Starting phenix.real_space_refine on Thu Jul 2 23:08:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8whb_37538/07_2026/8whb_37538.cif Found real_map, /net/cci-nas-00/data/ceres_data/8whb_37538/07_2026/8whb_37538.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8whb_37538/07_2026/8whb_37538.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8whb_37538/07_2026/8whb_37538.map" model { file = "/net/cci-nas-00/data/ceres_data/8whb_37538/07_2026/8whb_37538.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8whb_37538/07_2026/8whb_37538.cif" } resolution = 3.17 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= 0.003 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 268 5.49 5 S 12 5.16 5 C 6211 2.51 5 N 2067 2.21 5 O 2618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s 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: 11176 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 733 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "B" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 636 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 783 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 694 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 799 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 621 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "G" Number of atoms: 700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 700 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain: "H" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 716 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain: "I" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2729 Classifications: {'DNA': 134} Link IDs: {'rna3p': 133} Chain: "J" Number of atoms: 2765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2765 Classifications: {'DNA': 134} Link IDs: {'rna3p': 133} Time building chain proxies: 2.44, per 1000 atoms: 0.22 Number of scatterers: 11176 At special positions: 0 Unit cell: (118.845, 101.745, 127.395, 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 268 15.00 O 2618 8.00 N 2067 7.00 C 6211 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: 0.96 Conformation dependent library (CDL) restraints added in 235.7 milliseconds 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1352 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 74.4% alpha, 3.3% beta 86 base pairs and 224 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.668A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN A 55 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 74 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.639A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.747A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.697A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE B 61 " --> pdb=" O VAL B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.909A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 47 through 74 Processing helix chain 'C' and resid 80 through 91 Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 113 through 117 removed outlier: 3.966A pdb=" N LEU C 117 " --> pdb=" O ASN C 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 74 Processing helix chain 'D' and resid 80 through 109 removed outlier: 3.736A pdb=" N ASN D 109 " --> pdb=" O LEU D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 127 removed outlier: 3.732A pdb=" N ILE D 119 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN D 120 " --> pdb=" O SER D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 149 removed outlier: 3.743A pdb=" N SER D 137 " --> pdb=" O LYS D 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 55 removed outlier: 3.606A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.586A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.791A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR E 99 " --> pdb=" O ALA E 95 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 130 removed outlier: 3.804A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.871A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR F 73 " --> pdb=" O ALA F 69 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.689A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 38 Processing helix chain 'G' and resid 46 through 74 removed outlier: 4.452A pdb=" N VAL G 50 " --> pdb=" O ALA G 46 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU G 59 " --> pdb=" O VAL G 55 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU G 66 " --> pdb=" O GLU G 62 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 91 removed outlier: 3.602A pdb=" N ASP G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 98 Processing helix chain 'H' and resid 62 through 74 Processing helix chain 'H' and resid 80 through 109 removed outlier: 3.786A pdb=" N ASN H 109 " --> pdb=" O LEU H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 127 removed outlier: 3.879A pdb=" N THR H 121 " --> pdb=" O ARG H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 148 removed outlier: 3.667A pdb=" N ALA H 132 " --> pdb=" O PRO H 128 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N HIS H 134 " --> pdb=" O GLU H 130 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER H 137 " --> pdb=" O LYS H 133 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.960A pdb=" N ARG A 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 45 through 46 removed outlier: 7.545A pdb=" N ARG B 45 " --> pdb=" O ILE E 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 98 removed outlier: 7.000A pdb=" N THR B 96 " --> pdb=" O THR C 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.449A pdb=" N ARG C 43 " --> pdb=" O ILE D 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA8, first strand: chain 'F' and resid 96 through 98 removed outlier: 6.609A pdb=" N THR F 96 " --> pdb=" O THR G 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.158A pdb=" N ARG G 43 " --> pdb=" O ILE H 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79 359 hydrogen bonds defined for protein. 1056 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 216 hydrogen bonds 432 hydrogen bond angles 0 basepair planarities 86 basepair parallelities 224 stacking parallelities Total time for adding SS restraints: 1.79 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1313 1.32 - 1.44: 4203 1.44 - 1.56: 5846 1.56 - 1.68: 537 1.68 - 1.80: 22 Bond restraints: 11921 Sorted by residual: bond pdb=" C1' DT I 134 " pdb=" N1 DT I 134 " ideal model delta sigma weight residual 1.468 1.549 -0.081 1.40e-02 5.10e+03 3.37e+01 bond pdb=" C1' DC J 20 " pdb=" N1 DC J 20 " ideal model delta sigma weight residual 1.468 1.548 -0.080 1.40e-02 5.10e+03 3.23e+01 bond pdb=" C1' DC I 125 " pdb=" N1 DC I 125 " ideal model delta sigma weight residual 1.468 1.544 -0.076 1.40e-02 5.10e+03 2.95e+01 bond pdb=" C1' DC J 34 " pdb=" N1 DC J 34 " ideal model delta sigma weight residual 1.468 1.542 -0.074 1.40e-02 5.10e+03 2.81e+01 bond pdb=" C1' DA J 21 " pdb=" N9 DA J 21 " ideal model delta sigma weight residual 1.468 1.402 0.066 1.40e-02 5.10e+03 2.23e+01 ... (remaining 11916 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.22: 16982 3.22 - 6.43: 249 6.43 - 9.65: 8 9.65 - 12.87: 3 12.87 - 16.08: 5 Bond angle restraints: 17247 Sorted by residual: angle pdb=" N THR E 107 " pdb=" CA THR E 107 " pdb=" C THR E 107 " ideal model delta sigma weight residual 113.18 102.29 10.89 1.21e+00 6.83e-01 8.10e+01 angle pdb=" O5' DT I 115 " pdb=" C5' DT I 115 " pdb=" C4' DT I 115 " ideal model delta sigma weight residual 109.40 114.98 -5.58 8.00e-01 1.56e+00 4.86e+01 angle pdb=" O3' DT J 9 " pdb=" C3' DT J 9 " pdb=" C2' DT J 9 " ideal model delta sigma weight residual 109.40 125.48 -16.08 2.50e+00 1.60e-01 4.14e+01 angle pdb=" O3' DA I 106 " pdb=" C3' DA I 106 " pdb=" C2' DA I 106 " ideal model delta sigma weight residual 109.40 124.99 -15.59 2.50e+00 1.60e-01 3.89e+01 angle pdb=" O3' DG I 126 " pdb=" C3' DG I 126 " pdb=" C2' DG I 126 " ideal model delta sigma weight residual 109.40 124.43 -15.03 2.50e+00 1.60e-01 3.61e+01 ... (remaining 17242 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.91: 5232 34.91 - 69.82: 1200 69.82 - 104.74: 34 104.74 - 139.65: 2 139.65 - 174.56: 4 Dihedral angle restraints: 6472 sinusoidal: 4381 harmonic: 2091 Sorted by residual: dihedral pdb=" CA GLU H 118 " pdb=" C GLU H 118 " pdb=" N ILE H 119 " pdb=" CA ILE H 119 " ideal model delta harmonic sigma weight residual 180.00 152.95 27.05 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA LEU E 60 " pdb=" C LEU E 60 " pdb=" N LEU E 61 " pdb=" CA LEU E 61 " ideal model delta harmonic sigma weight residual -180.00 -157.21 -22.79 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA GLU E 133 " pdb=" C GLU E 133 " pdb=" N ARG E 134 " pdb=" CA ARG E 134 " ideal model delta harmonic sigma weight residual 180.00 159.16 20.84 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 6469 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.178: 1962 0.178 - 0.357: 5 0.357 - 0.535: 0 0.535 - 0.713: 2 0.713 - 0.892: 3 Chirality restraints: 1972 Sorted by residual: chirality pdb=" C3' DG I 126 " pdb=" C4' DG I 126 " pdb=" O3' DG I 126 " pdb=" C2' DG I 126 " both_signs ideal model delta sigma weight residual False -2.73 -1.84 -0.89 2.00e-01 2.50e+01 1.99e+01 chirality pdb=" C3' DA I 106 " pdb=" C4' DA I 106 " pdb=" O3' DA I 106 " pdb=" C2' DA I 106 " both_signs ideal model delta sigma weight residual False -2.73 -1.94 -0.80 2.00e-01 2.50e+01 1.58e+01 chirality pdb=" C3' DT J 24 " pdb=" C4' DT J 24 " pdb=" O3' DT J 24 " pdb=" C2' DT J 24 " both_signs ideal model delta sigma weight residual False -2.73 -1.98 -0.75 2.00e-01 2.50e+01 1.40e+01 ... (remaining 1969 not shown) Planarity restraints: 1249 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC J 27 " 0.045 2.00e-02 2.50e+03 2.09e-02 9.82e+00 pdb=" N1 DC J 27 " -0.015 2.00e-02 2.50e+03 pdb=" C2 DC J 27 " -0.016 2.00e-02 2.50e+03 pdb=" O2 DC J 27 " -0.010 2.00e-02 2.50e+03 pdb=" N3 DC J 27 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DC J 27 " 0.007 2.00e-02 2.50e+03 pdb=" N4 DC J 27 " 0.025 2.00e-02 2.50e+03 pdb=" C5 DC J 27 " -0.010 2.00e-02 2.50e+03 pdb=" C6 DC J 27 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 106 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.12e+00 pdb=" C ASP E 106 " 0.052 2.00e-02 2.50e+03 pdb=" O ASP E 106 " -0.019 2.00e-02 2.50e+03 pdb=" N THR E 107 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR F 51 " -0.015 2.00e-02 2.50e+03 3.00e-02 9.01e+00 pdb=" C TYR F 51 " 0.052 2.00e-02 2.50e+03 pdb=" O TYR F 51 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU F 52 " -0.018 2.00e-02 2.50e+03 ... (remaining 1246 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2427 2.80 - 3.32: 9588 3.32 - 3.85: 20983 3.85 - 4.37: 25240 4.37 - 4.90: 35944 Nonbonded interactions: 94182 Sorted by model distance: nonbonded pdb=" O ASP C 91 " pdb=" OG SER C 95 " model vdw 2.272 3.040 nonbonded pdb=" OH TYR G 58 " pdb=" OE2 GLU G 62 " model vdw 2.335 3.040 nonbonded pdb=" NE ARG E 131 " pdb=" OE2 GLU E 133 " model vdw 2.342 3.120 nonbonded pdb=" OH TYR C 40 " pdb=" OE1 GLU D 96 " model vdw 2.415 3.040 nonbonded pdb=" NH2 ARG E 131 " pdb=" OE2 GLU E 133 " model vdw 2.420 3.120 ... (remaining 94177 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 43 through 133) } ncs_group { reference = (chain 'B' and resid 24 through 100) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 18 through 110) selection = chain 'G' } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 61 through 149) } 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: 1.290 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.920 Find NCS groups from input model: 0.110 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 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 : 0.008 0.081 11921 Z= 0.566 Angle : 1.024 16.081 17247 Z= 0.739 Chirality : 0.067 0.892 1972 Planarity : 0.006 0.055 1249 Dihedral : 27.902 174.559 5120 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.53 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % 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: -2.07 (0.29), residues: 707 helix: -0.87 (0.22), residues: 510 sheet: None (None), residues: 0 loop : -2.40 (0.37), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 89 TYR 0.013 0.003 TYR H 65 PHE 0.049 0.003 PHE C 26 HIS 0.006 0.001 HIS G 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00784 / 0.57 (11921) covalent geometry : angle 1.02424 / 0.74 (17247) hydrogen bonds : bond 0.20894 / 13.98 ( 575) hydrogen bonds : angle 7.77230 / 5.45 ( 1488) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.295 Fit side-chains REVERT: C 105 ASN cc_start: 0.8857 (t0) cc_final: 0.8656 (t0) REVERT: C 111 ASN cc_start: 0.8084 (t0) cc_final: 0.7741 (p0) REVERT: D 111 LYS cc_start: 0.8478 (mmtm) cc_final: 0.8191 (mtpt) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.1894 time to fit