Starting phenix.real_space_refine on Tue Jun 10 15:30:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tan_25777/06_2025/7tan_25777.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tan_25777/06_2025/7tan_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7tan_25777/06_2025/7tan_25777.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tan_25777/06_2025/7tan_25777.map" model { file = "/net/cci-nas-00/data/ceres_data/7tan_25777/06_2025/7tan_25777.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tan_25777/06_2025/7tan_25777.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.41, per 1000 atoms: 0.69 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: 3.13 Conformation dependent library (CDL) restraints added in 936.5 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: 5.09 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: 3.96 Time building geometry restraints manager: 3.39 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=" C GLU G 61 " pdb=" O GLU G 61 " ideal model delta sigma weight residual 1.236 1.248 -0.011 1.15e-02 7.56e+03 9.21e-01 bond pdb=" CB ARG B 92 " pdb=" CG ARG B 92 " ideal model delta sigma weight residual 1.520 1.493 0.027 3.00e-02 1.11e+03 8.19e-01 bond pdb=" C ASN B 64 " pdb=" O ASN B 64 " ideal model delta sigma weight residual 1.236 1.246 -0.010 1.15e-02 7.56e+03 7.16e-01 bond pdb=" CA ASP B 24 " pdb=" CB ASP B 24 " ideal model delta sigma weight residual 1.530 1.544 -0.014 1.69e-02 3.50e+03 6.80e-01 bond pdb=" C GLY A 102 " pdb=" O GLY A 102 " ideal model delta sigma weight residual 1.234 1.243 -0.009 1.20e-02 6.94e+03 5.97e-01 ... (remaining 12925 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 18268 1.28 - 2.55: 412 2.55 - 3.83: 27 3.83 - 5.11: 8 5.11 - 6.38: 1 Bond angle restraints: 18716 Sorted by residual: angle pdb=" C ARG B 23 " pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta sigma weight residual 121.54 127.92 -6.38 1.91e+00 2.74e-01 1.12e+01 angle pdb=" C SER L 388 " pdb=" N ARG L 389 " pdb=" CA ARG L 389 " ideal model delta sigma weight residual 121.56 124.96 -3.40 1.56e+00 4.11e-01 4.74e+00 angle pdb=" N ARG L 389 " pdb=" CA ARG L 389 " pdb=" C ARG L 389 " ideal model delta sigma weight residual 110.42 113.42 -3.00 1.46e+00 4.69e-01 4.23e+00 angle pdb=" CA ASP B 24 " pdb=" CB ASP B 24 " pdb=" CG ASP B 24 " ideal model delta sigma weight residual 112.60 114.44 -1.84 1.00e+00 1.00e+00 3.38e+00 angle pdb=" C SER K 388 " pdb=" N ARG K 389 " pdb=" CA ARG K 389 " ideal model delta sigma weight residual 122.82 125.37 -2.55 1.42e+00 4.96e-01 3.22e+00 ... (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: 1793 0.040 - 0.081: 285 0.081 - 0.121: 49 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: 16.730 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: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 33.160 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 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:12.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 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 : 0.003 0.030 12930 Z= 0.161 Angle : 0.469 6.382 18716 Z= 0.283 Chirality : 0.031 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.003 0.001 HIS G 31 PHE 0.008 0.001 PHE B 61 TYR 0.008 0.001 TYR B 51 ARG 0.005 0.000 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.19398 ( 516) hydrogen bonds : angle 5.97015 ( 1395) covalent geometry : bond 0.00348 (12930) covalent geometry : angle 0.46936 (18716) *********************** 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 : 0.891 Fit side-chains REVERT: C 104 GLN cc_start: 0.8357 (mm-40) cc_final: 0.8096 (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: 2.2031 time to fit residues: 284.4331 Evaluate side-chains 100 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3798 r_free = 0.3798 target = 0.147270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.097710 restraints weight = 15514.584| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.22 r_work: 0.2909 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1236 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= 0.154 Angle : 0.471 4.785 18716 Z= 0.288 Chirality : 0.031 0.140 2132 Planarity : 0.003 0.037 1347 Dihedral : 29.699 80.113 4058 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.56 % Allowed : 9.84 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.32), residues: 748 helix: 3.02 (0.23), residues: 509 sheet: None (None), residues: 0 loop : -1.75 (0.33), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.008 0.001 PHE B 61 TYR 0.007 0.001 TYR D 121 ARG 0.005 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.06213 ( 516) hydrogen bonds : angle 2.73971 ( 1395) covalent geometry : bond 0.00324 (12930) covalent geometry : angle 0.47088 (18716) *********************** 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 111 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 1.345 Fit side-chains REVERT: A 129 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8447 (tpt-90) REVERT: C 104 GLN cc_start: 0.8712 (mm-40) cc_final: 0.8462 (mm-40) REVERT: D 51 ASP cc_start: 0.7906 (p0) cc_final: 0.7494 (p0) REVERT: H 34 LYS cc_start: 0.8062 (mptt) cc_final: 0.7764 (mmtp) outliers start: 10 outliers final: 6 residues processed: 106 average time/residue: 2.3116 time to fit residues: 258.1202 Evaluate side-chains 102 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ARG 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 114 VAL 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 27 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 50 optimal weight: 0.0570 chunk 47 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 26 optimal