Starting phenix.real_space_refine on Tue Mar 11 18:43:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j58_35983/03_2025/8j58_35983.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j58_35983/03_2025/8j58_35983.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j58_35983/03_2025/8j58_35983.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j58_35983/03_2025/8j58_35983.map" model { file = "/net/cci-nas-00/data/ceres_data/8j58_35983/03_2025/8j58_35983.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j58_35983/03_2025/8j58_35983.cif" } resolution = 3.15 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= 0.015 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: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 4409 2.51 5 N 1072 2.21 5 O 1161 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6666 Number of models: 1 Model: "" Number of chains: 10 Chain: "1" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 550 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "2" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 560 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "3" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 550 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "4" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 550 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "5" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 550 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "6" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 550 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "7" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 550 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "8" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 550 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "9" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 550 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "a" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1706 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 9, 'TRANS': 210} Chain breaks: 2 Time building chain proxies: 7.34, per 1000 atoms: 1.10 Number of scatterers: 6666 At special positions: 0 Unit cell: (71.54, 91.98, 79.57, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 1161 8.00 N 1072 7.00 C 4409 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: 1.60 Conformation dependent library (CDL) restraints added in 981.6 milliseconds 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1586 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 1 sheets defined 89.6% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain '1' and resid 2 through 42 removed outlier: 3.751A pdb=" N ALA 1 34 " --> pdb=" O VAL 1 30 " (cutoff:3.500A) Processing helix chain '1' and resid 43 through 46 Processing helix chain '1' and resid 47 through 48 No H-bonds generated for 'chain '1' and resid 47 through 48' Processing helix chain '1' and resid 49 through 77 Processing helix chain '2' and resid 3 through 42 removed outlier: 3.788A pdb=" N ALA 2 34 " --> pdb=" O VAL 2 30 " (cutoff:3.500A) Processing helix chain '2' and resid 45 through 76 removed outlier: 4.605A pdb=" N THR 2 51 " --> pdb=" O GLY 2 47 " (cutoff:3.500A) Proline residue: 2 52 - end of helix Processing helix chain '3' and resid 3 through 42 removed outlier: 3.722A pdb=" N ALA 3 34 " --> pdb=" O VAL 3 30 " (cutoff:3.500A) Processing helix chain '3' and resid 44 through 77 removed outlier: 4.036A pdb=" N ARG 3 48 " --> pdb=" O GLU 3 44 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N THR 3 51 " --> pdb=" O GLY 3 47 " (cutoff:3.500A) Proline residue: 3 52 - end of helix removed outlier: 3.740A pdb=" N ALA 3 62 " --> pdb=" O GLY 3 58 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA 3 63 " --> pdb=" O LEU 3 59 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TYR 3 64 " --> pdb=" O VAL 3 60 " (cutoff:3.500A) Processing helix chain '4' and resid 3 through 42 removed outlier: 3.831A pdb=" N ALA 4 34 " --> pdb=" O VAL 4 30 " (cutoff:3.500A) Processing helix chain '4' and resid 45 through 77 removed outlier: 4.520A pdb=" N THR 4 51 " --> pdb=" O GLY 4 47 " (cutoff:3.500A) Proline residue: 4 52 - end of helix removed outlier: 3.588A pdb=" N ALA 4 63 " --> pdb=" O LEU 4 59 " (cutoff:3.500A) Processing helix chain '5' and resid 3 through 42 removed outlier: 3.839A pdb=" N ALA 5 34 " --> pdb=" O VAL 5 30 " (cutoff:3.500A) Processing helix chain '5' and resid 45 through 77 removed outlier: 4.880A pdb=" N THR 5 51 " --> pdb=" O GLY 5 47 " (cutoff:3.500A) Proline residue: 5 52 - end of helix removed outlier: 3.536A pdb=" N ALA 5 63 " --> pdb=" O LEU 5 59 " (cutoff:3.500A) Processing helix chain '6' and resid 3 through 42 removed outlier: 3.697A pdb=" N ALA 6 34 " --> pdb=" O VAL 6 30 " (cutoff:3.500A) Processing helix chain '6' and resid 45 through 77 removed outlier: 4.074A pdb=" N THR 6 51 " --> pdb=" O GLY 6 47 " (cutoff:3.500A) Proline residue: 6 52 - end of helix removed outlier: 3.611A pdb=" N ASN 6 67 " --> pdb=" O ALA 6 63 " (cutoff:3.500A) Processing helix chain '7' and resid 3 through 42 removed outlier: 3.796A pdb=" N ALA 7 34 " --> pdb=" O VAL 7 30 " (cutoff:3.500A) Processing helix chain '7' and resid 45 through 77 removed outlier: 4.713A pdb=" N THR 7 51 " --> pdb=" O GLY 7 47 " (cutoff:3.500A) Proline residue: 7 52 - end of helix removed outlier: 3.548A pdb=" N ALA 7 63 " --> pdb=" O LEU 7 59 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR 7 64 " --> pdb=" O VAL 7 60 " (cutoff:3.500A) Processing helix chain '8' and resid 3 through 42 removed outlier: 3.832A pdb=" N ALA 8 34 " --> pdb=" O VAL 8 30 " (cutoff:3.500A) Processing helix chain '8' and resid 45 through 77 removed outlier: 3.637A pdb=" N PHE 8 50 " --> pdb=" O GLN 8 46 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N THR 8 51 " --> pdb=" O GLY 8 47 " (cutoff:3.500A) Proline residue: 8 52 - end of helix removed outlier: 3.545A pdb=" N ALA 8 63 " --> pdb=" O LEU 8 59 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR 8 64 " --> pdb=" O VAL 8 60 " (cutoff:3.500A) Processing helix chain '9' and resid 3 through 42 removed outlier: 3.788A pdb=" N ALA 9 34 " --> pdb=" O VAL 9 30 " (cutoff:3.500A) Processing helix chain '9' and resid 45 through 77 removed outlier: 3.536A pdb=" N PHE 9 50 " --> pdb=" O GLN 9 46 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N THR 9 51 " --> pdb=" O GLY 9 47 " (cutoff:3.500A) Proline residue: 9 52 - end of helix removed outlier: 3.592A pdb=" N ALA 9 63 " --> pdb=" O LEU 9 59 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR 9 64 " --> pdb=" O VAL 9 60 " (cutoff:3.500A) Processing helix chain 'a' and resid 29 through 50 Processing helix chain 'a' and resid 58 through 79 removed outlier: 3.748A pdb=" N SER a 77 " --> pdb=" O ASN a 73 " (cutoff:3.500A) Processing helix chain 'a' and resid 86 through 104 removed outlier: 3.811A pdb=" N LEU a 90 " --> pdb=" O PHE a 86 " (cutoff:3.500A) Processing helix chain 'a' and resid 105 through 107 No H-bonds generated for 'chain 'a' and resid 105 through 107' Processing helix chain 'a' and resid 124 through 128 Processing helix chain 'a' and resid 129 through 152 removed outlier: 4.226A pdb=" N LEU a 135 " --> pdb=" O TYR a 131 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL a 139 " --> pdb=" O LEU a 135 " (cutoff:3.500A) Processing helix chain 'a' and resid 165 through 167 No H-bonds generated for 'chain 'a' and resid 165 through 167' Processing helix chain 'a' and resid 168 through 201 removed outlier: 4.036A pdb=" N ASN a 172 " --> pdb=" O LEU a 168 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU a 173 " --> pdb=" O ALA a 169 " (cutoff:3.500A) Proline residue: a 180 - end of helix removed outlier: 3.600A pdb=" N GLY a 194 " --> pdb=" O ASN a 190 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA a 199 " --> pdb=" O GLY a 195 " (cutoff:3.500A) Processing helix chain 'a' and resid 202 through 204 No H-bonds generated for 'chain 'a' and resid 202 through 204' Processing helix chain 'a' and resid 205 through 244 removed outlier: 4.383A pdb=" N TRP a 210 " --> pdb=" O PRO a 206 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ALA a 211 " --> pdb=" O TYR a 207 " (cutoff:3.500A) Proline residue: a 212 - end of helix Processing sheet with id=AA1, first strand: chain 'a' and resid 17 through 19 652 hydrogen bonds defined for protein. 