residues: 47.1971 Evaluate side-chains 152 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.0670 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 10.0000 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN C 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.128294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.091531 restraints weight = 21093.871| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.51 r_work: 0.3048 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11921 Z= 0.179 Angle : 0.733 8.000 17247 Z= 0.437 Chirality : 0.050 0.246 1972 Planarity : 0.005 0.059 1249 Dihedral : 31.155 175.899 3713 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.51 % Allowed : 10.91 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.31), residues: 707 helix: 0.59 (0.23), residues: 519 sheet: None (None), residues: 0 loop : -2.07 (0.39), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 67 TYR 0.010 0.001 TYR D 62 PHE 0.019 0.001 PHE C 26 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.18 (11921) covalent geometry : angle 0.73309 / 0.44 (17247) hydrogen bonds : bond 0.07144 / 4.73 ( 575) hydrogen bonds : angle 3.53457 / 2.46 ( 1488) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 154 time to evaluate : 0.292 Fit side-chains REVERT: C 18 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.7690 (mpp80) REVERT: C 74 ASN cc_start: 0.7352 (m-40) cc_final: 0.6764 (t0) REVERT: C 105 ASN cc_start: 0.9061 (t0) cc_final: 0.8348 (t0) REVERT: C 111 ASN cc_start: 0.8397 (t0) cc_final: 0.7809 (p0) REVERT: D 111 LYS cc_start: 0.8478 (mmtm) cc_final: 0.8121 (mtpt) REVERT: E 58 THR cc_start: 0.9397 (p) cc_final: 0.9160 (p) REVERT: F 79 LYS cc_start: 0.9037 (mtpt) cc_final: 0.8782 (mtmt) REVERT: F 96 THR cc_start: 0.9117 (m) cc_final: 0.8863 (p) REVERT: G 89 ARG cc_start: 0.8571 (mmt180) cc_final: 0.8367 (mmt180) REVERT: H 104 LYS cc_start: 0.8553 (ttmt) cc_final: 0.8248 (ttmm) outliers start: 9 outliers final: 2 residues processed: 157 average time/residue: 0.1614 time to fit residues: 32.2196 Evaluate side-chains 152 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 149 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 44 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 3 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 70 optimal weight: 20.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN F 75 HIS H 74 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.125689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.089890 restraints weight = 21166.828| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.53 r_work: 0.3052 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11921 Z= 0.169 Angle : 0.659 8.559 17247 Z= 0.394 Chirality : 0.046 0.240 1972 Planarity : 0.005 0.045 1249 Dihedral : 31.258 179.254 3713 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.68 % Allowed : 12.58 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.32), residues: 707 helix: 1.54 (0.23), residues: 520 sheet: None (None), residues: 0 loop : -1.83 (0.40), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 89 TYR 0.010 0.001 TYR A 54 PHE 0.017 0.001 PHE C 26 HIS 0.003 0.001 HIS D 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.17 (11921) covalent geometry : angle 0.65880 / 0.39 (17247) hydrogen bonds : bond 0.05934 / 3.97 ( 575) hydrogen bonds : angle 3.01485 / 2.11 ( 1488) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 155 time to evaluate : 0.289 Fit side-chains REVERT: C 18 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.7931 (mpp80) REVERT: C 74 ASN cc_start: 0.7346 (m-40) cc_final: 0.6802 (t0) REVERT: C 105 ASN cc_start: 0.9061 (t0) cc_final: 0.8237 (t0) REVERT: C 111 ASN cc_start: 0.8384 (t0) cc_final: 0.7840 (p0) REVERT: D 104 LYS cc_start: 0.8201 (mmtm) cc_final: 0.7875 (mptt) REVERT: D 111 LYS cc_start: 0.8542 (mmtm) cc_final: 0.8236 (mtpt) REVERT: E 58 THR cc_start: 0.9555 (p) cc_final: 0.9351 (p) REVERT: F 44 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8674 (mtmt) REVERT: H 104 LYS cc_start: 0.8597 (ttmt) cc_final: 0.8135 (ttmm) outliers start: 10 outliers final: 6 residues processed: 158 average time/residue: 0.1745 time to fit residues: 34.7893 Evaluate side-chains 151 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 143 