Starting phenix.real_space_refine on Sat Jul 4 14:38:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mmk_48392/07_2026/9mmk_48392.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mmk_48392/07_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_48392/07_2026/9mmk_48392.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mmk_48392/07_2026/9mmk_48392.map" model { file = "/net/cci-nas-00/data/ceres_data/9mmk_48392/07_2026/9mmk_48392.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mmk_48392/07_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-dev-6108/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: 3.74, 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: 1.95 Conformation dependent library (CDL) restraints added in 486.4 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: 3.90 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: 5.35 Time building geometry restraints manager: 2.61 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: 34747 1.32 - 2.63: 4667 2.63 - 3.95: 446 3.95 - 5.27: 135 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: 5.780 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: 0.130 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 23.750 Find NCS groups from input model: 0.140 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.590 ------------------------------------------------------------------------------- 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 : 1.005 6.584 18242 Z= 0.846 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 1.00527 / 0.85 (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 : 0.407 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 104 average time/residue: 0.3481 time to fit residues: 45.2264 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 : 0.446 ------------------------------------------------------------------------------- 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 = 0.3381 r_free = 0.3381 target = 0.080419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.056698 restraints weight = 70050.066| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 1.59 r_work: 0.2714 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12601 Z= 0.218 Angle : 0.701 5.873 18242 Z= 0.461 Chirality : 0.048 0.181 2072 Planarity : 0.006 0.051 1318 Dihedral : 29.244 83.017 3959 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.24 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: 1.45 (0.29), residues: 736 helix: 1.67 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -1.01 (0.34), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 100 TYR 0.011 0.002 TYR F 73 PHE 0.014 0.001 PHE D 66 HIS 0.006 0.002 HIS C 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.22 (12601) covalent geometry : angle 0.70075 / 0.46 (18242) hydrogen bonds : bond 0.08129 / 5.42 ( 738) hydrogen bonds : angle 3.43380 / 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 : 0.485 Fit side-chains REVERT: F 25 ASP cc_start: 0.7815 (t70) cc_final: 0.7586 (t0) outliers start: 3 outliers final: 3 residues processed: 58 average time/residue: 0.2129 time to fit residues: 17.7239 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 : 0.392 ------------------------------------------------------------------------------- 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: 0.6980 chunk 7 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 69 optimal weight: 0.1980 chunk 16 optimal weight: 6.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3412 r_free = 0.3412 target = 0.081890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.057907 restraints weight = 69412.671| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 1.60 r_work: 0.2755 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12601 Z= 0.167 Angle : 0.599 5.343 18242 Z= 0.413 Chirality : 0.042 0.149 2072 Planarity : 0.005 0.044 1318 Dihedral : 29.551 83.321 3959 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.97 % Allowed : 5.15 % Favored : 93.88 % 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: 1.90 (0.30), residues: 736 helix: 2.13 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -1.24 (0.34), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 100 TYR 0.009 0.001 TYR C 51 PHE 0.013 0.001 PHE H 71 HIS 0.004 0.001 HIS D 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.17 (12601) covalent geometry : angle 0.59866 / 0.41 (18242) hydrogen bonds : bond 0.06654 / 4.39 ( 738) hydrogen bonds : angle 3.06423 / 2.24 ( 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 : 0.460 Fit side-chains REVERT: D 77 GLU cc_start: 0.8950 (tp30) cc_final: 0.8509 (tp30) REVERT: F 25 ASP cc_start: 0.7746 (t70) cc_final: 0.7474 (t0) outliers start: 6 outliers final: 3 residues processed: 59 average time/residue: 0.2649 time to fit residues: 21.6683 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 : 0.411 ------------------------------------------------------------------------------- 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: 1.9990 chunk 47 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 96 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3410 r_free = 0.3410 target = 0.081628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.057555 restraints weight = 70006.081| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 1.60 r_work: 0.2745 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12601 Z= 0.164 Angle : 0.589 5.651 18242 Z= 0.394 Chirality : 0.042 0.155 2072 Planarity : 0.004 0.044 1318 Dihedral : 29.600 82.404 3959 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.64 % Allowed : 5.48 % Favored : 93.88 % 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: 2.00 (0.30), residues: 736 helix: 2.27 