Starting phenix.real_space_refine on Tue Feb 11 18:41:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6tar_10425/02_2025/6tar_10425.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tar_10425/02_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_10425/02_2025/6tar_10425.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tar_10425/02_2025/6tar_10425.map" model { file = "/net/cci-nas-00/data/ceres_data/6tar_10425/02_2025/6tar_10425.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tar_10425/02_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-5592/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: 2.71, per 1000 atoms: 0.40 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: 1.37 Conformation dependent library (CDL) restraints added in 837.3 milliseconds 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: 1.59 Time building geometry restraints manager: 1.62 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: 0.05 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: 0.160 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: 0.240 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 16.050 Find NCS groups from input model: 0.140 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:12.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.340 ------------------------------------------------------------------------------- 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 : 0.987 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: 0.9812 time to fit residues: 134.0522 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 : 0.764 ------------------------------------------------------------------------------- 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 : 0.718 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: 0.6695 time to fit residues: 93.6070 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 : 0.781 ------------------------------------------------------------------------------- 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: 0.0270 chunk 22 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 4 optimal weight: 0.0070 chunk 5 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.4060 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.119546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.106757 restraints weight = 11727.340| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.90 r_work: 0.3440 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2824 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= 0.173 Angle : 0.504 5.372 9285 Z= 0.273 Chirality : 0.042 0.248 980 Planarity : 0.003 0.023 1205 Dihedral : 4.117 14.366 880 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.81 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 0.010 0.001 TRP A 108 HIS 0.004 0.001 HIS E 182 PHE 0.022 0.001 PHE B 52 TYR 0.015 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 : 0.787 Fit side-chains REVERT: A 73 ASP cc_start: 0.8714 (t0) cc_final: 0.8512 (t0) REVERT: A 101 VAL cc_start: 0.8616 (t) cc_final: 0.8234 (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: 0.8782 (OUTLIER) cc_final: 0.8402 (tp) REVERT: B 182 HIS cc_start: 0.8360 (m-70) cc_final: 0.8034 (m170) REVERT: C 73 ASP cc_start: 0.8547 (t0) cc_final: 0.8311 (t0) REVERT: D 73 ASP cc_start: 0.8538 (t0) cc_final: 0.8237 (t0) REVERT: D 174 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7828 (mt) REVERT: E 154 LEU cc_start: 0.8511 (tp) cc_final: 0.8107 (tp) outliers start: 30 outliers final: 16 residues processed: 123 average time/residue: 0.6463 time to fit residues: 87.3388 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 : 0.738 ------------------------------------------------------------------------------- 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: 2.9990 chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 49 optimal weight: 10.0000 chunk 33 optimal weight: 0.6980 chunk 77 optimal weight: 7.9990 chunk 75 optimal weight: 0.0050 chunk 23 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.1198 ------------------------------------------------------------------------------- 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 = 0.3705 r_free = 0.3705 target = 0.118299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.105266 restraints weight = 11984.993| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 3.01 r_work: 0.3453 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3093 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= 0.153 Angle : 0.481 5.206 9285 Z= 0.261 Chirality : 0.041 0.265 980 Planarity : 0.003 0.023 1205 Dihedral : 3.964 14.180 880 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 3.89 % Allowed : 22.36 % 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: -0.26 (0.31), residues: 810 helix: 1.41 (0.27), residues: 455 sheet: None (None), residues: 0 loop : -2.44 (0.29), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 108 HIS 0.002 0.000 HIS E 203 PHE 0.018 0.001 PHE B 52 TYR 0.017 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 128 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.717 Fit side-chains REVERT: A 101 VAL cc_start: 0.8611 (t) cc_final: 0.8254 (t) REVERT: A 141 ASP cc_start: 