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain G residue 102 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 31 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 109 ASN F 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.119670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.083084 restraints weight = 20655.629| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.53 r_work: 0.2925 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 11921 Z= 0.183 Angle : 0.675 7.802 17247 Z= 0.390 Chirality : 0.046 0.254 1972 Planarity : 0.005 0.049 1249 Dihedral : 31.249 179.471 3713 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.35 % Allowed : 12.92 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.32), residues: 707 helix: 1.86 (0.23), residues: 521 sheet: None (None), residues: 0 loop : -1.58 (0.41), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 92 TYR 0.014 0.002 TYR D 62 PHE 0.023 0.002 PHE C 26 HIS 0.005 0.001 HIS D 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.18 (11921) covalent geometry : angle 0.67537 / 0.39 (17247) hydrogen bonds : bond 0.06327 / 4.10 ( 575) hydrogen bonds : angle 2.97611 / 2.09 ( 1488) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: C 18 ARG cc_start: 0.9197 (OUTLIER) cc_final: 0.8106 (mtp85) REVERT: C 73 ASP cc_start: 0.8172 (m-30) cc_final: 0.7863 (m-30) REVERT: C 74 ASN cc_start: 0.7784 (m-40) cc_final: 0.7208 (t0) REVERT: C 90 ASN cc_start: 0.8551 (m-40) cc_final: 0.8272 (m-40) REVERT: C 105 ASN cc_start: 0.8996 (t0) cc_final: 0.8183 (t0) REVERT: C 111 ASN cc_start: 0.8477 (t0) cc_final: 0.8004 (p0) REVERT: D 104 LYS cc_start: 0.8275 (mmtm) cc_final: 0.7950 (mptt) REVERT: D 111 LYS cc_start: 0.8669 (mmtm) cc_final: 0.8337 (mtpt) REVERT: H 63 LYS cc_start: 0.9098 (mptt) cc_final: 0.8794 (mptt) outliers start: 14 outliers final: 8 residues processed: 164 average time/residue: 0.1703 time to fit residues: 35.0859 Evaluate side-chains 156 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 147 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain G residue 102 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 82 optimal weight: 20.0000 chunk 41 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 50 optimal weight: 0.1980 chunk 84 optimal weight: 20.0000 chunk 4 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.120586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.084487 restraints weight = 20580.433| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.51 r_work: 0.2943 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 11921 Z= 0.142 Angle : 0.619 8.174 17247 Z= 0.366 Chirality : 0.044 0.255 1972 Planarity : 0.005 0.091 1249 Dihedral : 31.206 179.742 3713 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.18 % Allowed : 14.09 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.32), residues: 707 helix: 2.17 (0.23), residues: 524 sheet: None (None), residues: 0 loop : -1.53 (0.42), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 92 TYR 0.009 0.001 TYR B 51 PHE 0.012 0.001 PHE C 26 HIS 0.008 0.001 HIS H 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.14 (11921) covalent geometry : angle 0.61935 / 0.37 (17247) hydrogen bonds : bond 0.05233 / 3.46 ( 575) hydrogen bonds : angle 2.81737 / 1.98 ( 1488) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 153 time to evaluate : 0.298 Fit side-chains REVERT: C 18 ARG cc_start: 0.9147 (OUTLIER) cc_final: 0.8096 (mpp80) REVERT: C 73 ASP cc_start: 0.8138 (m-30) cc_final: 0.7827 (m-30) REVERT: C 74 ASN cc_start: 0.7636 (m-40) cc_final: 0.7036 (t0) REVERT: C 90 ASN cc_start: 0.8490 (m-40) cc_final: 0.8221 (m-40) REVERT: C 105 ASN cc_start: 0.8981 (t0) cc_final: 0.8472 (t0) REVERT: C 111 ASN cc_start: 0.8455 (t0) cc_final: 0.7929 (p0) REVERT: D 104 LYS cc_start: 0.8250 (mmtm) cc_final: 0.7905 (mptt) REVERT: D 111 LYS cc_start: 0.8699 (mmtm) cc_final: 0.8318 (mtpt) REVERT: F 44 LYS cc_start: 0.8887 (mtmt) cc_final: 0.8657 (mtmt) REVERT: H 63 LYS cc_start: 0.9149 (mptt) cc_final: 0.8791 (mptt) REVERT: H 104 LYS cc_start: 0.8571 (ttmt) cc_final: 0.8161 (ttmm) outliers start: 13 outliers final: 8 residues processed: 157 average time/residue: 0.1618 time to fit residues: 32.6549 Evaluate side-chains 158 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 149 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain H residue 68 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 15 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 91 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 chunk 51 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 81 optimal weight: 20.0000 chunk 12 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 79 optimal weight: 20.