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -1.41 (0.34), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 33 TYR 0.007 0.001 TYR F 52 PHE 0.009 0.001 PHE D 66 HIS 0.003 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.16 (12601) covalent geometry : angle 0.58898 / 0.39 (18242) hydrogen bonds : bond 0.06404 / 4.25 ( 738) hydrogen bonds : angle 2.98835 / 2.18 ( 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 55 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.459 Fit side-chains REVERT: F 25 ASP cc_start: 0.7814 (t70) cc_final: 0.7536 (t0) outliers start: 4 outliers final: 3 residues processed: 54 average time/residue: 0.2408 time to fit residues: 18.1139 Evaluate side-chains 51 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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=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: 2.9990 chunk 98 optimal weight: 30.0000 chunk 5 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.3389 r_free = 0.3389 target = 0.080507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.056357 restraints weight = 69698.141| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 1.60 r_work: 0.2715 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2592 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12601 Z= 0.172 Angle : 0.576 4.556 18242 Z= 0.390 Chirality : 0.041 0.151 2072 Planarity : 0.005 0.048 1318 Dihedral : 29.648 81.538 3959 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % 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 (0.30), residues: 736 helix: 2.38 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -1.64 (0.34), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 100 TYR 0.008 0.001 TYR F 73 PHE 0.012 0.001 PHE D 66 HIS 0.004 0.001 HIS E 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.17 (12601) covalent geometry : angle 0.57566 / 0.39 (18242) hydrogen bonds : bond 0.06690 / 4.45 ( 738) hydrogen bonds : angle 2.96620 / 2.15 ( 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 : 0.320 Fit side-chains REVERT: F 25 ASP cc_start: 0.7812 (t70) cc_final: 0.7537 (t0) outliers start: 1 outliers final: 1 residues processed: 52 average time/residue: 0.2157 time to fit residues: 16.0153 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 : 0.392 ------------------------------------------------------------------------------- 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: 9.9990 chunk 48 optimal weight: 0.8980 chunk 73 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3399 r_free = 0.3399 target = 0.080941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.056836 restraints weight = 69638.363| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 1.59 r_work: 0.2729 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12601 Z= 0.152 Angle : 0.562 4.889 18242 Z= 0.380 Chirality : 0.040 0.156 2072 Planarity : 0.004 0.046 1318 Dihedral : 29.647 81.526 3959 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.32 % Allowed : 6.76 % 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: 2.11 (0.31), residues: 736 helix: 2.43 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -1.63 (0.34), 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 0.011 0.001 PHE D 66 HIS 0.002 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.15 (12601) covalent geometry : angle 0.56184 / 0.38 (18242) hydrogen bonds : bond 0.06356 / 4.23 ( 738) hydrogen bonds : angle 2.93138 / 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: 2 poor density : 49 time to evaluate : 0.444 Fit side-chains REVERT: F 25 ASP cc_start: 0.7788 (t70) cc_final: 0.7511 (t0) outliers start: 2 outliers final: 1 residues processed: 50 average time/residue: 0.2184 time to fit residues: 15.4398 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 : 0.442 ------------------------------------------------------------------------------- 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: 2.9990 chunk 50 optimal weight: 1.9990 chunk 71 optimal weight: 30.0000 chunk 96 optimal weight: 10.0000 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: 0.9990 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 = 0.3373 r_free = 0.3373 target = 0.079541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.055377 restraints weight = 70087.808| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 1.58 r_work: 0.2691 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12601 Z= 0.184 Angle : 0.582 6.447 18242 Z= 0.384 Chirality : 0.040 0.157 2072 Planarity : 0.004 0.050 1318 Dihedral : 29.666 81.018 3959 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % 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: 1.92 (0.31), residues: 736 helix: 2.35 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -1.90 (0.35), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 72 TYR 0.008 0.001 TYR E 100 PHE 0.013 0.001 PHE D 66 HIS 0.004 0.001 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.18 (12601) covalent geometry : angle 0.58246 / 0.38 (18242) hydrogen bonds : bond 0.06956 / 4.65 ( 738) hydrogen bonds : angle 3.01618 / 2.19 ( 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 51 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.351 Fit side-chains REVERT: F 25 ASP cc_start: 0.7794 (t70) cc_final: 0.7567 (t0) outliers start: 1 outliers final: 1 residues processed: 51 average time/residue: 0.2194 time to fit residues: 16.1506 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 : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 78 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 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: 9.9990 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 = 0.3377 r_free = 0.3377 target = 0.079771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.055664 