Starting phenix.real_space_refine on Tue Mar 11 18:11:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6tar_10425/03_2025/6tar_10425.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tar_10425/03_2025/6tar_10425.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6tar_10425/03_2025/6tar_10425.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tar_10425/03_2025/6tar_10425.map" model { file = "/net/cci-nas-00/data/ceres_data/6tar_10425/03_2025/6tar_10425.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tar_10425/03_2025/6tar_10425.cif" } resolution = 2.8 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= 0.001 sd= 0.010 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 15 5.16 5 C 4270 2.51 5 N 1170 2.21 5 O 1260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 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: 6715 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1343 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 4, 'TRANS': 159} Restraints were copied for chains: C, B, E, D Time building chain proxies: 3.21, per 1000 atoms: 0.48 Number of scatterers: 6715 At special positions: 0 Unit cell: (117.467, 112.623, 60.55, 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 15 16.00 O 1260 8.00 N 1170 7.00 C 4270 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: 1.57 Conformation dependent library (CDL) restraints added in 1.1 seconds 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1530 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 0 sheets defined 68.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 57 through 76 removed outlier: 3.618A pdb=" N VAL A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY A 76 " --> pdb=" O LYS A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 85 removed outlier: 3.835A pdb=" N LYS A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 89 removed outlier: 3.540A pdb=" N LEU A 89 " --> pdb=" O ILE A 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 86 through 89' Processing helix chain 'A' and resid 92 through 102 removed outlier: 4.114A pdb=" N THR A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TRP A 97 " --> pdb=" O MET A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 108 through 119 Processing helix chain 'A' and resid 124 through 135 removed outlier: 4.032A pdb=" N ILE A 128 " --> pdb=" O PRO A 124 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN A 135 " --> pdb=" O GLU A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 154 removed outlier: 3.903A pdb=" N PHE A 146 " --> pdb=" O PRO A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 172 removed outlier: 3.560A pdb=" N GLU A 167 " --> pdb=" O ASP A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 181 Processing helix chain 'A' and resid 190 through 205 removed outlier: 3.550A pdb=" N LEU A 194 " --> pdb=" O THR A 190 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASN A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 76 removed outlier: 3.618A pdb=" N VAL B 61 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 85 removed outlier: 3.836A pdb=" N LYS B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 89 removed outlier: 3.540A pdb=" N LEU B 89 " --> pdb=" O ILE B 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 86 through 89' Processing helix chain 'B' and resid 92 through 102 removed outlier: 4.112A pdb=" N THR B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TRP B 97 " --> pdb=" O MET B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 105 No H-bonds generated for 'chain 'B' and resid 103 through 105' Processing helix chain 'B' and resid 108 through 119 Processing helix chain 'B' and resid 124 through 135 removed outlier: 4.032A pdb=" N ILE B 128 " --> pdb=" O PRO B 124 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN B 135 " --> pdb=" O GLU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 154 removed outlier: 3.903A pdb=" N PHE B 146 " --> pdb=" O PRO B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 172 removed outlier: 3.559A pdb=" N GLU B 167 " --> pdb=" O ASP B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 181 Processing helix chain 'B' and resid 190 through 205 removed outlier: 3.550A pdb=" N LEU B 194 " --> pdb=" O THR B 190 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASN