Starting phenix.real_space_refine on Wed Aug 5 16:52:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8whb_37538/08_2026/8whb_37538.cif Found real_map, /net/cci-nas-00/data/ceres_data/8whb_37538/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8whb_37538/08_2026/8whb_37538.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8whb_37538/08_2026/8whb_37538.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8whb_37538/08_2026/8whb_37538.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8whb_37538/08_2026/8whb_37538.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.85, per 1000 atoms: 0.17 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: 0.77 Conformation dependent library (CDL) restraints added in 266.6 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: 1.62 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: 2.09 Time building geometry restraints manager: 1.15 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: 16977 3.22 - 6.43: 254 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: 1.510 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.740 Find NCS groups from input model: 0.280 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.200 ------------------------------------------------------------------------------- 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= 0.570 Angle : 1.033 16.081 17247 Z= 0.749 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 1.03268 / 0.75 (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 : 0.281 Fit side-chains REVERT: C 105 ASN cc_start: 0.8857 (t0) cc_final: 0.8657 (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: 0.8192 (mtpt) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.1731 time to fit residues: 43.4135 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 : 0.285 ------------------------------------------------------------------------------- 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: 6.9990 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 = 0.3802 r_free = 0.3802 target = 0.128399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.091086 restraints weight = 21142.799| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.67 r_work: 0.3036 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11921 Z= 0.180 Angle : 0.760 9.921 17247 Z= 0.441 Chirality : 0.051 0.276 1972 Planarity : 0.006 0.060 1249 Dihedral : 31.107 176.804 3713 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.68 % Allowed : 10.91 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.31), residues: 707 helix: 0.66 (0.23), residues: 518 sheet: None (None), residues: 0 loop : -2.06 (0.39), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 67 TYR 0.009 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 0.00293 / 0.18 (11921) covalent geometry : angle 0.75978 / 0.44 (17247) hydrogen bonds : bond 0.06988 / 4.63 ( 575) hydrogen bonds : angle 3.47970 / 2.43 ( 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 168 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 158 time to evaluate : 0.284 Fit side-chains REVERT: C 18 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.7693 (mpp80) REVERT: C 74 ASN cc_start: 0.7274 (m-40) cc_final: 0.6705 (t0) REVERT: C 105 ASN cc_start: 0.9074 (t0) cc_final: 0.8337 (t0) REVERT: C 111 ASN cc_start: 0.8394 (t0) cc_final: 0.7709 (p0) REVERT: D 111 LYS cc_start: 0.8429 (mmtm) cc_final: 0.8017 (mtpt) REVERT: D 141 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8510 (ttmt) REVERT: E 58 THR cc_start: 0.9394 (p) cc_final: 0.9161 (p) REVERT: F 79 LYS cc_start: 0.9035 (mtpt) cc_final: 0.8717 (mtmt) REVERT: F 96 THR cc_start: 0.9131 (m) cc_final: 0.8834 (p) REVERT: G 89 ARG cc_start: 0.8590 (mmt180) cc_final: 0.8381 (mmt180) REVERT: H 104 LYS cc_start: 0.8462 (ttmt) cc_final: 0.7954 (ttmm) outliers start: 10 outliers final: 3 residues processed: 162 average time/residue: 0.1483 time to fit residues: 30.6116 Evaluate side-chains 158 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 153 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 141 LYS 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: 1.9990 chunk 13 optimal weight: 0.6980 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: 