Starting phenix.real_space_refine on Fri Sep 11 21:39:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tan_25777/09_2026/7tan_25777.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tan_25777/09_2026/7tan_25777.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tan_25777/09_2026/7tan_25777.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tan_25777/09_2026/7tan_25777.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tan_25777/09_2026/7tan_25777.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tan_25777/09_2026/7tan_25777.map" } resolution = 3.0 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 294 5.49 5 S 12 5.16 5 C 6691 2.51 5 N 2284 2.21 5 O 2838 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s 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: 12119 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 828 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 828 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3033 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2994 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Chain: "L" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Time building chain proxies: 2.70, per 1000 atoms: 0.22 Number of scatterers: 12119 At special positions: 0 Unit cell: (77.35, 122.85, 126.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 294 15.00 O 2838 8.00 N 2284 7.00 C 6691 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 426.4 milliseconds 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1436 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 9 sheets defined 69.4% alpha, 2.9% beta 60 base pairs and 258 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 removed outlier: 4.064A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.653A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.582A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.586A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.962A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.223A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.720A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 4.024A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.825A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.587A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 124 removed outlier: 3.840A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 55 removed outlier: 3.503A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.698A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.539A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.588A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.615A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.018A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.761A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.968A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.759A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL H 48 " --> pdb=" O VAL H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.651A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.933A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER H 124 " --> pdb=" O LYS H 120 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.828A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.798A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.490A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.890A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.455A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 369 hydrogen bonds defined for protein. 1101 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 147 hydrogen bonds 294 hydrogen bond angles 0 basepair planarities 60 basepair parallelities 258 stacking parallelities Total time for adding SS restraints: 2.38 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2205 1.33 - 1.45: 4172 1.45 - 1.57: 5945 1.57 - 1.69: 586 1.69 - 1.80: 22 Bond restraints: 12930 Sorted by residual: bond pdb=" C3' DT J -65 " pdb=" C2' DT J -65 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.28e+00 bond pdb=" C3' DG I -49 " pdb=" C2' DG I -49 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.69e+00 bond pdb=" C3' DT I 66 " pdb=" C2' DT I 66 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.39e+00 bond pdb=" C3' DA J -67 " pdb=" C2' DA J -67 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.73e+00 bond pdb=" C3' DG I -22 " pdb=" C2' DG I -22 " ideal model delta sigma weight residual 1.516 1.534 -0.018 8.00e-03 1.56e+04 5.15e+00 ... (remaining 12925 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 17332 1.28 - 2.55: 1305 2.55 - 3.83: 70 3.83 - 5.11: 8 5.11 - 6.38: 1 Bond angle restraints: 18716 Sorted by residual: angle pdb=" N3 DT J -42 " pdb=" C4 DT J -42 " pdb=" O4 DT J -42 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 angle pdb=" N3 DT I -17 " pdb=" C4 DT I -17 " pdb=" O4 DT I -17 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.78e+01 