restraints weight = 69643.372| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 1.58 r_work: 0.2701 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2580 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12601 Z= 0.164 Angle : 0.560 4.809 18242 Z= 0.374 Chirality : 0.040 0.154 2072 Planarity : 0.004 0.052 1318 Dihedral : 29.663 81.150 3959 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 1.69 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: 1.97 (0.31), residues: 736 helix: 2.40 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -1.93 (0.35), 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 0.012 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 0.56021 / 0.37 (18242) hydrogen bonds : bond 0.06681 / 4.45 ( 738) hydrogen bonds : angle 2.95970 / 2.15 ( 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 49 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.423 Fit side-chains REVERT: F 25 ASP cc_start: 0.7779 (t70) cc_final: 0.7510 (t0) REVERT: H 72 GLU cc_start: 0.8521 (tm-30) cc_final: 0.8302 (tm-30) outliers start: 1 outliers final: 1 residues processed: 49 average time/residue: 0.2136 time to fit residues: 14.9052 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 : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 5 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 77 optimal weight: 8.9990 chunk 22 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3386 r_free = 0.3386 target = 0.080235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.056304 restraints weight = 69912.655| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 1.57 r_work: 0.2714 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 12601 Z= 0.146 Angle : 0.557 6.912 18242 Z= 0.373 Chirality : 0.039 0.154 2072 Planarity : 0.004 0.051 1318 Dihedral : 29.658 81.151 3959 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % 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: 2.04 (0.31), residues: 736 helix: 2.45 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -1.88 (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 H 41 PHE 0.011 0.001 PHE D 66 HIS 0.002 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.15 (12601) covalent geometry : angle 0.55695 / 0.37 (18242) hydrogen bonds : bond 0.06333 / 4.22 ( 738) hydrogen bonds : angle 2.92373 / 2.12 ( 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 50 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.351 Fit side-chains REVERT: F 25 ASP cc_start: 0.7748 (t70) cc_final: 0.7473 (t0) REVERT: H 72 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8285 (tm-30) outliers start: 1 outliers final: 1 residues processed: 50 average time/residue: 0.2050 time to fit residues: 14.7374 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 : 0.418 ------------------------------------------------------------------------------- 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: 2.9990 chunk 95 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 92 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.079125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.055185 restraints weight = 70105.767| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 1.56 r_work: 0.2688 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12601 Z= 0.190 Angle : 0.569 4.714 18242 Z= 0.376 Chirality : 0.040 0.147 2072 Planarity : 0.004 0.052 1318 Dihedral : 29.666 80.911 3959 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 1.74 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: 1.93 (0.31), residues: 736 helix: 2.40 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -2.04 (0.35), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 129 TYR 0.009 0.001 TYR A 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 0.00362 / 0.19 (12601) covalent geometry : angle 0.56897 / 0.38 (18242) hydrogen bonds : bond 0.06936 / 4.63 ( 738) hydrogen bonds : angle 2.99037 / 2.17 ( 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 : 0.473 Fit side-chains REVERT: F 25 ASP cc_start: 0.7786 (t70) cc_final: 0.7518 (t0) REVERT: H 72 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8293 (tm-30) outliers start: 1 outliers final: 1 residues processed: 50 average time/residue: 0.2227 time to fit residues: 15.9403 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 : 0.439 ------------------------------------------------------------------------------- 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: 10.0000 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: 2.9990 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 = 0.3369 r_free = 0.3369 target = 0.079307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.055241 restraints weight = 70232.780| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 1.58 r_work: 0.2687 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2566 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12601 Z= 0.172 Angle : 0.560 8.644 18242 Z= 0.370 Chirality : 0.039 0.134 2072 Planarity : 0.004 0.053 1318 Dihedral : 29.677 81.335 3959 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % 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: 1.95 (0.31), residues: 736 helix: 2.42 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -2.05 (0.34), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 72 TYR 0.007 0.001 TYR A 100 PHE 0.012 0.001 PHE D 66 HIS 0.004 0.001 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.17 (12601) covalent geometry : angle 0.55980 / 0.37 (18242) hydrogen bonds : bond 0.06708 / 4.47 ( 738) hydrogen bonds : angle 2.97637 / 2.16 ( 1831) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4771.31 seconds wall clock time: 81 minutes 24.20 seconds (4884.20 seconds total)