Starting phenix.real_space_refine on Wed Aug 5 23:52:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wc0_65853/08_2026/9wc0_65853.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wc0_65853/08_2026/9wc0_65853.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wc0_65853/08_2026/9wc0_65853.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wc0_65853/08_2026/9wc0_65853.map" model { file = "/net/cci-nas-00/data/ceres_data/9wc0_65853/08_2026/9wc0_65853.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wc0_65853/08_2026/9wc0_65853.cif" } resolution = 2.4 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= 0.005 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 308 5.49 5 S 12 5.16 5 C 6840 2.51 5 N 2339 2.21 5 O 2932 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 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: 12431 Number of models: 1 Model: "" Number of chains: 11 Chain: "B" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 717 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 828 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: "H" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 3139 Classifications: {'DNA': 154} Link IDs: {'rna3p': 153} Chain: "J" Number of atoms: 3175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 3175 Classifications: {'DNA': 154} Link IDs: {'rna3p': 153} Chain: "K" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "O" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 81 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Time building chain proxies: 2.82, per 1000 atoms: 0.23 Number of scatterers: 12431 At special positions: 0 Unit cell: (80.6462, 122.323, 117.451, 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 12 16.00 P 308 15.00 O 2932 8.00 N 2339 7.00 C 6840 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 374.8 milliseconds 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1460 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 70.7% alpha, 3.1% beta 153 base pairs and 279 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'B' and resid 16 through 22 removed outlier: 3.744A pdb=" N LYS B 20 " --> pdb=" O LYS B 16 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL B 21 " --> pdb=" O ARG B 17 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU B 22 " --> pdb=" O HIS B 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 16 through 22' Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.760A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.424A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 124 removed outlier: 3.541A pdb=" N HIS D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.634A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.533A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.505A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.762A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 removed outlier: 3.509A pdb=" N ARG G 20 " --> pdb=" O THR G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.487A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 Processing helix chain 'K' and resid 44 through 49 Processing helix chain 'K' and resid 50 through 53 Processing helix chain 'K' and resid 63 through 79 removed outlier: 4.045A pdb=" N ASP K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE K 78 " --> pdb=" O ILE K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 114 removed outlier: 3.507A pdb=" N ALA K 114 " --> pdb=" O CYS K 110 " (cutoff:3.500A) Processing helix chain 'K' and resid 120 through 131 Processing helix chain 'O' and resid 10 through 15 Processing sheet with id=AA1, first strand: chain 'B' and resid 45 through 46 removed outlier: 7.362A pdb=" N ARG B 45 " --> pdb=" O ILE K 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.048A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.807A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.830A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.044A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 395 hydrogen bonds defined for protein. 