0.8279 (m-30) cc_final: 0.8033 (m-30) REVERT: B 137 GLN cc_start: 0.8611 (tt0) cc_final: 0.8293 (tm-30) REVERT: B 154 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8329 (tp) REVERT: B 182 HIS cc_start: 0.8466 (m-70) cc_final: 0.8152 (m170) REVERT: C 137 GLN cc_start: 0.8964 (tm-30) cc_final: 0.8640 (tm-30) REVERT: D 73 ASP cc_start: 0.8548 (t0) cc_final: 0.8187 (t0) REVERT: D 137 GLN cc_start: 0.8688 (tm-30) cc_final: 0.8249 (tm-30) REVERT: D 174 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7731 (mt) REVERT: E 154 LEU cc_start: 0.8381 (tp) cc_final: 0.7947 (tp) outliers start: 28 outliers final: 16 residues processed: 123 average time/residue: 0.6137 time to fit residues: 82.9663 Evaluate side-chains 112 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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 D residue 68 ILE 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: 5.9990 chunk 25 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 = 0.3611 r_free = 0.3611 target = 0.111178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.098530 restraints weight = 12095.049| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.97 r_work: 0.3367 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3425 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= 0.272 Angle : 0.575 7.963 9285 Z= 0.311 Chirality : 0.045 0.301 980 Planarity : 0.003 0.026 1205 Dihedral : 4.450 14.332 880 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 5.28 % Allowed : 21.81 % Favored : 72.92 % 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: -0.71 (0.31), residues: 810 helix: 1.11 (0.26), residues: 475 sheet: None (None), residues: 0 loop : -3.00 (0.30), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 108 HIS 0.003 0.001 HIS C 182 PHE 0.016 0.002 PHE B 52 TYR 0.018 0.002 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 159 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 121 time to evaluate : 0.707 Fit side-chains REVERT: A 101 VAL cc_start: 0.8671 (t) cc_final: 0.8446 (t) REVERT: A 141 ASP cc_start: 0.8134 (m-30) cc_final: 0.7865 (m-30) REVERT: A 205 ASN cc_start: 0.6782 (t0) cc_final: 0.5624 (m-40) REVERT: B 154 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8466 (tp) REVERT: B 182 HIS cc_start: 0.8399 (m-70) cc_final: 0.8124 (m170) REVERT: C 73 ASP cc_start: 0.8764 (t0) cc_final: 0.8475 (t0) REVERT: C 137 GLN cc_start: 0.9057 (tm-30) cc_final: 0.8711 (tm-30) REVERT: D 73 ASP cc_start: 0.8737 (t0) cc_final: 0.8474 (t0) outliers start: 38 outliers final: 20 residues processed: 149 average time/residue: 0.6755 time to fit residues: 109.9334 Evaluate side-chains 133 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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 182 HIS 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 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 159 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.3973 > 50: distance: 11 - 15: 11.894 distance: 15 - 16: 26.184 distance: 15 - 21: 28.393 distance: 16 - 17: 7.685 distance: 16 - 19: 12.634 distance: 17 - 18: 9.932 distance: 17 - 22: 33.708 distance: 19 - 20: 19.014 distance: 20 - 21: 27.204 distance: 22 - 23: 14.208 distance: 23 - 24: 8.096 distance: 23 - 26: 16.032 distance: 24 - 25: 28.543 distance: 24 - 29: 12.115 distance: 26 - 27: 25.573 distance: 26 - 28: 24.078 distance: 29 - 30: 14.092 distance: 30 - 31: 14.741 distance: 30 - 33: 14.129 distance: 31 - 32: 23.285 distance: 31 - 38: 16.312 distance: 33 - 34: 12.802 distance: 34 - 35: 9.245 distance: 35 - 36: 4.852 distance: 36 - 37: 10.963 distance: 38 - 39: 8.912 distance: 38 - 44: 3.817 distance: 39 - 40: 7.881 distance: 39 - 42: 11.954 distance: 40 - 41: 13.590 distance: 40 - 45: 11.862 distance: 42 - 43: 11.023 distance: 43 - 44: 7.510 distance: 45 - 46: 3.704 distance: 46 - 47: 6.279 distance: 46 - 49: 4.229 distance: 47 - 50: 7.653 distance: 48 - 79: 12.070 distance: 50 - 51: 3.111 distance: 51 - 52: 6.281 distance: 51 - 54: 7.526 distance: 52 - 53: 6.249 distance: 52 - 62: 6.358 distance: 53 - 91: 8.461 distance: 54 - 55: 3.210 distance: 55 - 56: 5.500 distance: 56 - 58: 6.712 distance: 58 - 60: 5.032 distance: 60 - 61: 4.487 distance: 62 - 63: 6.559 distance: 63 - 64: 3.020 distance: 63 - 66: 3.934 distance: 64 - 65: 10.334 distance: 64 - 71: 3.539 distance: 65 - 99: 17.606 distance: 66 - 67: 8.739 distance: 68 - 69: 3.273 distance: 71 - 72: 6.228 distance: 72 - 73: 9.698 distance: 72 - 75: 4.748 distance: 73 - 74: 13.571 distance: 73 - 79: 14.766 distance: 74 - 108: 13.821 distance: 75 - 76: 4.843 distance: 75 - 77: 9.870 distance: 76 - 78: 6.216 distance: 79 - 80: 6.233 distance: 80 - 81: 8.777 distance: 80 - 83: 6.981 distance: 81 - 82: 7.195 distance: 81 - 91: 14.018 distance: 82 - 115: 20.023 distance: 83 - 84: 12.285 distance: 84 - 85: 5.175 distance: 84 - 86: 5.840 distance: 85 - 87: 4.133 distance: 86 - 88: 6.401 distance: 87 - 89: 5.092 distance: 88 - 89: 4.422 distance: 89 - 90: 3.126 distance: 91 - 92: 6.613 distance: 92 - 93: 4.275 distance: 92 - 95: 11.161 distance: 93 - 94: 6.381 distance: 93 - 99: 4.101 distance: 94 - 122: 13.528 distance: 95 - 96: 3.529 distance: 96 - 97: 20.701 distance: 97 - 98: 17.326