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 25 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.118804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.082971 restraints weight = 20731.553| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.51 r_work: 0.2926 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11921 Z= 0.163 Angle : 0.610 8.279 17247 Z= 0.360 Chirality : 0.042 0.239 1972 Planarity : 0.004 0.033 1249 Dihedral : 31.116 179.656 3713 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.01 % Allowed : 14.77 % Favored : 83.22 % 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: 2.17 (0.33), residues: 707 helix: 2.38 (0.23), residues: 523 sheet: None (None), residues: 0 loop : -1.48 (0.42), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 92 TYR 0.007 0.001 TYR B 51 PHE 0.016 0.001 PHE C 26 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.16 (11921) covalent geometry : angle 0.60992 / 0.36 (17247) hydrogen bonds : bond 0.05208 / 3.42 ( 575) hydrogen bonds : angle 2.75374 / 1.94 ( 1488) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: C 18 ARG cc_start: 0.9163 (OUTLIER) cc_final: 0.8156 (mpp80) REVERT: C 74 ASN cc_start: 0.7768 (m-40) cc_final: 0.7222 (t0) REVERT: C 90 ASN cc_start: 0.8510 (m-40) cc_final: 0.8235 (m-40) REVERT: C 105 ASN cc_start: 0.9028 (t0) cc_final: 0.8456 (t0) REVERT: C 111 ASN cc_start: 0.8458 (t0) cc_final: 0.8070 (p0) REVERT: D 104 LYS cc_start: 0.8331 (mmtm) cc_final: 0.7958 (mtmm) REVERT: D 111 LYS cc_start: 0.8612 (mmtm) cc_final: 0.8208 (mtpt) REVERT: F 44 LYS cc_start: 0.8882 (mtmt) cc_final: 0.8647 (mtmt) REVERT: G 75 LYS cc_start: 0.9055 (mmmt) cc_final: 0.8831 (mmtm) outliers start: 12 outliers final: 6 residues processed: 154 average time/residue: 0.1543 time to fit residues: 30.1396 Evaluate side-chains 155 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 148 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain H residue 68 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 76 optimal weight: 9.9990 chunk 36 optimal weight: 0.7980 chunk 61 optimal weight: 8.9990 chunk 84 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 68 optimal weight: 30.0000 chunk 11 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.116615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.079339 restraints weight = 20560.602| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.63 r_work: 0.2822 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11921 Z= 0.145 Angle : 0.589 7.064 17247 Z= 0.350 Chirality : 0.041 0.212 1972 Planarity : 0.004 0.040 1249 Dihedral : 31.034 179.681 3713 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.34 % Allowed : 16.11 % Favored : 82.55 % 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: 2.27 (0.33), residues: 707 helix: 2.45 (0.23), residues: 525 sheet: None (None), residues: 0 loop : -1.49 (0.42), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 92 TYR 0.011 0.001 TYR H 62 PHE 0.012 0.001 PHE C 26 HIS 0.004 0.001 HIS H 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.14 (11921) covalent geometry : angle 0.58913 / 0.35 (17247) hydrogen bonds : bond 0.04835 / 3.18 ( 575) hydrogen bonds : angle 2.69559 / 1.89 ( 1488) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 151 time to evaluate : 0.393 Fit side-chains REVERT: C 18 ARG cc_start: 0.9106 (OUTLIER) cc_final: 0.8151 (mpp80) REVERT: C 74 ASN cc_start: 0.7714 (m-40) cc_final: 0.7148 (t0) REVERT: C 90 ASN cc_start: 0.8450 (m-40) cc_final: 0.8186 (m-40) REVERT: C 105 ASN cc_start: 0.9018 (t0) cc_final: 0.8420 (t0) REVERT: C 111 ASN cc_start: 0.8483 (t0) cc_final: 0.7949 (p0) REVERT: D 104 LYS cc_start: 0.8160 (mmtm) cc_final: 0.7769 (mtmm) REVERT: D 111 LYS cc_start: 0.8614 (mmtm) cc_final: 0.8077 (mtpt) REVERT: F 44 LYS cc_start: 0.8927 (mtmt) cc_final: 0.8671 (mtmt) outliers start: 8 outliers final: 5 residues processed: 153 average time/residue: 