1176 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 391 hydrogen bonds 762 hydrogen bond angles 0 basepair planarities 153 basepair parallelities 279 stacking parallelities Total time for adding SS restraints: 2.34 Time building geometry restraints manager: 1.46 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: 2342 1.33 - 1.45: 4435 1.45 - 1.57: 5865 1.57 - 1.69: 614 1.69 - 1.81: 22 Bond restraints: 13278 Sorted by residual: bond pdb=" C3' DT J 7 " pdb=" C2' DT J 7 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.19e+01 bond pdb=" C3' DC I 95 " pdb=" C2' DC I 95 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" C3' DT I 9 " pdb=" C2' DT I 9 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 bond pdb=" C3' DT J 96 " pdb=" C2' DT J 96 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DT I 104 " pdb=" C2' DT I 104 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 ... (remaining 13273 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 17972 1.56 - 3.11: 1230 3.11 - 4.67: 52 4.67 - 6.23: 7 6.23 - 7.78: 2 Bond angle restraints: 19263 Sorted by residual: angle pdb=" O4' DG J 4 " pdb=" C4' DG J 4 " pdb=" C3' DG J 4 " ideal model delta sigma weight residual 106.00 103.23 2.77 6.00e-01 2.78e+00 2.13e+01 angle pdb=" N3 DT I 112 " pdb=" C4 DT I 112 " pdb=" O4 DT I 112 " ideal model delta sigma weight residual 119.90 122.63 -2.73 6.00e-01 2.78e+00 2.07e+01 angle pdb=" N3 DT I 32 " pdb=" C4 DT I 32 " pdb=" O4 DT I 32 " ideal model delta sigma weight residual 119.90 122.63 -2.73 6.00e-01 2.78e+00 2.06e+01 angle pdb=" N3 DT J 99 " pdb=" C4 DT J 99 " pdb=" O4 DT J 99 " ideal model delta sigma weight residual 119.90 122.61 -2.71 6.00e-01 2.78e+00 2.04e+01 angle pdb=" N3 DT J 83 " pdb=" C4 DT J 83 " pdb=" O4 DT J 83 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.03e+01 ... (remaining 19258 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.32: 5612 35.32 - 70.64: 1544 70.64 - 105.96: 13 105.96 - 141.28: 0 141.28 - 176.60: 3 Dihedral angle restraints: 7172 sinusoidal: 4914 harmonic: 2258 Sorted by residual: dihedral pdb=" CA ARG K 53 " pdb=" C ARG K 53 " pdb=" N TYR K 54 " pdb=" CA TYR K 54 " ideal model delta harmonic sigma weight residual -180.00 -155.67 -24.33 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" C4' DT J 15 " pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sinusoidal sigma weight residual -140.00 36.60 -176.60 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC I 12 " pdb=" C3' DC I 12 " pdb=" O3' DC I 12 " pdb=" P DG I 13 " ideal model delta sinusoidal sigma weight residual 220.00 52.71 167.29 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 7169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1274 0.034 - 0.067: 641 0.067 - 0.101: 227 0.101 - 0.135: 51 0.135 - 0.168: 7 Chirality restraints: 2200 Sorted by residual: chirality pdb=" C3' DT J 15 " pdb=" C4' DT J 15 " pdb=" O3' DT J 15 " pdb=" C2' DT J 15 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.07e-01 chirality pdb=" C3' DC I 12 " pdb=" C4' DC I 12 " pdb=" O3' DC I 12 " pdb=" C2' DC I 12 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.69e-01 chirality pdb=" C3' DC I 53 " pdb=" C4' DC I 53 " pdb=" O3' DC I 53 " pdb=" C2' DC I 53 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.12e-01 ... (remaining 2197 not shown) Planarity restraints: 1372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 100 " -0.031 2.00e-02 2.50e+03 1.30e-02 5.07e+00 pdb=" N9 DG I 100 " 0.030 2.00e-02 2.50e+03 pdb=" C8 DG I 100 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DG I 100 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DG I 100 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 100 " -0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 100 " -0.011 2.00e-02 2.50e+03 pdb=" N1 DG I 100 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DG I 100 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 100 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DG I 100 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DG I 100 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 91 " 0.022 2.00e-02 2.50e+03 1.01e-02 2.80e+00 pdb=" N9 DA I 91 " -0.023 2.00e-02 2.50e+03 pdb=" C8 DA I 91 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DA I 91 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA I 91 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DA I 91 " 0.002 2.00e-02 2.50e+03 pdb=" N6 DA I 91 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DA I 91 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 91 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DA