Starting phenix.real_space_refine on Sun Sep 13 06:42:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mmk_48392/09_2026/9mmk_48392.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mmk_48392/09_2026/9mmk_48392.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mmk_48392/09_2026/9mmk_48392.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mmk_48392/09_2026/9mmk_48392.map" model { file = "/net/cci-nas-00/data/ceres_data/9mmk_48392/09_2026/9mmk_48392.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mmk_48392/09_2026/9mmk_48392.cif" } resolution = 3.2 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= 0.012 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: 6 Type Number sf(0) Gaussians P 285 5.49 5 S 14 5.16 5 C 6530 2.51 5 N 2214 2.21 5 O 2763 1.98 5 H 9467 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21273 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1616 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1283 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1715 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1471 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1616 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1315 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1715 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1471 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 4519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 4519 Classifications: {'DNA': 143} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 142} Chain: "J" Number of atoms: 4552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 4552 Classifications: {'DNA': 143} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 142} Time building chain proxies: 3.80, per 1000 atoms: 0.18 Number of scatterers: 21273 At special positions: 0 Unit cell: (77.77, 120.12, 120.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 14 16.00 P 285 15.00 O 2763 8.00 N 2214 7.00 C 6530 6.00 H 9467 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.94 Conformation dependent library (CDL) restraints added in 431.9 milliseconds 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1398 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 10 sheets defined 72.2% alpha, 2.9% beta 141 base pairs and 262 stacking pairs defined. Time for finding SS restraints: 3.56 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.547A pdb=" N GLN A 77 " --> pdb=" O ARG A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 114 removed outlier: 3.863A pdb=" N VAL A 90 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N MET A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N CYS A 111 " --> pdb=" O ASP A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 133 removed outlier: 3.660A pdb=" N ILE A 125 " --> pdb=" O MET A 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 30 Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 50 through 77 removed outlier: 3.711A pdb=" N GLU B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY B 57 " --> pdb=" O GLU B 53 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU B 64 " --> pdb=" O LYS B 60 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASN B 65 " --> pdb=" O VAL B 61 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL B 66 " --> pdb=" O PHE B 62 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP B 69 " --> pdb=" O ASN B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 94 removed outlier: 3.650A pdb=" N GLN B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 27 through 38 Processing helix chain 'C' and resid 47 through 74 removed outlier: 4.007A pdb=" N LEU C 66 " --> pdb=" O GLU C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'C' and resid 93 through 98 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'D' and resid 38 through 50 Processing helix chain 'D' and resid 56 through 85 removed outlier: 3.864A pdb=" N ASN D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN D 85 " --> pdb=" O LEU D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 103 Processing helix chain 'D' and resid 104 through 125 removed outlier: 3.815A pdb=" N SER D 113 " --> pdb=" O LYS D 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 58 removed outlier: 3.569A pdb=" N ARG E 50 " --> pdb=" O THR E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 77 removed outlier: 3.555A pdb=" N GLN E 77 " --> pdb=" O ARG E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 115 removed outlier: 3.863A pdb=" N VAL E 90 " --> pdb=" O GLN E 86 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N MET E 91 " --> pdb=" O SER E 87 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU E 110 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA E 115 " --> pdb=" O CYS E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 133 