angle pdb=" N3 DT J 3 " pdb=" C4 DT J 3 " pdb=" O4 DT J 3 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.77e+01 angle pdb=" N3 DT J 34 " pdb=" C4 DT J 34 " pdb=" O4 DT J 34 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT I -63 " pdb=" C4 DT I -63 " pdb=" O4 DT I -63 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 ... (remaining 18711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.03: 4575 17.03 - 34.07: 1014 34.07 - 51.10: 1023 51.10 - 68.13: 379 68.13 - 85.16: 25 Dihedral angle restraints: 7016 sinusoidal: 4792 harmonic: 2224 Sorted by residual: dihedral pdb=" CG ARG E 128 " pdb=" CD ARG E 128 " pdb=" NE ARG E 128 " pdb=" CZ ARG E 128 " ideal model delta sinusoidal sigma weight residual -180.00 -136.48 -43.52 2 1.50e+01 4.44e-03 1.01e+01 dihedral pdb=" CB GLU G 41 " pdb=" CG GLU G 41 " pdb=" CD GLU G 41 " pdb=" OE1 GLU G 41 " ideal model delta sinusoidal sigma weight residual 0.00 -85.16 85.16 1 3.00e+01 1.11e-03 9.77e+00 dihedral pdb=" CG ARG C 71 " pdb=" CD ARG C 71 " pdb=" NE ARG C 71 " pdb=" CZ ARG C 71 " ideal model delta sinusoidal sigma weight residual -90.00 -132.16 42.16 2 1.50e+01 4.44e-03 9.61e+00 ... (remaining 7013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1445 0.040 - 0.081: 571 0.081 - 0.121: 111 0.121 - 0.161: 4 0.161 - 0.202: 1 Chirality restraints: 2132 Sorted by residual: chirality pdb=" CB ILE D 54 " pdb=" CA ILE D 54 " pdb=" CG1 ILE D 54 " pdb=" CG2 ILE D 54 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA ASP B 24 " pdb=" N ASP B 24 " pdb=" C ASP B 24 " pdb=" CB ASP B 24 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" CA ILE G 111 " pdb=" N ILE G 111 " pdb=" C ILE G 111 " pdb=" CB ILE G 111 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.87e-01 ... (remaining 2129 not shown) Planarity restraints: 1347 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.024 5.00e-02 4.00e+02 3.62e-02 2.09e+00 pdb=" N PRO C 80 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU H 105 " 0.007 2.00e-02 2.50e+03 1.35e-02 1.82e+00 pdb=" CD GLU H 105 " -0.023 2.00e-02 2.50e+03 pdb=" OE1 GLU H 105 " 0.008 2.00e-02 2.50e+03 pdb=" OE2 GLU H 105 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 32 " 0.018 2.00e-02 2.50e+03 7.59e-03 1.73e+00 pdb=" N9 DG I 32 " -0.019 2.00e-02 2.50e+03 pdb=" C8 DG I 32 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DG I 32 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DG I 32 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 32 " 0.002 2.00e-02 2.50e+03 pdb=" O6 DG I 32 " 0.004 2.00e-02 2.50e+03 pdb=" N1 DG I 32 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DG I 32 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 32 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DG I 32 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 32 " -0.002 2.00e-02 2.50e+03 ... (remaining 1344 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 3496 2.86 - 3.37: 10080 3.37 - 3.88: 21084 3.88 - 4.39: 25540 4.39 - 4.90: 36647 Nonbonded interactions: 96847 Sorted by model distance: nonbonded pdb=" OG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 2.351 3.040 nonbonded pdb=" N2 DG I 74 " pdb=" O2 DC J -73 " model vdw 2.381 3.120 nonbonded pdb=" O GLN E 125 " pdb=" NH2 ARG E 134 " model vdw 2.427 3.120 nonbonded pdb=" NZ LYS B 59 " pdb=" OE2 GLU B 63 " model vdw 2.487 3.120 nonbonded pdb=" O2 DT I 69 " pdb=" N2 DG J -68 " model vdw 2.503 3.120 ... (remaining 96842 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' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 21 through 101) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'L' } 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: 4.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.470 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 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 : 0.005 0.030 12930 Z= 0.489 Angle : 0.668 6.382 18716 Z= 0.606 Chirality : 0.042 0.202 2132 Planarity : 0.003 0.036 1347 Dihedral : 27.155 85.162 5580 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 2.18 (0.32), residues: 748 helix: 2.89 (0.24), residues: 503 sheet: None (None), residues: 0 loop : -1.88 (0.33), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 92 TYR 0.008 0.001 TYR B 51 PHE 0.008 0.001 PHE B 61 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.49 (12930) covalent geometry : angle 0.66803 / 0.61 (18716) hydrogen bonds : bond 0.19398 / 12.64 ( 516) hydrogen bonds : angle 5.97015 / 4.04 ( 1395) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.266 Fit side-chains REVERT: C 104 GLN cc_start: 0.8357 (mm-40) cc_final: 0.8097 (mm-40) REVERT: D 51 ASP cc_start: 0.7542 (p0) cc_final: 0.7295 (p0) REVERT: H 34 LYS cc_start: 0.7917 (mptt) cc_final: 0.7653 (mmtp) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.9694 time to fit residues: 125.3300 Evaluate side-chains 101 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 