weight: 0.0770 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN D 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.147197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.097659 restraints weight = 15770.541| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.25 r_work: 0.2906 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1511 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= 0.148 Angle : 0.449 4.958 18716 Z= 0.276 Chirality : 0.030 0.133 2132 Planarity : 0.003 0.036 1347 Dihedral : 29.643 82.724 4058 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.56 % Allowed : 11.09 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.32), residues: 748 helix: 3.11 (0.23), residues: 509 sheet: None (None), residues: 0 loop : -1.65 (0.34), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 82 PHE 0.008 0.001 PHE B 61 TYR 0.007 0.001 TYR D 121 ARG 0.003 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.05976 ( 516) hydrogen bonds : angle 2.65492 ( 1395) covalent geometry : bond 0.00311 (12930) covalent geometry : angle 0.44939 (18716) *********************** 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: 10 poor density : 103 time to evaluate : 1.078 Fit side-chains REVERT: A 129 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.8381 (tpt-90) REVERT: C 104 GLN cc_start: 0.8725 (mm-40) cc_final: 0.8484 (mm-40) REVERT: D 51 ASP cc_start: 0.7923 (p0) cc_final: 0.7486 (p0) REVERT: H 34 LYS cc_start: 0.8107 (mptt) cc_final: 0.7802 (mmtp) REVERT: H 93 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.7784 (mp0) outliers start: 10 outliers final: 5 residues processed: 107 average time/residue: 2.5335 time to fit residues: 285.3542 Evaluate side-chains 105 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 91 GLU 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 97 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 25 optimal weight: 0.0570 chunk 59 optimal weight: 0.0570 chunk 20 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 18 optimal weight: 0.0370 overall best weight: 0.3694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.146729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.097628 restraints weight = 15668.497| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.22 r_work: 0.2913 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12930 Z= 0.139 Angle : 0.448 5.544 18716 Z= 0.276 Chirality : 0.029 0.158 2132 Planarity : 0.003 0.036 1347 Dihedral : 29.643 82.787 4058 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.72 % Allowed : 12.50 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.32), residues: 748 helix: 3.18 (0.23), residues: 511 sheet: None (None), residues: 0 loop : -1.57 (0.35), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.008 0.001 PHE B 61 TYR 0.006 0.001 TYR F 51 ARG 0.005 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.05608 ( 516) hydrogen bonds : angle 2.65696 ( 1395) covalent geometry : bond 0.00278 (12930) covalent geometry : angle 0.44801 (18716) *********************** 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 113 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 1.108 Fit side-chains REVERT: A 129 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8383 (tpt-90) REVERT: C 104 GLN cc_start: 0.8714 (mm-40) cc_final: 0.8471 (mm-40) REVERT: D 51 ASP cc_start: 0.7871 (p0) cc_final: 0.7455 (p0) REVERT: H 34 LYS cc_start: 0.8098 (mptt) cc_final: 0.7794 (mmtp) REVERT: H 93 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.7772 (mp0) outliers start: 11 outliers final: 5 residues processed: 105 average time/residue: 2.0589 time to fit residues: 227.6841 Evaluate side-chains 108 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 18 SER 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 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 82 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 99 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 chunk 53 optimal weight: 0.0270 chunk 30 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.1642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.144422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.094361 restraints weight = 15558.057| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.23 r_work: 0.2853 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12930 Z= 0.180 Angle : 0.485 5.022 18716 Z= 0.294 Chirality : 0.032 0.149 2132 Planarity : 0.004 0.037 1347 Dihedral : 29.712 85.737 4058 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.19 % Allowed : 12.81 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.32), residues: 748 helix: 3.05 (0.23), residues: 509 sheet: None (None), residues: 0 loop : -1.66 (0.35), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 113 PHE 0.010 0.002 PHE B 61 TYR 0.009 0.001 TYR D 121 ARG 0.006 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.07305 ( 516) hydrogen bonds : angle 2.77656 ( 1395) covalent geometry : bond 0.00397 (12930) covalent geometry : angle 0.48462 (18716) *********************** 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 116 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 1.107 Fit side-chains REVERT: A 129 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8392 (tpt-90) REVERT: C 24 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8092 (mp10) REVERT: C 75 LYS cc_start: 0.8662 (mptt) cc_final: 0.8249 (mmtm) REVERT: C 104 GLN cc_start: 0.8763 (mm-40) cc_final: 0.8519 (mm-40) REVERT: D 51 ASP cc_start: 0.7935 (p0) cc_final: 0.7504 (p0) REVERT: D 108 LYS cc_start: 0.7866 (mtmt) cc_final: 0.7661 (mttm) REVERT: H 93 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.7787 (mp0) outliers start: 14 outliers final: 