removed outlier: 3.668A pdb=" N ILE E 125 " --> pdb=" O MET E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 30 removed outlier: 4.140A pdb=" N ILE F 27 " --> pdb=" O ARG F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 42 Processing helix chain 'F' and resid 50 through 77 removed outlier: 3.836A pdb=" N GLU F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL F 61 " --> pdb=" O GLY F 57 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE F 62 " --> pdb=" O VAL F 58 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP F 69 " --> pdb=" O ASN F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 95 removed outlier: 3.639A pdb=" N VAL F 87 " --> pdb=" O THR F 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 23 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 47 through 73 Processing helix chain 'G' and resid 80 through 90 Processing helix chain 'G' and resid 93 through 98 Processing helix chain 'H' and resid 38 through 50 Processing helix chain 'H' and resid 56 through 85 removed outlier: 3.510A pdb=" N ILE H 62 " --> pdb=" O LYS H 58 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL H 67 " --> pdb=" O MET H 63 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 103 Processing helix chain 'H' and resid 104 through 125 removed outlier: 3.657A pdb=" N LYS H 109 " --> pdb=" O GLY H 105 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS H 110 " --> pdb=" O GLU H 106 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.590A pdb=" N ARG A 84 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120 removed outlier: 3.525A pdb=" N ILE A 120 " --> pdb=" O ARG B 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 98 through 99 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.099A pdb=" N ARG C 43 " --> pdb=" O ILE D 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 103 Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85 removed outlier: 6.953A pdb=" N ARG E 84 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 119 through 120 Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.219A pdb=" N ARG G 43 " --> pdb=" O ILE H 90 " (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 79 376 hydrogen bonds defined for protein. 1107 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 362 hydrogen bonds 724 hydrogen bond angles 0 basepair planarities 141 basepair parallelities 262 stacking parallelities Total time for adding SS restraints: 4.94 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9463 1.03 - 1.23: 111 1.23 - 1.42: 5353 1.42 - 1.61: 7117 1.61 - 1.81: 24 Bond restraints: 22068 Sorted by residual: bond pdb=" C3' DC I 69 " pdb=" C2' DC I 69 " ideal model delta sigma weight residual 1.516 1.555 -0.039 8.00e-03 1.56e+04 2.36e+01 bond pdb=" C3' DA I -5 " pdb=" C2' DA I -5 " ideal model delta sigma weight residual 1.516 1.554 -0.038 8.00e-03 1.56e+04 2.21e+01 bond pdb=" C3' DT J 15 " pdb=" C2' DT J 15 " ideal model delta sigma weight residual 1.516 1.551 -0.035 8.00e-03 1.56e+04 1.88e+01 bond pdb=" C3' DT J 69 " pdb=" C2' DT J 69 " ideal model delta sigma weight residual 1.516 1.548 -0.032 8.00e-03 1.56e+04 1.63e+01 bond pdb=" C3' DC I -62 " pdb=" C2' DC I -62 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.50e+01 ... (remaining 22063 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 34676 1.32 - 2.63: 4704 2.63 - 3.95: 479 3.95 - 5.27: 136 5.27 - 6.58: 7 Bond angle restraints: 40002 Sorted by residual: angle pdb=" O4' DC I 66 " pdb=" C1' DC I 66 " pdb=" N1 DC I 66 " ideal model delta sigma weight residual 108.00 113.13 -5.13 7.00e-01 2.04e+00 5.38e+01 angle pdb=" O4' DG J 27 " pdb=" C1' DG J 27 " pdb=" N9 DG J 27 " ideal model delta sigma weight residual 108.00 112.93 -4.93 7.00e-01 2.04e+00 4.96e+01 angle pdb=" O4' DT I 34 " pdb=" C1' DT I 34 " pdb=" N1 DT I 34 " ideal model delta sigma weight residual 108.00 112.42 -4.42 7.00e-01 2.04e+00 3.98e+01 angle pdb=" O4' DC I -27 " pdb=" C1' DC I -27 " pdb=" N1 DC I -27 " ideal model delta sigma weight residual 108.00 112.26 -4.26 7.00e-01 2.04e+00 3.70e+01 angle pdb=" O4' DT I -16 " pdb=" C1' DT I -16 " pdb=" N1 DT I -16 " ideal model delta sigma weight residual 108.00 112.20 -4.20 7.00e-01 2.04e+00 3.59e+01 ... (remaining 39997 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 6425 17.18 - 34.35: 1201 34.35 - 51.53: 919 51.53 - 68.70: 606 68.70 - 85.88: 13 Dihedral angle restraints: 9164 sinusoidal: 6728 harmonic: 2436 Sorted by residual: dihedral pdb=" CG ARG H 100 " pdb=" CD ARG H 100 " pdb=" NE ARG H 100 " pdb=" CZ ARG H 100 " ideal model delta sinusoidal sigma weight residual -90.00 -43.87 -46.13 2 1.50e+01 4.44e-03 1.11e+01 dihedral pdb=" CG ARG F 56 " pdb=" CD ARG F 56 " pdb=" NE ARG F 56 " pdb=" CZ ARG F 56 " ideal model delta sinusoidal sigma weight residual 180.00 135.60 