Starting phenix.real_space_refine on Fri Jul 3 05:42:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wc0_65853/07_2026/9wc0_65853.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wc0_65853/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9wc0_65853/07_2026/9wc0_65853.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wc0_65853/07_2026/9wc0_65853.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wc0_65853/07_2026/9wc0_65853.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wc0_65853/07_2026/9wc0_65853.map" } 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-dev-6108/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: 2.67, per 1000 atoms: 0.21 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: 0.91 Conformation dependent library (CDL) restraints added in 461.6 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: 1.91 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: 1.99 Time building geometry restraints manager: 1.29 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: 18008 1.56 - 3.11: 1194 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: 5.990 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: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.010 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.640 ------------------------------------------------------------------------------- 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= 0.570 Angle : 0.764 7.782 19263 Z= 0.680 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 0.76358 / 0.68 (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 : 0.330 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 181 average time/residue: 0.9857 time to fit residues: 186.9693 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 : 0.315 ------------------------------------------------------------------------------- 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 = 0.3791 r_free = 0.3791 target = 0.114997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.079523 restraints weight = 20814.811| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.67 r_work: 0.2940 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13278 Z= 0.168 Angle : 0.646 6.666 19263 Z= 0.379 Chirality : 0.047 0.287 2200 Planarity : 0.004 0.043 1372 Dihedral : 31.284 173.576 4218 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.21 % Allowed : 15.30 % Favored : 82.49 % 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: 2.64 (0.29), residues: 759 helix: 2.60 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.50 (0.35), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 92 TYR 0.011 0.001 TYR D 83 PHE 0.008 0.001 PHE B 61 HIS 0.005 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.17 (13278) covalent geometry : angle 0.64620 / 0.38 (19263) hydrogen bonds : bond 0.06864 / 4.72 ( 786) hydrogen bonds : angle 3.03704 / 2.22 ( 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 : 0.259 Fit side-chains REVERT: C 99 ARG cc_start: 0.8886 (mmm-85) cc_final: 0.8268 (mmm160) REVERT: D 108 LYS cc_start: 0.8600 (mtpp) cc_final: 0.8299 (tttm) REVERT: E 59 GLU cc_start: 0.8211 (pm20) cc_final: 0.7951 (pm20) REVERT: F 77 LYS cc_start: 0.9238 (mptp) cc_final: 0.9004 (mttp) REVERT: G 92 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8293 (mt-10) REVERT: H 68 ASP cc_start: 0.9008 (t0) cc_final: 0.8801 (t0) outliers start: 14 outliers final: 4 residues processed: 167 average time/residue: 0.9346 time to fit residues: 163.8989 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 : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 59 LYS 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: 3.9990 chunk 14 optimal weight: 4.9990 chunk 77 optimal weight: 50.0000 chunk 38 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 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: 3.3788 ------------------------------------------------------------------------------- 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 = 0.3764 r_free = 0.3764 target = 0.113615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.078136 restraints weight = 21067.198| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.70 r_work: 0.2906 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13278 Z= 0.220 Angle : 0.637 6.755 19263 Z= 0.372 Chirality : 0.047 0.302 2200 Planarity : 0.004 0.038 1372 Dihedral : 31.390 174.147 4215 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.68 % Allowed : 14.35 % Favored : 82.97 % 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: 2.73 (0.30), residues: 759 helix: 2.67 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.49 (0.35), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 33 TYR 0.009 0.002 TYR E 54 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 0.00447 / 0.22 (13278) covalent geometry : angle 0.63671 / 0.37 (19263) hydrogen bonds : bond 0.07234 / 4.95 ( 786) hydrogen bonds : angle 2.93582 / 2.15 ( 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 177 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 0.309 Fit side-chains REVERT: C 99 ARG cc_start: 0.8905 (mmm-85) cc_final: 0.8272 (mmm160) REVERT: D 108 LYS cc_start: 0.8610 (mtpp) cc_final: 0.8282 (tttm) REVERT: E 59 GLU cc_start: 0.8382 (pm20) cc_final: 0.8116 (pm20) REVERT: E 122 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8463 (pttp) REVERT: F 77 LYS cc_start: 0.9235 (mptp) cc_final: 0.8889 (mttp) REVERT: G 90 ASP cc_start: 0.8758 (t70) cc_final: 0.8448 (t0) REVERT: G 92 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8276 (mt-10) REVERT: H 68 ASP cc_start: 0.9037 (t0) cc_final: 0.8778 (t0) outliers start: 17 outliers final: 11 residues processed: 168 average time/residue: 0.8823 time to fit residues: 155.6314 Evaluate side-chains 171 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 158 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 24 ASP 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: 0.7980 chunk 7 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 87 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 63 optimal weight: 50.0000 chunk 67 optimal weight: 20.0000 chunk 29 optimal weight: 2.9990 chunk 3 optimal weight: 0.1980 chunk 71 optimal weight: 10.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 76 GLN G 110 ASN H 63 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.114862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.079435 restraints weight = 21044.300| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.68 r_work: 0.2942 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13278 Z= 0.154 Angle : 0.599 6.229 19263 Z= 0.354 Chirality : 0.044 0.301 2200 Planarity : 0.004 0.042 1372 Dihedral : 31.336 175.656 4215 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.89 % Allowed : 16.25 % Favored : 81.86 % 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: 2.93 (0.30), residues: 759 helix: 2.81 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.39 (0.36), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 33 TYR 0.010 0.001 TYR D 83 PHE 0.007 0.001 PHE B 61 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.15 (13278) covalent geometry : angle 0.59901 / 0.35 (19263) hydrogen bonds : bond 0.06273 / 4.33 ( 786) hydrogen bonds : angle 2.84283 / 2.08 ( 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 176 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 164 time to evaluate : 0.433 Fit side-chains REVERT: C 99 ARG cc_start: 0.8902 (mmm-85) cc_final: 0.8287 (mmm160) REVERT: D 68 ASP cc_start: 0.9125 (t0) cc_final: 0.8889 (t0) REVERT: D 108 LYS cc_start: 0.8589 (mtpp) cc_final: 0.8273 (tttm) REVERT: E 59 GLU cc_start: 0.8391 (pm20) cc_final: 0.8095 (pm20) REVERT: F 77 LYS cc_start: 0.9217 (mptp) cc_final: 0.8877 (mttp) REVERT: F 93 GLN cc_start: 0.8582 (mt0) cc_final: 0.8298 (mm-40) REVERT: G 19 SER cc_start: 0.9191 (p) cc_final: 0.8974 (p) REVERT: G 90 ASP cc_start: 0.8783 (t70) cc_final: 0.8475 (t0) REVERT: G 92 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8237 (mt-10) REVERT: H 68 ASP cc_start: 0.9014 (t0) cc_final: 0.8756 (t0) REVERT: H 116 LYS cc_start: 0.9176 (ttmt) cc_final: 0.8915 (ttmt) outliers start: 12 outliers final: 8 residues processed: 169 average time/residue: 0.9509 time to fit residues: 168.8844 Evaluate side-chains 173 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 164 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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 87 SER 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: 5.9990 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: 30.0000 chunk 48 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 76 GLN F 25 ASN G 110 ASN H 63 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.112026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.076562 restraints weight = 21058.247| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.69 r_work: 0.2880 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 13278 Z= 0.318 Angle : 0.678 7.609 19263 Z= 0.384 Chirality : 0.050 0.315 2200 Planarity : 0.005 0.043 1372 Dihedral : 31.519 175.738 4215 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.68 % Allowed : 15.46 % Favored : 81.86 % 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: 2.64 (0.30), residues: 759 helix: 2.64 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.60 (0.36), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 33 TYR 0.012 0.002 TYR H 121 PHE 0.010 0.002 PHE C 25 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00684 / 0.32 (13278) covalent geometry : angle 0.67849 / 0.38 (19263) hydrogen bonds : bond 0.08225 / 5.60 ( 786) hydrogen bonds : angle 2.98861 / 2.19 ( 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 179 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 0.342 Fit side-chains REVERT: B 79 LYS cc_start: 0.8999 (mtpp) cc_final: 0.8521 (mttp) REVERT: D 108 LYS cc_start: 0.8667 (mtpp) cc_final: 0.8335 (tttm) REVERT: E 59 GLU cc_start: 0.8512 (pm20) cc_final: 0.8128 (pm20) REVERT: E 122 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8574 (pttp) REVERT: F 77 LYS cc_start: 0.9262 (mptp) cc_final: 0.8924 (mttp) REVERT: G 90 ASP cc_start: 0.8827 (t70) cc_final: 0.8489 (t0) REVERT: G 110 ASN cc_start: 0.8954 (t0) cc_final: 0.8650 (t0) REVERT: H 116 LYS cc_start: 0.9202 (ttmt) cc_final: 0.8947 (ttmt) outliers start: 17 outliers final: 12 residues processed: 170 average time/residue: 0.9783 time to fit residues: 174.7955 Evaluate side-chains 174 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 161 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 THR 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 G residue 62 ILE 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: 0.9990 chunk 59 optimal weight: 3.9990 chunk 68 optimal weight: 20.0000 chunk 4 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 75 optimal weight: 20.0000 chunk 51 optimal weight: 0.7980 chunk 63 optimal weight: 50.0000 chunk 47 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3775 r_free = 0.3775 target = 0.114202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.078747 restraints weight = 20956.600| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.69 r_work: 0.2931 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 13278 Z= 0.137 Angle : 0.622 12.866 19263 Z= 0.359 Chirality : 0.046 0.306 2200 Planarity : 0.004 0.039 1372 Dihedral : 31.489 177.114 4215 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.89 % Allowed : 16.88 % Favored : 81.23 % 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: 2.92 (0.30), residues: 759 helix: 2.82 (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 0.009 0.001 ARG H 33 TYR 0.016 0.002 TYR D 83 PHE 0.008 0.001 PHE B 61 HIS 0.002 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.14 (13278) covalent geometry : angle 0.62203 / 0.36 (19263) hydrogen bonds : bond 0.06390 / 4.41 ( 786) hydrogen bonds : angle 2.88383 / 2.11 ( 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 180 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 168 time to evaluate : 0.354 Fit side-chains REVERT: C 99 ARG cc_start: 0.8923 (mmm-85) cc_final: 0.8317 (mmm160) REVERT: D 108 LYS cc_start: 0.8585 (mtpp) cc_final: 0.8276 (tttm) REVERT: E 59 GLU cc_start: 0.8488 (pm20) cc_final: 0.8101 (pm20) REVERT: E 122 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8479 (pttp) REVERT: F 77 LYS cc_start: 0.9241 (mptp) cc_final: 0.8878 (mttp) REVERT: F 93 GLN cc_start: 0.8733 (mm-40) cc_final: 0.8372 (mm-40) REVERT: G 90 ASP cc_start: 0.8785 (t70) cc_final: 0.8404 (t0) REVERT: G 110 ASN cc_start: 0.8900 (t0) cc_final: 0.8611 (t0) REVERT: H 116 LYS cc_start: 0.9189 (ttmt) cc_final: 0.8933 (ttmt) outliers start: 12 outliers final: 8 residues processed: 173 average time/residue: 0.8754 time to fit residues: 159.4132 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 : 0.396 ------------------------------------------------------------------------------- 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 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: 4.9990 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: 0.9990 chunk 46 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 76 GLN E 125 GLN H 63 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.114373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.078928 restraints weight = 20953.445| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.68 r_work: 0.2937 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13278 Z= 0.156 Angle : 0.603 11.021 19263 Z= 0.352 Chirality : 0.044 0.305 2200 Planarity : 0.004 0.054 1372 Dihedral : 31.364 177.813 4215 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.58 % Allowed : 17.03 % Favored : 81.39 % 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: 3.02 (0.30), residues: 759 helix: 2.89 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.40 (0.36), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG H 33 TYR 0.012 0.002 TYR D 83 