B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 76 removed outlier: 3.618A pdb=" N VAL C 61 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY C 76 " --> pdb=" O LYS C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 85 removed outlier: 3.835A pdb=" N LYS C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 89 removed outlier: 3.540A pdb=" N LEU C 89 " --> pdb=" O ILE C 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 86 through 89' Processing helix chain 'C' and resid 92 through 102 removed outlier: 4.113A pdb=" N THR C 96 " --> pdb=" O GLY C 92 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TRP C 97 " --> pdb=" O MET C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 108 through 119 Processing helix chain 'C' and resid 124 through 135 removed outlier: 4.033A pdb=" N ILE C 128 " --> pdb=" O PRO C 124 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASN C 135 " --> pdb=" O GLU C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 154 removed outlier: 3.903A pdb=" N PHE C 146 " --> pdb=" O PRO C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 172 removed outlier: 3.559A pdb=" N GLU C 167 " --> pdb=" O ASP C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 181 Processing helix chain 'C' and resid 190 through 205 removed outlier: 3.551A pdb=" N LEU C 194 " --> pdb=" O THR C 190 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASN C 205 " --> pdb=" O ILE C 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 76 removed outlier: 3.617A pdb=" N VAL D 61 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY D 76 " --> pdb=" O LYS D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 85 removed outlier: 3.836A pdb=" N LYS D 84 " --> pdb=" O GLU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 89 removed outlier: 3.540A pdb=" N LEU D 89 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 86 through 89' Processing helix chain 'D' and resid 92 through 102 removed outlier: 4.114A pdb=" N THR D 96 " --> pdb=" O GLY D 92 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TRP D 97 " --> pdb=" O MET D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 105 No H-bonds generated for 'chain 'D' and resid 103 through 105' Processing helix chain 'D' and resid 108 through 119 Processing helix chain 'D' and resid 124 through 135 removed outlier: 4.032A pdb=" N ILE D 128 " --> pdb=" O PRO D 124 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN D 135 " --> pdb=" O GLU D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 154 removed outlier: 3.903A pdb=" N PHE D 146 " --> pdb=" O PRO D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 172 removed outlier: 3.559A pdb=" N GLU D 167 " --> pdb=" O ASP D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 181 Processing helix chain 'D' and resid 190 through 205 removed outlier: 3.551A pdb=" N LEU D 194 " --> pdb=" O THR D 190 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASN D 205 " --> pdb=" O ILE D 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 76 removed outlier: 3.617A pdb=" N VAL E 61 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY E 76 " --> pdb=" O LYS E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 85 removed outlier: 3.834A pdb=" N LYS E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 89 removed outlier: 3.540A pdb=" N LEU E 89 " --> pdb=" O ILE E 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 86 through 89' Processing helix chain 'E' and resid 92 through 102 removed outlier: 4.113A pdb=" N THR E 96 " --> pdb=" O GLY E 92 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TRP E 97 " --> pdb=" O MET E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 105 No H-bonds generated for 'chain 'E' and resid 103 through 105' Processing helix chain 'E' and resid 108 through 119 Processing helix chain 'E' and resid 124 through 135 removed outlier: 4.031A pdb=" N ILE E 128 " --> pdb=" O PRO E 124 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASN E 135 " --> pdb=" O GLU E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 154 removed outlier: 3.903A pdb=" N PHE E 146 " --> pdb=" O PRO E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 172 removed outlier: 3.560A pdb=" N GLU E 167 " --> pdb=" O ASP E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 181 Processing helix chain 'E' and resid 190 through 205 removed outlier: 3.549A pdb=" N LEU E 194 " --> pdb=" O THR E 190 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASN E 205 " --> pdb=" O ILE E 201 " (cutoff:3.500A) 295 hydrogen bonds defined for protein. 