0.1505 time to fit residues: 29.3509 Evaluate side-chains 153 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 147 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain H residue 68 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 85 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 67 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 134 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.112198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.074811 restraints weight = 20390.026| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 1.66 r_work: 0.2733 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.4807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11921 Z= 0.205 Angle : 0.647 7.873 17247 Z= 0.374 Chirality : 0.045 0.202 1972 Planarity : 0.005 0.034 1249 Dihedral : 31.024 179.546 3713 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.34 % Allowed : 15.77 % Favored : 82.89 % 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: 2.07 (0.32), residues: 707 helix: 2.32 (0.23), residues: 523 sheet: None (None), residues: 0 loop : -1.57 (0.42), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 43 TYR 0.010 0.001 TYR B 51 PHE 0.022 0.002 PHE C 26 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.21 (11921) covalent geometry : angle 0.64726 / 0.37 (17247) hydrogen bonds : bond 0.06345 / 4.16 ( 575) hydrogen bonds : angle 2.92486 / 2.06 ( 1488) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 154 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: C 18 ARG cc_start: 0.9158 (OUTLIER) cc_final: 0.8165 (mpp80) REVERT: C 73 ASP cc_start: 0.8511 (m-30) cc_final: 0.8204 (m-30) REVERT: C 74 ASN cc_start: 0.8148 (m-40) cc_final: 0.7639 (t0) REVERT: C 105 ASN cc_start: 0.9037 (t0) cc_final: 0.8451 (t0) REVERT: C 111 ASN cc_start: 0.8588 (t0) cc_final: 0.8242 (p0) REVERT: D 101 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7977 (tp30) REVERT: D 104 LYS cc_start: 0.8293 (mmtm) cc_final: 0.7958 (mtmm) REVERT: D 111 LYS cc_start: 0.8676 (mmtm) cc_final: 0.8217 (mtpt) REVERT: F 44 LYS cc_start: 0.8979 (mtmt) cc_final: 0.8709 (mtmt) REVERT: G 75 LYS cc_start: 0.9165 (mmmt) cc_final: 0.8855 (mmtm) outliers start: 8 outliers final: 5 residues processed: 156 average time/residue: 0.1511 time to fit residues: 29.7879 Evaluate side-chains 157 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 151 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain H residue 68 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 66 optimal weight: 1.9990 chunk 80 optimal weight: 30.0000 chunk 61 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 91 optimal weight: 20.0000 chunk 51 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.113214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.075936 restraints weight = 20259.773| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.60 r_work: 0.2758 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.4870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11921 Z= 0.154 Angle : 0.611 8.237 17247 Z= 0.357 Chirality : 0.043 0.191 1972 Planarity : 0.004 0.032 1249 Dihedral : 31.007 179.780 3713 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.34 % Allowed : 15.44 % Favored : 83.22 % 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: 2.15 (0.32), residues: 707 helix: 2.40 (0.23), residues: 523 sheet: None (None), residues: 0 loop : -1.59 (0.42), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 52 TYR 0.012 0.001 TYR B 51 PHE 0.013 0.001 PHE C 26 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.15 (11921) covalent geometry : angle 0.61055 / 0.36 (17247) hydrogen bonds : bond 0.05523 / 3.63 ( 575) hydrogen bonds : angle 2.81717 / 1.98 ( 1488) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 152 time to evaluate : 0.279 Fit side-chains REVERT: C 18 ARG cc_start: 0.9142 (OUTLIER) cc_final: 0.8146 (mpp80) REVERT: C 73 ASP cc_start: 0.8461 (m-30) cc_final: 0.8159 (m-30) REVERT: C 74 ASN cc_start: 0.8076 (m-40) cc_final: 0.7544 (t0) REVERT: C 105 ASN cc_start: 0.9029 (t0) cc_final: 0.8438 (t0) REVERT: C 111 ASN cc_start: 0.8525 (t0) cc_final: 0.8133 (p0) REVERT: D 101 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7952 (tp30) REVERT: D 104 LYS cc_start: 0.8236 (mmtm) cc_final: 0.7892 (mtmm) REVERT: D 111 LYS