Starting phenix.real_space_refine (version: dev) on Sat Feb 18 01:06:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tar_10425/02_2023/6tar_10425.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tar_10425/02_2023/6tar_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_2023/6tar_10425.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tar_10425/02_2023/6tar_10425.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tar_10425/02_2023/6tar_10425.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tar_10425/02_2023/6tar_10425.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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-4877/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: 4.29, per 1000 atoms: 0.64 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: 2.65 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: 0.31 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: 1.49 Time building geometry restraints manager: 2.70 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 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. 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: 0.220 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: 1.500 Check model and map are aligned: 0.100 Process input model: 20.660 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.060 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:11.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 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 % 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 *********************** 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 : 0.844 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 128 average time/residue: 0.9807 time to fit residues: 133.9191 Evaluate side-chains 92 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.800 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 20 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 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: 0.0060 overall best weight: 1.6004 ------------------------------------------------------------------------------- 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: 0.8109 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.021 6880 Z= 0.183 Angle : 0.513 5.567 9285 Z= 0.284 Chirality : 0.041 0.219 980 Planarity : 0.003 0.025 1205 Dihedral : 4.404 14.104 880 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer Outliers : 3.75 % 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: -1.68 (0.28), residues: 810 helix: 0.22 (0.25), residues: 445 sheet: None (None), residues: 0 loop : -2.93 (0.27), residues: 365 *********************** 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 132 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 105 time to evaluate : 0.891 Fit side-chains outliers start: 27 outliers final: 13 residues processed: 124 average time/residue: 0.6675 time to fit residues: 90.6945 Evaluate side-chains 105 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 92 time to evaluate : 0.765 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 8 residues processed: 6 average time/residue: 0.0934 time to fit residues: 1.9814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 78 optimal weight: 8.9990 chunk 64 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 E 182 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2859 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= 0.197 Angle : 0.519 5.484 9285 Z= 0.281 Chirality : 0.043 0.250 980 Planarity : 0.003 0.024 1205 Dihedral : 4.222 13.834 880 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer Outliers : 4.86 % 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: -0.91 (0.30), residues: 810 helix: 0.86 (0.26), residues: 455 sheet: None (None), residues: 0 loop : -2.70 (0.29), residues: 355 *********************** 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 137 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 102 time to evaluate : 0.734 Fit side-chains outliers start: 35 outliers final: 19 residues processed: 129 average time/residue: 0.6943 time to fit residues: 97.7446 Evaluate side-chains 111 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 92 time to evaluate : 0.864 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 15 residues processed: 5 average time/residue: 0.1158 time to fit residues: 2.0333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 34 optimal weight: 0.4980 chunk 48 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3422 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= 0.282 Angle : 0.596 11.385 9285 Z= 0.318 Chirality : 0.045 0.272 980 Planarity : 0.003 0.026 1205 Dihedral : 4.604 14.406 880 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer Outliers : 6.39 % 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: 1.04 (0.26), residues: 450 sheet: None (None), residues: 0 loop : -2.71 (0.29), residues: 360 *********************** 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 156 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 110 time to evaluate : 0.805 Fit side-chains outliers start: 46 outliers final: 25 residues processed: 146 average time/residue: 0.6055 time to fit residues: 97.2027 Evaluate side-chains 127 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 102 time to evaluate : 0.868 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 20 residues processed: 5 average time/residue: 0.2836 time to fit residues: 2.8914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0570 chunk 57 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 19 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 overall best weight: 1.4704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 GLN B 182 HIS C 99 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 6880 Z= 0.179 Angle : 0.531 9.278 9285 Z= 0.278 Chirality : 0.041 0.199 980 Planarity : 0.003 0.023 1205 Dihedral : 4.161 14.500 880 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer Outliers : 5.69 % 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: -0.38 (0.31), residues: 810 helix: 1.41 (0.27), residues: 450 sheet: None (None), residues: 0 loop : -2.60 (0.30), residues: 360 *********************** 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 134 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 93 time to evaluate : 0.816 Fit side-chains outliers start: 41 outliers final: 25 residues processed: 128 average time/residue: 0.5763 time to fit residues: 81.7027 Evaluate side-chains 114 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 89 time to evaluate : 0.742 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 20 residues processed: 5 average time/residue: 0.2644 time to fit residues: 2.7436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 45 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 35 optimal weight: 0.0010 chunk 6 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.6586 ------------------------------------------------------------------------------- 