885 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: 1.70 Time building geometry restraints manager: 1.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2186 1.34 - 1.46: 1085 1.46 - 1.57: 3584 1.57 - 1.69: 0 1.69 - 1.80: 25 Bond restraints: 6880 Sorted by residual: bond pdb=" N PHE E 133 " pdb=" CA PHE E 133 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.31e-02 5.83e+03 5.94e+00 bond pdb=" N PHE C 133 " pdb=" CA PHE C 133 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.31e-02 5.83e+03 5.87e+00 bond pdb=" N PHE A 133 " pdb=" CA PHE A 133 " ideal model delta sigma weight residual 1.456 1.488 -0.031 1.31e-02 5.83e+03 5.70e+00 bond pdb=" N PHE B 133 " pdb=" CA PHE B 133 " ideal model delta sigma weight residual 1.456 1.488 -0.031 1.31e-02 5.83e+03 5.66e+00 bond pdb=" N PHE D 133 " pdb=" CA PHE D 133 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.31e-02 5.83e+03 5.50e+00 ... (remaining 6875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 8763 1.80 - 3.59: 437 3.59 - 5.39: 65 5.39 - 7.19: 10 7.19 - 8.98: 10 Bond angle restraints: 9285 Sorted by residual: angle pdb=" C HIS E 118 " pdb=" N PHE E 119 " pdb=" CA PHE E 119 " ideal model delta sigma weight residual 122.60 116.50 6.10 1.56e+00 4.11e-01 1.53e+01 angle pdb=" C HIS C 118 " pdb=" N PHE C 119 " pdb=" CA PHE C 119 " ideal model delta sigma weight residual 122.60 116.51 6.09 1.56e+00 4.11e-01 1.52e+01 angle pdb=" CA THR A 122 " pdb=" CB THR A 122 " pdb=" CG2 THR A 122 " ideal model delta sigma weight residual 110.50 117.13 -6.63 1.70e+00 3.46e-01 1.52e+01 angle pdb=" C PRO C 121 " pdb=" N THR C 122 " pdb=" CA THR C 122 " ideal model delta sigma weight residual 121.54 128.99 -7.45 1.91e+00 2.74e-01 1.52e+01 angle pdb=" CA THR D 122 " pdb=" CB THR D 122 " pdb=" CG2 THR D 122 " ideal model delta sigma weight residual 110.50 117.13 -6.63 1.70e+00 3.46e-01 1.52e+01 ... (remaining 9280 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.14: 3375 14.14 - 28.29: 480 28.29 - 42.43: 150 42.43 - 56.58: 35 56.58 - 70.72: 5 Dihedral angle restraints: 4045 sinusoidal: 1675 harmonic: 2370 Sorted by residual: dihedral pdb=" CA ASN E 44 " pdb=" CB ASN E 44 " pdb=" CG ASN E 44 " pdb=" OD1 ASN E 44 " ideal model delta sinusoidal sigma weight residual -90.00 -160.72 70.72 2 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CA ASN B 44 " pdb=" CB ASN B 44 " pdb=" CG ASN B 44 " pdb=" OD1 ASN B 44 " ideal model delta sinusoidal sigma weight residual -90.00 -160.67 70.67 2 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CA ASN C 44 " pdb=" CB ASN C 44 " pdb=" CG ASN C 44 " pdb=" OD1 ASN C 44 " ideal model delta sinusoidal sigma weight residual -90.00 -160.67 70.67 2 2.00e+01 2.50e-03 1.07e+01 ... (remaining 4042 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 785 0.062 - 0.123: 136 0.123 - 0.185: 44 0.185 - 0.246: 5 0.246 - 0.308: 10 Chirality restraints: 980 Sorted by residual: chirality pdb=" CB ILE C 183 " pdb=" CA ILE C 183 " pdb=" CG1 ILE C 183 " pdb=" CG2 ILE C 183 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CB ILE A 183 " pdb=" CA ILE A 183 " pdb=" CG1 ILE A 183 " pdb=" CG2 ILE A 183 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CB ILE E 183 " pdb=" CA ILE E 183 " pdb=" CG1 ILE E 183 " pdb=" CG2 ILE E 183 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 977 not shown) Planarity restraints: 1205 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 112 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.06e+00 pdb=" C ILE B 112 " 0.035 2.00e-02 2.50e+03 pdb=" O ILE B 112 " -0.013 2.00e-02 2.50e+03 pdb=" N ALA B 113 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 112 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.98e+00 pdb=" C ILE E 112 " -0.034 2.00e-02 2.50e+03 pdb=" O ILE E 112 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA E 113 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 112 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.94e+00 pdb=" C ILE A 112 " 0.034 2.00e-02 2.50e+03 pdb=" O ILE A 112 " -0.013 2.00e-02 2.50e+03 pdb=" N ALA A 113 " -0.012 2.00e-02 2.50e+03 ... (remaining 1202 