0.1980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.0020 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 125 GLN F 25 ASN ** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.147723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.097975 restraints weight = 15549.558| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.25 r_work: 0.2910 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12930 Z= 0.147 Angle : 0.525 5.532 18716 Z= 0.324 Chirality : 0.040 0.159 2132 Planarity : 0.004 0.036 1347 Dihedral : 29.963 79.814 4058 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.94 % Allowed : 9.84 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.32), residues: 748 helix: 3.03 (0.23), residues: 509 sheet: None (None), residues: 0 loop : -1.75 (0.34), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 42 TYR 0.006 0.001 TYR F 51 PHE 0.008 0.001 PHE D 70 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.15 (12930) covalent geometry : angle 0.52486 / 0.32 (18716) hydrogen bonds : bond 0.07162 / 4.77 ( 516) hydrogen bonds : angle 2.88901 / 2.05 ( 1395) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 102 time to evaluate : 0.319 Fit side-chains REVERT: C 104 GLN cc_start: 0.8709 (mm-40) cc_final: 0.8456 (mm-40) REVERT: D 51 ASP cc_start: 0.7920 (p0) cc_final: 0.7489 (p0) REVERT: H 34 LYS cc_start: 0.8072 (mptt) cc_final: 0.7780 (mmtp) outliers start: 6 outliers final: 4 residues processed: 105 average time/residue: 0.9127 time to fit residues: 101.1921 Evaluate side-chains 101 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 97 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain H residue 122 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 21 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 86 optimal weight: 30.0000 chunk 79 optimal weight: 9.9990 chunk 23 optimal weight: 0.8980 chunk 45 optimal weight: 0.0870 chunk 94 optimal weight: 9.9990 chunk 7 optimal weight: 0.0470 chunk 39 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.148425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.098950 restraints weight = 15644.829| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.21 r_work: 0.2929 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12930 Z= 0.138 Angle : 0.474 5.085 18716 Z= 0.296 Chirality : 0.037 0.166 2132 Planarity : 0.003 0.035 1347 Dihedral : 30.114 82.921 4058 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.41 % Allowed : 11.41 % Favored : 87.19 % 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: 2.62 (0.32), residues: 748 helix: 3.13 (0.23), residues: 511 sheet: None (None), residues: 0 loop : -1.64 (0.34), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 86 TYR 0.006 0.001 TYR D 121 PHE 0.007 0.001 PHE B 61 HIS 0.002 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.14 (12930) covalent geometry : angle 0.47448 / 0.30 (18716) hydrogen bonds : bond 0.06133 / 4.12 ( 516) hydrogen bonds : angle 2.70587 / 1.92 ( 1395) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.323 Fit side-chains REVERT: A 120 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8312 (mtt) REVERT: C 104 GLN cc_start: 0.8701 (mm-40) cc_final: 0.8443 (mm-40) REVERT: D 51 ASP cc_start: 0.7907 (p0) cc_final: 0.7494 (p0) REVERT: H 34 LYS cc_start: 0.8059 (mptt) cc_final: 0.7748 (mmtp) REVERT: H 93 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.7877 (mp0) outliers start: 9 outliers final: 6 residues processed: 108 average time/residue: 0.8927 time to fit residues: 101.8489 Evaluate side-chains 106 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 93 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 80 optimal weight: 9.9990 chunk 27 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 79 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 2 optimal weight: 0.0570 chunk 41 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 overall best weight: 0.9502 ------------------------------------------------------------------------------- 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 = 0.3775 r_free = 0.3775 target = 0.145781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.095784 restraints weight = 15792.979| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.25 r_work: 0.2882 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12930 Z= 0.150 Angle : 0.494 4.864 18716 Z= 0.302 Chirality : 0.038 0.148 2132 Planarity : 0.004 0.036 1347 Dihedral : 30.122 84.482 4058 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.34 % Allowed : 11.41 % Favored : 86.25 % 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: 2.57 (0.32), residues: 748 helix: 3.11 (0.23), residues: 509 sheet: None (None), residues: 0 loop : -1.67 (0.35), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 42 TYR 0.008 0.001 TYR D 121 PHE 0.009 0.001 PHE B 61 HIS 0.003 0.001 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.15 (12930) covalent geometry : angle 0.49356 / 0.30 (18716) hydrogen bonds : bond 0.06872 / 4.62 ( 516) hydrogen bonds : angle 2.73671 / 1.95 ( 1395) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.332 Fit side-chains REVERT: A 120 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8484 (mtt) REVERT: C 104 GLN cc_start: 0.8757 (mm-40) cc_final: 0.8505 (mm-40) REVERT: D 51 ASP cc_start: 0.7935 (p0) cc_final: 0.7501 (p0) REVERT: H 34 LYS cc_start: 0.8115 (mptt) cc_final: 0.7899 (mmtp) REVERT: H 93 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7784 (mp0) outliers start: 15 outliers final: 7 residues processed: 108 average time/residue: 0.9263 time to fit residues: 105.4336 Evaluate side-chains 106 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 122 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 24 optimal weight: 0.9990 chunk 89 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 85 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 90 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 chunk 88 optimal weight: 10.0000 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.146041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.095971 restraints weight = 15776.687| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.24 r_work: 0.2881 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12930 Z= 0.149 Angle : 0.491 4.971 18716 Z= 0.300 Chirality : 0.038 0.165 2132 Planarity : 0.004 0.037 1347 Dihedral : 30.165 85.183 4058 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.19 % Allowed : 12.19 % Favored : 85.62 % 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: 2.53 (0.32), residues: 748 helix: 3.07 (0.23), residues: 509 sheet: None (None), residues: 0 loop : -1.65 (0.35), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 42 TYR 0.008 0.001 TYR D 121 PHE 0.009 0.001 PHE B 61 HIS 0.002 0.001 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.15 (12930) covalent geometry : angle 0.49082 / 0.30 (18716) hydrogen bonds : bond 0.06805 / 4.60 ( 516) hydrogen bonds : angle 2.72725 / 1.94 ( 1395) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.285 Fit side-chains REVERT: A 120 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8447 (mtt) REVERT: A 129 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8370 (tpt-90) REVERT: C 104 GLN cc_start: 0.8750 (mm-40) cc_final: 0.8505 (mm-40) REVERT: D 51 ASP cc_start: 0.7935 (p0) cc_final: 0.7506 (p0) REVERT: D 93 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7177 (mp0) REVERT: H 34 LYS cc_start: 0.8121 (mptt) cc_final: 0.7905 (mmtp) REVERT: H 93 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.7766 (mp0) outliers start: 14 outliers final: 8 residues processed: 109 average time/residue: 0.8870 time to fit residues: 102.2075 Evaluate side-chains 113 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 122 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.0970 chunk 31 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 85 optimal weight: 20.0000 chunk 50 optimal weight: 0.9980 chunk 82 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 70 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 95 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3779 r_free = 0.3779 target = 0.146162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.096230 restraints weight = 15733.630| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.24 r_work: 0.2885 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12930 Z= 0.140 Angle : 0.486 4.879 18716 Z= 0.298 Chirality : 0.037 0.184 2132 Planarity : 0.003 0.037 1347 Dihedral : 30.161 85.167 4058 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.03 % Allowed : 13.12 % Favored : 84.84 % 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: 2.59 (0.32), residues: 748 helix: 3.12 (0.23), residues: 509 sheet: None (None), residues: 0 loop : -1.62 (0.35), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 42 TYR 0.007 0.001 TYR D 121 PHE 0.009 0.001 PHE B 61 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.14 (12930) covalent geometry : angle 0.48560 / 0.30 (18716) hydrogen bonds : bond 0.06623 / 4.47 ( 516) hydrogen bonds : angle 2.72487 / 1.94 ( 1395) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.318 Fit side-chains REVERT: A 120 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8439 (mtt) REVERT: A 129 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8360 (tpt-90) REVERT: C 24 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8044 (mp10) REVERT: C 104 GLN cc_start: 0.8747 (mm-40) cc_final: 0.8501 (mm-40) REVERT: D 51 ASP cc_start: 0.7938 (p0) cc_final: 0.7505 (p0) REVERT: D 93 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7171 (mp0) REVERT: H 34 LYS cc_start: 0.8122 (mptt) cc_final: 0.7905 (mmtp) REVERT: H 93 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.7761 (mp0) outliers start: 13 outliers final: 8 residues processed: 110 