1947 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.23 Time building geometry restraints manager: 1.92 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: 1351 1.33 - 1.45: 1497 1.45 - 1.57: 3912 1.57 - 1.70: 0 1.70 - 1.82: 47 Bond restraints: 6807 Sorted by residual: bond pdb=" C ALA a 49 " pdb=" N LYS a 50 " ideal model delta sigma weight residual 1.330 1.437 -0.107 1.52e-02 4.33e+03 4.99e+01 bond pdb=" C TRP a 149 " pdb=" N ARG a 150 " ideal model delta sigma weight residual 1.334 1.395 -0.061 1.33e-02 5.65e+03 2.08e+01 bond pdb=" CE1 HIS a 144 " pdb=" NE2 HIS a 144 " ideal model delta sigma weight residual 1.321 1.362 -0.041 1.00e-02 1.00e+04 1.72e+01 bond pdb=" C GLY 3 47 " pdb=" N ARG 3 48 " ideal model delta sigma weight residual 1.331 1.272 0.059 1.43e-02 4.89e+03 1.71e+01 bond pdb=" CE1 HIS a 164 " pdb=" NE2 HIS a 164 " ideal model delta sigma weight residual 1.321 1.362 -0.041 1.00e-02 1.00e+04 1.67e+01 ... (remaining 6802 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 7593 2.16 - 4.33: 1588 4.33 - 6.49: 86 6.49 - 8.65: 2 8.65 - 10.81: 1 Bond angle restraints: 9270 Sorted by residual: angle pdb=" C TYR a 131 " pdb=" N VAL a 132 " pdb=" CA VAL a 132 " ideal model delta sigma weight residual 122.66 111.85 10.81 9.70e-01 1.06e+00 1.24e+02 angle pdb=" O ALA a 49 " pdb=" C ALA a 49 " pdb=" N LYS a 50 " ideal model delta sigma weight residual 122.07 130.59 -8.52 1.03e+00 9.43e-01 6.84e+01 angle pdb=" CA PHE a 204 " pdb=" C PHE a 204 " pdb=" N PRO a 205 " ideal model delta sigma weight residual 118.23 123.83 -5.60 9.20e-01 1.18e+00 3.70e+01 angle pdb=" O GLY 6 47 " pdb=" C GLY 6 47 " pdb=" N ARG 6 48 " ideal model delta sigma weight residual 122.18 127.29 -5.11 9.60e-01 1.09e+00 2.84e+01 angle pdb=" N TYR a 131 " pdb=" CA TYR a 131 " pdb=" C TYR a 131 " ideal model delta sigma weight residual 112.87 106.60 6.27 1.20e+00 6.94e-01 2.73e+01 ... (remaining 9265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 3521 16.87 - 33.73: 261 33.73 - 50.60: 31 50.60 - 67.46: 23 67.46 - 84.33: 2 Dihedral angle restraints: 3838 sinusoidal: 1317 harmonic: 2521 Sorted by residual: dihedral pdb=" CA ALA 5 77 " pdb=" C ALA 5 77 " pdb=" N THR 5 78 " pdb=" CA THR 5 78 " ideal model delta harmonic sigma weight residual -180.00 -158.70 -21.30 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" C THR 3 51 " pdb=" N THR 3 51 " pdb=" CA THR 3 51 " pdb=" CB THR 3 51 " ideal model delta harmonic sigma weight residual -122.00 -131.69 9.69 0 2.50e+00 1.60e-01 1.50e+01 dihedral pdb=" C LEU a 245 " pdb=" N LEU a 245 " pdb=" CA LEU a 245 " pdb=" CB LEU a 245 " ideal model delta harmonic sigma weight residual -122.60 -131.91 9.31 0 2.50e+00 1.60e-01 1.39e+01 ... (remaining 3835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 614 0.067 - 0.134: 348 0.134 - 0.201: 96 0.201 - 0.269: 39 0.269 - 0.336: 9 Chirality restraints: 1106 Sorted by residual: chirality pdb=" CA PRO 4 79 " pdb=" N PRO 4 79 " pdb=" C PRO 4 79 " pdb=" CB PRO 4 79 " both_signs ideal model delta sigma weight residual False 2.72 2.38 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA THR 3 51 " pdb=" N THR 3 51 " pdb=" C THR 3 51 " pdb=" CB THR 3 51 " both_signs ideal model delta sigma weight residual False 2.53 2.21 0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CA PHE 3 54 " pdb=" N PHE 3 54 " pdb=" C PHE 3 54 " pdb=" CB PHE 3 54 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 1103 not shown) Planarity restraints: 1191 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP a 216 " 0.159 2.00e-02 2.50e+03 7.86e-02 1.54e+02 pdb=" CG TRP a 216 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP a 216 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP a 216 " -0.078 2.00e-02 2.50e+03 pdb=" NE1 TRP a 216 " -0.037 2.00e-02 2.50e+03 pdb=" CE2 TRP a 216 " -0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP a 216 " -0.099 2.00e-02 2.50e+03 pdb=" CZ2 TRP a 216 " 0.092 2.00e-02 2.50e+03 pdb=" CZ3 TRP a 216 " -0.030 2.00e-02 2.50e+03 pdb=" CH2 TRP a 216 " 0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP a 103 " -0.108 2.00e-02 2.50e+03 5.49e-02 7.54e+01 pdb=" CG TRP a 103 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TRP a 103 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP a 103 " 0.050 2.00e-02 2.50e+03 pdb=" NE1 TRP a 103 " 0.031 2.00e-02 2.50e+03 pdb=" CE2 TRP a 103 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP a 103 " 0.070 2.00e-02 2.50e+03 pdb=" CZ2 TRP a 103 " -0.069 2.00e-02 2.50e+03 pdb=" CZ3 TRP a 103 " 0.027 2.00e-02 2.50e+03 pdb=" CH2 TRP a 103 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP a 210 " -0.094 2.00e-02 2.50e+03 4.69e-02 5.49e+01 pdb=" CG TRP a 210 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP a 210 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TRP a 210 " 0.034 2.00e-02 2.50e+03 pdb=" NE1 TRP a 210 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TRP