44.40 2 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CG ARG G 33 " pdb=" CD ARG G 33 " pdb=" NE ARG G 33 " pdb=" CZ ARG G 33 " ideal model delta sinusoidal sigma weight residual -90.00 -133.75 43.75 2 1.50e+01 4.44e-03 1.02e+01 ... (remaining 9161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1154 0.043 - 0.086: 556 0.086 - 0.129: 260 0.129 - 0.172: 89 0.172 - 0.215: 13 Chirality restraints: 2072 Sorted by residual: chirality pdb=" C4' DC I 69 " pdb=" C5' DC I 69 " pdb=" O4' DC I 69 " pdb=" C3' DC I 69 " both_signs ideal model delta sigma weight residual False -2.53 -2.32 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" C4' DC I 21 " pdb=" C5' DC I 21 " pdb=" O4' DC I 21 " pdb=" C3' DC I 21 " both_signs ideal model delta sigma weight residual False -2.53 -2.32 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C3' DC I 7 " pdb=" C4' DC I 7 " pdb=" O3' DC I 7 " pdb=" C2' DC I 7 " both_signs ideal model delta sigma weight residual False -2.73 -2.52 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 2069 not shown) Planarity restraints: 2263 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 33 " 0.023 9.50e-02 1.11e+02 3.93e-02 3.35e+01 pdb=" NE ARG C 33 " -0.034 2.00e-02 2.50e+03 pdb=" CZ ARG C 33 " 0.031 2.00e-02 2.50e+03 pdb=" NH1 ARG C 33 " 0.072 2.00e-02 2.50e+03 pdb=" NH2 ARG C 33 " -0.018 2.00e-02 2.50e+03 pdb="HH11 ARG C 33 " 0.002 2.00e-02 2.50e+03 pdb="HH12 ARG C 33 " -0.073 2.00e-02 2.50e+03 pdb="HH21 ARG C 33 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG C 33 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 87 " -0.409 9.50e-02 1.11e+02 1.39e-01 3.28e+01 pdb=" NE ARG H 87 " -0.003 2.00e-02 2.50e+03 pdb=" CZ ARG H 87 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG H 87 " 0.035 2.00e-02 2.50e+03 pdb=" NH2 ARG H 87 " 0.046 2.00e-02 2.50e+03 pdb="HH11 ARG H 87 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARG H 87 " -0.018 2.00e-02 2.50e+03 pdb="HH21 ARG H 87 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG H 87 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 60 " -0.034 2.00e-02 2.50e+03 2.61e-02 1.87e+01 pdb=" N1 DC J 60 " 0.072 2.00e-02 2.50e+03 pdb=" C2 DC J 60 " -0.033 2.00e-02 2.50e+03 pdb=" O2 DC J 60 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DC J 60 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DC J 60 " -0.002 2.00e-02 2.50e+03 pdb=" N4 DC J 60 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DC J 60 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DC J 60 " 0.002 2.00e-02 2.50e+03 pdb=" H5 DC J 60 " -0.006 2.00e-02 2.50e+03 pdb=" H6 DC J 60 " -0.004 2.00e-02 2.50e+03 ... (remaining 2260 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 595 2.19 - 2.79: 34680 2.79 - 3.39: 49566 3.39 - 4.00: 70495 4.00 - 4.60: 111624 Nonbonded interactions: 266960 Sorted by model distance: nonbonded pdb=" OE1 GLU E 74 " pdb="HD21 ASN F 26 " model vdw 1.586 2.450 nonbonded pdb=" OD2 ASP E 107 " pdb="HH11 ARG E 132 " model vdw 1.603 2.450 nonbonded pdb=" OD2 ASP D 69 " pdb=" HH TYR F 99 " model vdw 1.611 2.450 nonbonded pdb=" O LEU C 86 " pdb="HD21 ASN C 90 " model vdw 1.636 2.450 nonbonded pdb="HE21 GLN C 25 " pdb=" OE1 GLN D 48 " model vdw 1.651 2.450 ... (remaining 266955 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' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 25 through 102) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.120 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 23.330 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 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 : 0.007 0.069 12601 Z= 0.617 Angle : 1.019 6.584 18242 Z= 0.861 Chirality : 0.062 0.215 2072 Planarity : 0.013 0.152 1318 Dihedral : 26.172 85.877 5435 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 0.16 % Allowed : 3.22 % Favored : 96.62 % 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: 0.24 (0.27), residues: 736 helix: 0.46 (0.20), residues: 531 sheet: None (None), residues: 0 loop : -0.33 (0.35), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.003 ARG E 64 TYR 0.020 0.005 TYR G 58 PHE 0.017 0.003 PHE D 66 HIS 0.012 0.003 HIS D 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00690 / 0.62 (12601) covalent geometry : angle 1.01865 / 0.86 (18242) hydrogen bonds : bond 0.13252 / 8.82 ( 738) hydrogen bonds : angle 3.78051 / 2.76 ( 1831) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.433 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 104 average time/residue: 0.3863 time to fit residues: 50.5289 Evaluate side-chains 55 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 26 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.080553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.056718 restraints weight = 70256.210| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 