Starting phenix.real_space_refine on Tue Feb 13 15:22:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tar_10425/02_2024/6tar_10425.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tar_10425/02_2024/6tar_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tar_10425/02_2024/6tar_10425.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tar_10425/02_2024/6tar_10425.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tar_10425/02_2024/6tar_10425.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tar_10425/02_2024/6tar_10425.pdb" } 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 Residue "A ARG 102": "NH1" <-> "NH2" Residue "A GLU 104": "OE1" <-> "OE2" Residue "A ARG 161": "NH1" <-> "NH2" Residue "A ARG 180": "NH1" <-> "NH2" Residue "A ARG 185": "NH1" <-> "NH2" Residue "A ARG 199": "NH1" <-> "NH2" Residue "B ARG 102": "NH1" <-> "NH2" Residue "B GLU 104": "OE1" <-> "OE2" Residue "B ARG 161": "NH1" <-> "NH2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "B ARG 185": "NH1" <-> "NH2" Residue "B ARG 199": "NH1" <-> "NH2" Residue "C ARG 102": "NH1" <-> "NH2" Residue "C GLU 104": "OE1" <-> "OE2" Residue "C ARG 161": "NH1" <-> "NH2" Residue "C ARG 180": "NH1" <-> "NH2" Residue "C ARG 185": "NH1" <-> "NH2" Residue "C ARG 199": "NH1" <-> "NH2" Residue "D ARG 102": "NH1" <-> "NH2" Residue "D GLU 104": "OE1" <-> "OE2" Residue "D ARG 161": "NH1" <-> "NH2" Residue "D ARG 180": "NH1" <-> "NH2" Residue "D ARG 185": "NH1" <-> "NH2" Residue "D ARG 199": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E GLU 104": "OE1" <-> "OE2" Residue "E ARG 161": "NH1" <-> "NH2" Residue "E ARG 180": "NH1" <-> "NH2" Residue "E ARG 185": "NH1" <-> "NH2" Residue "E ARG 199": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6715 Number of models: 1 Model: "" Number of chains: 5 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} Chain: "B" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1343 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 4, 'TRANS': 159} Chain: "C" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1343 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 4, 'TRANS': 159} Chain: "D" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1343 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 4, 'TRANS': 159} Chain: "E" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1343 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 4, 'TRANS': 159} Time building chain proxies: 4.05, per 1000 atoms: 0.60 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 - 3.50 Amino acid : False - 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: 2.33 Conformation dependent library (CDL) restraints added in 1.3 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: 0.64 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: 1.47 Time building geometry restraints manager: 2.53 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: 100.21 - 106.99: 161 106.99 - 113.77: 3670 113.77 - 120.55: 2974 120.55 - 127.33: 2385 127.33 - 134.11: 95 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 2.440 nonbonded pdb=" O SER D 78 " pdb=" OG SER D 78 " model vdw 2.319 2.440 nonbonded pdb=" O SER B 78 " pdb=" OG SER B 78 " model vdw 2.320 2.440 nonbonded pdb=" O SER C 78 " pdb=" OG SER C 78 " model vdw 2.320 2.440 nonbonded pdb=" O SER E 78 " pdb=" OG SER E 78 " model vdw 2.321 2.440 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 0.130 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: 1.090 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 20.980 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.170 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 5 poor density : 123 time to evaluate : 0.810 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: 0.9255 time to fit residues: 126.3484 Evaluate side-chains 95 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 91 time to evaluate : 0.766 ------------------------------------------------------------------------------- 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: 0.9990 chunk 33 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- 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 E 203 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 6880 Z= 0.167 Angle : 0.494 5.468 9285 Z= 0.274 Chirality : 0.041 0.228 980 Planarity : 0.003 0.025 1205 Dihedral : 5.629 49.279 888 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 3.06 % Allowed : 18.33 % Favored : 78.61 % 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: -1.65 (0.28), residues: 810 helix: 0.18 (0.25), residues: 450 sheet: None (None), residues: 0 loop : -2.86 (0.27), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 108 HIS 0.004 0.001 HIS B 182 PHE 0.010 0.001 PHE B 133 TYR 0.011 0.001 TYR B 126 ARG 0.002 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 133 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 111 time to evaluate : 0.820 Fit side-chains REVERT: A 141 ASP cc_start: 0.7856 (m-30) cc_final: 0.7561 (m-30) REVERT: E 120 SER cc_start: 0.7336 (t) cc_final: 0.7082 (m) outliers start: 22 outliers final: 8 residues processed: 126 average time/residue: 0.6633 time to fit residues: 91.1507 Evaluate side-chains 104 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 96 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain B residue 106 THR 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 159 