I 91 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DA I 91 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 121 " -0.022 2.00e-02 2.50e+03 9.50e-03 2.71e+00 pdb=" N9 DG I 121 " 0.023 2.00e-02 2.50e+03 pdb=" C8 DG I 121 " 0.003 2.00e-02 2.50e+03 pdb=" N7 DG I 121 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DG I 121 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DG I 121 " -0.002 2.00e-02 2.50e+03 pdb=" O6 DG I 121 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DG I 121 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DG I 121 " -0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 121 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DG I 121 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DG I 121 " 0.003 2.00e-02 2.50e+03 ... (remaining 1369 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 83 2.59 - 3.17: 9000 3.17 - 3.75: 22812 3.75 - 4.32: 32392 4.32 - 4.90: 44743 Nonbonded interactions: 109030 Sorted by model distance: nonbonded pdb=" N2 DG I 14 " pdb=" O2 DC J 134 " model vdw 2.018 2.496 nonbonded pdb=" O2 DC I 95 " pdb=" N2 DG J 53 " model vdw 2.081 2.496 nonbonded pdb=" O2 DC I 53 " pdb=" N2 DG J 95 " model vdw 2.097 2.496 nonbonded pdb=" O2 DC I 23 " pdb=" N2 DG J 125 " model vdw 2.146 2.496 nonbonded pdb=" O2 DC I 70 " pdb=" N2 DG J 78 " model vdw 2.153 2.496 ... (remaining 109025 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 'B' and ((resid 17 and (name N or name CA or name C or name O or name CB \ )) or resid 18 or (resid 19 through 20 and (name N or name CA or name C or name \ O or name CB )) or resid 21 through 22 or (resid 23 and (name N or name CA or na \ me C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and resid 17 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 117 or (resid 118 and (name N or \ name CA or name C or name O or name CB )))) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 32 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 56 or (resid 57 through 58 and (na \ me N or name CA or name C or name O or name CB )) or resid 59 through 124)) } ncs_group { reference = chain 'E' selection = (chain 'K' and resid 40 through 134) } 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 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: 4.400 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: 0.440 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 13.870 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 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 0.040 13278 Z= 0.571 Angle : 0.772 7.782 19263 Z= 0.687 Chirality : 0.044 0.168 2200 Planarity : 0.005 0.041 1372 Dihedral : 28.804 176.600 5712 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.95 % Allowed : 14.98 % Favored : 84.07 % 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: 2.25 (0.29), residues: 759 helix: 2.36 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -0.58 (0.34), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 52 TYR 0.019 0.002 TYR F 88 PHE 0.009 0.002 PHE G 25 HIS 0.008 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00623 / 0.57 (13278) covalent geometry : angle 0.77184 / 0.69 (19263) hydrogen bonds : bond 0.11867 / 8.29 ( 786) hydrogen bonds : angle 3.68589 / 2.72 ( 1938) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 179 time to evaluate : 0.352 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 181 average time/residue: 1.0825 time to fit residues: 205.2849 Evaluate side-chains 159 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 157 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain H residue 88 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 30.0000 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.4980 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 95 GLN G 110 ASN H 84 ASN K 68 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.114922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.079529 restraints weight = 20812.965| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.66 r_work: 0.2936 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13278 Z= 0.167 Angle : 0.661 6.582 19263 Z= 0.385 Chirality : 0.048 0.303 2200 Planarity : 0.005 0.042 1372 Dihedral : 31.186 174.086 4218 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.21 % Allowed : 15.46 % Favored : 82.33 % 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: 2.62 (0.29), residues: 759 helix: 2.58 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.51 (0.35), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 92 TYR 0.011 0.001 TYR D 83 PHE 0.008 0.001 PHE K 67 HIS 0.005 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.17 (13278) covalent geometry : angle 0.66127 / 0.39 (19263) hydrogen bonds : bond 0.06906 / 4.75 ( 786) hydrogen bonds : angle 3.08522 / 2.25 ( 1938) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 0.353 Fit side-chains REVERT: C 92 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8642 (mp0) REVERT: C 99 ARG cc_start: 0.8869 (mmm-85) cc_final: 0.8250 (mmm160) REVERT: D 108 LYS cc_start: 0.8580 (mtpp) cc_final: 0.8284 (tttm) REVERT: E 59 GLU cc_start: 0.8207 (pm20) cc_final: 0.7969 (pm20) REVERT: F 77 LYS cc_start: 0.9243 (mptp) cc_final: 0.9034 (mttp) REVERT: G 92 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8294 (mt-10) outliers start: 14 outliers final: 3 residues processed: 167 average time/residue: 1.0075 time to fit residues: 176.7096 Evaluate side-chains 163 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 158 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain K residue 94 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 101 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 77 optimal weight: 50.0000 chunk 38 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 90 optimal weight: 20.0000 chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 76 GLN G 110 ASN H 63 ASN K 68 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.114223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.078447 restraints weight = 21136.572| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.71 r_work: 0.2924 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13278 Z= 0.188 Angle : 0.633 6.401 19263 Z= 0.367 Chirality : 0.046 0.331 2200 Planarity : 0.005 0.045 1372 Dihedral : 31.288 175.170 4215 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.68 % Allowed : 14.98 % Favored : 82.33 % 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: 2.80 (0.30), residues: 759 helix: 2.72 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.47 (0.36), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 86 TYR 0.010 0.002 TYR D 83 PHE 0.010 0.002 PHE C 25 HIS 0.005 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.19 (13278) covalent geometry : angle 0.63331 / 0.37 (19263) hydrogen bonds : bond 0.06780 / 4.64 ( 786) hydrogen bonds : angle 2.89130 / 2.12 ( 1938) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 0.321 Fit side-chains REVERT: C 99 ARG cc_start: 0.8911 (mmm-85) cc_final: 0.8284 (mmm160) REVERT: D 108 LYS cc_start: 0.8594 (mtpp) cc_final: 0.8265 (tttm) REVERT: E 59 GLU cc_start: 0.8372 (pm20) cc_final: 0.7989 (pm20) REVERT: E 122 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8460 (pttp) REVERT: F 24 ASP cc_start: 0.7274 (t0) cc_final: 0.7024 (t0) REVERT: F 77 LYS cc_start: 0.9213 (mptp) cc_final: 0.8886 (mttp) REVERT: F 93 GLN cc_start: 0.8605 (mt0) cc_final: 0.8286 (mm-40) REVERT: G 19 SER cc_start: 0.9184 (p) cc_final: 0.8968 (p) REVERT: G 90 ASP cc_start: 0.8769 (t70) cc_final: 0.8485 (t0) REVERT: G 92 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8251 (mt-10) outliers start: 17 outliers final: 9 residues processed: 174 average time/residue: 0.9489 time to fit residues: 173.6733 Evaluate side-chains 172 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 161 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain K residue 94 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 54 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 95 optimal weight: 0.0170 chunk 100 optimal weight: 0.9990 chunk 87 optimal weight: 20.0000 chunk 22 optimal weight: 0.9980 chunk 63 optimal weight: 50.0000 chunk 67 optimal weight: 20.0000 chunk 29 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 71 optimal weight: 20.0000 overall best weight: 1.