0.0980 chunk 5 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 70 optimal weight: 20.0000 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 75 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.126564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.089659 restraints weight = 21322.736| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.66 r_work: 0.3008 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 11921 Z= 0.157 Angle : 0.639 8.315 17247 Z= 0.385 Chirality : 0.045 0.245 1972 Planarity : 0.004 0.038 1249 Dihedral : 31.089 178.451 3713 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.68 % Allowed : 13.26 % Favored : 85.07 % 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: 0.97 (0.32), residues: 707 helix: 1.46 (0.23), residues: 521 sheet: None (None), residues: 0 loop : -1.74 (0.41), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 92 TYR 0.009 0.001 TYR H 65 PHE 0.010 0.001 PHE A 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.16 (11921) covalent geometry : angle 0.63905 / 0.38 (17247) hydrogen bonds : bond 0.05554 / 3.74 ( 575) hydrogen bonds : angle 3.00913 / 2.09 ( 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 163 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 153 time to evaluate : 0.285 Fit side-chains REVERT: C 18 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.7709 (mpp80) REVERT: C 74 ASN cc_start: 0.7147 (m-40) cc_final: 0.6552 (t0) REVERT: C 105 ASN cc_start: 0.9062 (t0) cc_final: 0.8268 (t0) REVERT: C 111 ASN cc_start: 0.8405 (t0) cc_final: 0.7691 (p0) REVERT: D 104 LYS cc_start: 0.8011 (mmtm) cc_final: 0.7802 (mptt) REVERT: D 111 LYS cc_start: 0.8437 (mmtm) cc_final: 0.8056 (mtpt) REVERT: D 141 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8477 (ttpp) REVERT: E 58 THR cc_start: 0.9479 (p) cc_final: 0.9248 (p) REVERT: F 79 LYS cc_start: 0.9054 (mtpt) cc_final: 0.8714 (mtmt) REVERT: H 84 MET cc_start: 0.8839 (tpt) cc_final: 0.8487 (tpt) REVERT: H 104 LYS cc_start: 0.8439 (ttmt) cc_final: 0.7883 (ttmm) REVERT: H 130 GLU cc_start: 0.8094 (tp30) cc_final: 0.7840 (tp30) outliers start: 10 outliers final: 4 residues processed: 156 average time/residue: 0.1620 time to fit residues: 31.8335 Evaluate side-chains 152 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 146 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain D residue 141 LYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 31 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 109 ASN H 74 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.121325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.084829 restraints weight = 20772.743| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.53 r_work: 0.2961 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 11921 Z= 0.183 Angle : 0.677 7.659 17247 Z= 0.392 Chirality : 0.046 0.242 1972 Planarity : 0.005 0.041 1249 Dihedral : 31.110 179.710 3713 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.35 % Allowed : 12.58 % Favored : 85.07 % 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: 1.49 (0.32), residues: 707 helix: 1.81 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -1.44 (0.41), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 35 TYR 0.017 0.002 TYR D 65 PHE 0.026 0.002 PHE C 26 HIS 0.005 0.001 HIS D 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.18 (11921) covalent geometry : angle 0.67698 / 0.39 (17247) hydrogen bonds : bond 0.06061 / 3.95 ( 575) hydrogen bonds : angle 2.98637 / 2.10 ( 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 164 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.276 Fit side-chains REVERT: B 84 MET cc_start: 0.8552 (mmm) cc_final: 0.8310 (mmp) REVERT: C 18 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.8004 (mtp85) REVERT: C 74 ASN cc_start: 0.7649 (m-40) cc_final: 0.7128 (t0) REVERT: C 90 ASN cc_start: 0.8604 (m-40) cc_final: 0.8331 (m-40) REVERT: C 105 ASN cc_start: 0.9060 (t0) cc_final: 0.8215 (t0) REVERT: C 111 ASN cc_start: 0.8465 (t0) cc_final: 0.7923 (p0) REVERT: D 104 LYS cc_start: 0.8225 (mmtm) cc_final: 0.7866 (mptt) REVERT: D 141 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8664 (ttpp) REVERT: H 104 LYS cc_start: 0.8661 (ttmt) cc_final: 0.8167 (ttmm) outliers start: 14 outliers final: 8 residues processed: 154 average time/residue: 0.1600 time to fit residues: 31.1554 Evaluate side-chains 157 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 147 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 95 SER Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain D residue 141 LYS 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: 30.0000 chunk 41 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 84 optimal weight: 20.0000 chunk 4 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN A 68 GLN C 25 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.122177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.086191 restraints weight = 20638.638| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.51 r_work: 0.2978 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11921 Z= 0.141 Angle : 0.614 7.122 17247 Z= 0.362 Chirality : 0.043 0.241 1972 Planarity : 0.004 0.033 1249 Dihedral : 31.093 179.777 3713 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.52 % Allowed : 13.76 % 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: 1.96 (0.33), residues: 707 helix: 2.19 (0.23), residues: 523 sheet: None (None), residues: 0 loop : -1.42 (0.42), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 107 TYR 0.009 0.001 TYR B 51 PHE 0.012 0.001 PHE C 26 HIS 0.002 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.14 (11921) covalent geometry : angle 0.61434 / 0.36 (17247) hydrogen bonds : bond 0.05151 / 3.40 ( 575) hydrogen bonds : angle 2.78571 / 1.96 ( 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 164 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 0.293 Fit side-chains REVERT: B 84 MET cc_start: 0.8515 (mmm) cc_final: 0.8275 (mmp) REVERT: C 18 ARG cc_start: 0.9098 (OUTLIER) cc_final: 0.8059 (mpp80) REVERT: C 74 ASN cc_start: 0.7554 (m-40) cc_final: 0.7000 (t0) REVERT: C 90 ASN cc_start: 0.8491 (m-40) cc_final: 0.8183 (m-40) REVERT: C 105 ASN cc_start: 0.8986 (t0) cc_final: 0.8446 (t0) REVERT: C 111 ASN cc_start: 0.8357 (t0) cc_final: 0.7829 (p0) REVERT: D 104 LYS cc_start: 0.8137 (mmtm) cc_final: 0.7791 (mptt) REVERT: D 141 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8640 (ttpp) REVERT: G 78 ARG cc_start: 0.8975 (mtm-85) cc_final: 0.8773 (mtp85) REVERT: H 104 LYS cc_start: 0.8523 (ttmt) cc_final: 0.8312 (ttmm) outliers start: 15 outliers final: 8 residues processed: 152 average time/residue: 0.1598 time to fit residues: 30.8283 Evaluate side-chains 155 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 145 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS 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 D residue 141 LYS Chi-restraints excluded: chain E residue 94 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 15 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 chunk 51 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 81 optimal weight: 20.0000 chunk 12 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 79 optimal weight: 20.0000 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 = 0.3635 r_free = 0.3635 target = 0.116038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.078618 restraints weight = 20612.457| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 1.62 r_work: 0.2808 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11921 Z= 0.169 Angle : 0.642 8.935 17247 Z= 0.372 Chirality : 0.044 0.241 1972 Planarity : 0.005 0.053 1249 Dihedral : 31.051 179.516 3713 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.02 % Allowed : 14.60 % Favored : 82.38 % 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 (0.32), residues: 707 helix: 2.35 (0.23), residues: 521 sheet: None (None), residues: 0 loop : -1.32 (0.42), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 107 TYR 0.009 0.001 TYR H 62 PHE 0.020 0.002 PHE C 26 HIS 0.008 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.17 (11921) covalent geometry : angle 0.64160 / 0.37 (17247) hydrogen bonds : bond 0.05648 / 3.69 ( 575) hydrogen bonds : angle 2.80818 / 1.98 ( 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 178 