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 2092 2.84 - 3.35: 5496 3.35 - 3.87: 9302 3.87 - 4.38: 9425 4.38 - 4.90: 17315 Nonbonded interactions: 43630 Sorted by model distance: nonbonded pdb=" O SER A 78 " pdb=" OG SER A 78 " model vdw 2.319 3.040 nonbonded pdb=" O SER D 78 " pdb=" OG SER D 78 " model vdw 2.319 3.040 nonbonded pdb=" O SER B 78 " pdb=" OG SER B 78 " model vdw 2.320 3.040 nonbonded pdb=" O SER C 78 " pdb=" OG SER C 78 " model vdw 2.320 3.040 nonbonded pdb=" O SER E 78 " pdb=" OG SER E 78 " model vdw 2.321 3.040 ... (remaining 43625 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } 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: 0.310 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: 0.060 Process input model: 18.540 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:14.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6880 Z= 0.334 Angle : 0.915 8.983 9285 Z= 0.574 Chirality : 0.060 0.308 980 Planarity : 0.006 0.041 1205 Dihedral : 14.526 70.721 2515 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 0.69 % Allowed : 10.14 % Favored : 89.17 % 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: -3.91 (0.23), residues: 810 helix: -1.87 (0.20), residues: 440 sheet: None (None), residues: 0 loop : -3.56 (0.23), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 108 HIS 0.004 0.001 HIS C 203 PHE 0.012 0.002 PHE D 45 TYR 0.016 0.002 TYR A 126 ARG 0.003 0.001 ARG C 185 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 123 time to evaluate : 0.772 Fit side-chains REVERT: A 45 PHE cc_start: 0.8601 (OUTLIER) cc_final: 0.8010 (t80) REVERT: A 141 ASP cc_start: 0.7559 (m-30) cc_final: 0.7262 (m-30) REVERT: B 103 LYS cc_start: 0.8453 (mttt) cc_final: 0.8200 (mtmm) REVERT: C 45 PHE cc_start: 0.9016 (OUTLIER) cc_final: 0.8695 (t80) REVERT: D 45 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.8216 (t80) REVERT: D 73 ASP cc_start: 0.8168 (t0) cc_final: 0.7944 (t0) REVERT: E 45 PHE cc_start: 0.8819 (OUTLIER) cc_final: 0.7568 (t80) outliers start: 5 outliers final: 0 residues processed: 128 average time/residue: 0.9553 time to fit residues: 130.0665 Evaluate side-chains 95 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 91 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain C residue 45 PHE Chi-restraints excluded: chain D residue 45 PHE Chi-restraints excluded: chain E residue 45 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 33 optimal weight: 0.2980 chunk 20 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 24 optimal weight: 0.2980 chunk 38 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN A 162 HIS A 203 HIS B 44 ASN B 162 HIS B 182 HIS C 44 ASN C 162 HIS C 203 HIS D 44 ASN D 149 GLN D 162 HIS D 203 HIS E 44 ASN E 162 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.117231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.104283 restraints weight = 11633.991| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.93 r_work: 0.3436 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 6880 Z= 0.210 Angle : 0.536 5.598 9285 Z= 0.298 Chirality : 0.042 0.233 980 Planarity : 0.004 0.025 1205 Dihedral : 5.641 48.146 888 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 3.47 % Allowed : 16.53 % Favored : 80.00 % 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: -1.64 (0.28), residues: 810 helix: 0.22 (0.25), residues: 445 sheet: None (None), residues: 0 loop : -2.87 (0.27), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 108 HIS 0.004 0.001 HIS B 182 PHE 0.013 0.001 PHE B 133 TYR 0.012 0.002 TYR A 126 ARG 0.003 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.730 Fit side-chains REVERT: A 73 ASP cc_start: 0.8768 (t0) cc_final: 0.8542 (t0) REVERT: A 141 ASP cc_start: 0.8200 (m-30) cc_final: 0.7889 (m-30) REVERT: B 182 HIS cc_start: 0.8301 (m-70) cc_final: 0.8053 (m170) REVERT: C 73 ASP cc_start: 0.8487 (t0) cc_final: 0.8224 (t0) REVERT: C 137 GLN cc_start: 0.8962 (tt0) cc_final: 0.8590 (tm-30) REVERT: D 137 GLN cc_start: 0.8695 (tt0) cc_final: 0.8167 (tm-30) outliers start: 25 outliers final: 12 residues processed: 128 average time/residue: 0.6801 time to fit residues: 94.7073 Evaluate side-chains 109 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain E residue 159 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 41 