Starting phenix.real_space_refine on Fri Nov 15 16:24:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vgn_43212/11_2024/8vgn_43212.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vgn_43212/11_2024/8vgn_43212.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vgn_43212/11_2024/8vgn_43212.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vgn_43212/11_2024/8vgn_43212.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vgn_43212/11_2024/8vgn_43212.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vgn_43212/11_2024/8vgn_43212.cif" } resolution = 2.5 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= 1.031 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 54 5.16 5 C 5836 2.51 5 N 1500 2.21 5 O 1760 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 9150 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1668 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 13, 'TRANS': 210} Chain: "B" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1623 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 199} Chain: "G" Number of atoms: 1284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1284 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 7, 'TRANS': 157} Chain breaks: 1 Chain: "H" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1668 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 13, 'TRANS': 210} Chain: "I" Number of atoms: 1284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1284 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 7, 'TRANS': 157} Chain breaks: 1 Chain: "L" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1623 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 199} Time building chain proxies: 7.03, per 1000 atoms: 0.77 Number of scatterers: 9150 At special positions: 0 Unit cell: (62.6919, 154.39, 124.448, 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 54 16.00 O 1760 8.00 N 1500 7.00 C 5836 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 144 " - pdb=" SG CYS A 200 " distance=2.03 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS B 214 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS G 167 " - pdb=" SG CYS G 183 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 144 " - pdb=" SG CYS H 200 " distance=2.03 Simple disulfide: pdb=" SG CYS H 220 " - pdb=" SG CYS L 214 " distance=2.03 Simple disulfide: pdb=" SG CYS I 167 " - pdb=" SG CYS I 183 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 1.1 seconds 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2224 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 22 sheets defined 29.7% alpha, 37.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.686A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 64 Processing helix chain 'A' and resid 83 through 87 Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 191 through 196 removed outlier: 4.386A pdb=" N THR A 195 " --> pdb=" O SER A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 208 Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.518A pdb=" N ALA B 83 " --> pdb=" O ALA B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 Processing helix chain 'B' and resid 183 through 187 Processing helix chain 'G' and resid 48 through 71 Processing helix chain 'G' and resid 79 through 84 Processing helix chain 'G' and resid 85 through 98 Processing helix chain 'G' and resid 99 through 102 Processing helix chain 'G' and resid 114 through 143 Processing helix chain 'G' and resid 152 through 157 Processing helix chain 'G' and resid 171 through 176 removed outlier: 3.832A pdb=" N ASN G 176 " --> pdb=" O SER G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 219 removed outlier: 4.569A pdb=" N ASN G 214 " --> pdb=" O GLY G 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.686A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 131 through 133 No H-bonds generated for 'chain 'H' and resid 131 through 133' Processing helix chain 'H' and resid 160 through 162 No H-bonds generated for 'chain 'H' and resid 160 through 162' Processing helix chain 'H' and resid 191 through 196 removed outlier: 4.388A pdb=" N THR H 195 " --> pdb=" O SER H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 205 through 208 Processing helix chain 'I' and resid 48 through 71 Processing helix chain 'I' and resid 79 through 84 Processing helix chain 'I' and resid 85 through 98 Processing helix chain 'I' and resid 99 through 102 Processing helix chain 'I' and resid 114 through 143 Processing helix chain 'I' and resid 152 through 157 Processing helix chain 'I' and resid 171 through 176 removed outlier: 3.831A pdb=" N ASN I 176 " --> pdb=" O SER I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 219 removed outlier: 4.562A pdb=" N ASN I 214 " --> pdb=" O GLY I 210 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.518A pdb=" N ALA L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 126 Processing helix chain 'L' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 12 removed outlier: 4.021A pdb=" N ASN A 33 " --> pdb=" O SER A 95 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N MET A 34 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ALA