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 149 GLN B 182 HIS C 99 GLN D 58 HIS D 182 HIS E 58 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3788 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= 0.133 Angle : 0.483 8.090 9285 Z= 0.252 Chirality : 0.039 0.204 980 Planarity : 0.003 0.024 1205 Dihedral : 3.698 13.976 880 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer Outliers : 4.17 % 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: 0.04 (0.32), residues: 810 helix: 1.80 (0.27), residues: 450 sheet: None (None), residues: 0 loop : -2.48 (0.30), residues: 360 *********************** 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 120 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 90 time to evaluate : 0.804 Fit side-chains outliers start: 30 outliers final: 22 residues processed: 117 average time/residue: 0.5730 time to fit residues: 74.2369 Evaluate side-chains 106 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 84 time to evaluate : 0.721 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 21 residues processed: 2 average time/residue: 0.1216 time to fit residues: 1.4069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 D 182 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 6880 Z= 0.154 Angle : 0.511 11.228 9285 Z= 0.264 Chirality : 0.040 0.242 980 Planarity : 0.003 0.023 1205 Dihedral : 3.683 13.408 880 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer Outliers : 4.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.32), residues: 810 helix: 1.87 (0.27), residues: 455 sheet: None (None), residues: 0 loop : -2.35 (0.31), residues: 355 *********************** 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 124 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 92 time to evaluate : 0.794 Fit side-chains outliers start: 32 outliers final: 23 residues processed: 122 average time/residue: 0.6333 time to fit residues: 85.0438 Evaluate side-chains 110 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 87 time to evaluate : 0.752 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 22 residues processed: 1 average time/residue: 0.0483 time to fit residues: 1.1086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.0980 chunk 49 optimal weight: 0.0570 chunk 52 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 overall best weight: 1.0302 ------------------------------------------------------------------------------- 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 D 182 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 6880 Z= 0.150 Angle : 0.515 10.595 9285 Z= 0.267 Chirality : 0.040 0.246 980 Planarity : 0.003 0.023 1205 Dihedral : 3.680 13.298 880 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer Outliers : 4.17 % 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: 0.33 (0.32), residues: 810 helix: 1.97 (0.27), residues: 455 sheet: None (None), residues: 0 loop : -2.30 (0.31), residues: 355 *********************** 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 121 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 91 time to evaluate : 0.810 Fit side-chains outliers start: 30 outliers final: 25 residues processed: 119 average time/residue: 0.6037 time to fit residues: 79.2647 Evaluate side-chains 113 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 88 time to evaluate : 0.744 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 24 residues processed: 1 average time/residue: 0.0822 time to fit residues: 1.2715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 31 optimal weight: 0.2980 chunk 56 optimal weight: 0.5980 chunk 22 optimal weight: 0.0980 chunk 64 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- 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 149 GLN D 182 HIS E 182 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 6880 Z= 0.131 Angle : 0.505 12.701 9285 Z= 0.257 Chirality : 0.040 0.253 980 Planarity : 0.003 0.022 1205 Dihedral : 3.371 13.018 880 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer Outliers : 3.89 % 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: 0.52 (0.32), residues: 810 helix: 2.07 (0.26), residues: 465 sheet: None (None), residues: 0 loop : -2.25 (0.32), residues: 345 *********************** 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 116 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 88 time to evaluate : 0.820 Fit side-chains outliers start: 28 outliers final: 23 residues processed: 115 average time/residue: 0.6716 time to fit residues: 84.5282 Evaluate side-chains 104 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 81 time to evaluate : 0.737 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 23 residues processed: 0 time to fit residues: 1.0361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 79 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 6 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 149 GLN B 182 HIS C 99 GLN C 182 HIS D 182 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 6880 Z= 0.191 Angle : 0.565 15.750 9285 Z= 0.290 Chirality : 0.042 0.268 980 Planarity : 0.003 0.021 1205 Dihedral : 3.795 13.865 880 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer Outliers : 3.75 % 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: 0.50 (0.32), residues: 810 helix: 2.12 (0.26), residues: 455 sheet: None (None), residues: 0 loop : -2.25 (0.31), residues: 355 ********************** 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 125 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 98 time to evaluate : 0.756 Fit side-chains outliers start: 27 outliers final: 22 residues processed: 123 average time/residue: 0.6624 time to fit residues: 89.2552 Evaluate side-chains 113 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 91 time to evaluate : 0.808 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 21 residues processed: 1 average time/residue: 0.0768 time to fit residues: 1.2865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 65 optimal weight: 0.0050 chunk 8 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- 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 182 HIS D 182 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.119962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.107542 restraints weight = 11770.546| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.86 r_work: 0.3482 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 6880 Z= 0.140 Angle : 0.546 14.746 9285 Z= 0.274 Chirality : 0.040 0.254 980 Planarity : 0.003 0.021 1205 Dihedral : 3.547 14.781 880 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer Outliers : 3.61 % 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: 0.66 (0.32), residues: 810 helix: 2.20 (0.26), residues: 460 sheet: None (None), residues: 0 loop : -2.15 (0.31), residues: 350 =============================================================================== Job complete usr+sys time: 2055.85 seconds wall clock time: 37 minutes 48.64 seconds (2268.64 seconds total)