a 210 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP a 210 " 0.062 2.00e-02 2.50e+03 pdb=" CZ2 TRP a 210 " -0.056 2.00e-02 2.50e+03 pdb=" CZ3 TRP a 210 " 0.024 2.00e-02 2.50e+03 pdb=" CH2 TRP a 210 " -0.045 2.00e-02 2.50e+03 ... (remaining 1188 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 276 2.75 - 3.29: 7400 3.29 - 3.82: 11124 3.82 - 4.36: 14496 4.36 - 4.90: 24135 Nonbonded interactions: 57431 Sorted by model distance: nonbonded pdb=" CD1 ILE a 79 " pdb=" CE MET a 243 " model vdw 2.208 3.880 nonbonded pdb=" N THR a 52 " pdb=" OE1 GLN a 61 " model vdw 2.452 3.120 nonbonded pdb=" N GLU 3 44 " pdb=" OE1 GLU 3 44 " model vdw 2.472 3.120 nonbonded pdb=" O ASP 9 2 " pdb=" N ILE 9 5 " model vdw 2.487 3.120 nonbonded pdb=" OE1 GLN 6 42 " pdb=" NH2 ARG 6 48 " model vdw 2.488 3.120 ... (remaining 57426 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 '1' selection = (chain '2' and resid 2 through 80) selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' } 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: 13.080 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.660 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 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:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 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 : 0.012 0.107 6807 Z= 0.783 Angle : 1.613 10.813 9270 Z= 1.163 Chirality : 0.092 0.336 1106 Planarity : 0.015 0.121 1191 Dihedral : 13.092 84.329 2252 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % 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: -1.50 (0.25), residues: 908 helix: -0.50 (0.16), residues: 765 sheet: None (None), residues: 0 loop : -3.01 (0.46), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.159 0.033 TRP a 216 HIS 0.014 0.003 HIS a 15 PHE 0.067 0.012 PHE a 192 TYR 0.057 0.009 TYR 7 64 ARG 0.009 0.001 ARG 3 41 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.646 Fit side-chains revert: symmetry clash REVERT: 1 17 MET cc_start: 0.8433 (mmm) cc_final: 0.8111 (mmt) REVERT: 2 17 MET cc_start: 0.8152 (mmm) cc_final: 0.7836 (mmp) REVERT: 4 71 MET cc_start: 0.8446 (tmm) cc_final: 0.8213 (tmm) REVERT: 5 71 MET cc_start: 0.9038 (tmm) cc_final: 0.8824 (tmm) REVERT: a 79 ILE cc_start: 0.7053 (pt) cc_final: 0.6792 (tp) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.1590 time to fit residues: 33.1119 Evaluate side-chains 113 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 26 optimal weight: 0.1980 chunk 40 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 42 GLN a 15 HIS a 172 ASN ** a 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.158296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.115643 restraints weight = 8104.187| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.02 r_work: 0.3341 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6807 Z= 0.230 Angle : 0.632 7.958 9270 Z= 0.330 Chirality : 0.044 0.157 1106 Planarity : 0.006 0.044 1191 Dihedral : 4.108 25.697 960 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.43 % Allowed : 10.33 % Favored : 88.24 % 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: 1.95 (0.28), residues: 908 helix: 1.67 (0.18), residues: 821 sheet: None (None), residues: 0 loop : -2.30 (0.62), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP a 216 HIS 0.004 0.001 HIS a 15 PHE 0.018 0.002 PHE a 192 TYR 0.024 0.002 TYR a 143 ARG 0.003 0.001 ARG 5 41 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 0.710 Fit side-chains REVERT: 1 17 MET cc_start: 0.9044 (mmm) cc_final: 0.8757 (mmt) REVERT: 6 41 ARG cc_start: 0.8362 (ttt180) cc_final: 0.8039 (ttt-90) REVERT: 6 71 MET cc_start: 0.8924 (tmm) cc_final: 0.8683 (tmm) REVERT: 7 42 GLN cc_start: 0.7608 (pp30) cc_final: 0.7312 (pp30) REVERT: a 43 LEU cc_start: 0.5971 (mt) cc_final: 0.5726 (mp) REVERT: a 176 GLU cc_start: 0.7867 (mp0) cc_final: 0.7607 (mp0) REVERT: a 201 ILE cc_start: 0.7683 (tp) cc_final: 0.7328 (tt) outliers start: 9 outliers final: 4 residues processed: 129 average time/residue: 0.1809 time to fit residues: 31.3605 Evaluate side-chains 110 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 106 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 78 THR Chi-restraints excluded: chain a residue 109 VAL Chi-restraints excluded: chain a residue 182 SER Chi-restraints excluded: chain a residue 223 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 44 