A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TRP A 36 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 9 through 12 removed outlier: 7.034A pdb=" N CYS A 92 " --> pdb=" O TRP A 103 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TRP A 103 " --> pdb=" O CYS A 92 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ARG A 94 " --> pdb=" O ASN A 101 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP A 100A" --> pdb=" O TYR A 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 124 through 128 removed outlier: 5.710A pdb=" N TYR A 180 " --> pdb=" O ASP A 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 135 through 136 removed outlier: 5.710A pdb=" N TYR A 180 " --> pdb=" O ASP A 148 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 155 through 158 Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.243A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N GLN B 37 " --> pdb=" O PRO B 46 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.243A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 114 through 118 removed outlier: 5.061A pdb=" N SER B 131 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LEU B 181 " --> pdb=" O SER B 131 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N VAL B 133 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LEU B 179 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LEU B 135 " --> pdb=" O SER B 177 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N SER B 177 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ASN B 137 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU B 175 " --> pdb=" O ASN B 137 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 153 through 154 Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AB4, first strand: chain 'H' and resid 9 through 12 removed outlier: 4.023A pdb=" N ASN H 33 " --> pdb=" O SER H 95 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 9 through 12 removed outlier: 7.036A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ARG H 94 " --> pdb=" O ASN H 101 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP H 100A" --> pdb=" O TYR H 98 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 124 through 128 removed outlier: 5.709A pdb=" N TYR H 180 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 135 through 136 removed outlier: 5.709A pdb=" N TYR H 180 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 155 through 158 Processing sheet with id=AB9, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC1, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.245A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLN L 37 " --> pdb=" O PRO L 46 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.245A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.064A pdb=" N SER L 131 " --> pdb=" O LEU L 181 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LEU L 181 " --> pdb=" O SER L 131 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N VAL L 133 " --> pdb=" O LEU L 179 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LEU L 179 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N LEU L 135 " --> pdb=" O SER L 177 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N SER L 177 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ASN L 137 " --> pdb=" O LEU L 175 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU L 175 " --> pdb=" O ASN L 137 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 153 through 154 514 hydrogen bonds defined for protein. 1332 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: 3.03 Time building geometry restraints manager: 2.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2828 1.34 - 1.46: 2141 1.46 - 1.58: 4323 1.58 - 1.70: 0 1.70 - 1.82: 82 Bond restraints: 9374 Sorted by residual: bond pdb=" C GLU A 216 " pdb=" N PRO A 217 " ideal model delta sigma weight residual 1.334 1.352 -0.019 8.40e-03 1.42e+04 4.92e+00 bond pdb=" C GLU H 216 " pdb=" N PRO H 217 " ideal model delta sigma weight residual 1.334 1.351 -0.017 8.40e-03 1.42e+04 4.23e+00 bond pdb=" CG1 ILE G 95 " pdb=" CD1 ILE G 95 " ideal model delta sigma weight residual 1.513 1.457 0.056 3.90e-02 6.57e+02 2.04e+00 bond pdb=" CG1 ILE I 95 " pdb=" CD1 ILE I 95 " ideal model delta sigma weight residual 1.513 1.459 0.054 3.90e-02 6.57e+02 1.91e+00 bond pdb=" CB ARG L 61 " pdb=" CG ARG L 61 " ideal model delta sigma weight residual 1.520 1.483 0.037 3.00e-02 1.11e+03 1.50e+00 ... (remaining 9369 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 11954 1.59 - 3.18: 659 3.18 - 4.76: 109 4.76 - 6.35: 14 6.35 - 7.94: 10 Bond angle restraints: 12746 Sorted by residual: angle pdb=" N GLY G 75 " pdb=" CA GLY G 75 " pdb=" C GLY G 75 " ideal model delta sigma weight residual 111.52 118.49 -6.97 1.31e+00 5.83e-01 2.83e+01 angle pdb=" N GLY I 75 " pdb=" CA GLY I 75 " pdb=" C GLY I 75 " ideal model delta sigma weight residual 111.52 118.34 -6.82 1.31e+00 5.83e-01 2.71e+01 angle pdb=" N GLY G 91 " pdb=" CA GLY G 91 " pdb=" C GLY G 91 " ideal model delta sigma weight residual 112.64 116.80 -4.16 1.21e+00 6.83e-01 1.18e+01 angle pdb=" N GLY I 91 " pdb=" CA GLY I 91 " pdb=" C GLY I 91 " ideal model delta sigma weight residual 112.64 116.71 -4.07 1.21e+00 6.83e-01 1.13e+01 angle pdb=" N LYS I 142 " pdb=" CA LYS I 142 " pdb=" C LYS I 142 " ideal model delta sigma weight residual 113.72 117.63 -3.91 1.30e+00 5.92e-01 9.04e+00 ... (remaining 12741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.26: 5123 17.26 - 34.53: 369 34.53 - 51.79: 62 51.79 - 69.06: 28 69.06 - 86.32: 16 Dihedral angle restraints: 5598 sinusoidal: 2120 harmonic: 3478 Sorted by residual: dihedral pdb=" CA PRO A 153 " pdb=" C PRO A 153 " pdb=" N VAL A 154 " pdb=" CA VAL A 154 " ideal model delta harmonic sigma weight residual 180.00 151.44 28.56 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA PRO H 153 " pdb=" C PRO H 153 " pdb=" N VAL H 154 " pdb=" CA VAL H 154 " ideal model delta harmonic sigma weight residual 180.00 151.47 28.53 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA LYS H 218 " pdb=" C LYS H 218 " pdb=" N SER H 219 " pdb=" CA SER H 219 " ideal model delta harmonic sigma weight residual 180.00 151.99 28.01 0 5.00e+00 4.00e-02 3.14e+01 ... (remaining 5595 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1120 0.058 - 0.115: 276 0.115 - 0.173: 45 0.173 - 0.231: 1 0.231 - 0.288: 2 Chirality restraints: 1444 Sorted by residual: chirality pdb=" CA PHE H 150 " pdb=" N PHE H 150 " pdb=" C PHE H 150 " pdb=" CB PHE H 150 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CA PHE A 150 " pdb=" N PHE A 150 " pdb=" C PHE A 150 " pdb=" CB PHE A 150 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" CA PRO L 141 " pdb=" N PRO L 141 " pdb=" C PRO L 141 " pdb=" CB PRO L 141 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.17 2.00e-01 2.50e+01 7.53e-01 ... (remaining 1441 not shown) Planarity restraints: 1598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 142 " -0.315 9.50e-02 1.11e+02 1.42e-01 1.56e+01 pdb=" NE ARG B 142 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG B 142 " -0.028 2.00e-02 2.50e+03 pdb=" NH1 ARG B 142 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG B 142 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 142 " -0.317 9.50e-02 1.11e+02 1.43e-01 1.56e+01 pdb=" NE ARG L 142 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG L 142 " -0.028 2.00e-02 2.50e+03 pdb=" NH1 ARG L 142 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG L 142 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 52 " -0.002 2.00e-02 2.50e+03 2.37e-02 1.12e+01 pdb=" CG TYR A 52 " 0.002 2.00e-02 2.50e+03 pdb=" CD1 TYR A 52 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR A 52 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 52 " 0.034 2.00e-02 2.50e+03 pdb=" CE2 TYR A 52 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 52 " 0.032 2.00e-02 2.50e+03 pdb=" OH TYR A 52 " -0.034 2.00e-02 2.50e+03 ... (remaining 1595 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2495 2.81 - 3.33: 8974 3.33 - 3.86: 16041 3.86 - 4.38: 19495 4.38 - 4.90: 32489 Nonbonded interactions: 79494 Sorted by model distance: nonbonded pdb=" OE2 GLU L 123 " pdb=" NZ LYS L 126 " model vdw 2.290 3.120 nonbonded pdb=" OE2 GLU B 123 " pdb=" NZ LYS B 126 " model vdw 2.290 3.120 nonbonded pdb=" OE1 GLU I 150 " pdb=" NH1 ARG I 156 " model vdw 2.307 3.120 nonbonded pdb=" OE1 GLU G 150 " pdb=" NH1 ARG G 156 " model vdw 2.310 3.120 nonbonded pdb=" OE2 GLU I 213 " pdb=" NZ LYS I 217 " model vdw 2.365 3.120 ... (remaining 79489 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'L' } ncs_group { reference = chain 'G' selection = chain 'I' } 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: 3.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 25.510 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 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 : 0.006 0.056 9374 Z= 0.363 Angle : 0.832 7.940 12746 Z= 0.466 Chirality : 0.051 0.288 1444 Planarity : 0.008 0.143 1598 Dihedral : 14.287 86.319 3338 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.13 % Favored : 94.53 % Rotamer: Outliers : 0.78 % Allowed : 3.52 % Favored : 95.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.56 (0.23), residues: 1188 helix: -0.92 (0.26), residues: 270 sheet: 0.31 (0.25), residues: 418 loop : -0.48 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP L 91 HIS 0.007 0.001 HIS B 34 PHE 0.038 0.003 PHE H 100D TYR 0.034 0.008 TYR H 52 ARG 0.032 0.004 ARG B 142 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 167 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8008 (t0) cc_final: 0.7565 (t70) REVERT: G 49 SER cc_start: 0.8224 (m) cc_final: 0.7982 (p) REVERT: G 117 MET cc_start: 0.8221 (mtp) cc_final: 0.7627 (mmm) REVERT: G 119 MET cc_start: 0.7190 (mmt) cc_final: 0.6540 (tpt) REVERT: G 149 MET cc_start: 0.8089 (mmt) cc_final: 0.7859 (mmp) REVERT: G 213 GLU cc_start: 0.8559 (tp30) cc_final: 0.8188 (tm-30) REVERT: G 215 GLU cc_start: 0.8466 (mm-30) cc_final: 0.7563 (mm-30) REVERT: G 216 TRP cc_start: 0.7980 (m100) cc_final: 0.7339 (m-10) REVERT: H 3 GLN cc_start: 0.8799 (tt0) cc_final: 0.8544 (tt0) REVERT: H 5 GLN cc_start: 0.8666 (mm-40) cc_final: 0.8318 (tp40) REVERT: H 72 ASP cc_start: 0.7999 (t0) cc_final: 0.7542 (t70) REVERT: I 49 SER cc_start: 0.8232 (m) cc_final: 0.7877 (p) REVERT: I 117 MET cc_start: 0.8248 (mtp) cc_final: 0.7244 (mmm) REVERT: I 119 MET cc_start: 0.7100 (mmt) cc_final: 0.6883 (mmt) REVERT: I 149 MET cc_start: 0.8076 (mmt) cc_final: 0.7840 (mmp) REVERT: I 213 GLU cc_start: 0.8544 (tp30) cc_final: 0.8181 (tm-30) REVERT: I 216 TRP cc_start: 0.7990 (m100) cc_final: 0.7340 (m-10) outliers start: 8 outliers final: 0 residues processed: 173 average time/residue: 1.3801 time to fit residues: 253.6019 Evaluate side-chains 114 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 60 optimal weight: 0.0870 chunk 47 optimal weight: 0.2980 chunk 92 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN B 53 ASN ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 171 ASN G 204 GLN H 61 GLN ** I 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 204 GLN L 53 ASN ** L 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9374 Z= 0.227 Angle : 0.680 6.528 12746 Z= 0.357 Chirality : 0.045 0.152 1444 Planarity : 0.005 0.049 1598 Dihedral : 5.585 28.556 1278 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.76 % Allowed : 9.47 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 (0.25), residues: 1188 helix: 1.48 (0.30), residues: 270 sheet: 0.43 (0.24), residues: 426 loop : 0.13 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP I 89 HIS 0.004 0.001 HIS B 189 PHE 0.019 0.002 PHE H 100D TYR 0.021 0.002 TYR G 86 ARG 0.011 0.001 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8136 (t0) cc_final: 0.7866 (t70) REVERT: A 199 ILE cc_start: 0.8253 (tp) cc_final: 0.8051 (tp) REVERT: B 170 ASP cc_start: 0.8303 (t0) cc_final: 0.8008 (t0) REVERT: G 49 SER cc_start: 0.8202 (m) cc_final: 0.8000 (p) REVERT: G 71 MET cc_start: 0.9001 (OUTLIER) cc_final: 0.8629 (mtp) REVERT: G 117 MET cc_start: 0.7970 (mtp) cc_final: 0.6806 (mmm) REVERT: G 118 ILE cc_start: 0.8371 (mm) cc_final: 0.8130 (mp) REVERT: G 119 MET cc_start: 0.7254 (mmt) cc_final: 0.6778 (tpt) REVERT: G 149 MET cc_start: 0.8193 (mmt) cc_final: 0.7940 (mmp) REVERT: G 213 GLU cc_start: 0.8149 (tp30) cc_final: 0.7792 (tm-30) REVERT: G 215 GLU cc_start: 0.8493 (mm-30) cc_final: 0.7493 (mm-30) REVERT: G 216 TRP cc_start: 0.8092 (m100) cc_final: 0.7162 (m-10) REVERT: H 72 ASP cc_start: 0.8141 (t0) cc_final: 0.7831 (t70) REVERT: H 212 ASP cc_start: 0.9134 (m-30) cc_final: 0.8903 (m-30) REVERT: I 117 MET cc_start: 0.8167 (mtp) cc_final: 0.6994 (mmm) REVERT: I 118 ILE cc_start: 0.8489 (mm) cc_final: 0.8159 (mp) REVERT: I 119 MET cc_start: 0.7296 (mmt) cc_final: 0.6808 (tpt) REVERT: I 149 MET cc_start: 0.8176 (mmt) cc_final: 0.7871 (mmp) REVERT: I 213 GLU cc_start: 0.8138 (tp30) cc_final: 0.7831 (tm-30) REVERT: I 215 GLU cc_start: 0.8513 (mm-30) cc_final: 0.7527 (mm-30) REVERT: I 216 TRP cc_start: 0.8097 (m100) cc_final: 0.7197 (m-10) REVERT: L 79 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7717 (mp0) REVERT: L 170 ASP cc_start: 0.8313 (t0) cc_final: 0.8008 (t0) outliers start: 18 outliers final: 0 residues processed: 158 average time/residue: 1.4215 time to fit residues: 238.0057 Evaluate side-chains 118 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 116 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 71 MET Chi-restraints excluded: chain L residue 79 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 115 optimal weight: 9.9990 chunk 95 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 86 optimal weight: 0.0570 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9374 Z= 0.255 Angle : 0.657 7.858 12746 Z= 0.340 Chirality : 0.044 0.146 1444 Planarity : 0.004 0.033 1598 Dihedral : 5.081 21.202 1278 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.54 % Allowed : 11.13 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.00 (0.25), residues: 1188 helix: 1.98 (0.31), residues: 270 sheet: 0.60 (0.24), residues: 428 loop : 0.09 (0.30), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP I 89 HIS 0.004 0.001 HIS B 189 PHE 0.022 0.002 PHE L 116 TYR 0.021 0.002 TYR I 86 ARG 0.009 0.001 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8224 (t0) cc_final: 0.7892 (t70) REVERT: A 216 GLU cc_start: 0.8358 (pm20) cc_final: 0.8097 (pp20) REVERT: B 170 ASP cc_start: 0.8366 (t0) cc_final: 0.7985 (t0) REVERT: G 46 MET cc_start: 0.5486 (ttp) cc_final: 0.5117 (mpt) REVERT: G 49 SER cc_start: 0.8226 (m) cc_final: 0.7946 (p) REVERT: G 71 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8625 (mtp) REVERT: G 117 MET cc_start: 0.7903 (mtp) cc_final: 0.6837 (mmm) REVERT: G 118 ILE cc_start: 0.8320 (mm) cc_final: 0.8080 (mp) REVERT: G 149 MET cc_start: 0.8259 (mmt) cc_final: 0.7915 (mmp) REVERT: G 213 GLU cc_start: 0.8236 (tp30) cc_final: 0.7873 (tm-30) REVERT: G 215 GLU cc_start: 0.8453 (mm-30) cc_final: 0.7552 (mm-30) REVERT: G 216 TRP cc_start: 0.8175 (m100) cc_final: 0.7209 (m-10) REVERT: G 217 LYS cc_start: 0.7957 (mmpt) cc_final: 0.7749 (mmpt) REVERT: H 72 ASP cc_start: 0.8243 (t0) cc_final: 0.7895 (t70) REVERT: H 216 GLU cc_start: 0.8375 (pm20) cc_final: 0.8101 (pp20) REVERT: I 117 MET cc_start: 0.7929 (mtp) cc_final: 0.6840 (mmm) REVERT: I 118 ILE cc_start: 