8 residues processed: 107 average time/residue: 2.2413 time to fit residues: 254.1543 Evaluate side-chains 112 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 122 THR Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 36 LYS 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 44 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 61 optimal weight: 0.0670 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.145115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.095183 restraints weight = 15804.486| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.24 r_work: 0.2865 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12930 Z= 0.156 Angle : 0.473 4.965 18716 Z= 0.290 Chirality : 0.031 0.179 2132 Planarity : 0.003 0.037 1347 Dihedral : 29.707 85.707 4058 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.88 % Allowed : 13.75 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.32), residues: 748 helix: 3.09 (0.23), residues: 509 sheet: None (None), residues: 0 loop : -1.63 (0.35), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 113 PHE 0.009 0.001 PHE B 61 TYR 0.008 0.001 TYR D 121 ARG 0.001 0.000 ARG E 131 Details of bonding type rmsd hydrogen bonds : bond 0.06889 ( 516) hydrogen bonds : angle 2.78935 ( 1395) covalent geometry : bond 0.00323 (12930) covalent geometry : angle 0.47317 (18716) *********************** 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 114 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.886 Fit side-chains REVERT: A 120 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8512 (mtt) REVERT: A 129 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8385 (tpt-90) REVERT: C 24 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8102 (mp10) REVERT: C 75 LYS cc_start: 0.8672 (mptt) cc_final: 0.8240 (mmtm) REVERT: C 104 GLN cc_start: 0.8758 (mm-40) cc_final: 0.8505 (mm-40) REVERT: D 51 ASP cc_start: 0.7939 (p0) cc_final: 0.7510 (p0) REVERT: H 93 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7777 (mp0) outliers start: 12 outliers final: 8 residues processed: 107 average time/residue: 1.8245 time to fit residues: 206.0413 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 : 0.847 ------------------------------------------------------------------------------- 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 122 THR Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 36 LYS 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 5 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 99 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 32 optimal weight: 0.0870 overall best weight: 1.5364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.143985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.093774 restraints weight = 15399.201| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.23 r_work: 0.2837 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12930 Z= 0.210 Angle : 0.515 5.134 18716 Z= 0.310 Chirality : 0.034 0.172 2132 Planarity : 0.004 0.038 1347 Dihedral : 29.821 88.129 4058 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.81 % Allowed : 12.97 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.31), residues: 748 helix: 2.88 (0.23), residues: 509 sheet: None (None), residues: 0 loop : -1.73 (0.35), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 113 PHE 0.011 0.002 PHE B 61 TYR 0.011 0.002 TYR D 121 ARG 0.007 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.08040 ( 516) hydrogen bonds : angle 2.85076 ( 1395) covalent geometry : bond 0.00476 (12930) covalent geometry : angle 0.51476 (18716) *********************** 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 122 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 1.032 Fit side-chains REVERT: A 129 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8410 (tpt-90) REVERT: C 24 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8051 (mp10) REVERT: C 104 GLN cc_start: 0.8779 (mm-40) cc_final: 0.8535 (mm-40) REVERT: D 51 ASP cc_start: 0.8001 (p0) cc_final: 0.7590 (p0) REVERT: H 93 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.7832 (mp0) outliers start: 18 outliers final: 9 residues processed: 111 average time/residue: 2.0247 time to fit residues: 237.0305 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 : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 59 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.144225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.093926 restraints weight = 15565.531| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.23 r_work: 0.2840 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12930 Z= 0.176 Angle : 0.502 5.004 18716 Z= 0.305 Chirality : 0.032 0.186 2132 Planarity : 0.004 0.039 1347 Dihedral : 29.817 88.072 4058 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.88 % Allowed : 14.22 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.31), residues: 748 helix: 2.89 (0.23), residues: 509 sheet: None (None), residues: 0 loop : -1.73 (0.35), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 113 PHE 0.010 0.002 PHE B 61 TYR 0.009 0.001 TYR D 121 ARG 0.009 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.07660 ( 516) hydrogen bonds : angle 2.86364 ( 1395) covalent geometry : bond 0.00378 (12930) covalent geometry : angle 0.50189 (18716) *********************** 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 112 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 1.104 Fit side-chains REVERT: A 129 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8396 (tpt-90) REVERT: C 24 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8025 (mp10) REVERT: C 104 GLN cc_start: 0.8774 (mm-40) cc_final: 0.8526 (mm-40) REVERT: D 51 ASP cc_start: 