PHE 0.008 0.001 PHE E 67 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.16 (13278) covalent geometry : angle 0.60292 / 0.35 (19263) hydrogen bonds : bond 0.06246 / 4.30 ( 786) hydrogen bonds : angle 2.81744 / 2.06 ( 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 169 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 159 time to evaluate : 0.360 Fit side-chains REVERT: C 99 ARG cc_start: 0.8921 (mmm-85) cc_final: 0.8319 (mmm160) REVERT: D 108 LYS cc_start: 0.8579 (mtpp) cc_final: 0.8265 (tttm) REVERT: E 59 GLU cc_start: 0.8471 (pm20) cc_final: 0.8070 (pm20) REVERT: F 77 LYS cc_start: 0.9224 (mptp) cc_final: 0.8903 (mttp) REVERT: F 93 GLN cc_start: 0.8760 (mm-40) cc_final: 0.8392 (mm-40) REVERT: G 19 SER cc_start: 0.9214 (p) cc_final: 0.8998 (p) REVERT: G 90 ASP cc_start: 0.8793 (t70) cc_final: 0.8490 (t0) REVERT: G 110 ASN cc_start: 0.8917 (t0) cc_final: 0.8643 (t0) REVERT: H 116 LYS cc_start: 0.9194 (ttmt) cc_final: 0.8933 (ttmt) outliers start: 10 outliers final: 7 residues processed: 164 average time/residue: 0.9269 time to fit residues: 160.1807 Evaluate side-chains 167 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 160 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 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=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: 4.9990 chunk 64 optimal weight: 40.0000 chunk 30 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 74 optimal weight: 20.0000 chunk 11 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 76 GLN E 125 GLN H 63 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.113923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.078349 restraints weight = 20901.385| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.69 r_work: 0.2920 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13278 Z= 0.179 Angle : 0.602 10.125 19263 Z= 0.351 Chirality : 0.044 0.305 2200 Planarity : 0.004 0.046 1372 Dihedral : 31.337 179.365 4215 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.21 % Allowed : 16.40 % Favored : 81.39 % 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: 2.99 (0.30), residues: 759 helix: 2.88 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.42 (0.36), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 33 TYR 0.014 0.002 TYR D 83 PHE 0.008 0.001 PHE E 67 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.18 (13278) covalent geometry : angle 0.60220 / 0.35 (19263) hydrogen bonds : bond 0.06453 / 4.44 ( 786) hydrogen bonds : angle 2.80837 / 2.06 ( 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 175 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 161 time to evaluate : 0.344 Fit side-chains REVERT: B 79 LYS cc_start: 0.8988 (mtpp) cc_final: 0.8491 (mttp) REVERT: C 99 ARG cc_start: 0.8914 (mmm-85) cc_final: 0.8302 (mmm160) REVERT: E 59 GLU cc_start: 0.8473 (pm20) cc_final: 0.8076 (pm20) REVERT: E 122 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8479 (pttp) REVERT: F 77 LYS cc_start: 0.9229 (mptp) cc_final: 0.8959 (mttp) REVERT: F 95 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8564 (ptp90) REVERT: G 19 SER cc_start: 0.9225 (p) cc_final: 0.9008 (p) REVERT: G 90 ASP cc_start: 0.8789 (t70) cc_final: 0.8429 (t0) REVERT: G 110 ASN cc_start: 0.8942 (t0) cc_final: 0.8686 (t0) REVERT: H 116 LYS cc_start: 0.9200 (ttmt) cc_final: 0.8939 (ttmt) outliers start: 14 outliers final: 8 residues processed: 168 average time/residue: 0.8613 time to fit residues: 152.3812 Evaluate side-chains 172 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 162 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 F residue 95 ARG 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: 1.9990 chunk 33 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 90 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 44 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3778 r_free = 0.3778 target = 0.114256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.078595 restraints weight = 21051.594| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.69 r_work: 0.2929 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13278 Z= 0.142 Angle : 0.601 9.728 19263 Z= 0.350 Chirality : 0.043 0.304 2200 Planarity : 0.004 0.040 1372 Dihedral : 31.340 179.482 4215 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.89 % Allowed : 16.72 % Favored : 81.39 % 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: 3.07 (0.30), residues: 759 helix: 2.94 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.39 (0.36), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 33 TYR 0.016 0.002 TYR D 83 PHE 0.009 0.001 PHE E 67 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.14 (13278) covalent geometry : angle 0.60144 / 0.35 (19263) hydrogen bonds : bond 0.06260 / 4.31 ( 786) hydrogen bonds : angle 2.80529 / 2.05 ( 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: 12 poor density : 162 time to evaluate : 0.347 Fit side-chains REVERT: C 99 ARG cc_start: 0.8912 (mmm-85) cc_final: 0.8298 (mmm160) REVERT: D 108 LYS cc_start: 0.8496 (mtpp) cc_final: 0.8186 (tttm) REVERT: E 59 GLU cc_start: 0.8462 (pm20) cc_final: 0.8055 (pm20) REVERT: E 122 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8459 (pttp) REVERT: F 77 LYS cc_start: 0.9218 (mptp) cc_final: 0.8946 (mttp) REVERT: G 19 SER cc_start: 0.9219 (p) cc_final: 0.8995 (p) REVERT: G 90 ASP cc_start: 0.8778 (t70) cc_final: 0.8414 (t0) REVERT: G 110 ASN cc_start: 0.8932 (t0) cc_final: 0.8678 (t0) REVERT: H 116 LYS cc_start: 0.9189 (ttmt) cc_final: 0.8929 (ttmt) outliers start: 12 outliers final: 8 residues processed: 168 average time/residue: 0.9371 time to fit residues: 165.8742 Evaluate side-chains 172 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 163 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 42 optimal weight: 5.9990 chunk 74 optimal weight: 20.0000 chunk 19 optimal weight: 0.8980 chunk 102 optimal weight: 6.9990 chunk 87 optimal weight: 20.0000 chunk 40 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 = 0.3776 r_free = 0.3776 target = 0.114109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.078637 restraints weight = 20975.572| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.67 r_work: 0.2930 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13278 Z= 0.174 Angle : 0.604 9.710 19263 Z= 0.350 Chirality : 0.044 0.304 2200 Planarity : 0.004 0.039 1372 Dihedral : 31.332 179.880 4215 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.21 % Allowed : 16.40 % Favored : 81.39 % 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: 3.03 (0.30), residues: 759 helix: 2.90 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.40 (0.36), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 33 TYR 0.017 0.002 TYR D 83 PHE 0.008 0.001 PHE E 67 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.17 (13278) covalent geometry : angle 0.60439 / 0.35 (19263) hydrogen bonds : bond 0.06264 / 4.31 ( 786) hydrogen bonds : angle 2.79481 / 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 176 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 0.355 Fit side-chains REVERT: B 79 LYS cc_start: 0.8985 (mtpp) cc_final: 0.8488 (mttp) REVERT: C 99 ARG cc_start: 0.8916 (mmm-85) cc_final: 0.8313 (mmm160) REVERT: D 108 LYS cc_start: 0.8497 (mtpp) cc_final: 0.8169 (tttm) REVERT: E 59 GLU cc_start: 0.8458 (pm20) cc_final: 0.8049 (pm20) REVERT: E 122 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8469 (pttp) REVERT: F 77 LYS cc_start: 0.9221 (mptp) cc_final: 0.8948 (mttp) REVERT: F 95 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8558 (ptp90) REVERT: G 19 SER cc_start: 0.9223 (p) cc_final: 0.9007 (p) REVERT: G 90 ASP cc_start: 0.8782 (t70) cc_final: 0.8424 (t0) REVERT: G 110 ASN cc_start: 0.8940 (t0) cc_final: 0.8672 (t0) REVERT: H 116 LYS cc_start: 0.9197 (ttmt) cc_final: 0.8937 (ttmt) outliers start: 14 outliers final: 8 residues processed: 170 average time/residue: 0.9363 time to fit residues: 167.6757 Evaluate side-chains 172 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 162 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 F residue 95 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 89 optimal weight: 20.0000 chunk 40 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 76 GLN E 125 GLN H 63 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.114567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.078862 restraints weight = 21019.381| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.68 r_work: 0.2938 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 13278 Z= 0.140 Angle : 0.600 9.631 19263 Z= 0.350 Chirality : 0.043 0.302 2200 Planarity : 0.004 0.037 1372 Dihedral : 31.326 179.981 4215 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.05 % Allowed : 16.72 % Favored : 81.23 % 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: 2.95 (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 0.008 0.000 ARG H 33 TYR 0.019 0.002 TYR D 83 PHE 0.009 0.001 PHE E 67 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.14 (13278) covalent geometry : angle 0.60026 / 0.35 (19263) hydrogen bonds : bond 0.06096 / 4.20 ( 786) hydrogen bonds : angle 2.78906 / 2.04 ( 1938) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6401.33 seconds wall clock time: 109 minutes 6.70 seconds (6546.70 seconds total)