0.8363 (mm) cc_final: 0.8161 (mp) REVERT: I 119 MET cc_start: 0.7337 (mmt) cc_final: 0.6903 (tpt) REVERT: I 149 MET cc_start: 0.8248 (mmt) cc_final: 0.7970 (mmp) REVERT: I 213 GLU cc_start: 0.8233 (tp30) cc_final: 0.7915 (tm-30) REVERT: I 215 GLU cc_start: 0.8456 (mm-30) cc_final: 0.7574 (mm-30) REVERT: I 216 TRP cc_start: 0.8172 (m100) cc_final: 0.7230 (m-10) REVERT: I 217 LYS cc_start: 0.7993 (mmpt) cc_final: 0.7774 (mmpt) REVERT: L 79 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7930 (mp0) REVERT: L 170 ASP cc_start: 0.8388 (t0) cc_final: 0.7998 (t0) outliers start: 26 outliers final: 5 residues processed: 151 average time/residue: 1.4159 time to fit residues: 226.6023 Evaluate side-chains 128 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 121 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain G residue 71 MET Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain I residue 49 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 79 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN A 168 HIS ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN H 168 HIS ** I 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9374 Z= 0.233 Angle : 0.617 8.307 12746 Z= 0.318 Chirality : 0.043 0.154 1444 Planarity : 0.004 0.038 1598 Dihedral : 4.806 19.420 1278 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.05 % Allowed : 12.40 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.13 (0.25), residues: 1188 helix: 2.19 (0.32), residues: 272 sheet: 0.70 (0.24), residues: 428 loop : 0.06 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP G 89 HIS 0.004 0.001 HIS L 189 PHE 0.014 0.002 PHE H 100D TYR 0.020 0.002 TYR I 86 ARG 0.015 0.001 ARG G 47 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8181 (t0) cc_final: 0.7821 (t70) REVERT: B 79 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8200 (mm-30) REVERT: B 170 ASP cc_start: 0.8538 (t0) cc_final: 0.8250 (t0) REVERT: G 48 GLU cc_start: 0.6813 (mm-30) cc_final: 0.6032 (mp0) REVERT: G 71 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8628 (mtp) REVERT: G 117 MET cc_start: 0.7927 (mtp) cc_final: 0.6901 (mmm) REVERT: G 119 MET cc_start: 0.7748 (tpp) cc_final: 0.7391 (tpt) REVERT: G 149 MET cc_start: 0.8228 (mmt) cc_final: 0.7956 (mmp) REVERT: G 213 GLU cc_start: 0.8311 (tp30) cc_final: 0.7993 (tm-30) REVERT: G 215 GLU cc_start: 0.8470 (mm-30) cc_final: 0.7445 (mm-30) REVERT: G 216 TRP cc_start: 0.8117 (m100) cc_final: 0.7129 (m-10) REVERT: H 72 ASP cc_start: 0.8258 (t0) cc_final: 0.7846 (t70) REVERT: H 216 GLU cc_start: 0.8452 (pm20) cc_final: 0.8201 (pp20) REVERT: I 117 MET cc_start: 0.7855 (mtp) cc_final: 0.6799 (mmm) REVERT: I 118 ILE cc_start: 0.8318 (mm) cc_final: 0.8106 (mp) REVERT: I 119 MET cc_start: 0.7299 (mmt) cc_final: 0.6874 (tpt) REVERT: I 149 MET cc_start: 0.8215 (mmt) cc_final: 0.7943 (mmp) REVERT: I 213 GLU cc_start: 0.8299 (tp30) cc_final: 0.7984 (tm-30) REVERT: I 215 GLU cc_start: 0.8462 (mm-30) cc_final: 0.7460 (mm-30) REVERT: I 216 TRP cc_start: 0.8114 (m100) cc_final: 0.7133 (m-10) REVERT: L 170 ASP cc_start: 0.8556 (t0) cc_final: 0.8261 (t0) outliers start: 21 outliers final: 8 residues processed: 141 average time/residue: 1.4359 time to fit residues: 215.1150 Evaluate side-chains 126 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain G residue 71 MET Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain I residue 49 SER Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 33 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 0.6980 chunk 64 optimal weight: 0.0570 chunk 1 optimal weight: 0.2980 chunk 84 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 0 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN A 5 GLN A 61 GLN ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 140 ASN G 166 ASN H 3 GLN H 5 GLN H 61 GLN H 159 ASN I 140 ASN I 166 ASN ** I 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 124 GLN L 189 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9374 Z= 0.208 Angle : 0.598 6.576 12746 Z= 0.308 Chirality : 0.042 0.156 1444 Planarity : 0.004 0.037 1598 Dihedral : 4.627 18.280 1278 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.95 % Allowed : 12.40 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.25 (0.25), residues: 1188 helix: 2.35 (0.32), residues: 272 sheet: 0.82 (0.24), residues: 428 loop : 0.05 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP I 89 HIS 0.006 0.001 HIS L 189 PHE 0.013 0.001 PHE G 200 TYR 0.019 0.001 TYR I 86 ARG 0.011 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8204 (t0) cc_final: 0.7814 (t70) REVERT: A 216 GLU cc_start: 0.8386 (pm20) cc_final: 0.8143 (pp20) REVERT: B 79 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8195 (mm-30) REVERT: B 167 ASP cc_start: 0.8482 (t0) cc_final: 0.8058 (t0) REVERT: B 169 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8745 (pptt) REVERT: B 170 ASP cc_start: 0.8620 (t0) cc_final: 0.8096 (t0) REVERT: G 48 GLU cc_start: 0.6949 (mm-30) cc_final: 0.6103 (mp0) REVERT: G 71 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8627 (mtp) REVERT: G 117 MET cc_start: 0.7863 (mtp) cc_final: 0.7194 (mmm) REVERT: G 119 MET cc_start: 0.7713 (tpp) cc_final: 0.7348 (tpt) REVERT: G 149 MET cc_start: 0.8168 (mmt) cc_final: 0.7903 (mmp) REVERT: G 213 GLU cc_start: 0.8278 (tp30) cc_final: 0.8018 (tm-30) REVERT: G 216 TRP cc_start: 0.8105 (m100) cc_final: 0.7125 (m-10) REVERT: H 72 ASP cc_start: 0.8243 (t0) cc_final: 0.7797 (t70) REVERT: H 216 GLU cc_start: 0.8469 (pm20) cc_final: 0.8232 (pp20) REVERT: I 50 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8373 (mptm) REVERT: I 117 MET cc_start: 0.7768 (mtp) cc_final: 0.6809 (mmm) REVERT: I 119 MET cc_start: 0.7260 (mmt) cc_final: 0.6822 (tpt) REVERT: I 149 MET cc_start: 0.8091 (mmt) cc_final: 0.7839 (mmp) REVERT: I 213 GLU cc_start: 0.8270 (tp30) cc_final: 0.8004 (tm-30) REVERT: I 215 GLU cc_start: 0.8383 (mm-30) cc_final: 0.7491 (mm-30) REVERT: I 216 TRP cc_start: 0.8088 (m100) cc_final: 0.7100 (m-10) REVERT: L 167 ASP cc_start: 0.8499 (t0) cc_final: 0.8084 (t0) REVERT: L 169 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8827 (pptt) REVERT: L 170 ASP cc_start: 0.8639 (t0) cc_final: 0.8115 (t0) outliers start: 20 outliers final: 5 residues processed: 136 average time/residue: 1.5739 time to fit residues: 227.9464 Evaluate side-chains 122 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain G residue 71 MET Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain I residue 50 LYS Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 118 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 169 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN A 5 GLN A 168 HIS ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 GLN H 3 GLN H 5 GLN H 168 HIS I 171 ASN L 124 GLN ** L 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 199 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 9374 Z= 0.511 Angle : 0.722 8.224 12746 Z= 0.370 Chirality : 0.048 0.165 1444 Planarity : 0.005 0.041 1598 Dihedral : 5.085 25.002 1278 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.15 % Allowed : 13.67 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.02 (0.24), residues: 1188 helix: 1.97 (0.31), residues: 270 sheet: 0.74 (0.24), residues: 432 loop : -0.03 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP G 89 HIS 0.005 0.002 HIS B 189 PHE 0.022 0.002 PHE H 150 TYR 0.025 0.002 TYR I 86 ARG 0.011 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8316 (t0) cc_final: 0.7937 (t70) REVERT: A 216 GLU cc_start: 0.8502 (pm20) cc_final: 0.8266 (pp20) REVERT: B 79 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8222 (mm-30) REVERT: B 169 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8854 (pptt) REVERT: B 170 ASP cc_start: 0.8664 (t0) cc_final: 0.8160 (t0) REVERT: G 49 SER cc_start: 0.8335 (m) cc_final: 0.7975 (p) REVERT: G 71 MET cc_start: 0.8944 (mtm) cc_final: 0.8575 (mtp) REVERT: G 76 ILE cc_start: 0.8375 (mm) cc_final: 0.8138 (pt) REVERT: G 117 MET cc_start: 0.8179 (mtp) cc_final: 0.7788 (tpp) REVERT: G 149 MET cc_start: 0.7935 (mmt) cc_final: 0.7686 (mmp) REVERT: G 213 GLU cc_start: 0.8323 (tp30) cc_final: 0.8076 (tm-30) REVERT: G 216 TRP cc_start: 0.8111 (m100) cc_final: 0.7141 (m-10) REVERT: H 72 ASP cc_start: 0.8395 (t0) cc_final: 0.7949 (t70) REVERT: H 159 ASN cc_start: 0.8089 (m-40) cc_final: 0.7863 (m110) REVERT: H 199 ILE cc_start: 0.8743 (pp) cc_final: 0.8518 (tp) REVERT: H 216 GLU cc_start: 0.8518 (pm20) cc_final: 0.8280 (pp20) REVERT: I 117 MET cc_start: 0.8084 (mtp) cc_final: 0.7502 (mmm) REVERT: I 119 MET cc_start: 0.7338 (mmt) cc_final: 0.7052 (tpp) REVERT: I 149 MET cc_start: 0.7943 (mmt) cc_final: 0.7692 (mmp) REVERT: I 213 GLU cc_start: 0.8320 (tp30) cc_final: 0.8099 (tm-30) REVERT: I 216 TRP cc_start: 0.8122 (m100) cc_final: 0.7159 (m-10) REVERT: L 169 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8851 (pptt) REVERT: L 170 ASP cc_start: 0.8678 (t0) cc_final: 0.8172 (t0) outliers start: 22 outliers final: 9 residues processed: 138 average time/residue: 1.4933 time to fit residues: 218.3936 Evaluate side-chains 121 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 142 LYS Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 118 ILE Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 169 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 64 optimal weight: 0.4980 chunk 96 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 61 GLN A 168 HIS B 137 ASN ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 GLN G 166 ASN H 5 GLN H 61 GLN H 168 HIS I 166 ASN L 124 GLN L 137 ASN ** L 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 199 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9374 Z= 0.256 Angle : 0.619 6.708 12746 Z= 0.318 Chirality : 0.043 0.149 1444 Planarity : 0.004 0.046 1598 Dihedral : 4.773 20.187 1278 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.15 % Allowed : 13.87 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.14 (0.24), residues: 1188 helix: 2.24 (0.31), residues: 270 sheet: 0.73 (0.24), residues: 424 loop : 0.03 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP I 89 HIS 0.006 0.001 HIS L 189 PHE 0.015 0.001 PHE G 200 TYR 0.019 0.002 TYR I 86 ARG 0.012 0.001 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8248 (t0) cc_final: 0.7857 (t70) REVERT: A 216 GLU cc_start: 0.8495 (pm20) cc_final: 0.8275 (pp20) REVERT: B 79 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8157 (mm-30) REVERT: B 169 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8864 (pptt) REVERT: B 170 ASP cc_start: 0.8695 (t0) cc_final: 0.8184 (t0) REVERT: G 48 GLU cc_start: 0.7111 (mm-30) cc_final: 0.6431 (mp0) REVERT: G 49 SER cc_start: 0.8140 (m) cc_final: 0.7891 (p) REVERT: G 71 MET cc_start: 0.8959 (mtm) cc_final: 0.8594 (mtp) REVERT: G 117 MET cc_start: 0.7858 (mtp) cc_final: 0.7542 (tpp) REVERT: G 119 MET cc_start: 0.7739 (tpp) cc_final: 0.7377 (tpt) REVERT: G 149 MET cc_start: 0.7981 (mmt) cc_final: 0.7764 (mmp) REVERT: G 213 GLU cc_start: 0.8285 (tp30) cc_final: 0.8051 (tm-30) REVERT: G 216 TRP cc_start: 0.8089 (m100) cc_final: 0.7058 (m-10) REVERT: H 72 ASP cc_start: 0.8332 (t0) cc_final: 0.7881 (t70) REVERT: H 216 GLU cc_start: 0.8529 (pm20) cc_final: 0.8327 (pp20) REVERT: I 117 MET cc_start: 0.7878 (mtp) cc_final: 0.7373 (tpp) REVERT: I 118 ILE cc_start: 0.8369 (mm) cc_final: 0.8144 (mp) REVERT: I 119 MET cc_start: 0.7269 (mmt) cc_final: 0.6784 (tpt) REVERT: I 149 MET cc_start: 0.8026 (mmt) cc_final: 0.7814 (mmp) REVERT: I 213 GLU cc_start: 0.8277 (tp30) cc_final: 0.8045 (tm-30) REVERT: I 216 TRP cc_start: 0.8103 (m100) cc_final: 0.7064 (m-10) REVERT: L 137 ASN cc_start: 0.8197 (OUTLIER) cc_final: 0.7985 (t0) REVERT: L 169 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8863 (pptt) REVERT: L 170 ASP cc_start: 0.8704 (t0) cc_final: 0.8189 (t0) outliers start: 22 outliers final: 7 residues processed: 130 average time/residue: 1.4626 time to fit residues: 201.7862 Evaluate side-chains 122 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 199 GLN Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 137 ASN Chi-restraints excluded: chain L residue 169 LYS Chi-restraints excluded: chain L residue 199 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 0.3980 chunk 45 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 GLN H 5 GLN L 124 GLN ** L 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 199 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9374 Z= 0.270 Angle : 0.633 7.616 12746 Z= 0.323 Chirality : 0.043 0.149 1444 Planarity : 0.005 0.053 1598 Dihedral : 4.727 20.801 1278 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.56 % Allowed : 14.94 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.17 (0.24), residues: 1188 helix: 2.23 (0.31), residues: 272 sheet: 0.76 (0.24), residues: 424 loop : 0.05 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP I 89 HIS 0.006 0.001 HIS L 189 PHE 0.015 0.002 PHE G 200 TYR 0.019 0.002 TYR I 86 ARG 0.013 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8304 (t0) cc_final: 0.7895 (t70) REVERT: A 216 GLU cc_start: 0.8507 (pm20) cc_final: 0.8293 (pp20) REVERT: B 79 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8171 (mm-30) REVERT: B 169 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8893 (pptt) REVERT: B 170 ASP cc_start: 0.8739 (t0) cc_final: 0.8232 (t0) REVERT: G 49 SER cc_start: 0.8209 (m) cc_final: 0.7928 (p) REVERT: G 71 MET cc_start: 0.8966 (mtm) cc_final: 0.8592 (mtp) REVERT: G 117 MET cc_start: 0.7928 (mtp) cc_final: 0.7608 (tpp) REVERT: G 119 MET cc_start: 0.7799 (tpp) cc_final: 0.7432 (tpt) REVERT: G 149 MET cc_start: 0.7987 (mmt) cc_final: 0.7765 (mmp) REVERT: G 213 GLU cc_start: 0.8289 (tp30) cc_final: 0.8056 (tm-30) REVERT: G 216 TRP cc_start: 0.8085 (m100) cc_final: 0.7113 (m-10) REVERT: H 72 ASP cc_start: 0.8344 (t0) cc_final: 0.7879 (t70) REVERT: I 117 MET cc_start: 0.7878 (mtp) cc_final: 0.7123 (mmm) REVERT: I 118 ILE cc_start: 0.8322 (mm) cc_final: 0.8116 (mp) REVERT: I 119 MET cc_start: 0.7295 (mmt) cc_final: 0.6846 (tpt) REVERT: I 149 MET cc_start: 0.7992 (mmt) cc_final: 0.7781 (mmp) REVERT: I 213 GLU cc_start: 0.8303 (tp30) cc_final: 0.8061 (tm-30) REVERT: I 216 TRP cc_start: 0.8102 (m100) cc_final: 0.7113 (m-10) REVERT: L 169 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8891 (pptt) REVERT: L 170 ASP cc_start: 0.8751 (t0) cc_final: 0.8241 (t0) outliers start: 16 outliers final: 6 residues processed: 125 average time/residue: 1.4937 time to fit residues: 197.7282 Evaluate side-chains 117 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 169 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 63 optimal weight: 0.4980 chunk 46 optimal weight: 0.5980 chunk 83 optimal weight: 0.3980 chunk 32 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 112 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 61 GLN H 5 GLN H 61 GLN I 166 ASN L 124 GLN ** L 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9374 Z= 0.218 Angle : 0.623 8.149 12746 Z= 0.318 Chirality : 0.042 0.145 1444 Planarity : 0.005 0.056 1598 Dihedral : 4.652 20.154 1278 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.78 % Allowed : 15.53 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.30 (0.24), residues: 1188 helix: 2.37 (0.31), residues: 272 sheet: 0.86 (0.24), residues: 422 loop : 0.09 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP I 89 