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 76 GLN E 125 GLN F 93 GLN G 110 ASN H 63 ASN K 68 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.114786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.079313 restraints weight = 20992.665| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.68 r_work: 0.2937 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13278 Z= 0.146 Angle : 0.620 6.260 19263 Z= 0.361 Chirality : 0.045 0.329 2200 Planarity : 0.004 0.035 1372 Dihedral : 31.278 175.537 4215 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.21 % Allowed : 15.77 % Favored : 82.02 % 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: 2.95 (0.30), residues: 759 helix: 2.85 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.44 (0.36), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 33 TYR 0.009 0.001 TYR F 51 PHE 0.009 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.15 (13278) covalent geometry : angle 0.61965 / 0.36 (19263) hydrogen bonds : bond 0.06440 / 4.42 ( 786) hydrogen bonds : angle 2.87222 / 2.10 ( 1938) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 163 time to evaluate : 0.237 Fit side-chains REVERT: C 99 ARG cc_start: 0.8901 (mmm-85) cc_final: 0.8270 (mmm160) REVERT: D 108 LYS cc_start: 0.8579 (mtpp) cc_final: 0.8265 (tttm) REVERT: E 59 GLU cc_start: 0.8353 (pm20) cc_final: 0.8070 (pm20) REVERT: F 77 LYS cc_start: 0.9206 (mptp) cc_final: 0.8879 (mttp) REVERT: F 93 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8251 (mm-40) REVERT: G 19 SER cc_start: 0.9179 (p) cc_final: 0.8961 (p) REVERT: G 90 ASP cc_start: 0.8780 (t70) cc_final: 0.8481 (t0) REVERT: G 92 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8221 (mt-10) REVERT: H 116 LYS cc_start: 0.9168 (ttmt) cc_final: 0.8905 (ttmt) outliers start: 14 outliers final: 9 residues processed: 168 average time/residue: 0.9063 time to fit residues: 160.0159 Evaluate side-chains 175 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 164 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain K residue 94 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 16 optimal weight: 7.9990 chunk 80 optimal weight: 30.0000 chunk 72 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 78 optimal weight: 50.0000 chunk 88 optimal weight: 20.0000 chunk 74 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 76 optimal weight: 40.0000 chunk 48 optimal weight: 4.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 76 GLN F 93 GLN G 110 ASN H 63 ASN K 68 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.112752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.076953 restraints weight = 21084.009| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.67 r_work: 0.2894 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 13278 Z= 0.271 Angle : 0.666 7.172 19263 Z= 0.377 Chirality : 0.049 0.334 2200 Planarity : 0.005 0.045 1372 Dihedral : 31.374 176.118 4215 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.84 % Allowed : 15.62 % Favored : 81.55 % 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: 2.75 (0.29), residues: 759 helix: 2.72 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.59 (0.35), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 33 TYR 0.010 0.002 TYR E 54 PHE 0.009 0.002 PHE C 25 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.27 (13278) covalent geometry : angle 0.66573 / 0.38 (19263) hydrogen bonds : bond 0.07536 / 5.15 ( 786) hydrogen bonds : angle 2.92837 / 2.14 ( 1938) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 0.357 Fit side-chains REVERT: B 79 LYS cc_start: 0.9004 (mtpp) cc_final: 0.8524 (mttp) REVERT: D 108 LYS cc_start: 0.8647 (mtpp) cc_final: 0.8321 (tttm) REVERT: E 59 GLU cc_start: 0.8478 (pm20) cc_final: 0.8101 (pm20) REVERT: E 122 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8540 (pttp) REVERT: F 24 ASP cc_start: 0.7409 (t0) cc_final: 0.7130 (OUTLIER) REVERT: F 93 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8284 (mm-40) REVERT: G 90 ASP cc_start: 0.8801 (t70) cc_final: 0.8463 (t0) REVERT: G 92 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8213 (mt-10) REVERT: G 110 ASN cc_start: 0.8941 (t0) cc_final: 0.8623 (t0) REVERT: H 68 ASP cc_start: 0.9043 (t0) cc_final: 0.8838 (t0) REVERT: H 116 LYS cc_start: 0.9196 (ttmt) cc_final: 0.8937 (ttmt) outliers start: 18 outliers final: 11 residues processed: 168 average time/residue: 0.7991 time to fit residues: 141.1570 Evaluate side-chains 172 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 159 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain K residue 94 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 68 optimal