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 34 optimal weight: 0.0970 chunk 5 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 42 GLN a 227 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.156322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.113468 restraints weight = 8223.456| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.04 r_work: 0.3338 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6807 Z= 0.212 Angle : 0.601 6.998 9270 Z= 0.304 Chirality : 0.042 0.167 1106 Planarity : 0.005 0.050 1191 Dihedral : 3.988 25.055 960 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.91 % Allowed : 12.08 % Favored : 86.01 % 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: 2.92 (0.29), residues: 908 helix: 2.31 (0.18), residues: 821 sheet: None (None), residues: 0 loop : -1.97 (0.66), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP a 216 HIS 0.001 0.000 HIS a 16 PHE 0.017 0.002 PHE a 192 TYR 0.022 0.001 TYR a 143 ARG 0.003 0.000 ARG 1 41 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.650 Fit side-chains REVERT: 1 17 MET cc_start: 0.9067 (mmm) cc_final: 0.8785 (mmt) REVERT: 6 71 MET cc_start: 0.8985 (tmm) cc_final: 0.8739 (tmm) REVERT: 7 42 GLN cc_start: 0.7474 (pp30) cc_final: 0.7088 (pp30) REVERT: 9 61 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8556 (mm-30) REVERT: a 43 LEU cc_start: 0.6110 (mt) cc_final: 0.5848 (mp) REVERT: a 47 LEU cc_start: 0.6670 (tp) cc_final: 0.6439 (tt) REVERT: a 176 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7558 (mp0) REVERT: a 201 ILE cc_start: 0.7652 (tp) cc_final: 0.7411 (tt) outliers start: 12 outliers final: 8 residues processed: 116 average time/residue: 0.1881 time to fit residues: 29.2009 Evaluate side-chains 108 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 78 THR Chi-restraints excluded: chain 2 residue 78 THR Chi-restraints excluded: chain a residue 23 MET Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 102 ASN Chi-restraints excluded: chain a residue 109 VAL Chi-restraints excluded: chain a residue 176 GLU Chi-restraints excluded: chain a residue 182 SER Chi-restraints excluded: chain a residue 223 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 31 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.153138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.110292 restraints weight = 8368.466| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.02 r_work: 0.3273 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6807 Z= 0.263 Angle : 0.621 7.698 9270 Z= 0.312 Chirality : 0.043 0.171 1106 Planarity : 0.005 0.051 1191 Dihedral : 3.999 24.451 960 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.23 % Allowed : 13.99 % Favored : 83.78 % 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: 3.15 (0.28), residues: 908 helix: 2.57 (0.18), residues: 772 sheet: None (None), residues: 0 loop : -0.93 (0.54), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP a 216 HIS 0.002 0.001 HIS a 164 PHE 0.014 0.002 PHE a 192 TYR 0.022 0.002 TYR a 131 ARG 0.006 0.001 ARG 8 41 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.686 Fit side-chains revert: symmetry clash REVERT: 3 67 ASN cc_start: 0.8715 (m-40) cc_final: 0.8439 (m-40) REVERT: 6 71 MET cc_start: 0.9038 (tmm) cc_final: 0.8796 (tmm) REVERT: 7 42 GLN cc_start: 0.7524 (pp30) cc_final: 0.6706 (pm20) REVERT: a 201 ILE cc_start: 0.7676 (tp) cc_final: 0.7427 (tt) outliers start: 14 outliers final: 8 residues processed: 118 average time/residue: 0.1941 time to fit residues: 30.4653 Evaluate side-chains 110 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 78 THR Chi-restraints excluded: chain 2 residue 78 THR Chi-restraints excluded: chain a residue 23 MET Chi-restraints excluded: chain a residue 31 LEU Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 109 VAL Chi-restraints excluded: chain a residue 176 GLU Chi-restraints excluded: chain a residue 182 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 35 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3988 r_free = 0.3988 target = 0.161684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.122120 restraints weight = 8241.103| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.89 r_work: 0.3360 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6807 Z= 0.200 Angle : 0.593 8.552 9270 Z= 0.292 Chirality : 0.042 0.180 1106 Planarity : 0.005 0.049 1191 Dihedral : 3.887 23.171 960 