SER Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 159 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 0.0970 chunk 60 optimal weight: 9.9990 chunk 49 optimal weight: 0.0770 chunk 20 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 64 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 overall best weight: 0.6136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 HIS C 182 HIS D 182 HIS E 58 HIS E 182 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2789 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= 0.131 Angle : 0.467 5.552 9285 Z= 0.248 Chirality : 0.041 0.255 980 Planarity : 0.003 0.021 1205 Dihedral : 3.681 13.200 880 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 3.19 % Allowed : 22.64 % Favored : 74.17 % 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: -0.74 (0.30), residues: 810 helix: 1.03 (0.27), residues: 455 sheet: None (None), residues: 0 loop : -2.66 (0.29), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 108 HIS 0.005 0.001 HIS B 182 PHE 0.016 0.001 PHE B 52 TYR 0.012 0.001 TYR C 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 120 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 97 time to evaluate : 0.769 Fit side-chains REVERT: A 101 VAL cc_start: 0.8545 (t) cc_final: 0.8198 (t) REVERT: A 141 ASP cc_start: 0.7866 (m-30) cc_final: 0.7641 (m-30) REVERT: B 154 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8385 (tt) outliers start: 23 outliers final: 8 residues processed: 112 average time/residue: 0.6482 time to fit residues: 79.5303 Evaluate side-chains 98 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 89 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain B residue 154 LEU 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 118 HIS Chi-restraints excluded: chain D residue 159 SER 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 54 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 48 optimal weight: 9.9990 chunk 73 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 64 optimal weight: 9.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN B 182 HIS E 58 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3039 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= 0.190 Angle : 0.508 5.317 9285 Z= 0.277 Chirality : 0.042 0.265 980 Planarity : 0.003 0.026 1205 Dihedral : 4.027 13.161 880 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 5.28 % Allowed : 22.50 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.31), residues: 810 helix: 1.36 (0.27), residues: 455 sheet: None (None), residues: 0 loop : -2.53 (0.29), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 108 HIS 0.006 0.001 HIS C 118 PHE 0.011 0.001 PHE B 52 TYR 0.018 0.002 TYR C 179 ARG 0.002 0.000 ARG D 102 *********************** 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 142 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 104 time to evaluate : 0.806 Fit side-chains REVERT: A 141 ASP cc_start: 0.7902 (m-30) cc_final: 0.7649 (m-30) REVERT: B 154 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8081 (tp) REVERT: C 120 SER cc_start: 0.7193 (t) cc_final: 0.6941 (m) REVERT: E 69 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7637 (mt-10) REVERT: E 154 LEU cc_start: 0.8443 (tt) cc_final: 0.8240 (tt) outliers start: 38 outliers final: 19 residues processed: 134 average time/residue: 0.6118 time to fit residues: 89.9249 Evaluate side-chains 115 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 94 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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 163 ASP 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 159 SER Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 174 LEU 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 163 ASP Chi-restraints excluded: chain E residue 69 GLU 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 43 optimal weight: 8.9990 chunk 1 optimal weight: 0.4980 chunk 57 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 65 optimal weight: 0.4980 chunk 53 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 HIS C 118 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6880 Z= 0.243 Angle : 0.566 9.132 9285 Z= 0.302 Chirality : 0.044 0.297 980 Planarity : 0.003 0.023 1205 Dihedral : 4.269 13.410 880 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 5.14 % Allowed : 25.00 % Favored : 69.86 % 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: 1.32 (0.26), residues: 455 sheet: None (None), residues: 0 loop : -2.50 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 108 HIS 0.006 0.001 HIS B 182 PHE 0.010 0.001 PHE B 133 TYR 0.017 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 144 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 107 time to evaluate : 0.830 Fit side-chains REVERT: A 141 ASP cc_start: 0.7849 (m-30) cc_final: 0.7604 (m-30) REVERT: A 205 ASN cc_start: 0.6708 (t0) cc_final: 0.5661 (m-40) REVERT: B 154 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8490 (tp) REVERT: E 69 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7613 (mt-10) REVERT: E 154 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8243 (tt) outliers start: 37 outliers final: 25 residues processed: 134 average time/residue: 0.6504 time to fit residues: 95.3149 Evaluate side-chains 126 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 98 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 