6832 (mp0) outliers start: 20 outliers final: 17 residues processed: 125 average time/residue: 0.1293 time to fit residues: 22.2122 Evaluate side-chains 126 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 108 ASN Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 92 GLN Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain O residue 39 HIS Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain Q residue 49 LEU Chi-restraints excluded: chain Q residue 50 ILE Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 38 ASN Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 87 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 76 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 59 optimal weight: 0.3980 chunk 89 optimal weight: 20.0000 chunk 85 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 54 optimal weight: 0.2980 chunk 46 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 7 optimal weight: 9.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.119769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.091511 restraints weight = 32135.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.093685 restraints weight = 16923.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.095120 restraints weight = 11360.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.095975 restraints weight = 9003.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.096530 restraints weight = 7923.138| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13403 Z= 0.150 Angle : 0.678 8.973 19459 Z= 0.393 Chirality : 0.052 0.379 2218 Planarity : 0.004 0.051 1377 Dihedral : 33.549 178.885 4271 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.69 % Allowed : 26.11 % Favored : 71.20 % 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: 1.62 (0.32), residues: 760 helix: 2.12 (0.23), residues: 524 sheet: None (None), residues: 0 loop : -1.42 (0.38), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 35 TYR 0.020 0.001 TYR M 80 PHE 0.006 0.001 PHE S 62 HIS 0.003 0.001 HIS I 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.15 (13403) covalent geometry : angle 0.67813 / 0.39 (19459) hydrogen bonds : bond 0.07638 / 8.28 ( 768) hydrogen bonds : angle 3.03590 / 3.90 ( 1860) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2121.96 seconds wall clock time: 37 minutes 10.37 seconds (2230.37 seconds total)