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.07 % Allowed : 15.26 % Favored : 82.67 % 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: 3.47 (0.28), residues: 908 helix: 2.81 (0.18), residues: 772 sheet: None (None), residues: 0 loop : -0.98 (0.53), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 216 HIS 0.001 0.000 HIS a 164 PHE 0.012 0.001 PHE a 63 TYR 0.021 0.001 TYR a 143 ARG 0.006 0.000 ARG 8 41 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.621 Fit side-chains REVERT: 4 42 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.8502 (pt0) REVERT: 7 42 GLN cc_start: 0.7467 (pp30) cc_final: 0.7085 (pp30) REVERT: 7 71 MET cc_start: 0.9015 (ttp) cc_final: 0.8569 (ttp) REVERT: a 167 LEU cc_start: 0.1860 (OUTLIER) cc_final: 0.1589 (tp) REVERT: a 176 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7480 (mp0) REVERT: a 201 ILE cc_start: 0.7697 (tp) cc_final: 0.7434 (tt) outliers start: 13 outliers final: 6 residues processed: 113 average time/residue: 0.2140 time to fit residues: 31.6573 Evaluate side-chains 99 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 78 THR Chi-restraints excluded: chain 2 residue 78 THR Chi-restraints excluded: chain 3 residue 80 VAL Chi-restraints excluded: chain 4 residue 5 ILE Chi-restraints excluded: chain 4 residue 42 GLN Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 167 LEU Chi-restraints excluded: chain a residue 176 GLU Chi-restraints excluded: chain a residue 182 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 81 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 chunk 61 optimal weight: 0.0570 chunk 4 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 = 0.4001 r_free = 0.4001 target = 0.162912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.123479 restraints weight = 8120.056| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.87 r_work: 0.3379 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6807 Z= 0.186 Angle : 0.591 8.561 9270 Z= 0.289 Chirality : 0.041 0.190 1106 Planarity : 0.004 0.044 1191 Dihedral : 3.773 22.843 960 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.75 % Allowed : 16.69 % Favored : 81.56 % 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: 3.70 (0.28), residues: 908 helix: 2.95 (0.18), residues: 773 sheet: None (None), residues: 0 loop : -0.87 (0.54), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP a 216 HIS 0.001 0.000 HIS a 164 PHE 0.015 0.001 PHE 4 70 TYR 0.021 0.002 TYR a 143 ARG 0.006 0.001 ARG 1 41 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.674 Fit side-chains REVERT: 7 42 GLN cc_start: 0.7378 (OUTLIER) cc_final: 0.6710 (pm20) REVERT: a 167 LEU cc_start: 0.1850 (OUTLIER) cc_final: 0.1649 (tp) REVERT: a 176 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7385 (mp0) REVERT: a 201 ILE cc_start: 0.7690 (tp) cc_final: 0.7418 (tt) outliers start: 11 outliers final: 5 residues processed: 108 average time/residue: 0.1858 time to fit residues: 26.9133 Evaluate side-chains 100 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 78 THR Chi-restraints excluded: chain 2 residue 78 THR Chi-restraints excluded: chain 3 residue 80 VAL Chi-restraints excluded: chain 7 residue 42 GLN Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 167 LEU Chi-restraints excluded: chain a residue 176 GLU Chi-restraints excluded: chain a residue 182 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 58 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 72 optimal weight: 0.3980 chunk 84 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 47 optimal weight: 0.0370 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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 = 0.3989 r_free = 0.3989 target = 0.157774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.115418 restraints weight = 8156.126| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.02 r_work: 0.3368 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6807 Z= 0.186 Angle : 0.598 8.770 9270 Z= 0.291 Chirality : 0.041 0.200 1106 Planarity : 0.004 0.044 1191 Dihedral : 3.759 22.029 960 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.07 % Allowed : 16.69 % Favored : 81.24 % 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: 3.72 (0.28), residues: 908 helix: 2.97 (0.18), residues: 773 sheet: None (None), residues: 0 loop : -0.89 (0.55), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP a 216 HIS 0.001 0.000 HIS a 164 PHE 0.011 0.001 PHE a 63 TYR 