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 0.224 Fit side-chains REVERT: C 18 ARG cc_start: 0.9146 (OUTLIER) cc_final: 0.8223 (mpp80) REVERT: C 74 ASN cc_start: 0.7780 (m-40) cc_final: 0.7177 (t0) REVERT: C 90 ASN cc_start: 0.8484 (m-40) cc_final: 0.8211 (m-40) REVERT: C 105 ASN cc_start: 0.8992 (t0) cc_final: 0.8409 (t0) REVERT: C 111 ASN cc_start: 0.8566 (t0) cc_final: 0.8119 (p0) REVERT: D 101 GLU cc_start: 0.8524 (tp30) cc_final: 0.8277 (tp30) REVERT: D 104 LYS cc_start: 0.8196 (mmtm) cc_final: 0.7794 (mtmm) REVERT: D 111 LYS cc_start: 0.8672 (mmtm) cc_final: 0.8189 (mtpt) REVERT: D 141 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8701 (ttpp) REVERT: G 20 SER cc_start: 0.9163 (m) cc_final: 0.8920 (m) REVERT: H 63 LYS cc_start: 0.9193 (mptt) cc_final: 0.8771 (mptt) REVERT: H 130 GLU cc_start: 0.8127 (tp30) cc_final: 0.7785 (tm-30) outliers start: 18 outliers final: 7 residues processed: 165 average time/residue: 0.1546 time to fit residues: 32.2157 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 : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP 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 141 LYS Chi-restraints excluded: chain E residue 94 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: 10.0000 chunk 36 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 84 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 68 optimal weight: 30.0000 chunk 11 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 = 0.3633 r_free = 0.3633 target = 0.115744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.078244 restraints weight = 20511.910| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.62 r_work: 0.2802 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11921 Z= 0.160 Angle : 0.611 7.048 17247 Z= 0.357 Chirality : 0.043 0.229 1972 Planarity : 0.004 0.042 1249 Dihedral : 31.035 179.621 3713 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.18 % Allowed : 15.60 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.32), residues: 707 helix: 2.40 (0.23), residues: 523 sheet: None (None), residues: 0 loop : -1.37 (0.42), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 107 TYR 0.007 0.001 TYR B 51 PHE 0.013 0.001 PHE C 26 HIS 0.003 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.16 (11921) covalent geometry : angle 0.61058 / 0.36 (17247) hydrogen bonds : bond 0.05243 / 3.45 ( 575) hydrogen bonds : angle 2.75492 / 1.94 ( 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 166 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 153 time to evaluate : 0.203 Fit side-chains REVERT: B 74 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8574 (mt-10) REVERT: C 18 ARG cc_start: 0.9118 (OUTLIER) cc_final: 0.8189 (mpp80) REVERT: C 74 ASN cc_start: 0.7845 (m-40) cc_final: 0.7258 (t0) REVERT: C 90 ASN cc_start: 0.8488 (m-40) cc_final: 0.8222 (m-40) REVERT: C 105 ASN cc_start: 0.8989 (t0) cc_final: 0.8465 (t0) REVERT: C 111 ASN cc_start: 0.8498 (t0) cc_final: 0.7939 (p0) REVERT: D 104 LYS cc_start: 0.8171 (mmtm) cc_final: 0.7793 (mtmm) REVERT: D 111 LYS cc_start: 0.8660 (mmtm) cc_final: 0.8156 (mtpt) REVERT: D 141 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8711 (ttpp) REVERT: G 20 SER cc_start: 0.9161 (m) cc_final: 0.8912 (m) REVERT: G 78 ARG cc_start: 0.8974 (mtm-85) cc_final: 0.8764 (mtp85) REVERT: H 104 LYS cc_start: 0.8596 (ttmm) cc_final: 0.8069 (ttmm) outliers start: 13 outliers final: 6 residues processed: 157 average time/residue: 0.1452 time to fit residues: 28.8773 Evaluate side-chains 162 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 153 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP 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 64 ILE Chi-restraints excluded: chain D residue 141 LYS 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: 9.9990 chunk 45 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 109 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.115702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.078738 restraints weight = 20504.986| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.60 r_work: 0.2814 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.4726 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= 