weight: 20.0000 chunk 4 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 75 optimal weight: 20.0000 chunk 51 optimal weight: 0.7980 chunk 63 optimal weight: 50.0000 chunk 47 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 76 GLN H 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.114832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.079407 restraints weight = 20980.853| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.69 r_work: 0.2943 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13278 Z= 0.138 Angle : 0.623 10.549 19263 Z= 0.358 Chirality : 0.045 0.331 2200 Planarity : 0.004 0.056 1372 Dihedral : 31.313 177.423 4215 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.05 % Allowed : 17.51 % Favored : 80.44 % 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: 3.01 (0.30), residues: 759 helix: 2.90 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.43 (0.36), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 33 TYR 0.013 0.002 TYR D 83 PHE 0.008 0.001 PHE E 67 HIS 0.002 0.000 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.14 (13278) covalent geometry : angle 0.62270 / 0.36 (19263) hydrogen bonds : bond 0.06158 / 4.26 ( 786) hydrogen bonds : angle 2.84086 / 2.08 ( 1938) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 168 time to evaluate : 0.350 Fit side-chains REVERT: C 99 ARG cc_start: 0.8941 (mmm-85) cc_final: 0.8367 (mmm160) REVERT: D 68 ASP cc_start: 0.9113 (t0) cc_final: 0.8894 (t0) REVERT: D 108 LYS cc_start: 0.8564 (mtpp) cc_final: 0.8258 (tttm) REVERT: E 59 GLU cc_start: 0.8430 (pm20) cc_final: 0.8062 (pm20) REVERT: E 122 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8464 (pttp) REVERT: G 19 SER cc_start: 0.9188 (p) cc_final: 0.8965 (p) REVERT: G 90 ASP cc_start: 0.8748 (t70) cc_final: 0.8452 (t0) REVERT: G 92 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8191 (mt-10) REVERT: G 110 ASN cc_start: 0.8905 (t0) cc_final: 0.8603 (t0) REVERT: H 68 ASP cc_start: 0.9013 (t0) cc_final: 0.8767 (t0) REVERT: H 116 LYS cc_start: 0.9189 (ttmt) cc_final: 0.8934 (ttmt) outliers start: 13 outliers final: 7 residues processed: 173 average time/residue: 0.9334 time to fit residues: 169.8498 Evaluate side-chains 175 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 166 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain K residue 94 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 10 optimal weight: 3.9990 chunk 73 optimal weight: 20.0000 chunk 64 optimal weight: 40.0000 chunk 5 optimal weight: 2.9990 chunk 91 optimal weight: 30.0000 chunk 56 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 76 GLN H 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.115364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.080031 restraints weight = 21003.481| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.70 r_work: 0.2964 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13278 Z= 0.142 Angle : 0.601 10.763 19263 Z= 0.350 Chirality : 0.044 0.329 2200 Planarity : 0.004 0.061 1372 Dihedral : 31.154 178.465 4215 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.74 % Allowed : 17.98 % Favored : 80.28 % 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: 3.11 (0.30), residues: 759 helix: 2.96 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.35 (0.36), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG H 33 TYR 0.015 0.001 TYR D 83 PHE 0.009 0.001 PHE E 67 HIS 0.002 0.000 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.14 (13278) covalent geometry : angle 0.60120 / 0.35 (19263) hydrogen bonds : bond 0.05977 / 4.13 ( 786) hydrogen bonds : angle 2.76046 / 2.02 ( 1938) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 162 time to evaluate : 0.302 Fit side-chains REVERT: C 99 ARG cc_start: 0.8912 (mmm-85) cc_final: 0.8319 (mmm160) REVERT: D 68 ASP cc_start: 0.9134 (t0) cc_final: 0.8876 (t0) REVERT: E 59 GLU cc_start: 0.8405 (pm20) cc_final: 0.8012 (pm20) REVERT: F 77 LYS cc_start: 0.9202 (mptp) cc_final: 0.8995 (mttp) REVERT: G 19 SER cc_start: 0.9203 (p) cc_final: 0.8982 (p) REVERT: G 90 ASP cc_start: 0.8785 (t70) cc_final: 0.8487 (t0) REVERT: G 92 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8179 (mt-10) REVERT: G 110 ASN cc_start: 0.8919 (t0) cc_final: 0.8636 (t0) REVERT: H 68 ASP cc_start: 0.9005 (t0) cc_final: 0.8749 (t0) REVERT: H 116 