0.021 0.001 TYR a 143 ARG 0.005 0.001 ARG 8 41 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.657 Fit side-chains REVERT: 4 42 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8493 (pt0) REVERT: 7 42 GLN cc_start: 0.7400 (OUTLIER) cc_final: 0.7192 (pm20) REVERT: a 81 MET cc_start: 0.7207 (tpt) cc_final: 0.6645 (tpp) REVERT: a 176 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7376 (mp0) REVERT: a 201 ILE cc_start: 0.7608 (tp) cc_final: 0.7369 (tt) outliers start: 13 outliers final: 8 residues processed: 103 average time/residue: 0.1863 time to fit residues: 25.5852 Evaluate side-chains 101 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 78 THR Chi-restraints excluded: chain 2 residue 5 ILE Chi-restraints excluded: chain 2 residue 78 THR Chi-restraints excluded: chain 3 residue 80 VAL Chi-restraints excluded: chain 4 residue 5 ILE Chi-restraints excluded: chain 4 residue 42 GLN Chi-restraints excluded: chain 7 residue 42 GLN Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 176 GLU Chi-restraints excluded: chain a residue 182 SER Chi-restraints excluded: chain a residue 184 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 4 optimal weight: 0.0060 chunk 13 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 67 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.157739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.115932 restraints weight = 8144.486| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.00 r_work: 0.3358 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6807 Z= 0.195 Angle : 0.611 9.024 9270 Z= 0.296 Chirality : 0.041 0.207 1106 Planarity : 0.004 0.041 1191 Dihedral : 3.734 21.960 960 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.91 % Allowed : 16.85 % Favored : 81.24 % 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: 3.74 (0.28), residues: 908 helix: 2.98 (0.18), residues: 773 sheet: None (None), residues: 0 loop : -0.84 (0.55), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP a 216 HIS 0.001 0.000 HIS a 164 PHE 0.016 0.001 PHE 1 70 TYR 0.021 0.001 TYR a 143 ARG 0.005 0.000 ARG 8 41 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.721 Fit side-chains REVERT: 1 67 ASN cc_start: 0.9054 (OUTLIER) cc_final: 0.8833 (t0) REVERT: 3 61 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7849 (mm-30) REVERT: 4 42 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8508 (pt0) REVERT: 7 42 GLN cc_start: 0.7402 (OUTLIER) cc_final: 0.6734 (pm20) REVERT: 7 71 MET cc_start: 0.8886 (ttp) cc_final: 0.8653 (ttp) REVERT: a 81 MET cc_start: 0.7189 (tpt) cc_final: 0.6667 (tpp) REVERT: a 176 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7349 (mp0) REVERT: a 201 ILE cc_start: 0.7633 (tp) cc_final: 0.7365 (tt) outliers start: 12 outliers final: 7 residues processed: 102 average time/residue: 0.1917 time to fit residues: 26.0058 Evaluate side-chains 103 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 67 ASN Chi-restraints excluded: chain 1 residue 78 THR Chi-restraints excluded: chain 2 residue 5 ILE Chi-restraints excluded: chain 2 residue 78 THR Chi-restraints excluded: chain 3 residue 80 VAL Chi-restraints excluded: chain 4 residue 42 GLN Chi-restraints excluded: chain 7 residue 42 GLN Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 176 GLU Chi-restraints excluded: chain a residue 182 SER Chi-restraints excluded: chain a residue 184 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 39 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 33 optimal weight: 0.4980 chunk 75 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 67 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.157447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.115573 restraints weight = 8185.154| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.99 r_work: 0.3359 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6807 Z= 0.200 Angle : 0.629 8.934 9270 Z= 0.303 Chirality : 0.041 0.211 1106 Planarity : 0.004 0.041 1191 Dihedral : 3.768 22.102 960 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.91 % Allowed : 17.01 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.73 (0.28), residues: 908 helix: 2.98 (0.18), residues: 773 sheet: None (None), residues: 0 loop : -0.88 (0.54), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP a 216 HIS 0.001 0.000 HIS a 164 PHE 0.017 0.001 PHE 4 70 TYR 0.021 0.002 TYR a 143 ARG 0.009 0.001 ARG 9 48 