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 4 optimal weight: 0.0980 chunk 5 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 182 HIS E 182 HIS E 203 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.119598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.106797 restraints weight = 11726.336| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.90 r_work: 0.3440 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6880 Z= 0.172 Angle : 0.503 5.372 9285 Z= 0.272 Chirality : 0.042 0.245 980 Planarity : 0.003 0.023 1205 Dihedral : 4.111 14.366 880 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 4.17 % Allowed : 20.28 % Favored : 75.56 % 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: -0.78 (0.30), residues: 810 helix: 0.94 (0.26), residues: 455 sheet: None (None), residues: 0 loop : -2.60 (0.29), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 108 HIS 0.005 0.001 HIS C 118 PHE 0.022 0.001 PHE B 52 TYR 0.014 0.002 TYR B 179 ARG 0.002 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 0.715 Fit side-chains REVERT: A 73 ASP cc_start: 0.8723 (t0) cc_final: 0.8520 (t0) REVERT: A 101 VAL cc_start: 0.8591 (t) cc_final: 0.8202 (t) REVERT: A 141 ASP cc_start: 0.8226 (m-30) cc_final: 0.8004 (m-30) REVERT: B 73 ASP cc_start: 0.8579 (t0) cc_final: 0.8366 (t0) REVERT: B 154 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8432 (tp) REVERT: B 182 HIS cc_start: 0.8362 (m-70) cc_final: 0.8030 (m170) REVERT: C 73 ASP cc_start: 0.8544 (t0) cc_final: 0.8309 (t0) REVERT: D 73 ASP cc_start: 0.8499 (t0) cc_final: 0.8185 (t0) REVERT: D 174 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7829 (mt) REVERT: E 154 LEU cc_start: 0.8513 (tp) cc_final: 0.8112 (tp) outliers start: 30 outliers final: 16 residues processed: 123 average time/residue: 0.6261 time to fit residues: 84.5977 Evaluate side-chains 108 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain E residue 159 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 1 optimal weight: 0.0970 chunk 22 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 75 optimal weight: 0.0870 chunk 23 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 overall best weight: 1.2360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 118 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.117809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.104867 restraints weight = 11996.637| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 3.00 r_work: 0.3447 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6880 Z= 0.160 Angle : 0.485 5.160 9285 Z= 0.263 Chirality : 0.041 0.268 980 Planarity : 0.003 0.025 1205 Dihedral : 3.995 14.196 880 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 4.31 % Allowed : 21.94 % Favored : 73.75 % 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: -0.25 (0.31), residues: 810 helix: 1.41 (0.27), residues: 455 sheet: None (None), residues: 0 loop : -2.43 (0.29), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 108 HIS 0.003 0.000 HIS D 203 PHE 0.019 0.001 PHE B 52 TYR 0.016 0.002 TYR C 179 ARG 0.001 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 0.738 Fit side-chains REVERT: A 101 VAL cc_start: 0.8622 (t) cc_final: 0.8266 (t) REVERT: A 141 ASP cc_start: 0.8273 (m-30) cc_final: 0.8027 (m-30) REVERT: B 137 GLN cc_start: 0.8634 (tt0) cc_final: 0.8347 (tm-30) REVERT: B 154 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8323 (tp) REVERT: B 182 HIS cc_start: 0.8513 (m-70) cc_final: 0.8188 (m170) REVERT: C 137 GLN cc_start: 0.8938 (tm-30) cc_final: 0.8685 (tm-30) REVERT: D 73 ASP cc_start: 0.8589 (t0) cc_final: 0.8230 (t0) REVERT: D 137 GLN cc_start: 0.8667 (tm-30) cc_final: 0.8270 (tm-30) REVERT: D 174 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7759 (mt) REVERT: E 154 LEU cc_start: 0.8393 (tp) cc_final: 0.7966 (tp) outliers start: 31 outliers final: 19 residues processed: 128 average time/residue: 0.6302 time to fit residues: 88.4816 Evaluate side-chains 118 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain E residue 159 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 6 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN A 182 HIS B 156 GLN C 118 HIS C 182 HIS E 156 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.113016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.100567 restraints weight = 