1.60 r_work: 0.2717 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12601 Z= 0.217 Angle : 0.706 5.919 18242 Z= 0.459 Chirality : 0.049 0.185 2072 Planarity : 0.006 0.045 1318 Dihedral : 29.289 83.682 3959 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.48 % Allowed : 5.48 % Favored : 94.04 % 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: 1.41 (0.29), residues: 736 helix: 1.65 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -1.06 (0.34), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 100 TYR 0.011 0.001 TYR F 73 PHE 0.013 0.001 PHE D 66 HIS 0.005 0.002 HIS C 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.22 (12601) covalent geometry : angle 0.70583 / 0.46 (18242) hydrogen bonds : bond 0.07999 / 5.33 ( 738) hydrogen bonds : angle 3.43941 / 2.51 ( 1831) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.449 Fit side-chains REVERT: F 25 ASP cc_start: 0.7839 (t70) cc_final: 0.7602 (t0) outliers start: 3 outliers final: 3 residues processed: 58 average time/residue: 0.2358 time to fit residues: 19.7142 Evaluate side-chains 55 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 31 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 67 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.3398 r_free = 0.3398 target = 0.081181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.057110 restraints weight = 69440.445| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 1.59 r_work: 0.2731 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12601 Z= 0.177 Angle : 0.613 5.217 18242 Z= 0.415 Chirality : 0.043 0.154 2072 Planarity : 0.005 0.040 1318 Dihedral : 29.531 83.094 3959 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.97 % Allowed : 4.83 % Favored : 94.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.30), residues: 736 helix: 2.09 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -1.38 (0.34), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 80 TYR 0.008 0.001 TYR F 52 PHE 0.016 0.001 PHE H 71 HIS 0.003 0.001 HIS D 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.18 (12601) covalent geometry : angle 0.61303 / 0.42 (18242) hydrogen bonds : bond 0.07004 / 4.64 ( 738) hydrogen bonds : angle 3.11686 / 2.27 ( 1831) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.377 Fit side-chains REVERT: D 77 GLU cc_start: 0.8968 (tp30) cc_final: 0.8546 (tp30) REVERT: F 25 ASP cc_start: 0.7776 (t70) cc_final: 0.7515 (t0) outliers start: 6 outliers final: 3 residues processed: 59 average time/residue: 0.2685 time to fit residues: 22.0607 Evaluate side-chains 57 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 13 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 47 optimal weight: 0.1980 chunk 92 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 96 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.3413 r_free = 0.3413 target = 0.081775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.057715 restraints weight = 70008.920| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 1.60 r_work: 0.2750 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12601 Z= 0.157 Angle : 0.584 5.876 18242 Z= 0.389 Chirality : 0.042 0.163 2072 Planarity : 0.004 0.050 1318 Dihedral : 29.627 82.739 3959 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.64 % Allowed : 5.31 % Favored : 94.04 % 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: 1.99 (0.30), residues: 736 helix: 2.28 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -1.47 (0.34), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 100 TYR 0.007 0.001 TYR A 100 PHE 0.010 0.001 PHE H 71 HIS 0.003 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.16 (12601) covalent geometry : angle 0.58437 / 0.39 (18242) hydrogen bonds : bond 0.06251 / 4.15 ( 738) hydrogen bonds : angle 2.96106 / 2.15 ( 1831) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.457 Fit side-chains REVERT: F 25 ASP cc_start: 0.7819 (t70) cc_final: 0.7546 (t0) outliers start: 4 outliers final: 2 residues processed: 55 average time/residue: 0.2654 time to fit residues: 20.5253 Evaluate side-chains 50 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 16 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 98 optimal weight: 20.0000 chunk 5 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.3392 r_free = 0.3392 target = 0.080584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.056490 restraints weight = 69695.150| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 1.59 r_work: 0.2722 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12601 Z= 0.172 Angle : 0.578 4.637 18242 Z= 0.388 Chirality : 0.041 0.153 2072 Planarity : 0.004 0.045 1318 Dihedral : 29.617 81.400 3959 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.16 % Allowed : 6.76 % Favored : 93.08 % 