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.553 Fit side-chains REVERT: 1 67 ASN cc_start: 0.9057 (OUTLIER) cc_final: 0.8806 (t0) REVERT: 7 42 GLN cc_start: 0.7390 (OUTLIER) cc_final: 0.6802 (pm20) REVERT: 7 71 MET cc_start: 0.8887 (ttp) cc_final: 0.8635 (ttt) REVERT: a 81 MET cc_start: 0.7210 (tpt) cc_final: 0.6666 (tpp) REVERT: a 176 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7341 (mp0) REVERT: a 201 ILE cc_start: 0.7567 (tp) cc_final: 0.7297 (tt) outliers start: 12 outliers final: 8 residues processed: 103 average time/residue: 0.2058 time to fit residues: 27.8732 Evaluate side-chains 106 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 67 ASN Chi-restraints excluded: chain 1 residue 78 THR Chi-restraints excluded: chain 2 residue 5 ILE Chi-restraints excluded: chain 2 residue 78 THR Chi-restraints excluded: chain 3 residue 80 VAL Chi-restraints excluded: chain 7 residue 42 GLN Chi-restraints excluded: chain 7 residue 80 VAL Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 176 GLU Chi-restraints excluded: chain a residue 182 SER Chi-restraints excluded: chain a residue 184 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 26 optimal weight: 0.9990 chunk 68 optimal weight: 8.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 7 optimal weight: 0.0980 chunk 18 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 67 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.158198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.116304 restraints weight = 8283.106| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.99 r_work: 0.3365 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6807 Z= 0.194 Angle : 0.633 9.044 9270 Z= 0.305 Chirality : 0.041 0.204 1106 Planarity : 0.004 0.042 1191 Dihedral : 3.773 21.746 960 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.75 % Allowed : 16.69 % Favored : 81.56 % 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: 3.70 (0.28), residues: 908 helix: 2.96 (0.18), residues: 773 sheet: None (None), residues: 0 loop : -0.93 (0.54), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP a 216 HIS 0.001 0.000 HIS a 164 PHE 0.015 0.001 PHE 1 70 TYR 0.021 0.001 TYR a 143 ARG 0.008 0.001 ARG 9 48 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.851 Fit side-chains REVERT: 1 67 ASN cc_start: 0.9020 (OUTLIER) cc_final: 0.8800 (t0) REVERT: 7 17 MET cc_start: 0.8799 (mmm) cc_final: 0.8496 (mmm) REVERT: 7 71 MET cc_start: 0.8906 (ttp) cc_final: 0.8575 (ttt) REVERT: a 47 LEU cc_start: 0.6779 (tp) cc_final: 0.6561 (tt) REVERT: a 81 MET cc_start: 0.7229 (tpt) cc_final: 0.6708 (tpp) REVERT: a 176 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7331 (mp0) REVERT: a 201 ILE cc_start: 0.7479 (tp) cc_final: 0.7211 (tt) outliers start: 11 outliers final: 8 residues processed: 100 average time/residue: 0.2104 time to fit residues: 27.5817 Evaluate side-chains 103 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 67 ASN Chi-restraints excluded: chain 1 residue 78 THR Chi-restraints excluded: chain 2 residue 5 ILE Chi-restraints excluded: chain 2 residue 78 THR Chi-restraints excluded: chain 3 residue 80 VAL Chi-restraints excluded: chain 7 residue 80 VAL Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 176 GLU Chi-restraints excluded: chain a residue 182 SER Chi-restraints excluded: chain a residue 184 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 78 optimal weight: 0.0870 chunk 24 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 26 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.164935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.125368 restraints weight = 8206.546| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.86 r_work: 0.3386 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6807 Z= 0.193 Angle : 0.634 9.193 9270 Z= 0.306 Chirality : 0.041 0.199 1106 Planarity : 0.005 0.060 1191 Dihedral : 3.754 21.895 960 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.43 % Allowed : 17.17 % Favored : 81.40 % 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: 3.70 (0.28), residues: 908 helix: 2.98 (0.18), residues: 773 sheet: None (None), residues: 0 loop : -1.07 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP a 216 HIS 0.001 0.000 HIS a 164 PHE 0.015 0.001 PHE 1 70 TYR 0.021 0.002 TYR a 143 ARG 0.008 0.001 ARG 9 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4353.09 seconds wall clock time: 74 minutes 56.12 seconds (4496.12 seconds total)