average time/residue: 0.8494 time to fit residues: 98.7441 Evaluate side-chains 116 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 122 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 70 optimal weight: 0.5980 chunk 98 optimal weight: 10.9990 chunk 22 optimal weight: 0.9990 chunk 8 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 = 0.3782 r_free = 0.3782 target = 0.146372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.096512 restraints weight = 15690.059| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.24 r_work: 0.2889 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12930 Z= 0.140 Angle : 0.483 4.938 18716 Z= 0.297 Chirality : 0.037 0.179 2132 Planarity : 0.003 0.037 1347 Dihedral : 30.153 85.167 4058 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.03 % Allowed : 12.81 % Favored : 85.16 % 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: 2.59 (0.32), residues: 748 helix: 3.11 (0.23), residues: 509 sheet: None (None), residues: 0 loop : -1.60 (0.35), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 42 TYR 0.007 0.001 TYR D 121 PHE 0.009 0.001 PHE B 61 HIS 0.002 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.14 (12930) covalent geometry : angle 0.48293 / 0.30 (18716) hydrogen bonds : bond 0.06550 / 4.42 ( 516) hydrogen bonds : angle 2.70917 / 1.93 ( 1395) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.322 Fit side-chains REVERT: A 120 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8433 (mtt) REVERT: A 129 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8360 (tpt-90) REVERT: C 24 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8030 (mp10) REVERT: C 104 GLN cc_start: 0.8737 (mm-40) cc_final: 0.8489 (mm-40) REVERT: D 51 ASP cc_start: 0.7930 (p0) cc_final: 0.7501 (p0) REVERT: D 93 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7170 (mp0) REVERT: H 34 LYS cc_start: 0.8115 (mptt) cc_final: 0.7899 (mmtp) REVERT: H 93 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7752 (mp0) outliers start: 13 outliers final: 7 residues processed: 110 average time/residue: 0.8977 time to fit residues: 104.3922 Evaluate side-chains 113 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 122 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 54 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 82 optimal weight: 10.0000 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3779 r_free = 0.3779 target = 0.146137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.096256 restraints weight = 15664.924| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.23 r_work: 0.2886 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12930 Z= 0.146 Angle : 0.487 4.955 18716 Z= 0.298 Chirality : 0.037 0.166 2132 Planarity : 0.004 0.039 1347 Dihedral : 30.133 85.445 4058 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.81 % Allowed : 12.34 % Favored : 84.84 % 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: 2.57 (0.32), residues: 748 helix: 3.09 (0.23), residues: 509 sheet: None (None), residues: 0 loop : -1.61 (0.35), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 42 TYR 0.008 0.001 TYR D 121 PHE 0.009 0.001 PHE B 61 HIS 0.002 0.001 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.15 (12930) covalent geometry : angle 0.48723 / 0.30 (18716) hydrogen bonds : bond 0.06594 / 4.45 ( 516) hydrogen bonds : angle 2.69373 / 1.92 ( 1395) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.277 Fit side-chains REVERT: A 120 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.8445 (mtt) REVERT: A 129 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8374 (tpt-90) REVERT: C 24 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8009 (mp10) REVERT: C 104 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8512 (mm-40) REVERT: D 51 ASP cc_start: 0.7956 (p0) cc_final: 0.7534 (p0) REVERT: D 71 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.8001 (tp30) REVERT: D 93 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7164 (mp0) REVERT: H 34 LYS cc_start: 0.8107 (mptt) cc_final: 0.7904 (mmtp) REVERT: H 93 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.7750 (mp0) outliers start: 18 outliers final: 9 residues processed: 109 average time/residue: 0.8848 time to fit residues: 101.8579 Evaluate side-chains 116 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 122 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 62 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 chunk 71 optimal weight: 0.9980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3781 r_free = 0.3781 target = 0.146282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.096418 restraints weight = 15658.436| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.22 r_work: 0.2886 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12930 Z= 0.143 Angle : 0.484 4.946 18716 Z= 0.296 Chirality : 0.037 0.167 2132 Planarity : 0.004 0.038 1347 Dihedral : 30.137 