0.148 Angle : 0.607 12.578 17247 Z= 0.356 Chirality : 0.042 0.213 1972 Planarity : 0.004 0.035 1249 Dihedral : 30.916 179.820 3713 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.51 % Allowed : 16.11 % Favored : 82.38 % 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: 2.36 (0.33), residues: 707 helix: 2.51 (0.23), residues: 525 sheet: None (None), residues: 0 loop : -1.42 (0.42), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 72 TYR 0.012 0.001 TYR H 62 PHE 0.010 0.001 PHE C 26 HIS 0.003 0.001 HIS H 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.15 (11921) covalent geometry : angle 0.60728 / 0.36 (17247) hydrogen bonds : bond 0.04884 / 3.21 ( 575) hydrogen bonds : angle 2.66666 / 1.87 ( 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 164 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 155 time to evaluate : 0.220 Fit side-chains REVERT: B 74 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8518 (mt-10) REVERT: C 18 ARG cc_start: 0.9122 (OUTLIER) cc_final: 0.8154 (mpp80) REVERT: C 74 ASN cc_start: 0.7808 (m-40) cc_final: 0.7279 (t0) REVERT: C 90 ASN cc_start: 0.8456 (m-40) cc_final: 0.8227 (m-40) REVERT: C 105 ASN cc_start: 0.9078 (t0) cc_final: 0.8472 (t0) REVERT: C 111 ASN cc_start: 0.8492 (t0) cc_final: 0.8099 (p0) REVERT: D 104 LYS cc_start: 0.8139 (mmtm) cc_final: 0.7794 (mtmm) REVERT: D 111 LYS cc_start: 0.8593 (mmtm) cc_final: 0.8064 (mtpt) REVERT: D 141 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8742 (ttpp) REVERT: G 20 SER cc_start: 0.9189 (m) cc_final: 0.8951 (m) REVERT: H 104 LYS cc_start: 0.8532 (ttmm) cc_final: 0.8022 (ttmm) outliers start: 9 outliers final: 6 residues processed: 157 average time/residue: 0.1495 time to fit residues: 29.6287 Evaluate side-chains 160 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 151 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP 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 64 ILE Chi-restraints excluded: chain D residue 141 LYS Chi-restraints excluded: chain E residue 122 LYS 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: 0.9980 chunk 80 optimal weight: 30.0000 chunk 61 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 91 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.114879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.077909 restraints weight = 20351.917| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.61 r_work: 0.2798 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11921 Z= 0.149 Angle : 0.590 7.015 17247 Z= 0.347 Chirality : 0.041 0.210 1972 Planarity : 0.004 0.039 1249 Dihedral : 30.845 179.919 3713 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.18 % Allowed : 15.44 % Favored : 82.38 % 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: 2.42 (0.33), residues: 707 helix: 2.56 (0.23), residues: 523 sheet: None (None), residues: 0 loop : -1.37 (0.42), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 107 TYR 0.009 0.001 TYR H 62 PHE 0.016 0.001 PHE H 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.15 (11921) covalent geometry : angle 0.59049 / 0.35 (17247) hydrogen bonds : bond 0.04906 / 3.23 ( 575) hydrogen bonds : angle 2.68212 / 1.89 ( 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 167 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 154 time to evaluate : 0.170 Fit side-chains REVERT: B 74 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8548 (mt-10) REVERT: C 18 ARG cc_start: 0.9119 (OUTLIER) cc_final: 0.8152 (mpp80) REVERT: C 74 ASN cc_start: 0.7899 (m-40) cc_final: 0.7437 (t0) REVERT: C 90 ASN cc_start: 0.8479 (m-40) cc_final: 0.8251 (m-40) REVERT: C 105 ASN cc_start: 0.9053 (t0) cc_final: 0.8443 (t0) REVERT: C 111 ASN cc_start: 0.8493 (t0) cc_final: 0.8060 (p0) REVERT: D 104 LYS cc_start: 0.8152 (mmtm) cc_final: 0.7833 (mtmm) REVERT: D 111 LYS cc_start: 0.8568 (mmtm) cc_final: 0.8014 (mtpt) REVERT: G 20 SER cc_start: 0.9170 (m) cc_final: 0.8950 (m) REVERT: G 78 ARG cc_start: 0.8908 (mtm-85) cc_final: 0.8652 (mtp85) REVERT: H 104 LYS cc_start: 0.8563 (ttmm) cc_final: 0.7884 (ttmm) REVERT: H 130 GLU cc_start: 0.8148 (tp30) cc_final: 0.7886 (tp30) outliers start: 13 outliers final: 