cc_start: 0.8659 (mmtm) cc_final: 0.8167 (mtpt) REVERT: F 44 LYS cc_start: 0.8959 (mtmt) cc_final: 0.8693 (mtmt) REVERT: H 104 LYS cc_start: 0.8621 (ttmm) cc_final: 0.8075 (ttmm) outliers start: 8 outliers final: 5 residues processed: 154 average time/residue: 0.1524 time to fit residues: 29.6293 Evaluate side-chains 156 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 150 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain H residue 68 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 44 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 83 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.113309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.076133 restraints weight = 20492.415| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.62 r_work: 0.2762 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.4930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11921 Z= 0.162 Angle : 0.605 7.198 17247 Z= 0.355 Chirality : 0.042 0.191 1972 Planarity : 0.004 0.032 1249 Dihedral : 30.979 179.833 3713 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.34 % Allowed : 15.44 % Favored : 83.22 % 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: 2.27 (0.32), residues: 707 helix: 2.50 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -1.59 (0.42), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 23 TYR 0.009 0.001 TYR B 51 PHE 0.020 0.001 PHE H 67 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.16 (11921) covalent geometry : angle 0.60453 / 0.35 (17247) hydrogen bonds : bond 0.05377 / 3.54 ( 575) hydrogen bonds : angle 2.79071 / 1.97 ( 1488) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 150 time to evaluate : 0.283 Fit side-chains REVERT: C 18 ARG cc_start: 0.9128 (OUTLIER) cc_final: 0.8112 (mpp80) REVERT: C 73 ASP cc_start: 0.8508 (m-30) cc_final: 0.8204 (m-30) REVERT: C 74 ASN cc_start: 0.8075 (m-40) cc_final: 0.7550 (t0) REVERT: C 105 ASN cc_start: 0.9058 (t0) cc_final: 0.8459 (t0) REVERT: C 109 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8004 (mtm) REVERT: C 111 ASN cc_start: 0.8521 (t0) cc_final: 0.8164 (p0) REVERT: D 101 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7960 (tp30) REVERT: D 104 LYS cc_start: 0.8218 (mmtm) cc_final: 0.7881 (mtmm) REVERT: D 111 LYS cc_start: 0.8657 (mmtm) cc_final: 0.8158 (mtpt) REVERT: E 131 ARG cc_start: 0.9104 (OUTLIER) cc_final: 0.8178 (mtp180) REVERT: F 44 LYS cc_start: 0.8965 (mtmt) cc_final: 0.8697 (mtmt) REVERT: H 104 LYS cc_start: 0.8601 (ttmm) cc_final: 0.8060 (ttmm) outliers start: 8 outliers final: 4 residues processed: 153 average time/residue: 0.1668 time to fit residues: 32.1887 Evaluate side-chains 156 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 149 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain H residue 68 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 63 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 81 optimal weight: 20.0000 chunk 82 optimal weight: 30.0000 chunk 93 optimal weight: 30.0000 chunk 40 optimal weight: 0.7980 chunk 80 optimal weight: 30.0000 chunk 56 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN B 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.110410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.073205 restraints weight = 20483.704| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 1.65 r_work: 0.2707 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.5341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11921 Z= 0.199 Angle : 0.651 8.514 17247 Z= 0.376 Chirality : 0.044 0.206 1972 Planarity : 0.005 0.040 1249 Dihedral : 30.954 179.941 3713 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.68 % Allowed : 15.77 % Favored : 82.55 % 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: 2.10 (0.32), residues: 707 helix: 2.35 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -1.56 (0.42), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 49 TYR 0.011 0.001 TYR B 51 PHE 0.016 0.002 PHE C 26 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.20 (11921) covalent geometry : angle 0.65079 / 0.38 (17247) hydrogen bonds : bond 0.06272 / 4.11 ( 575) hydrogen bonds : angle 2.91044 / 2.06 ( 1488) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2580.15 seconds wall clock time: 44 minutes 45.12 seconds (2685.12 seconds total)