HIS 0.007 0.001 HIS L 189 PHE 0.014 0.001 PHE G 200 TYR 0.018 0.001 TYR I 86 ARG 0.014 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8305 (t0) cc_final: 0.7868 (t70) REVERT: A 216 GLU cc_start: 0.8517 (pm20) cc_final: 0.8307 (pp20) REVERT: B 79 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8160 (mm-30) REVERT: B 169 LYS cc_start: 0.9220 (OUTLIER) cc_final: 0.8917 (pptt) REVERT: B 170 ASP cc_start: 0.8766 (t0) cc_final: 0.8251 (t0) REVERT: G 71 MET cc_start: 0.8979 (mtm) cc_final: 0.8640 (mtp) REVERT: G 117 MET cc_start: 0.7834 (mtp) cc_final: 0.7532 (tpp) REVERT: G 119 MET cc_start: 0.7722 (tpp) cc_final: 0.7380 (tpt) REVERT: G 149 MET cc_start: 0.7981 (mmt) cc_final: 0.7759 (mmp) REVERT: G 213 GLU cc_start: 0.8291 (tp30) cc_final: 0.8065 (tm-30) REVERT: G 216 TRP cc_start: 0.8072 (m100) cc_final: 0.7047 (m-10) REVERT: H 72 ASP cc_start: 0.8335 (t0) cc_final: 0.7850 (t70) REVERT: I 117 MET cc_start: 0.7751 (mtp) cc_final: 0.7332 (tpp) REVERT: I 119 MET cc_start: 0.7224 (mmt) cc_final: 0.6770 (tpt) REVERT: I 149 MET cc_start: 0.8033 (mmt) cc_final: 0.7808 (mmp) REVERT: I 213 GLU cc_start: 0.8284 (tp30) cc_final: 0.8062 (tm-30) REVERT: I 216 TRP cc_start: 0.8089 (m100) cc_final: 0.7035 (m-10) REVERT: L 169 LYS cc_start: 0.9240 (OUTLIER) cc_final: 0.8926 (pptt) REVERT: L 170 ASP cc_start: 0.8775 (t0) cc_final: 0.8270 (t0) outliers start: 8 outliers final: 4 residues processed: 121 average time/residue: 1.5491 time to fit residues: 198.2531 Evaluate side-chains 117 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 110 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 169 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 chunk 108 optimal weight: 0.7980 chunk 93 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 74 optimal weight: 0.0870 chunk 99 optimal weight: 2.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN H 5 GLN L 124 GLN ** L 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9374 Z= 0.233 Angle : 0.638 7.628 12746 Z= 0.326 Chirality : 0.042 0.141 1444 Planarity : 0.005 0.060 1598 Dihedral : 4.630 20.573 1278 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.88 % Allowed : 15.62 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.37 (0.24), residues: 1188 helix: 2.45 (0.30), residues: 270 sheet: 0.91 (0.24), residues: 422 loop : 0.12 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP I 89 HIS 0.009 0.001 HIS B 189 PHE 0.014 0.001 PHE G 200 TYR 0.018 0.001 TYR I 86 ARG 0.014 0.001 ARG B 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8315 (t0) cc_final: 0.7870 (t70) REVERT: A 159 ASN cc_start: 0.7845 (m-40) cc_final: 0.7621 (m110) REVERT: A 199 ILE cc_start: 0.8735 (pp) cc_final: 0.8517 (tp) REVERT: B 79 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8194 (mm-30) REVERT: B 169 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8933 (pptt) REVERT: B 170 ASP cc_start: 0.8787 (t0) cc_final: 0.8287 (t0) REVERT: G 49 SER cc_start: 0.8155 (m) cc_final: 0.7885 (p) REVERT: G 71 MET cc_start: 0.8980 (mtm) cc_final: 0.8610 (mtp) REVERT: G 117 MET cc_start: 0.7816 (mtp) cc_final: 0.7511 (tpp) REVERT: G 119 MET cc_start: 0.7769 (tpp) cc_final: 0.7424 (tpt) REVERT: G 149 MET cc_start: 0.7993 (mmt) cc_final: 0.7763 (mmp) REVERT: G 213 GLU cc_start: 0.8278 (tp30) cc_final: 0.8067 (tm-30) REVERT: G 216 TRP cc_start: 0.8107 (m100) cc_final: 0.7119 (m-10) REVERT: H 72 ASP cc_start: 0.8326 (t0) cc_final: 0.7860 (t70) REVERT: I 117 MET cc_start: 0.7729 (mtp) cc_final: 0.7278 (tpp) REVERT: I 119 MET cc_start: 0.7241 (mmt) cc_final: 0.6797 (tpt) REVERT: I 149 MET cc_start: 0.7993 (mmt) cc_final: 0.7769 (mmp) REVERT: I 216 TRP cc_start: 0.8073 (m100) cc_final: 0.7082 (m-10) REVERT: L 169 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.8922 (pptt) REVERT: L 170 ASP cc_start: 0.8790 (t0) cc_final: 0.8284 (t0) outliers start: 9 outliers final: 3 residues processed: 122 average time/residue: 1.3142 time to fit residues: 170.4148 Evaluate side-chains 116 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 169 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 26 optimal weight: 0.5980 chunk 93 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN H 61 GLN ** L 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.125018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.073448 restraints weight = 14448.204| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.41 r_work: 0.2832 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9374 Z= 0.242 Angle : 0.648 7.445 12746 Z= 0.334 Chirality : 0.042 0.141 1444 Planarity : 0.005 0.053 1598 Dihedral : 4.682 20.613 1278 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.68 % Allowed : 16.31 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.38 (0.24), residues: 1188 helix: 2.42 (0.30), residues: 270 sheet: 0.95 (0.24), residues: 422 loop : 0.11 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP I 89 HIS 0.010 0.001 HIS B 189 PHE 0.014 0.001 PHE G 200 TYR 0.018 0.001 TYR I 86 ARG 0.012 0.001 ARG B 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4243.62 seconds wall clock time: 79 minutes 7.43 seconds (4747.43 seconds total)