7 residues processed: 158 average time/residue: 0.1428 time to fit residues: 28.6821 Evaluate side-chains 159 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 150 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 64 ILE Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 122 LYS 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: 5.9990 chunk 45 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 83 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 109 ASN H 134 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.111544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.074247 restraints weight = 20473.899| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 1.65 r_work: 0.2720 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.5193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11921 Z= 0.199 Angle : 0.648 8.239 17247 Z= 0.372 Chirality : 0.045 0.207 1972 Planarity : 0.004 0.034 1249 Dihedral : 30.825 179.880 3713 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.51 % Allowed : 15.27 % 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: 2.19 (0.32), residues: 707 helix: 2.38 (0.23), residues: 523 sheet: None (None), residues: 0 loop : -1.40 (0.41), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 49 TYR 0.012 0.001 TYR H 62 PHE 0.016 0.002 PHE C 26 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.20 (11921) covalent geometry : angle 0.64788 / 0.37 (17247) hydrogen bonds : bond 0.06135 / 4.02 ( 575) hydrogen bonds : angle 2.89403 / 2.05 ( 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 164 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 155 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: B 74 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8594 (mt-10) REVERT: C 18 ARG cc_start: 0.9180 (OUTLIER) cc_final: 0.8258 (mpp80) REVERT: C 74 ASN cc_start: 0.8183 (m-40) cc_final: 0.7677 (t0) REVERT: C 90 ASN cc_start: 0.8585 (m-40) cc_final: 0.8380 (m-40) REVERT: C 105 ASN cc_start: 0.9075 (t0) cc_final: 0.8496 (t0) REVERT: C 111 ASN cc_start: 0.8574 (t0) cc_final: 0.8360 (p0) REVERT: D 104 LYS cc_start: 0.8260 (mmtm) cc_final: 0.7965 (mtmm) REVERT: D 111 LYS cc_start: 0.8687 (mmtm) cc_final: 0.8239 (mtpt) REVERT: H 68 LYS cc_start: 0.9318 (OUTLIER) cc_final: 0.9043 (mttt) REVERT: H 130 GLU cc_start: 0.8241 (tp30) cc_final: 0.8027 (tp30) outliers start: 9 outliers final: 5 residues processed: 157 average time/residue: 0.1496 time to fit residues: 29.9494 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 : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 64 ILE Chi-restraints excluded: chain E residue 122 LYS 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: 5.9990 chunk 6 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 81 optimal weight: 30.0000 chunk 82 optimal weight: 30.0000 chunk 93 optimal weight: 30.0000 chunk 40 optimal weight: 0.9990 chunk 80 optimal weight: 30.0000 chunk 56 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 25 ASN B 27 GLN D 109 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.111768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.074529 restraints weight = 20591.267| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 1.66 r_work: 0.2728 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.5277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11921 Z= 0.183 Angle : 0.628 7.853 17247 Z= 0.363 Chirality : 0.043 0.207 1972 Planarity : 0.004 0.033 1249 Dihedral : 30.818 179.933 3713 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.68 % Allowed : 15.60 % Favored : 82.72 % 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: 2.21 (0.32), residues: 707 helix: 2.41 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -1.46 (0.42), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 23 TYR 0.010 0.001 TYR H 62 PHE 0.016 0.002 PHE C 26 HIS 0.003 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.18 (11921) covalent geometry : angle 0.62800 / 0.36 (17247) hydrogen bonds : bond 0.05680 / 3.73 ( 575) hydrogen bonds : angle 2.80862 / 1.99 ( 1488) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2448.51 seconds wall clock time: 42 minutes 32.81 seconds (2552.81 seconds total)