LYS cc_start: 0.9202 (ttmt) cc_final: 0.8944 (ttmt) outliers start: 11 outliers final: 7 residues processed: 167 average time/residue: 0.8247 time to fit residues: 145.0467 Evaluate side-chains 170 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 162 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain K residue 94 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 80 optimal weight: 30.0000 chunk 55 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 64 optimal weight: 40.0000 chunk 30 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 74 optimal weight: 20.0000 chunk 11 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 76 GLN H 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.113510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.077906 restraints weight = 20884.948| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.66 r_work: 0.2908 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13278 Z= 0.220 Angle : 0.640 10.221 19263 Z= 0.363 Chirality : 0.046 0.336 2200 Planarity : 0.004 0.046 1372 Dihedral : 31.275 179.229 4215 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.89 % Allowed : 17.82 % Favored : 80.28 % 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: 2.96 (0.30), residues: 759 helix: 2.86 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.45 (0.36), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 33 TYR 0.013 0.002 TYR D 83 PHE 0.008 0.002 PHE K 67 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.22 (13278) covalent geometry : angle 0.63982 / 0.36 (19263) hydrogen bonds : bond 0.06890 / 4.72 ( 786) hydrogen bonds : angle 2.83789 / 2.08 ( 1938) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 162 time to evaluate : 0.269 Fit side-chains REVERT: C 99 ARG cc_start: 0.8927 (mmm-85) cc_final: 0.8319 (mmm160) REVERT: D 108 LYS cc_start: 0.8567 (mtpp) cc_final: 0.8221 (tttm) REVERT: E 59 GLU cc_start: 0.8475 (pm20) cc_final: 0.8078 (pm20) REVERT: F 24 ASP cc_start: 0.7421 (t0) cc_final: 0.7167 (OUTLIER) REVERT: G 19 SER cc_start: 0.9213 (p) cc_final: 0.8985 (p) REVERT: G 90 ASP cc_start: 0.8806 (t70) cc_final: 0.8445 (t0) REVERT: G 110 ASN cc_start: 0.8944 (t0) cc_final: 0.8673 (t0) REVERT: H 68 ASP cc_start: 0.9053 (t0) cc_final: 0.8794 (t0) REVERT: H 116 LYS cc_start: 0.9218 (ttmt) cc_final: 0.8960 (ttmt) outliers start: 12 outliers final: 10 residues processed: 167 average time/residue: 0.8420 time to fit residues: 148.2713 Evaluate side-chains 170 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 161 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain K residue 94 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 90 optimal weight: 20.0000 chunk 19 optimal weight: 0.7980 chunk 15 optimal weight: 0.4980 chunk 42 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 93 optimal weight: 0.0040 chunk 44 optimal weight: 10.0000 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 76 GLN H 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.114444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.078856 restraints weight = 20946.729| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.68 r_work: 0.2933 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 13278 Z= 0.135 Angle : 0.624 9.299 19263 Z= 0.359 Chirality : 0.044 0.334 2200 Planarity : 0.004 0.041 1372 Dihedral : 31.280 179.536 4215 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.74 % Allowed : 18.45 % Favored : 79.81 % 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: 3.12 (0.30), residues: 759 helix: 2.96 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.35 (0.36), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 33 TYR 0.019 0.002 TYR D 83 PHE 0.010 0.001 PHE E 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.13 (13278) covalent geometry : angle 0.62408 / 0.36 (19263) hydrogen bonds : bond 0.06309 / 4.35 ( 786) hydrogen bonds : angle 2.83549 / 2.08 ( 1938) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 163 time to evaluate : 0.251 Fit side-chains REVERT: C 99 ARG cc_start: 0.8898 (mmm-85) cc_final: 0.8267 (mmm160) REVERT: D 108 LYS cc_start: 0.8520 (mtpp) cc_final: 0.8184 (tttm) REVERT: E 59 GLU cc_start: 0.8444 (pm20) cc_final: 0.8049 (pm20) REVERT: F 24 ASP cc_start: 0.7359 (t0) cc_final: 0.7108 (OUTLIER) REVERT: G 19 SER cc_start: 0.9202 (p) cc_final: 0.8979 (p) REVERT: G 92 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8216 (mt-10) REVERT: G 110 ASN cc_start: 0.8908 (t0) cc_final: 0.8622 (t0) REVERT: H 68 ASP cc_start: 0.9013 (t0) cc_final: 0.8753 (t0) REVERT: H 116 LYS cc_start: 0.9190 (ttmt) cc_final: 0.8936 (ttmt) outliers start: 11 outliers final: 8 residues processed: 169 average time/residue: 0.9005 time to fit residues: 160.4272 Evaluate side-chains 170 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 162 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain K residue 94 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 42 optimal weight: 3.9990 chunk 74 optimal weight: 20.0000 chunk 19 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 87 optimal weight: 20.0000 chunk 40 optimal weight: 0.0870 chunk 95 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 71 optimal weight: 20.0000 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 76 GLN H 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.114361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.078893 restraints weight = 20962.988| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.68 r_work: 0.2932 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13278 Z= 0.151 Angle : 0.625 9.564 19263 Z= 0.357 Chirality : 0.045 0.333 2200 Planarity : 0.004 0.040 1372 Dihedral : 31.255 179.993 4215 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.74 % Allowed : 18.14 % Favored : 80.13 % 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: 3.11 (0.30), residues: 759 helix: 2.96 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.35 (0.36), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 33 TYR 0.015 0.002 TYR D 83 PHE 0.008 0.001 PHE E 67 HIS 0.002 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.15 (13278) covalent geometry : angle 0.62524 / 0.36 (19263) hydrogen bonds : bond 0.06183 / 4.27 ( 786) hydrogen bonds : angle 2.79967 / 2.05 ( 1938) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 160 time to evaluate : 0.346 Fit side-chains REVERT: C 99 ARG cc_start: 0.8926 (mmm-85) cc_final: 0.8322 (mmm160) REVERT: D 108 LYS cc_start: 0.8523 (mtpp) cc_final: 0.8186 (tttm) REVERT: E 59 GLU cc_start: 0.8441 (pm20) cc_final: 0.8038 (pm20) REVERT: F 24 ASP cc_start: 0.7365 (t0) cc_final: 0.7110 (OUTLIER) REVERT: G 19 SER cc_start: 0.9209 (p) cc_final: 0.8984 (p) REVERT: G 90 ASP cc_start: 0.8759 (t70) cc_final: 0.8413 (t0) REVERT: G 92 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8144 (mt-10) REVERT: G 110 ASN cc_start: 0.8903 (t0) cc_final: 0.8635 (t0) REVERT: H 68 ASP cc_start: 0.9024 (t0) cc_final: 0.8766 (t0) REVERT: H 116 LYS cc_start: 0.9203 (ttmt) cc_final: 0.8946 (ttmt) outliers start: 11 outliers final: 8 residues processed: 165 average time/residue: 0.8410 time to fit residues: 146.3924 Evaluate side-chains 169 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 161 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain K residue 94 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 89 optimal weight: 20.0000 chunk 40 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 16 optimal weight: 0.2980 chunk 3 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 76 GLN H 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.114611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.079144 restraints weight = 20982.304| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.68 r_work: 0.2939 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 13278 Z= 0.138 Angle : 0.618 9.376 19263 Z= 0.354 Chirality : 0.044 0.332 2200 Planarity : 0.004 0.037 1372 Dihedral : 31.249 179.924 4215 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.89 % Allowed : 17.98 % Favored : 80.13 % 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: 3.13 (0.30), residues: 759 helix: 2.97 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.33 (0.36), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 33 TYR 0.018 0.002 TYR D 83 PHE 0.008 0.001 PHE E 67 HIS 0.002 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.14 (13278) covalent geometry : angle 0.61788 / 0.35 (19263) hydrogen bonds : bond 0.06106 / 4.22 ( 786) hydrogen bonds : angle 2.79683 / 2.05 ( 1938) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6220.07 seconds wall clock time: 105 minutes 54.64 seconds (6354.64 seconds total)