12051.071| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.89 r_work: 0.3365 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6880 Z= 0.285 Angle : 0.587 8.822 9285 Z= 0.316 Chirality : 0.046 0.296 980 Planarity : 0.003 0.026 1205 Dihedral : 4.478 14.339 880 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 5.56 % Allowed : 21.81 % Favored : 72.64 % 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: -0.73 (0.31), residues: 810 helix: 1.08 (0.25), residues: 475 sheet: None (None), residues: 0 loop : -2.98 (0.30), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 108 HIS 0.003 0.001 HIS C 182 PHE 0.015 0.002 PHE B 52 TYR 0.018 0.003 TYR D 179 ARG 0.002 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 121 time to evaluate : 0.818 Fit side-chains REVERT: A 101 VAL cc_start: 0.8668 (t) cc_final: 0.8451 (t) REVERT: A 141 ASP cc_start: 0.8130 (m-30) cc_final: 0.7864 (m-30) REVERT: A 205 ASN cc_start: 0.6799 (t0) cc_final: 0.5645 (m-40) REVERT: B 154 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8475 (tp) REVERT: B 182 HIS cc_start: 0.8413 (m-70) cc_final: 0.8131 (m170) REVERT: C 73 ASP cc_start: 0.8753 (t0) cc_final: 0.8437 (t0) REVERT: C 137 GLN cc_start: 0.9043 (tm-30) cc_final: 0.8722 (tm-30) REVERT: D 73 ASP cc_start: 0.8727 (t0) cc_final: 0.8479 (t0) outliers start: 40 outliers final: 22 residues processed: 151 average time/residue: 0.6403 time to fit residues: 105.9748 Evaluate side-chains 132 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 203 HIS Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 203 HIS Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 159 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 78 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 37 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 HIS B 149 GLN B 156 GLN C 99 GLN C 182 HIS D 149 GLN E 156 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.117966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.105396 restraints weight = 11857.606| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.85 r_work: 0.3452 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6880 Z= 0.150 Angle : 0.508 7.506 9285 Z= 0.271 Chirality : 0.042 0.310 980 Planarity : 0.003 0.027 1205 Dihedral : 4.019 14.478 880 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 3.75 % Allowed : 25.69 % Favored : 70.56 % 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: -0.01 (0.31), residues: 810 helix: 1.67 (0.27), residues: 450 sheet: None (None), residues: 0 loop : -2.36 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 98 HIS 0.005 0.001 HIS C 118 PHE 0.014 0.001 PHE B 52 TYR 0.012 0.001 TYR D 179 ARG 0.002 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 0.845 Fit side-chains REVERT: A 73 ASP cc_start: 0.8733 (t0) cc_final: 0.8506 (t0) REVERT: A 101 VAL cc_start: 0.8536 (t) cc_final: 0.8250 (t) REVERT: A 141 ASP cc_start: 0.8050 (m-30) cc_final: 0.7794 (m-30) REVERT: B 137 GLN cc_start: 0.8690 (tt0) cc_final: 0.8459 (tm-30) REVERT: B 154 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8502 (tp) REVERT: B 182 HIS cc_start: 0.8582 (m-70) cc_final: 0.8373 (m170) REVERT: C 73 ASP cc_start: 0.8468 (t0) cc_final: 0.8223 (t0) REVERT: C 137 GLN cc_start: 0.8930 (tm-30) cc_final: 0.8672 (tm-30) REVERT: D 73 ASP cc_start: 0.8563 (t0) cc_final: 0.8253 (t0) REVERT: E 203 HIS cc_start: 0.4443 (OUTLIER) cc_final: 0.3699 (p-80) outliers start: 27 outliers final: 16 residues processed: 119 average time/residue: 0.6728 time to fit residues: 87.7101 Evaluate side-chains 109 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 203 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 12 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 17 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 HIS B 149 GLN C 99 GLN C 118 HIS C 182 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.116040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.103736 restraints weight = 11883.894| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.85 r_work: 0.3413 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6880 Z= 0.210 Angle : 0.550 14.432 9285 Z= 0.288 Chirality : 0.043 0.232 980 Planarity : 0.003 0.026 1205 Dihedral : 4.132 14.477 880 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 4.86 % Allowed : 25.14 % Favored : 70.00 % 