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: 2.05 (0.31), residues: 736 helix: 2.37 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -1.62 (0.35), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 72 TYR 0.007 0.001 TYR A 100 PHE 0.012 0.001 PHE H 71 HIS 0.003 0.001 HIS E 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.17 (12601) covalent geometry : angle 0.57845 / 0.39 (18242) hydrogen bonds : bond 0.06641 / 4.42 ( 738) hydrogen bonds : angle 2.94943 / 2.14 ( 1831) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.493 Fit side-chains REVERT: F 25 ASP cc_start: 0.7819 (t70) cc_final: 0.7544 (t0) outliers start: 1 outliers final: 1 residues processed: 52 average time/residue: 0.2379 time to fit residues: 17.8979 Evaluate side-chains 50 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 95 optimal weight: 10.0000 chunk 48 optimal weight: 0.6980 chunk 73 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3394 r_free = 0.3394 target = 0.080694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.056582 restraints weight = 69723.096| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 1.60 r_work: 0.2724 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12601 Z= 0.163 Angle : 0.570 5.001 18242 Z= 0.381 Chirality : 0.041 0.157 2072 Planarity : 0.004 0.043 1318 Dihedral : 29.628 81.574 3959 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.16 % Allowed : 6.92 % Favored : 92.91 % 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: 2.06 (0.31), residues: 736 helix: 2.41 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -1.70 (0.34), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 72 TYR 0.007 0.001 TYR A 100 PHE 0.011 0.001 PHE D 66 HIS 0.002 0.001 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.16 (12601) covalent geometry : angle 0.56999 / 0.38 (18242) hydrogen bonds : bond 0.06463 / 4.30 ( 738) hydrogen bonds : angle 2.93171 / 2.13 ( 1831) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.470 Fit side-chains REVERT: F 25 ASP cc_start: 0.7786 (t70) cc_final: 0.7518 (t0) outliers start: 1 outliers final: 1 residues processed: 51 average time/residue: 0.2499 time to fit residues: 18.2382 Evaluate side-chains 49 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 94 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 71 optimal weight: 30.0000 chunk 96 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.3367 r_free = 0.3367 target = 0.079211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.055116 restraints weight = 70189.619| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 1.58 r_work: 0.2681 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2558 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 12601 Z= 0.189 Angle : 0.590 5.115 18242 Z= 0.386 Chirality : 0.041 0.158 2072 Planarity : 0.005 0.047 1318 Dihedral : 29.635 81.283 3959 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.48 % Allowed : 7.25 % Favored : 92.27 % 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: 1.79 (0.31), residues: 736 helix: 2.27 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -2.00 (0.35), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 87 TYR 0.009 0.001 TYR E 100 PHE 0.014 0.001 PHE D 66 HIS 0.004 0.001 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.19 (12601) covalent geometry : angle 0.58969 / 0.39 (18242) hydrogen bonds : bond 0.07189 / 4.80 ( 738) hydrogen bonds : angle 3.06986 / 2.23 ( 1831) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.455 Fit side-chains REVERT: F 25 ASP cc_start: 0.7803 (t70) cc_final: 0.7583 (t0) outliers start: 3 outliers final: 2 residues processed: 53 average time/residue: 0.2423 time to fit residues: 18.6474 Evaluate side-chains 51 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 82 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.3372 r_free = 0.3372 target = 0.079484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.055428 restraints weight = 69839.557| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 1.58 r_work: 0.2689 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12601 Z= 0.164 Angle : 0.574 4.997 18242 Z= 0.379 Chirality : 0.040 0.156 2072 Planarity : 0.004 0.049 1318 Dihedral : 29.633 81.376 3959 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.32 % Allowed : 7.41 % Favored : 92.27 % 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: 1.85 (0.31), residues: 736 helix: 2.32 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -2.00 (0.34), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 72 TYR 0.008 0.001 TYR A 100 PHE 0.013 0.001 PHE D 66 HIS 0.003 0.001 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.16 (12601) covalent geometry : angle 0.57402 / 0.38 (18242) hydrogen bonds : bond 0.06904 / 4.60 ( 738) hydrogen bonds : angle 3.02679 / 2.20 ( 1831) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.480 Fit side-chains REVERT: F 25 ASP cc_start: 0.7793 (t70) cc_final: 0.7525 (t0) REVERT: H 72 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8314 (tm-30) outliers start: 2 outliers final: 2 residues processed: 50 average time/residue: 0.2414 time to fit residues: 17.4514 Evaluate side-chains 50 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 63 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 77 optimal weight: 8.9990 chunk 22 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3377 r_free = 0.3377 target = 0.079728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.055712 restraints weight = 70112.067| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 1.57 r_work: 0.2697 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12601 Z= 0.150 Angle : 0.565 4.990 18242 Z= 0.375 Chirality : 0.040 0.155 2072 Planarity : 0.004 0.049 1318 Dihedral : 29.630 81.390 3959 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.16 % Allowed : 7.57 % Favored : 92.27 % 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 (0.31), residues: 736 helix: 2.36 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -1.96 (0.35), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 33 TYR 0.007 0.001 TYR H 41 PHE 0.011 0.001 PHE D 66 HIS 0.003 0.001 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.15 (12601) covalent geometry : angle 0.56534 / 0.38 (18242) hydrogen bonds : bond 0.06677 / 4.45 ( 738) hydrogen bonds : angle 2.98741 / 2.17 ( 1831) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.452 Fit side-chains REVERT: F 25 ASP cc_start: 0.7776 (t70) cc_final: 0.7509 (t0) REVERT: H 72 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8293 (tm-30) outliers start: 1 outliers final: 1 residues processed: 49 average time/residue: 0.2286 time to fit residues: 16.2307 Evaluate side-chains 49 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 13 optimal weight: 1.9990 chunk 95 optimal weight: 9.9990 chunk 23 optimal weight: 0.0970 chunk 57 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 = 0.3379 r_free = 0.3379 target = 0.079868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.055873 restraints weight = 70172.429| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 1.59 r_work: 0.2700 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2579 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 12601 Z= 0.153 Angle : 0.563 4.993 18242 Z= 0.374 Chirality : 0.040 0.153 2072 Planarity : 0.004 0.049 1318 Dihedral : 29.635 81.370 3959 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.16 % Allowed : 7.57 % Favored : 92.27 % 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: 1.94 (0.31), residues: 736 helix: 2.39 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -1.96 (0.35), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 72 TYR 0.007 0.001 TYR F 52 PHE 0.012 0.001 PHE D 66 HIS 0.002 0.001 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.15 (12601) covalent geometry : angle 0.56309 / 0.37 (18242) hydrogen bonds : bond 0.06613 / 4.40 ( 738) hydrogen bonds : angle 2.96548 / 2.15 ( 1831) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.463 Fit side-chains REVERT: F 25 ASP cc_start: 0.7768 (t70) cc_final: 0.7492 (t0) REVERT: H 72 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8309 (tm-30) outliers start: 1 outliers final: 1 residues processed: 50 average time/residue: 0.2485 time to fit residues: 17.7281 Evaluate side-chains 49 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 51 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.3366 r_free = 0.3366 target = 0.079151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.055132 restraints weight = 70282.183| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 1.57 r_work: 0.2684 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2563 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12601 Z= 0.184 Angle : 0.573 4.736 18242 Z= 0.375 Chirality : 0.040 0.139 2072 Planarity : 0.005 0.050 1318 Dihedral : 29.640 80.976 3959 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.16 % Allowed : 7.73 % Favored : 92.11 % 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: 1.84 (0.31), residues: 736 helix: 2.35 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -2.11 (0.35), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 72 TYR 0.009 0.001 TYR A 100 PHE 0.014 0.001 PHE D 66 HIS 0.006 0.001 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.18 (12601) covalent geometry : angle 0.57314 / 0.38 (18242) hydrogen bonds : bond 0.06927 / 4.62 ( 738) hydrogen bonds : angle 3.00031 / 2.18 ( 1831) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5177.10 seconds wall clock time: 88 minutes 26.42 seconds (5306.42 seconds total)