163 ASP 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 106 THR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 163 ASP 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 120 SER Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 203 HIS Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 163 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 chunk 35 optimal weight: 0.1980 chunk 6 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 74 optimal weight: 0.4980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN B 149 GLN B 182 HIS C 99 GLN C 118 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6880 Z= 0.165 Angle : 0.520 9.475 9285 Z= 0.274 Chirality : 0.041 0.210 980 Planarity : 0.003 0.023 1205 Dihedral : 4.030 13.445 880 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 5.00 % Allowed : 25.42 % 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: -0.09 (0.31), residues: 810 helix: 1.67 (0.27), residues: 450 sheet: None (None), residues: 0 loop : -2.49 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 108 HIS 0.006 0.001 HIS B 182 PHE 0.008 0.001 PHE B 52 TYR 0.014 0.001 TYR D 179 ARG 0.001 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 131 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 95 time to evaluate : 0.801 Fit side-chains REVERT: A 141 ASP cc_start: 0.7811 (m-30) cc_final: 0.7574 (m-30) REVERT: B 154 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8510 (tp) REVERT: E 69 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7715 (mt-10) REVERT: E 154 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8210 (tt) outliers start: 36 outliers final: 25 residues processed: 122 average time/residue: 0.6373 time to fit residues: 85.2688 Evaluate side-chains 119 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 91 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 163 ASP 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 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 163 ASP 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 163 ASP Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 118 HIS Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 163 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 35 optimal weight: 0.1980 chunk 30 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN B 149 GLN B 182 HIS C 99 GLN C 118 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6880 Z= 0.263 Angle : 0.583 10.779 9285 Z= 0.308 Chirality : 0.045 0.326 980 Planarity : 0.003 0.025 1205 Dihedral : 4.335 13.674 880 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 5.56 % Allowed : 25.14 % 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: -0.61 (0.31), residues: 810 helix: 1.14 (0.25), residues: 485 sheet: None (None), residues: 0 loop : -2.98 (0.30), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 108 HIS 0.006 0.001 HIS B 182 PHE 0.010 0.001 PHE A 132 TYR 0.017 0.002 TYR D 179 ARG 0.001 0.000 ARG A 161 *********************** 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 148 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 108 time to evaluate : 0.796 Fit side-chains REVERT: A 101 VAL cc_start: 0.8677 (t) cc_final: 0.8414 (t) REVERT: A 205 ASN cc_start: 0.6825 (t0) cc_final: 0.5873 (m-40) REVERT: B 154 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8510 (tp) REVERT: B 201 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7933 (mm) REVERT: E 69 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7687 (mt-10) REVERT: E 154 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8243 (tt) outliers start: 40 outliers final: 26 residues processed: 138 average time/residue: 0.5738 time to fit residues: 87.5944 Evaluate side-chains 130 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 100 time to evaluate : 0.828 ------------------------------------------------------------------------------- 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 163 ASP 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 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 163 ASP 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 163 ASP Chi-restraints excluded: chain D residue 203 HIS Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 163 ASP 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 23 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 49 optimal weight: 0.2980 chunk 52 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN B 182 HIS C 99 GLN C 118 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6880 Z= 0.161 Angle : 0.515 8.765 9285 Z= 0.272 Chirality : 0.041 0.228 980 Planarity : 0.003 0.023 1205 Dihedral : 4.014 14.073 880 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 5.00 % Allowed : 26.94 % Favored : 68.06 % 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: 0.04 (0.31), residues: 810 helix: 1.75 (0.27), residues: 455 sheet: None (None), residues: 0 loop : -2.46 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 108 HIS 0.009 0.001 HIS B 182 PHE 0.008 0.001 PHE A 64 TYR 0.013 0.001 TYR D 179 ARG 0.001 0.000 ARG C 102 *********************** 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 129 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 93 time to evaluate : 0.819 Fit side-chains REVERT: A 205 ASN cc_start: 0.6605 (t0) cc_final: 0.5662 (m-40) REVERT: B 154 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8503 (tp) REVERT: E 154 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8186 (tt) outliers start: 36 outliers final: 24 residues processed: 124 average time/residue: 0.6206 time to fit residues: 84.5325 Evaluate side-chains 115 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 89 time to evaluate : 0.784 ------------------------------------------------------------------------------- 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 163 ASP 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 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 163 ASP 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 163 ASP Chi-restraints excluded: chain D residue 203 HIS Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 163 ASP 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 71 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 43 optimal weight: 0.1980 chunk 31 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 64 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 E 58 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6880 Z= 0.137 Angle : 0.525 15.885 9285 Z= 0.266 Chirality : 0.042 0.322 980 Planarity : 0.003 0.024 1205 Dihedral : 3.621 13.743 880 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 3.75 % Allowed : 28.89 % Favored : 67.36 % 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: 0.32 (0.32), residues: 810 helix: 1.93 (0.27), residues: 460 sheet: None (None), residues: 0 loop : -2.32 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 98 HIS 0.009 0.001 HIS B 182 PHE 0.009 0.001 PHE A 64 TYR 0.011 0.001 TYR D 179 ARG 0.001 0.000 ARG C 102 *********************** 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 110 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 83 time to evaluate : 0.799 Fit side-chains outliers start: 27 outliers final: 18 residues processed: 107 average time/residue: 0.6218 time to fit residues: 73.1250 Evaluate side-chains 100 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 82 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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 163 ASP Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 106 THR 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 106 THR Chi-restraints excluded: chain C residue 159 SER 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 163 ASP Chi-restraints excluded: chain D residue 203 HIS 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 36 optimal weight: 3.9990 chunk 52 optimal weight: 0.0370 chunk 79 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 49 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 19 optimal weight: 8.9990 overall best weight: 1.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 HIS B 182 HIS C 99 GLN C 118 HIS C 149 GLN E 182 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6880 Z= 0.157 Angle : 0.566 15.101 9285 Z= 0.280 Chirality : 0.043 0.348 980 Planarity : 0.003 0.021 1205 Dihedral : 3.702 13.938 880 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 3.33 % Allowed : 28.75 % Favored : 67.92 % 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: 0.43 (0.31), residues: 810 helix: 2.07 (0.26), residues: 455 sheet: None (None), residues: 0 loop : -2.30 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 98 HIS 0.009 0.001 HIS B 182 PHE 0.008 0.001 PHE A 64 TYR 0.013 0.001 TYR D 179 ARG 0.002 0.000 ARG E 185 ********************** 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 110 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 86 time to evaluate : 0.735 Fit side-chains outliers start: 24 outliers final: 19 residues processed: 108 average time/residue: 0.6680 time to fit residues: 78.9754 Evaluate side-chains 102 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 83 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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 163 ASP 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 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 106 THR Chi-restraints excluded: chain C residue 159 SER 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 163 ASP Chi-restraints excluded: chain D residue 203 HIS 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 58 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 8 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- 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 182 HIS C 99 GLN C 118 HIS D 182 HIS E 182 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.114318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.102421 restraints weight = 11886.533| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.81 r_work: 0.3398 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6880 Z= 0.237 Angle : 0.613 15.763 9285 Z= 0.310 Chirality : 0.044 0.272 980 Planarity : 0.003 0.024 1205 Dihedral : 4.105 14.417 880 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 4.03 % Allowed : 28.19 % Favored : 67.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.31), residues: 810 helix: 1.60 (0.25), residues: 485 sheet: None (None), residues: 0 loop : -2.82 (0.30), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 108 HIS 0.009 0.001 HIS B 182 PHE 0.010 0.001 PHE E 133 TYR 0.015 0.002 TYR D 179 ARG 0.002 0.000 ARG D 151 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2083.56 seconds wall clock time: 39 minutes 0.82 seconds (2340.82 seconds total)