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: 0.05 (0.31), residues: 810 helix: 1.65 (0.26), residues: 455 sheet: None (None), residues: 0 loop : -2.28 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 108 HIS 0.004 0.001 HIS A 203 PHE 0.010 0.001 PHE B 52 TYR 0.015 0.002 TYR D 179 ARG 0.002 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 101 time to evaluate : 0.778 Fit side-chains REVERT: A 101 VAL cc_start: 0.8579 (t) cc_final: 0.8311 (t) REVERT: A 205 ASN cc_start: 0.6759 (t0) cc_final: 0.5677 (m-40) REVERT: B 137 GLN cc_start: 0.8827 (tt0) cc_final: 0.8538 (tm-30) REVERT: B 154 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8466 (tp) REVERT: B 201 ILE cc_start: 0.7991 (OUTLIER) cc_final: 0.7751 (mm) REVERT: C 73 ASP cc_start: 0.8631 (t0) cc_final: 0.8381 (t0) REVERT: C 137 GLN cc_start: 0.8999 (tm-30) cc_final: 0.8711 (tm-30) REVERT: D 73 ASP cc_start: 0.8663 (t0) cc_final: 0.8419 (t0) outliers start: 35 outliers final: 23 residues processed: 129 average time/residue: 0.6871 time to fit residues: 96.5865 Evaluate side-chains 118 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 203 HIS Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 203 HIS Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 203 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 0 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 44 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 76 optimal weight: 0.0570 chunk 75 optimal weight: 2.9990 overall best weight: 1.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 HIS B 149 GLN B 182 HIS C 99 GLN C 182 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.118019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.105583 restraints weight = 12001.729| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.89 r_work: 0.3439 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6880 Z= 0.171 Angle : 0.532 9.570 9285 Z= 0.280 Chirality : 0.043 0.321 980 Planarity : 0.003 0.024 1205 Dihedral : 3.999 14.336 880 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 4.72 % Allowed : 25.83 % Favored : 69.44 % 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: 0.22 (0.32), residues: 810 helix: 1.78 (0.26), residues: 455 sheet: None (None), residues: 0 loop : -2.20 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 98 HIS 0.004 0.001 HIS A 203 PHE 0.011 0.001 PHE B 52 TYR 0.013 0.001 TYR D 179 ARG 0.002 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 89 time to evaluate : 0.771 Fit side-chains REVERT: A 101 VAL cc_start: 0.8573 (t) cc_final: 0.8316 (t) REVERT: B 137 GLN cc_start: 0.8745 (tt0) cc_final: 0.8449 (tm-30) REVERT: B 154 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8474 (tp) REVERT: B 182 HIS cc_start: 0.8183 (OUTLIER) cc_final: 0.7959 (m170) REVERT: C 73 ASP cc_start: 0.8555 (t0) cc_final: 0.8290 (t0) REVERT: C 137 GLN cc_start: 0.8951 (tm-30) cc_final: 0.8687 (tm-30) REVERT: D 73 ASP cc_start: 0.8591 (t0) cc_final: 0.8334 (t0) outliers start: 34 outliers final: 25 residues processed: 116 average time/residue: 0.6472 time to fit residues: 82.2266 Evaluate side-chains 117 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 182 HIS Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 203 HIS Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 203 HIS Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 203 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 37 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 70 optimal weight: 0.0970 chunk 28 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 HIS B 149 GLN B 182 HIS C 99 GLN C 118 HIS C 149 GLN C 182 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.116289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.103980 restraints weight = 12082.447| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.88 r_work: 0.3415 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6880 Z= 0.200 Angle : 0.541 8.797 9285 Z= 0.286 Chirality : 0.043 0.254 980 Planarity : 0.003 0.024 1205 Dihedral : 4.021 14.488 880 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 4.58 % Allowed : 25.83 % Favored : 69.58 % 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: 0.25 (0.31), residues: 810 helix: 1.82 (0.26), residues: 455 sheet: None (None), residues: 0 loop : -2.19 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 