85.446 4058 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.34 % Allowed : 12.81 % Favored : 84.84 % 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: 2.58 (0.32), residues: 748 helix: 3.11 (0.23), residues: 509 sheet: None (None), residues: 0 loop : -1.61 (0.35), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 42 TYR 0.008 0.001 TYR D 121 PHE 0.009 0.001 PHE B 61 HIS 0.002 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.14 (12930) covalent geometry : angle 0.48445 / 0.30 (18716) hydrogen bonds : bond 0.06555 / 4.43 ( 516) hydrogen bonds : angle 2.68746 / 1.91 ( 1395) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.321 Fit side-chains REVERT: A 120 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8446 (mtt) REVERT: A 129 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8372 (tpt-90) REVERT: C 24 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8006 (mp10) REVERT: C 104 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8507 (mm-40) REVERT: D 51 ASP cc_start: 0.7958 (p0) cc_final: 0.7534 (p0) REVERT: D 71 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7991 (tp30) REVERT: D 93 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7167 (mp0) REVERT: H 34 LYS cc_start: 0.8112 (mptt) cc_final: 0.7910 (mmtp) REVERT: H 93 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.7752 (mp0) outliers start: 15 outliers final: 9 residues processed: 108 average time/residue: 0.8826 time to fit residues: 100.7514 Evaluate side-chains 116 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 62 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 99 optimal weight: 20.0000 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 86 optimal weight: 40.0000 chunk 34 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3791 r_free = 0.3791 target = 0.146853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.096818 restraints weight = 15365.844| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.22 r_work: 0.2895 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12930 Z= 0.146 Angle : 0.488 4.951 18716 Z= 0.297 Chirality : 0.037 0.172 2132 Planarity : 0.003 0.038 1347 Dihedral : 30.175 85.501 4058 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.34 % Allowed : 12.97 % Favored : 84.69 % 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: 2.56 (0.32), residues: 748 helix: 3.09 (0.23), residues: 509 sheet: None (None), residues: 0 loop : -1.61 (0.35), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 42 TYR 0.014 0.001 TYR B 88 PHE 0.009 0.001 PHE B 61 HIS 0.002 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.15 (12930) covalent geometry : angle 0.48847 / 0.30 (18716) hydrogen bonds : bond 0.06599 / 4.46 ( 516) hydrogen bonds : angle 2.68183 / 1.91 ( 1395) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.317 Fit side-chains REVERT: A 120 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8461 (mtt) REVERT: A 129 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8377 (tpt-90) REVERT: C 24 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.7965 (mp10) REVERT: C 104 GLN cc_start: 0.8737 (mm-40) cc_final: 0.8488 (mm-40) REVERT: D 51 ASP cc_start: 0.7958 (p0) cc_final: 0.7547 (p0) REVERT: D 71 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7939 (tp30) REVERT: D 93 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7165 (mp0) REVERT: H 93 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7758 (mp0) outliers start: 15 outliers final: 7 residues processed: 109 average time/residue: 0.8576 time to fit residues: 98.8323 Evaluate side-chains 115 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 59 optimal weight: 0.1980 chunk 45 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 82 optimal weight: 9.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3794 r_free = 0.3794 target = 0.147101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.097048 restraints weight = 15436.514| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.20 r_work: 0.2896 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12930 Z= 0.137 Angle : 0.486 6.077 18716 Z= 0.296 Chirality : 0.037 0.174 2132 Planarity : 0.003 0.038 1347 Dihedral : 30.173 85.477 4058 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.19 % Allowed : 13.28 % Favored : 84.53 % 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: 2.59 (0.32), residues: 748 helix: 3.11 (0.23), residues: 509 sheet: None (None), residues: 0 loop : -1.59 (0.35), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 42 TYR 0.007 0.001 TYR D 121 PHE 0.009 0.001 PHE B 61 HIS 0.002 0.001 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.14 (12930) covalent geometry : angle 0.48604 / 0.30 (18716) hydrogen bonds : bond 0.06445 / 4.36 ( 516) hydrogen bonds : angle 2.68637 / 1.91 ( 1395) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4154.54 seconds wall clock time: 71 minutes 13.81 seconds (4273.81 seconds total)