0.7994 (p0) cc_final: 0.7585 (p0) REVERT: H 93 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7816 (mp0) outliers start: 12 outliers final: 9 residues processed: 107 average time/residue: 2.0974 time to fit residues: 236.9018 Evaluate side-chains 112 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 59 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 41 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 8 optimal weight: 0.3980 chunk 23 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 27 optimal weight: 0.4980 chunk 78 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 69 optimal weight: 0.0670 chunk 5 optimal weight: 0.6980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.144773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.094968 restraints weight = 15506.197| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.22 r_work: 0.2856 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12930 Z= 0.152 Angle : 0.491 7.065 18716 Z= 0.299 Chirality : 0.031 0.190 2132 Planarity : 0.004 0.038 1347 Dihedral : 29.805 87.935 4058 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.03 % Allowed : 14.38 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.32), residues: 748 helix: 2.96 (0.23), residues: 509 sheet: None (None), residues: 0 loop : -1.70 (0.35), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 113 PHE 0.009 0.001 PHE B 61 TYR 0.008 0.001 TYR D 121 ARG 0.010 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.07191 ( 516) hydrogen bonds : angle 2.87427 ( 1395) covalent geometry : bond 0.00300 (12930) covalent geometry : angle 0.49050 (18716) *********************** 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 115 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.889 Fit side-chains REVERT: A 129 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8391 (tpt-90) REVERT: C 24 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8021 (mp10) REVERT: C 104 GLN cc_start: 0.8758 (mm-40) cc_final: 0.8510 (mm-40) REVERT: D 51 ASP cc_start: 0.8002 (p0) cc_final: 0.7597 (p0) REVERT: H 93 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7803 (mp0) outliers start: 13 outliers final: 9 residues processed: 109 average time/residue: 2.0233 time to fit residues: 232.8133 Evaluate side-chains 111 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 46 LYS Chi-restraints excluded: chain D residue 59 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 18 optimal weight: 3.9990 chunk 54 optimal weight: 0.0670 chunk 69 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 8 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.8722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.144831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.094826 restraints weight = 15310.376| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.23 r_work: 0.2860 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1914 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= 0.165 Angle : 0.490 5.656 18716 Z= 0.299 Chirality : 0.032 0.188 2132 Planarity : 0.004 0.038 1347 Dihedral : 29.789 87.859 4058 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.03 % Allowed : 14.38 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.32), residues: 748 helix: 2.96 (0.23), residues: 509 sheet: None (None), residues: 0 loop : -1.70 (0.35), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 113 PHE 0.009 0.001 PHE B 61 TYR 0.009 0.001 TYR D 121 ARG 0.007 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.07293 ( 516) hydrogen bonds : angle 2.81087 ( 1395) covalent geometry : bond 0.00349 (12930) covalent geometry : angle 0.48984 (18716) ********************** 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 113 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 1.049 Fit side-chains REVERT: A 40 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.7947 (tpt90) REVERT: A 129 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8392 (tpt-90) REVERT: C 24 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8014 (mp10) REVERT: C 104 GLN cc_start: 0.8759 (mm-40) cc_final: 0.8509 (mm-40) REVERT: D 51 ASP cc_start: 0.8002 (p0) cc_final: 0.7594 (p0) REVERT: H 93 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.7805 (mp0) outliers start: 13 outliers final: 7 residues processed: 107 average time/residue: 2.9845 time to fit residues: 337.6019 Evaluate side-chains 111 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ARG 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 46 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 63 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 19 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.144850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.094816 restraints weight = 15339.648| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.23 r_work: 0.2857 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 12930 Z= 0.172 Angle : 0.492 6.376 18716 Z= 0.300 Chirality : 0.032 0.187 2132 Planarity : 0.004 0.039 1347 Dihedral : 29.781 87.814 4058 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.03 % Allowed : 14.38 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.32), residues: 748 helix: 2.96 (0.23), residues: 509 sheet: None (None), residues: 0 loop : -1.71 (0.35), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 113 PHE 0.010 0.001 PHE B 61 TYR 0.009 0.001 TYR D 121 ARG 0.007 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.07300 ( 516) hydrogen bonds : angle 2.80068 ( 1395) covalent geometry : bond 0.00371 (12930) covalent geometry : angle 0.49242 (18716) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9454.77 seconds wall clock time: 168 minutes 51.57 seconds (10131.57 seconds total)