108 HIS 0.004 0.001 HIS A 203 PHE 0.009 0.001 PHE B 52 TYR 0.017 0.002 TYR D 179 ARG 0.002 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 91 time to evaluate : 0.756 Fit side-chains REVERT: A 101 VAL cc_start: 0.8577 (t) cc_final: 0.8329 (t) REVERT: A 205 ASN cc_start: 0.7002 (t0) cc_final: 0.5473 (m-40) REVERT: B 137 GLN cc_start: 0.8792 (tt0) cc_final: 0.8509 (tm-30) REVERT: B 154 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8476 (tp) REVERT: B 182 HIS cc_start: 0.8328 (OUTLIER) cc_final: 0.8104 (m170) REVERT: C 73 ASP cc_start: 0.8611 (t0) cc_final: 0.8366 (t0) REVERT: D 73 ASP cc_start: 0.8626 (t0) cc_final: 0.8384 (t0) outliers start: 33 outliers final: 25 residues processed: 115 average time/residue: 0.6936 time to fit residues: 86.9037 Evaluate side-chains 115 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 88 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 182 HIS Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 203 HIS Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 203 HIS Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 203 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 73 optimal weight: 0.2980 chunk 50 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 HIS B 149 GLN B 182 HIS C 99 GLN C 118 HIS C 182 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.114999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.102369 restraints weight = 12199.787| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.97 r_work: 0.3419 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6880 Z= 0.191 Angle : 0.548 8.367 9285 Z= 0.290 Chirality : 0.044 0.354 980 Planarity : 0.003 0.024 1205 Dihedral : 4.010 14.532 880 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 4.31 % Allowed : 26.39 % Favored : 69.31 % 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: 0.33 (0.32), residues: 810 helix: 1.88 (0.26), residues: 455 sheet: None (None), residues: 0 loop : -2.16 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 108 HIS 0.004 0.001 HIS A 203 PHE 0.010 0.001 PHE B 52 TYR 0.015 0.001 TYR D 179 ARG 0.003 0.000 ARG C 199 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 86 time to evaluate : 0.782 Fit side-chains REVERT: A 101 VAL cc_start: 0.8552 (t) cc_final: 0.8308 (t) REVERT: A 205 ASN cc_start: 0.6881 (t0) cc_final: 0.5399 (m-40) REVERT: B 137 GLN cc_start: 0.8810 (tt0) cc_final: 0.8502 (tm-30) REVERT: B 154 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8462 (tp) REVERT: B 182 HIS cc_start: 0.8189 (OUTLIER) cc_final: 0.7892 (m170) REVERT: C 73 ASP cc_start: 0.8617 (t0) cc_final: 0.8362 (t0) REVERT: C 137 GLN cc_start: 0.8980 (tm-30) cc_final: 0.8694 (tm-30) REVERT: D 73 ASP cc_start: 0.8640 (t0) cc_final: 0.8392 (t0) outliers start: 31 outliers final: 25 residues processed: 110 average time/residue: 0.6667 time to fit residues: 80.2654 Evaluate side-chains 114 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 87 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 182 HIS Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 203 HIS Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 203 HIS Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 203 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 76 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 HIS B 149 GLN B 182 HIS C 99 GLN C 118 HIS C 149 GLN C 182 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.116270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.103996 restraints weight = 12043.609| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.86 r_work: 0.3416 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6880 Z= 0.201 Angle : 0.546 8.105 9285 Z= 0.289 Chirality : 0.043 0.267 980 Planarity : 0.003 0.024 1205 Dihedral : 4.024 14.509 880 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 4.58 % Allowed : 25.69 % Favored : 69.72 % 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: 0.37 (0.31), residues: 810 helix: 1.92 (0.26), residues: 455 sheet: None (None), residues: 0 loop : -2.16 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 108 HIS 0.004 0.001 HIS A 203 PHE 0.009 0.001 PHE B 52 TYR 0.016 0.001 TYR D 179 ARG 0.002 0.000 ARG C 199 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3716.13 seconds wall clock time: 64 minutes 10.28 seconds (3850.28 seconds total)